Systems Biology of Cancer Metastasis

Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has...

Full description

Saved in:
Bibliographic Details
Published inCell systems Vol. 9; no. 2; pp. 109 - 127
Main Authors Suhail, Yasir, Cain, Margo P., Vanaja, Kiran, Kurywchak, Paul A., Levchenko, Andre, Kalluri, Raghu, Kshitiz
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 28.08.2019
Subjects
Online AccessGet full text

Cover

Loading…
Abstract Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon. Cancer metastasis is a complex disease, arising from a growing tumor from which cells escape to other parts of the body. For long, cancer metastasis was considered as a combination of steps, which were studied separately, limiting our understanding of this complex disease. Here, we present the new developments and our perspective on how the new systems biology approach is changing our view of cancer metastasis as an integrated multiscale phenomenon comprising interlinked parts that allow tumors to metastasize.
AbstractList Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon.Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon.
Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon. Cancer metastasis is a complex disease, arising from a growing tumor from which cells escape to other parts of the body. For long, cancer metastasis was considered as a combination of steps, which were studied separately, limiting our understanding of this complex disease. Here, we present the new developments and our perspective on how the new systems biology approach is changing our view of cancer metastasis as an integrated multiscale phenomenon comprising interlinked parts that allow tumors to metastasize.
Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon.
Cancer metastasis is no longer viewed as a linear cascade of events, but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. Lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multi-scale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon. Cancer metastasis is a complex disease, arising from a growing tumor from which cells escape to other parts of the body. For long, cancer metastasis was considered as a combination of steps, which were studied separately, limiting our understanding of this complex disease. Here we present the new developments, and our perspective on how the new systems biology approach is changing our view of cancer metastasis as an integrated multiscale phenomenon comprising of interlinked parts that allow tumors to metastasize.
Author Cain, Margo P.
Kshitiz
Kurywchak, Paul A.
Suhail, Yasir
Kalluri, Raghu
Vanaja, Kiran
Levchenko, Andre
AuthorAffiliation 1. Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT
3. Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX
2. Cancer Systems Biology @ Yale (CaSB@Yale), Yale University, West Haven, CT
AuthorAffiliation_xml – name: 1. Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT
– name: 3. Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX
– name: 2. Cancer Systems Biology @ Yale (CaSB@Yale), Yale University, West Haven, CT
Author_xml – sequence: 1
  givenname: Yasir
  surname: Suhail
  fullname: Suhail, Yasir
  organization: Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, USA
– sequence: 2
  givenname: Margo P.
  surname: Cain
  fullname: Cain, Margo P.
  organization: Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA
– sequence: 3
  givenname: Kiran
  surname: Vanaja
  fullname: Vanaja, Kiran
  organization: Cancer Systems Biology @ Yale (CaSB@Yale), Yale University, West Haven, CT, USA
– sequence: 4
  givenname: Paul A.
  surname: Kurywchak
  fullname: Kurywchak, Paul A.
  organization: Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA
– sequence: 5
  givenname: Andre
  surname: Levchenko
  fullname: Levchenko, Andre
  organization: Cancer Systems Biology @ Yale (CaSB@Yale), Yale University, West Haven, CT, USA
– sequence: 6
  givenname: Raghu
  surname: Kalluri
  fullname: Kalluri, Raghu
  organization: Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA
– sequence: 7
  surname: Kshitiz
  fullname: Kshitiz
  email: kshitiz@uchc.edu
  organization: Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, USA
BackLink https://www.ncbi.nlm.nih.gov/pubmed/31465728$$D View this record in MEDLINE/PubMed
BookMark eNp9UUtLAzEQDqL4_gMepAcPXrom2exmF0TQ4gsUD-p5yGNWU7YbTbaF_ntT2op6EAYyzHyPMN8e2ex8h4QcMZoxysqzcWawjRmnrM6ozCjNN8guF7QYCsnp5nfP-A45jHFMKWWiTkO-TXZyJspC8mqXnDzPY4-TOLhyvvVv84FvBiPVGQyDR-xVTOXiAdlqVBvxcPXuk9eb65fR3fDh6fZ-dPkwNKIo-qFFUWldN1bXyuhKN1gpK4wVvLBKY215Q2slcpZrqSUtZa6ULdLHjGlkU9h8n1wsdT-meoLWYNcH1cJHcBMV5uCVg9-bzr3Dm59BKVlZcpYETlcCwX9OMfYwcTHdqVUd-mkEzqucseQsE_T4p9e3yfo0CVAtASb4GAM2YFyveucX1q4FRmERBIxhEQQsggAqIQWRqPwPda3-L-l8SUoLnDkMEI3DlIR1AU0P1rv_6F93SaJf
CitedBy_id crossref_primary_10_1038_s41420_021_00516_x
crossref_primary_10_1007_s13402_021_00611_2
crossref_primary_10_1016_j_jff_2024_106255
crossref_primary_10_3389_fcell_2022_854721
crossref_primary_10_1016_j_apsb_2024_08_003
crossref_primary_10_1080_21655979_2021_1971919
crossref_primary_10_2298_GENSR2401089T
crossref_primary_10_4274_hamidiyemedj_galenos_2024_72692
crossref_primary_10_3389_fonc_2022_857743
crossref_primary_10_1016_j_mocell_2024_100128
crossref_primary_10_1007_s13577_020_00427_6
crossref_primary_10_3389_fcell_2022_927631
crossref_primary_10_1007_s12247_024_09865_3
crossref_primary_10_1186_s13045_022_01392_3
crossref_primary_10_17085_apm_24041
crossref_primary_10_1039_D3LC00301A
crossref_primary_10_3390_ma14061435
crossref_primary_10_1002_cbin_11906
crossref_primary_10_1016_j_addr_2021_113909
crossref_primary_10_3389_fgene_2024_1362420
crossref_primary_10_3390_ijms22041886
crossref_primary_10_1148_radiol_221598
crossref_primary_10_1038_s41392_024_01885_2
crossref_primary_10_1038_s42003_023_05732_y
crossref_primary_10_2139_ssrn_4191374
crossref_primary_10_3390_pharmaceutics15041117
crossref_primary_10_1002_jcla_24023
crossref_primary_10_1039_D2MD00280A
crossref_primary_10_1016_j_compbiolchem_2023_107997
crossref_primary_10_1016_j_ejmech_2021_113935
crossref_primary_10_1007_s11033_022_07502_1
crossref_primary_10_2174_0113892029300608240531111743
crossref_primary_10_1016_j_intimp_2023_109775
crossref_primary_10_1016_j_heliyon_2023_e20656
crossref_primary_10_7554_eLife_76632
crossref_primary_10_1002_adfm_202107599
crossref_primary_10_1016_j_bios_2024_116947
crossref_primary_10_1051_vcm_2021003
crossref_primary_10_1016_j_bbcan_2023_189001
crossref_primary_10_1016_j_canlet_2020_03_014
crossref_primary_10_1080_1120009X_2023_2264585
crossref_primary_10_3389_fbioe_2021_756314
crossref_primary_10_1186_s13046_023_02741_x
crossref_primary_10_7554_eLife_53839
crossref_primary_10_1016_j_heliyon_2023_e23918
crossref_primary_10_1007_s00018_020_03449_3
crossref_primary_10_1038_s41598_023_39742_x
crossref_primary_10_1002_jcla_24609
crossref_primary_10_1016_j_biopha_2023_114590
crossref_primary_10_1155_2022_1217918
crossref_primary_10_1021_acsbiomaterials_3c00239
crossref_primary_10_1097_MD_0000000000036602
crossref_primary_10_1186_s13046_022_02493_0
crossref_primary_10_1002_cam4_6935
crossref_primary_10_3389_fcell_2022_794329
crossref_primary_10_1093_bioinformatics_btad374
crossref_primary_10_1016_j_critrevonc_2024_104269
crossref_primary_10_1038_s41392_024_01823_2
crossref_primary_10_1016_j_molstruc_2021_131929
crossref_primary_10_1007_s12672_025_01997_3
crossref_primary_10_3390_jpm13111590
crossref_primary_10_1080_14756366_2023_2247579
crossref_primary_10_3390_nu14132622
crossref_primary_10_3390_cancers15143549
crossref_primary_10_1002_smtd_202400861
crossref_primary_10_1021_acsami_1c15838
crossref_primary_10_1038_s41416_020_01172_1
crossref_primary_10_1186_s12935_020_01409_2
crossref_primary_10_1038_s41598_024_81150_2
crossref_primary_10_1007_s12672_024_01010_3
crossref_primary_10_1016_j_biopha_2023_115277
crossref_primary_10_1111_cas_15920
crossref_primary_10_3724_abbs_2023244
crossref_primary_10_3892_or_2024_8719
crossref_primary_10_3390_ijms22179546
crossref_primary_10_1016_j_heliyon_2024_e32626
crossref_primary_10_3390_cancers13184502
crossref_primary_10_1007_s00775_020_01841_9
crossref_primary_10_1002_advs_202003972
crossref_primary_10_3389_fonc_2022_1060495
crossref_primary_10_3390_cancers16050969
crossref_primary_10_31083_j_fbl2803053
crossref_primary_10_1186_s12859_022_04731_w
crossref_primary_10_31083_j_fbl2803058
crossref_primary_10_1016_j_jddst_2022_104081
crossref_primary_10_1002_iub_2786
crossref_primary_10_1016_j_trecan_2023_02_005
crossref_primary_10_1016_j_canlet_2024_216837
crossref_primary_10_1016_j_inoche_2025_114027
crossref_primary_10_1016_j_jpha_2022_12_003
crossref_primary_10_1038_s41571_023_00781_y
crossref_primary_10_3390_biom13071080
crossref_primary_10_12688_f1000research_138951_1
crossref_primary_10_3389_fimmu_2024_1258475
crossref_primary_10_1016_j_mbm_2024_100070
crossref_primary_10_1021_acs_molpharmaceut_3c00148
crossref_primary_10_1002_mog2_70000
crossref_primary_10_1042_BSR20211494
crossref_primary_10_1002_pros_24141
crossref_primary_10_3389_fphar_2022_1008222
crossref_primary_10_3390_cancers14040962
crossref_primary_10_1002_ardp_202200051
crossref_primary_10_1016_j_clcc_2024_05_010
crossref_primary_10_1016_j_ijscr_2022_107498
crossref_primary_10_1007_s43657_021_00043_w
crossref_primary_10_1177_1934578X211057694
crossref_primary_10_1016_j_ecoenv_2024_116579
crossref_primary_10_1021_acsptsci_4c00608
crossref_primary_10_1016_j_lfs_2023_121499
crossref_primary_10_2217_bmm_2023_0215
crossref_primary_10_3390_cells13020140
crossref_primary_10_3390_ijms25105569
crossref_primary_10_1021_acsami_2c01105
crossref_primary_10_1038_s41598_023_31880_6
crossref_primary_10_1186_s12935_019_0984_x
crossref_primary_10_3233_CBM_210232
crossref_primary_10_3389_fimmu_2020_02166
crossref_primary_10_3390_biom14080916
crossref_primary_10_3892_ijmm_2022_5180
crossref_primary_10_1097_MS9_0000000000003043
crossref_primary_10_1016_S1875_5364_23_60521_7
crossref_primary_10_1016_j_intimp_2023_110284
crossref_primary_10_1007_s00210_025_03902_9
crossref_primary_10_1080_2162402X_2021_2006529
crossref_primary_10_3389_fbioe_2022_907232
crossref_primary_10_1016_j_smaim_2022_07_005
crossref_primary_10_3390_biom13060883
crossref_primary_10_1016_j_euo_2024_10_010
crossref_primary_10_3390_nu16162790
crossref_primary_10_3389_fimmu_2022_875718
crossref_primary_10_1039_D4NJ00819G
crossref_primary_10_1186_s12964_022_01019_7
crossref_primary_10_1002_jcla_23791
crossref_primary_10_1080_14786419_2021_2000980
crossref_primary_10_3389_fcell_2021_625221
crossref_primary_10_1007_s12274_022_5141_5
crossref_primary_10_31083_j_fbl2910345
crossref_primary_10_1007_s11033_023_08910_7
crossref_primary_10_3389_fonc_2021_803266
crossref_primary_10_3390_ijms23147732
crossref_primary_10_1007_s00432_024_05773_8
crossref_primary_10_1038_s41392_024_01937_7
crossref_primary_10_1016_j_bcp_2024_116141
crossref_primary_10_1002_med4_38
crossref_primary_10_2217_bmm_2019_0145
crossref_primary_10_1007_s00262_022_03223_3
crossref_primary_10_3390_ph16020253
crossref_primary_10_1016_j_isci_2023_106719
crossref_primary_10_1186_s12943_024_02033_8
crossref_primary_10_3389_fmolb_2020_00079
crossref_primary_10_1016_j_phrs_2021_105861
crossref_primary_10_1016_j_ejmech_2022_114915
crossref_primary_10_1002_jcp_31084
crossref_primary_10_1042_BSR20220395
crossref_primary_10_3390_biomedicines12092137
crossref_primary_10_1002_mc_23214
crossref_primary_10_1371_journal_pone_0316146
crossref_primary_10_3390_md21090489
crossref_primary_10_1016_j_biocel_2022_106307
crossref_primary_10_1208_s12249_024_02765_2
crossref_primary_10_1016_j_isci_2022_103969
crossref_primary_10_17816_onco629570
crossref_primary_10_3389_fonc_2023_1133828
crossref_primary_10_3390_ijms22042219
crossref_primary_10_1186_s12859_021_04389_w
crossref_primary_10_2147_IJGM_S407266
crossref_primary_10_1007_s11033_021_06660_y
crossref_primary_10_3389_fimmu_2024_1441914
crossref_primary_10_1155_2022_2055900
crossref_primary_10_1186_s40164_023_00389_z
crossref_primary_10_1073_pnas_2111256119
crossref_primary_10_3390_jcm10040595
crossref_primary_10_3389_fcell_2023_1275668
crossref_primary_10_1089_omi_2023_0285
crossref_primary_10_3389_fonc_2022_965838
crossref_primary_10_1096_fj_202301064RR
crossref_primary_10_1016_j_isci_2023_107346
crossref_primary_10_1038_s41598_023_33792_x
crossref_primary_10_1097_RCT_0000000000001218
crossref_primary_10_1186_s12951_023_01989_x
crossref_primary_10_3748_wjg_v30_i11_1497
crossref_primary_10_3389_fonc_2023_1203439
crossref_primary_10_3390_cancers14092197
crossref_primary_10_3389_fonc_2021_778258
crossref_primary_10_3390_diseases13010001
crossref_primary_10_1016_j_ijpharm_2024_125059
crossref_primary_10_1089_thy_2022_0687
crossref_primary_10_1007_s11033_023_08920_5
crossref_primary_10_1016_j_ejphar_2023_175770
crossref_primary_10_1155_2022_8317466
crossref_primary_10_1016_j_celrep_2022_111513
crossref_primary_10_1016_j_heliyon_2024_e38628
crossref_primary_10_3390_cancers15092618
crossref_primary_10_1016_j_pharmthera_2024_108711
crossref_primary_10_31011_reaid_2024_v_98_n_3_art_1971
crossref_primary_10_1016_j_ecoenv_2023_114980
crossref_primary_10_1186_s12935_022_02822_5
crossref_primary_10_1186_s12967_024_05493_0
crossref_primary_10_3390_cancers15010069
crossref_primary_10_1016_j_cels_2022_11_003
crossref_primary_10_3390_ijms24119590
crossref_primary_10_1016_j_canlet_2023_216283
crossref_primary_10_2147_IJN_S476601
crossref_primary_10_1186_s11658_021_00301_9
crossref_primary_10_1186_s12906_021_03262_w
crossref_primary_10_35429_JBEB_2019_7_3_8_17
crossref_primary_10_1016_j_matbio_2020_05_001
crossref_primary_10_1186_s40364_022_00356_6
crossref_primary_10_1084_jem_20190218
crossref_primary_10_1016_j_isci_2024_111023
crossref_primary_10_1007_s00259_022_06056_5
crossref_primary_10_3389_fphar_2025_1494545
crossref_primary_10_3390_cells12151940
crossref_primary_10_18137_cardiometry_2023_27_5462
crossref_primary_10_1016_j_bbamcr_2024_119697
crossref_primary_10_3390_cancers16061213
crossref_primary_10_1016_j_clnesp_2023_06_038
crossref_primary_10_1016_j_tranon_2020_100845
crossref_primary_10_1186_s12943_024_01992_2
crossref_primary_10_3389_fphar_2023_1172939
crossref_primary_10_1016_j_mechmat_2021_104094
crossref_primary_10_1038_s41392_022_00994_0
crossref_primary_10_1016_j_ijbiomac_2023_123606
crossref_primary_10_3390_cancers15071974
crossref_primary_10_3390_ijms26030904
crossref_primary_10_3390_ijms21144992
crossref_primary_10_3390_biomedicines10092148
crossref_primary_10_1186_s12967_023_04447_2
crossref_primary_10_1186_s12935_022_02766_w
crossref_primary_10_1097_CAD_0000000000001221
crossref_primary_10_1016_j_copbio_2019_12_006
crossref_primary_10_3390_nu14173519
crossref_primary_10_1016_j_bioorg_2024_107237
crossref_primary_10_1093_gastro_goae055
crossref_primary_10_3390_ijms22158214
crossref_primary_10_1038_s41598_024_64197_z
crossref_primary_10_1080_21655979_2021_1977553
crossref_primary_10_3389_fsysb_2023_1099951
crossref_primary_10_1038_s41392_022_01199_1
crossref_primary_10_1016_j_clbc_2025_02_009
crossref_primary_10_3390_medicines8080045
crossref_primary_10_1021_acsbiomaterials_4c01226
crossref_primary_10_1134_S1990750823600577
crossref_primary_10_1186_s12935_022_02568_0
crossref_primary_10_3390_molecules26133963
crossref_primary_10_1002_chem_202401805
crossref_primary_10_1089_dna_2022_0322
crossref_primary_10_1371_journal_pone_0268073
crossref_primary_10_1007_s13577_024_01092_9
crossref_primary_10_3390_molecules26247659
crossref_primary_10_1016_j_bioorg_2024_107700
crossref_primary_10_1016_j_jbo_2022_100461
crossref_primary_10_1038_s41598_023_42985_3
crossref_primary_10_62347_OBES4130
crossref_primary_10_1002_wrna_1786
crossref_primary_10_1038_s41598_025_93192_1
crossref_primary_10_1080_15384047_2024_2321768
crossref_primary_10_1016_j_fitote_2024_106222
crossref_primary_10_3389_fphar_2024_1437022
crossref_primary_10_3390_mps3030060
crossref_primary_10_1021_acs_jmedchem_2c01895
crossref_primary_10_3390_cancers15164173
crossref_primary_10_1016_j_tox_2025_154054
crossref_primary_10_3390_ijms22041700
crossref_primary_10_1016_j_heliyon_2024_e29736
crossref_primary_10_1248_bpb_b21_00292
crossref_primary_10_3390_ijms222413443
crossref_primary_10_1016_j_ygeno_2023_110569
crossref_primary_10_1089_ars_2023_0272
crossref_primary_10_1016_j_ijbiomac_2023_123377
crossref_primary_10_3390_cells10061529
crossref_primary_10_1186_s12957_022_02821_w
Cites_doi 10.1016/j.cell.2011.11.025
10.1101/cshperspect.a028332
10.1242/dmm.034330
10.1186/1752-0509-4-104
10.1371/journal.pcbi.1004025
10.1016/j.stem.2018.02.011
10.1038/s41467-017-01666-2
10.18632/oncotarget.8247
10.1016/j.ccell.2016.11.014
10.1126/science.aah4573
10.15252/msb.20156458
10.1038/s41598-017-15882-9
10.1038/ncomms15078
10.1038/s41598-018-34037-y
10.12688/f1000research.8090.1
10.1016/j.cell.2016.02.025
10.1038/s41598-017-09098-0
10.1016/j.bpj.2016.08.011
10.1038/nrg3788
10.1016/j.cels.2017.05.001
10.1038/nature21350
10.1002/jcb.25972
10.1038/nrc.2016.73
10.1007/978-1-4939-2519-3_12
10.1002/ar.20849
10.1016/j.cell.2013.11.029
10.1158/0008-5472.CAN-13-0356
10.1039/C3IB40267C
10.1016/j.ccr.2014.05.002
10.1007/s00418-008-0529-1
10.1073/pnas.1620755114
10.1172/JCI69244
10.1016/j.cell.2018.05.056
10.1093/bioinformatics/bty766
10.4161/23723556.2014.975027
10.1038/ncb2767
10.1038/nn.4620
10.7554/eLife.04640
10.1038/s41467-018-05261-x
10.1126/science.aad0501
10.1038/nature25167
10.1158/2159-8290.CD-15-0012
10.1371/journal.pone.0183810
10.1016/j.copbio.2008.07.002
10.1016/j.clml.2019.01.003
10.1158/0008-5472.CAN-18-0221
10.1038/nature16064
10.1126/scitranslmed.3010467
10.3389/fonc.2019.00138
10.1016/j.ydbio.2017.04.015
10.1101/gad.294104
10.1093/bioinformatics/btt471
10.1016/j.cell.2016.03.029
10.1038/nbt1217-1211c
10.1038/s41586-019-1004-y
10.1056/NEJMoa065411
10.1016/j.cub.2016.11.057
10.1126/science.aaf2403
10.1172/JCI70935
10.1158/1078-0432.CCR-05-0658
10.1038/s41467-017-00136-z
10.18632/oncotarget.3712
10.1016/j.celrep.2017.07.052
10.1016/j.ccell.2016.10.009
10.1038/nrm2720
10.1038/nature25432
10.1007/978-1-61779-163-5_24
10.1098/rsif.2013.0011
10.1186/s13058-015-0523-1
10.1038/ncomms4963
10.1073/pnas.1508541113
10.1002/cncr.26456
10.1007/978-3-642-03246-2_1
10.1016/j.trecan.2016.06.004
10.1016/j.cell.2015.02.038
10.1172/JCI65105
10.1002/cam4.751
10.1245/s10434-010-0921-7
10.1373/clinchem.2015.253609
10.1093/bioinformatics/bts432
10.1038/ncb3484
10.1038/nature06385
10.1002/hep.22806
10.7150/thno.22717
10.1242/jcs.119974
10.15252/emmm.201303675
10.1007/978-1-4614-1445-2_5
10.1007/s10549-016-4026-2
10.1063/1.5000377
10.1158/0008-5472.CAN-14-3319
10.1039/C8LC00596F
10.1371/journal.pone.0185844
10.1038/nmeth.4627
10.1016/j.chom.2015.06.001
10.1038/nature20609
10.1038/nature15748
10.1038/ncomms15773
10.1016/j.cell.2012.03.031
10.1038/nature13490
10.1101/gr.209973.116
10.1038/s41467-017-01174-3
10.1002/(SICI)1097-0215(19960717)67:2<275::AID-IJC20>3.0.CO;2-9
10.1016/j.copbio.2016.02.007
10.1038/s41598-018-22226-8
10.1016/j.canlet.2013.10.010
10.1093/nar/gkj092
10.1371/journal.pcbi.1005618
10.1016/j.cell.2016.11.037
10.1021/acschembio.8b00099
10.1088/2057-1739/aa7a8d
10.1038/srep42369
10.1073/pnas.1700054114
10.1073/pnas.1210182109
10.1016/j.bpj.2017.08.022
10.1038/srep14739
10.1126/scitranslmed.3007094
10.15252/msb.20177651
10.1038/ncb3513
10.18632/oncotarget.8166
10.1126/scisignal.aaa2155
10.1038/s41598-017-05002-y
10.1371/journal.pcbi.1005991
10.1038/nmeth.4225
10.1089/106652700750050961
10.1073/pnas.1701333114
10.1016/j.cell.2014.07.013
10.1038/nature15756
10.1155/2018/9780349
10.1038/nature14971
10.1016/j.trecan.2018.01.008
10.1016/bs.acr.2016.07.005
10.1242/bio.019703
10.1038/nmeth.2869
10.1371/journal.pone.0028074
10.1126/science.aat9804
10.1093/bioinformatics/bts025
10.1016/j.neuroimage.2018.09.008
10.1016/j.semcancer.2014.04.001
10.1038/nature23306
10.1002/stem.2286
10.1186/s13045-015-0204-7
10.1371/journal.pone.0118060
10.1080/17460441.2017.1297416
10.3390/ijms17071151
10.1038/ncomms12685
10.1007/s10549-010-0747-9
10.1038/srep38244
10.1074/jbc.M112.392332
10.1038/nature13480
10.1038/ncb3465
10.1073/pnas.1121160109
10.1016/S1097-2765(02)00528-2
10.1038/nature15376
10.1371/journal.pone.0034637
10.1016/j.ccr.2005.08.003
10.1158/0008-5472.CAN-16-2844
10.1126/scisignal.2004008
10.1158/0008-5472.CAN-14-1428
10.1172/jci.insight.121490
10.1038/s41467-017-01171-6
10.1038/s41598-018-35695-8
10.1093/bioinformatics/btg015
10.1038/nature17038
10.1002/adhm.201700903
10.3389/fbioe.2016.00012
10.1038/bjc.2014.533
10.1074/jbc.M114.615534
10.1038/nmeth.4179
10.1038/sj.onc.1209755
10.1038/s41467-017-02481-5
10.1186/s13059-015-0700-7
10.1074/mcp.RA117.000370
10.1073/pnas.1700600114
10.1158/2159-8290.CD-15-0933
10.1016/j.cell.2014.09.021
10.1073/pnas.96.8.4494
10.1371/journal.pcbi.1003460
10.1242/dmm.030403
10.1038/ncb3169
10.1038/nprot.2007.99
10.1093/imammb/dqq011
10.1186/s41236-017-0005-8
10.1016/j.critrevonc.2015.08.009
10.1038/nrc1098
10.1016/j.celrep.2014.08.029
10.1016/j.cell.2015.11.062
10.1586/14737159.2015.1091311
10.1158/1078-0432.CCR-12-3180
10.1098/rsif.2005.0109
10.1038/cr.2012.89
10.1103/PhysRevB.95.245134
10.1016/j.tibtech.2016.02.016
10.1126/science.1228522
10.1136/gutjnl-2016-313372
10.1158/2159-8290.CD-14-0380
10.1016/j.drudis.2018.01.039
10.1038/s41467-017-00786-z
10.1038/msb.2013.1
10.1126/science.aaf6546
10.1038/nature14897
10.1038/srep26286
10.1158/0008-5472.CAN-14-0225
10.1016/j.cell.2018.05.015
10.1038/srep00802
10.1016/j.celrep.2018.10.004
10.1038/srep19103
10.1038/nbt.3569
10.1016/j.ymeth.2017.07.019
10.1016/j.jbi.2011.11.015
10.1038/nm.1789
10.1186/s12859-016-1361-6
10.1038/ncb1616
10.1016/S1470-2045(16)30067-5
10.1186/s13045-018-0560-1
ContentType Journal Article
Copyright 2019 The Authors
Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.
Copyright_xml – notice: 2019 The Authors
– notice: Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.
DBID 6I.
AAFTH
AAYXX
CITATION
CGR
CUY
CVF
ECM
EIF
NPM
7X8
5PM
DOI 10.1016/j.cels.2019.07.003
DatabaseName ScienceDirect Open Access Titles
Elsevier:ScienceDirect:Open Access
CrossRef
Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
MEDLINE - Academic
PubMed Central (Full Participant titles)
DatabaseTitle CrossRef
MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
MEDLINE - Academic
DatabaseTitleList MEDLINE - Academic

MEDLINE

Database_xml – sequence: 1
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 2
  dbid: EIF
  name: MEDLINE
  url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search
  sourceTypes: Index Database
DeliveryMethod fulltext_linktorsrc
EISSN 2405-4720
EndPage 127
ExternalDocumentID PMC6716621
31465728
10_1016_j_cels_2019_07_003
S2405471219302340
Genre Journal Article
Review
Research Support, N.I.H., Extramural
GrantInformation_xml – fundername: NCI NIH HHS
  grantid: U54 CA209992
GroupedDBID 0R~
457
6I.
AACTN
AAEDW
AAFTH
AAIAV
AAIKJ
AALRI
AAVLU
AAXUO
ABJNI
ABMAC
ABVKL
ACGFS
ADBBV
ADJPV
AFTJW
AHDRD
ALMA_UNASSIGNED_HOLDINGS
AMRAJ
EBS
EJD
FDB
JIG
M41
O9-
OK1
RCE
AAMRU
AAYWO
AAYXX
ABDGV
ACVFH
ADCNI
ADVLN
AEUPX
AFPUW
AGCQF
AIGII
AITUG
AKAPO
AKBMS
AKRWK
AKYEP
APXCP
CITATION
ROL
SSZ
CGR
CUY
CVF
ECM
EFKBS
EIF
NPM
7X8
5PM
ID FETCH-LOGICAL-c455t-de48bb9fdb9acb8bfe8ad4cd425dabe9d2f09a4313b7b70673aad5000ccf7f5d3
ISSN 2405-4712
2405-4720
IngestDate Thu Aug 21 18:28:50 EDT 2025
Fri Jul 11 06:29:37 EDT 2025
Mon Jul 21 06:06:39 EDT 2025
Thu Apr 24 23:00:32 EDT 2025
Tue Jul 01 04:22:57 EDT 2025
Fri Feb 23 02:33:22 EST 2024
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 2
Keywords
Language English
License This is an open access article under the CC BY license.
Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.
LinkModel OpenURL
MergedId FETCHMERGED-LOGICAL-c455t-de48bb9fdb9acb8bfe8ad4cd425dabe9d2f09a4313b7b70673aad5000ccf7f5d3
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
ObjectType-Review-3
content type line 23
Authors contributed equally to the manuscript.
OpenAccessLink https://dx.doi.org/10.1016/j.cels.2019.07.003
PMID 31465728
PQID 2283110677
PQPubID 23479
PageCount 19
ParticipantIDs pubmedcentral_primary_oai_pubmedcentral_nih_gov_6716621
proquest_miscellaneous_2283110677
pubmed_primary_31465728
crossref_citationtrail_10_1016_j_cels_2019_07_003
crossref_primary_10_1016_j_cels_2019_07_003
elsevier_sciencedirect_doi_10_1016_j_cels_2019_07_003
ProviderPackageCode CITATION
AAYXX
PublicationCentury 2000
PublicationDate 2019-08-28
PublicationDateYYYYMMDD 2019-08-28
PublicationDate_xml – month: 08
  year: 2019
  text: 2019-08-28
  day: 28
PublicationDecade 2010
PublicationPlace United States
PublicationPlace_xml – name: United States
PublicationTitle Cell systems
PublicationTitleAlternate Cell Syst
PublicationYear 2019
Publisher Elsevier Inc
Publisher_xml – name: Elsevier Inc
References Herrick, Lin, Peterson, Schnittke, Schwob (bib68) 2017; 114
Ronaldson-Bouchard, Vunjak-Novakovic (bib159) 2018; 22
Morales, Arenas, Urosevic, Guiu, Fernández, Planet, Fenwick, Fernández-Ruiz, Salvatella, Reverter (bib137) 2014; 6
Korkut, Wang, Demir, Aksoy, Jing, Molinelli, Babur, Bemis, Onur Sumer, Solit (bib98) 2015; 4
Singh, Brito, Lammerding (bib180) 2018; 4
Chaturvedi, Gilkes, Wong, Kshitiz, Luo, Zhang, Wei, Takano, Schito, Levchenko (bib28) 2013; 123
Zheng, Carstens, Kim, Scheible, Kaye, Sugimoto, Wu, LeBleu, Kalluri (bib224) 2015; 527
Scott, Basanta, Anderson, Gerlee (bib169) 2013; 10
Teschendorff, Severini (bib192) 2010; 4
Court, Ankeny, Hou, Tseng, Tomlinson (bib39) 2015; 15
Joseph, Gnanapragasam (bib85) 2011; 755
Rojas-Puentes, Cardona, Carranza, Vargas, Jaramillo, Zea, Cetina, Wills, Ruiz-Garcia, Arrieta (bib158) 2016; 5
Seo, Bhardwaj, Choi, Gonzalez, Andresen Eguiluz, Wang, Mohanan, Morris, Du, Zhou (bib172) 2015; 7
Schindler, Regnault, Neupert (bib167) 2017; 95
Jeon, Bersini, Whisler, Chen, Dubini, Charest, Moretti, Kamm (bib79) 2014; 6
Lehmann, Te Boekhorst, Odenthal, Bianchi, van Helvert, Ikenberg, Ilina, Stoma, Xandry, Jiang (bib108) 2017; 27
Whittle, Lewis, Lindeman, Visvader (bib210) 2015; 17
Walsh, Alvarez, Sabio, Reyngold, Makarov, Mukherjee, Lee, Desrichard, Turcan, Dalin (bib203) 2017; 20
Alexander, Koehl, Hirschberg, Geissler, Friedl (bib6) 2008; 130
Liu, Stojadinovic, Hrycushko, Wardak, Lau, Lu, Yan, Jiang, Zhen, Timmerman (bib120) 2017; 12
Miller, Oudin, Sullivan, Wang, Meyer, Im, Frederick, Tadros, Griffith, Lee (bib133) 2016; 6
In, Mason, Lin, Newton, Kuhn, Nieva (bib78) 2017; 3
Liang, Wu, Lei, Chong, Wei, Lu, Tagkopoulos, Kung, Yang, Hu (bib116) 2012; 287
Hoshino, Costa-Silva, Shen, Rodrigues, Hashimoto, Tesic Mark, Molina, Kohsaka, Di Giannatale, Ceder (bib71) 2015; 527
Lopez, Muhlich, Bachman, Sorger (bib121) 2013; 9
Han, Yuan, Zheng, Yang, Li, Edgerton, Diao, Xu, Verhaak, Liang (bib62) 2014; 5
Pradeep, Kim, Wu, Nishimura, Chaluvally-Raghavan, Miyake, Pecot, Kim, Choi, Bischoff (bib151) 2014; 26
Klein, Schmidt-Kittler, Schardt, Pantel, Speicher, Riethmüller (bib93) 1999; 96
Pennisi, Cavalieri, Motta, Pappalardo (bib147) 2016; 17
Li, Knutsdottir, Hui, Weiss, He, Philosophe, Cameron, Wolfgang, Pawlik, Ghiaur (bib113) 2019; 4
Ilina, Campanello, Gritsenko, Vullings, Wang, Bult, Losert, Friedl (bib77) 2018; 11
Enokida, Shiina, Urakami, Igawa, Ogishima, Li, Kawahara, Nakagawa, Kane, Carroll (bib43) 2005; 11
Ilie, Hofman, Ortholan, Bonnetaud, Coëlle, Mouroux, Hofman (bib76) 2012; 118
Clark, Kumar, Wheeler, Young, Venkataramanan, Stolz, Griffith, Lauffenburger, Wells (bib36) 2018; 17
Roy, Steyer, Gargesha, Stone, Wilson (bib161) 2009; 292
Goldsmith, Fiala, Dukeman, Ghobadi, Stockerl-Goldstein, Schroeder, Tomasson, Wildes, Vij (bib59) 2019; 19
Jia, Jolly, Tripathi, Den Hollander, Huang, Lu, Celiktas, Ramirez-Peña, Ben-Jacob, Onuchic (bib81) 2017; 1
Letort, Montagud, Stoll, Heiland, Barillot, Macklin, Zinovyev, Calzone (bib110) 2019; 35
Tape, Ling, Dimitriadi, McMahon, Worboys, Leong, Norrie, Miller, Poulogiannis, Lauffenburger (bib189) 2016; 165
Giese, Loo, Tran, Haskett, Coons, Berens (bib57) 1996; 67
Park, Holmes, Lee, Kim, Kim, Kwak, Wang, Edelstein-Keshet, Levchenko (bib145) 2017; 114
van Maaren, de Munck, de Bock, Jobsen, van Dalen, Linn, Poortmans, Strobbe, Siesling (bib197) 2016; 17
Lee, Stone, Porrett, Thomas, Komar, Li, Delman, Graham, Gladney, Hua (bib106) 2019; 567
Poleszczuk, Hahnfeldt, Enderling (bib150) 2015; 11
Chen, Alvarez, Talos, Dhruv, Rieckhof, Iyer, Diefes, Aldape, Berens, Shen (bib30) 2014; 159
Lange, Oh-Hohenhorst, Joosse, Pantel, Hahn, Gosau, Dyshlovoy, Wellbrock, Feldhaus, Maar (bib104) 2018; 8
Bakhoum, Ngo, Laughney, Cavallo, Murphy, Ly, Shah, Sriram, Watkins, Taunk (bib8) 2018; 553
Shin, Lee, Gong, Cho (bib177) 2017; 8
Barault, Amatu, Siravegna, Ponzetti, Moran, Cassingena, Mussolin, Falcomatà, Binder, Cristiano (bib9) 2018; 67
Cheung, Padmanaban, Silvestri, Schipper, Cohen, Fairchild, Gorin, Verdone, Pienta, Bader (bib34) 2016; 113
Wang, Mu, Chervoneva, Austin, Ye, Rossi, Palazzo, Sun, Abu-Khalaf, Myers (bib204) 2017; 161
Samek, Wiegand, Müller (bib164) 2017
Litjens, Sánchez, Timofeeva, Hermsen, Nagtegaal, Kovacs, Hulsbergen-van de Kaa, Bult, van Ginneken, van der Laak (bib118) 2016; 6
Yu, Ma, Fisher, Kreisberg, Raphael, Ideker (bib216) 2018; 173
Carcereri de Prati, Butturini, Rigo, Oppici, Rossin, Boriero, Mariotto (bib25) 2017; 118
Kalhor, Kalhor, Mejia, Leeper, Graveline, Mali, Church (bib87) 2018; 361
Li, Jiang, Zhao, Zhao, Cao, Zhao, Han, Wang, Yu, Peng (bib114) 2016; 7
Friedl, Gilmour (bib49) 2009; 10
Zhang, He, Zhang (bib221) 2019; 9
Gómez-Cuadrado, Tracey, Ma, Qian, Brunton (bib60) 2017; 10
Diehl, Schmidt, Choti, Romans, Goodman, Li, Thornton, Agrawal, Sokoll, Szabo (bib41) 2008; 14
Ting, Wittner, Ligorio, Vincent Jordan, Shah, Miyamoto, Aceto, Bersani, Brannigan, Xega (bib193) 2014; 8
Bush, Ray, Alvarez, Realubit, Li, Karan, Califano, Sims (bib21) 2017; 8
Kadakia, Tomlins, Sanghvi, Cani, Omata, Hovelson, Liu, Cooney (bib86) 2015; 8
Pal, Heidenreich, Vormoor (bib144) 2016; 30
Uhl, Muzykantov, Liu (bib196) 2018; 12
Friedman, Linial, Nachman, Pe'er (bib50) 2000; 7
Basanta, Anderson (bib10) 2017; 7
Rhee, Seo, Kim (bib154) 2018
Katt, Placone, Wong, Xu, Searson (bib90) 2016; 4
Lambert, Pattabiraman, Weinberg (bib103) 2017; 168
Zhao, Li, Yang, Li, Tian, Li (bib222) 2018; 17
Karamboulas, Bruce, Hope, Meens, Huang, Erdmann, Hyatt, Pereira, Goldstein, Weinreb (bib89) 2018; 25
McGillivray, Golden, Kaushal (bib130) 2015; 290
Heinrich, Neel, Rapoport (bib67) 2002; 9
Wheeler, Clark, Taylor, Young, Pillai, Stolz, Venkataramanan, Lauffenburger, Griffith, Wells (bib209) 2014; 111
Entenberg, Pastoriza, Oktay, Voiculescu, Wang, Sosa, Aguirre-Ghiso, Condeelis (bib44) 2017; 128
Herzog, Jiang, Herman, Zhao, Sanganahalli, Mason, Hyder, Rothman, Sherwin, Behar (bib69) 2013; 123
Moncada, Wagner, Chiodin, Devlin, Baron, Hajdu, Simeone, Yanai (bib136) 2019
Rongvaux, Willinger, Martinek, Strowig, Gearty, Teichmann, Saito, Marches, Halene, Palucka (bib160) 2017; 35
Harper, Sosa, Entenberg, Hosseini, Cheung, Nobre, Avivar-Valderas, Nagi, Girnius, Davis (bib64) 2016; 540
Garcia, Millat-Carus, Bertucci, Finetti, Birnbaum, Bidaut (bib52) 2012; 28
Hatzikirou, Basanta, Simon, Schaller, Deutsch (bib65) 2012; 29
Schillaci, Fontana, Monteleone, Taverna, Di Bella, Di Vizio, Alessandro (bib166) 2017; 7
Zangooei, Habibi (bib217) 2017; 12
Speer, Petrosky, Retsky, Wardwell (bib182) 1984; 44
Al-Ahmadie, Iyer, Hohl, Asthana, Inagaki, Schultz, Hanrahan, Scott, Brannon, McDermott (bib5) 2014; 4
Le Novère, Bornstein, Broicher, Courtot, Donizelli, Dharuri, Li, Sauro, Schilstra, Shapiro (bib105) 2006; 34
Brown, Schiavone, Tazzyman, Heymann, Chico (bib20) 2017; 12
Xue, Lu, Eisele, Sulistijo, Khan, Fan, Miller-Jensen (bib213) 2015; 8
Villani, Satija, Reynolds, Sarkizova, Shekhar, Fletcher, Griesbeck, Butler, Zheng, Lazo (bib201) 2017; 356
Board, Wardley, Dixon, Armstrong, Howell, Renshaw, Donald, Greystoke, Ranson, Hughes (bib16) 2010; 120
Liu, Huang, Wheeler, Xu, Wells, Song, Wiita (bib119) 2017; 4
Sikandar, Kuo, Kalisky, Cai, Zabala, Hsieh, Lobo, Scheeren, Sim, Qian (bib179) 2017; 8
Kalluri (bib88) 2016; 16
Zheng, Chen, Li, Haura, Sharma, Bepler (bib225) 2007; 356
Yu, Bardia, Wittner, Stott, Smas, Ting, Isakoff, Ciciliano, Wells, Shah (bib215) 2013; 339
Meyer, Liu (bib131) 2014; 15
Hwang, Thumar, Lundgren, Rezaul, Mayya, Wu, Eng, Wright, Han (bib74) 2007; 26
Massagué, Obenauf (bib129) 2016; 529
Aguilar, Marin de Mas, Zodda, Marin, Morrish, Selivanov, Meca-Cortés, Delowar, Pons, Izquierdo (bib3) 2016; 34
Neelakantan, Zhou, Oliphant, Zhang, Simon, Henke, Shaw, Wu, Hilsenbeck, White (bib140) 2017; 8
Heilmann, Ratnakumar, Langdon, Kansler, Kim, Campbell, Perry, McMahon, Kaufman, van Rooijen (bib66) 2015; 75
Shangguan, Gan, Zhang, Wu, Miao, Zhang, Li, Mi (bib175) 2018; 8
Kyriakakis, Markaki, Tavernarakis (bib102) 2015; 2
Nagrath, Sequist, Maheswaran, Bell, Irimia, Ulkus, Smith, Kwak, Digumarthy, Muzikansky (bib139) 2007; 450
Persi, Duran-Frigola, Damaghi, Roush, Aloy, Cleveland, Gillies, Ruppin (bib149) 2018; 9
Lu, Zeng, Liang, Chen, Zhang, Zhang, Liu, Jiang, Shen, Huang (bib122) 2015; 5
Tape (bib188) 2016; 34
Jiang, Wang, Yang, Chen, Pang, Guo, Cai, Wery, Li, Li (bib83) 2015; 6
Konen, Summerbell, Dwivedi, Galior, Hou, Rusnak, Chen, Saltz, Zhou, Boise (bib96) 2017; 8
Camacho, Collins, Powers, Costello, Collins (bib22) 2018; 173
West, Bianconi, Severini, Teschendorff (bib208) 2012; 2
Becker, Thakur, Weiss, Kim, Peinado, Lyden (bib11) 2016; 30
Ghajar, Peinado, Mori, Matei, Evason, Brazier, Almeida, Koller, Hajjar, Stainier (bib55) 2013; 15
Knox, Kim, Zhu, Chan (bib94) 2018; 13
Cancer Genome Atlas Research (bib23) 2014; 513
Seidel, Kimble (bib170) 2011; 6
Waclaw, Bozic, Pittman, Hruban, Vogelstein, Nowak (bib202) 2015; 525
Li, Liu, Wang, Li, Wang, Huang, Huang, Yuan (bib112) 2010; 17
Ma, Yu, Fong, Ono, Sage, Demchak, Sharan, Ideker (bib123) 2018; 15
Ma, Zhang (bib124) 2018
Costa-Silva, Aiello, Ocean, Singh, Zhang, Thakur, Becker, Hoshino, Mark, Molina (bib38) 2015; 17
Wells, Griffith, Wells, Taylor (bib207) 2013; 73
Cheung, Gabrielson, Werb, Ewald (bib33) 2013; 155
Becker, Feist, Mo, Hannum, Palsson, Herrgard (bib12) 2007; 2
Giesen, Wang, Schapiro, Zivanovic, Jacobs, Hattendorf, Schüffler, Grolimund, Buhmann, Brandt (bib58) 2014; 11
Linde, Casanova-Acebes, Sosa, Mortha, Rahman, Farias, Harper, Tardio, Reyes Torres, Jones (bib117) 2018; 9
Schubert, Ludwig, Kogadeeva, Zimmermann, Rosenberger, Gengenbacher, Gillet, Collins, Röst, Kaufmann (bib168) 2015; 18
Chow, Guzman, Wang, Schmidt, Youngblood, Ye, Errami, Dong, Martinez, Zhang (bib35) 2017; 20
Garrigou, Perkins, Garlan, Normand, Didelot, Le Corre, Peyvandi, Mulot, Niarra, Aucouturier (bib53) 2016; 62
Dzeroski, Todorovski (bib42) 2008; 19
Jolly, Tripathi, Jia, Mooney, Celiktas, Hanash, Mani, Pienta, Ben-Jacob, Levine (bib84) 2016; 7
Suijkerbuijk, van Rheenen (bib186) 2017; 428
Setty, Tadmor, Reich-Zeliger, Angel, Salame, Kathail, Choi, Bendall, Friedman, Pe'er (bib173) 2016; 34
Ahmad, Deris,
Ewald (10.1016/j.cels.2019.07.003_bib45) 2017; 19
Blanco (10.1016/j.cels.2019.07.003_bib14) 2012; 22
Wolf (10.1016/j.cels.2019.07.003_bib211) 2007; 9
Broecker (10.1016/j.cels.2019.07.003_bib19) 2017; 7
Goldsmith (10.1016/j.cels.2019.07.003_bib59) 2019; 19
Litjens (10.1016/j.cels.2019.07.003_bib118) 2016; 6
Bakhoum (10.1016/j.cels.2019.07.003_bib8) 2018; 553
Krebs (10.1016/j.cels.2019.07.003_bib100) 2017; 19
Shen (10.1016/j.cels.2019.07.003_bib176) 2017; 14
Giese (10.1016/j.cels.2019.07.003_bib57) 1996; 67
Carcereri de Prati (10.1016/j.cels.2019.07.003_bib25) 2017; 118
Garrigou (10.1016/j.cels.2019.07.003_bib53) 2016; 62
Milanovic (10.1016/j.cels.2019.07.003_bib132) 2018; 553
Harney (10.1016/j.cels.2019.07.003_bib63) 2015; 5
Entenberg (10.1016/j.cels.2019.07.003_bib44) 2017; 128
Fischer (10.1016/j.cels.2019.07.003_bib47) 2015; 527
Miloushev (10.1016/j.cels.2019.07.003_bib134) 2018; 78
Wang (10.1016/j.cels.2019.07.003_bib205) 2016
Cheung (10.1016/j.cels.2019.07.003_bib34) 2016; 113
Miller (10.1016/j.cels.2019.07.003_bib133) 2016; 6
Zhao (10.1016/j.cels.2019.07.003_bib222) 2018; 17
Zheng (10.1016/j.cels.2019.07.003_bib223) 2018; 11
Pal (10.1016/j.cels.2019.07.003_bib144) 2016; 30
Aguilar (10.1016/j.cels.2019.07.003_bib3) 2016; 34
Katt (10.1016/j.cels.2019.07.003_bib90) 2016; 4
Kshitiz Gupta (10.1016/j.cels.2019.07.003_bib101) 2019
Malladi (10.1016/j.cels.2019.07.003_bib126) 2016; 165
Ilina (10.1016/j.cels.2019.07.003_bib77) 2018; 11
Lu (10.1016/j.cels.2019.07.003_bib122) 2015; 5
Shangguan (10.1016/j.cels.2019.07.003_bib175) 2018; 8
Ilie (10.1016/j.cels.2019.07.003_bib76) 2012; 118
Liu (10.1016/j.cels.2019.07.003_bib119) 2017; 4
Al-Ahmadie (10.1016/j.cels.2019.07.003_bib5) 2014; 4
Jiang (10.1016/j.cels.2019.07.003_bib83) 2015; 6
Li (10.1016/j.cels.2019.07.003_bib113) 2019; 4
Gómez-Cuadrado (10.1016/j.cels.2019.07.003_bib60) 2017; 10
Court (10.1016/j.cels.2019.07.003_bib39) 2015; 15
Marcotte (10.1016/j.cels.2019.07.003_bib127) 2016; 164
Jespersen (10.1016/j.cels.2019.07.003_bib80) 2017; 8
Pennisi (10.1016/j.cels.2019.07.003_bib147) 2016; 17
Sosa (10.1016/j.cels.2019.07.003_bib181) 2013; 734
10.1016/j.cels.2019.07.003_bib148
Dzeroski (10.1016/j.cels.2019.07.003_bib42) 2008; 19
Friedman (10.1016/j.cels.2019.07.003_bib50) 2000; 7
Kalhor (10.1016/j.cels.2019.07.003_bib87) 2018; 361
Korkut (10.1016/j.cels.2019.07.003_bib98) 2015; 4
Chen (10.1016/j.cels.2019.07.003_bib31) 2015; 160
Aguado (10.1016/j.cels.2019.07.003_bib2) 2018; 7
Alexander (10.1016/j.cels.2019.07.003_bib6) 2008; 130
Joseph (10.1016/j.cels.2019.07.003_bib85) 2011; 755
Le Novère (10.1016/j.cels.2019.07.003_bib105) 2006; 34
Chow (10.1016/j.cels.2019.07.003_bib35) 2017; 20
Sikandar (10.1016/j.cels.2019.07.003_bib179) 2017; 8
Gyori (10.1016/j.cels.2019.07.003_bib61) 2017; 13
Knox (10.1016/j.cels.2019.07.003_bib94) 2018; 13
Spill (10.1016/j.cels.2019.07.003_bib183) 2016; 40
Linde (10.1016/j.cels.2019.07.003_bib117) 2018; 9
McGillivray (10.1016/j.cels.2019.07.003_bib130) 2015; 290
Setty (10.1016/j.cels.2019.07.003_bib173) 2016; 34
van Maaren (10.1016/j.cels.2019.07.003_bib197) 2016; 17
Jolly (10.1016/j.cels.2019.07.003_bib84) 2016; 7
Clark (10.1016/j.cels.2019.07.003_bib36) 2018; 17
Costa-Silva (10.1016/j.cels.2019.07.003_bib38) 2015; 17
Karamboulas (10.1016/j.cels.2019.07.003_bib89) 2018; 25
Lange (10.1016/j.cels.2019.07.003_bib104) 2018; 8
Ma (10.1016/j.cels.2019.07.003_bib124) 2018
Persi (10.1016/j.cels.2019.07.003_bib149) 2018; 9
Roy (10.1016/j.cels.2019.07.003_bib161) 2009; 292
Leiserson (10.1016/j.cels.2019.07.003_bib109) 2015; 16
Chaturvedi (10.1016/j.cels.2019.07.003_bib28) 2013; 123
Furukawa (10.1016/j.cels.2019.07.003_bib51) 2015; 10
Ibrahim-Hashim (10.1016/j.cels.2019.07.003_bib75) 2017; 77
Steinway (10.1016/j.cels.2019.07.003_bib185) 2014; 74
Kyriakakis (10.1016/j.cels.2019.07.003_bib102) 2015; 2
Zheng (10.1016/j.cels.2019.07.003_bib225) 2007; 356
Fidler (10.1016/j.cels.2019.07.003_bib46) 2003; 3
Li (10.1016/j.cels.2019.07.003_bib114) 2016; 7
Zheng (10.1016/j.cels.2019.07.003_bib224) 2015; 527
Liang (10.1016/j.cels.2019.07.003_bib116) 2012; 287
Ghajar (10.1016/j.cels.2019.07.003_bib55) 2013; 15
Chen (10.1016/j.cels.2019.07.003_bib29) 2018; 23
Giesen (10.1016/j.cels.2019.07.003_bib58) 2014; 11
Basanta (10.1016/j.cels.2019.07.003_bib10) 2017; 7
Tanay (10.1016/j.cels.2019.07.003_bib187) 2017; 541
Rhim (10.1016/j.cels.2019.07.003_bib155) 2012; 148
Herrick (10.1016/j.cels.2019.07.003_bib68) 2017; 114
Carmona-Fontaine (10.1016/j.cels.2019.07.003_bib26) 2017; 114
Kipf (10.1016/j.cels.2019.07.003_bib91) 2016
Rojas-Puentes (10.1016/j.cels.2019.07.003_bib158) 2016; 5
Hua (10.1016/j.cels.2019.07.003_bib72) 2006; 3
In (10.1016/j.cels.2019.07.003_bib78) 2017; 3
Ståhl (10.1016/j.cels.2019.07.003_bib184) 2016; 353
Min (10.1016/j.cels.2019.07.003_bib135) 2017; 18
Cao (10.1016/j.cels.2019.07.003_bib24) 2016; 111
Harper (10.1016/j.cels.2019.07.003_bib64) 2016; 540
van Marion (10.1016/j.cels.2019.07.003_bib198) 2016; 97
Barault (10.1016/j.cels.2019.07.003_bib9) 2018; 67
Kirouac (10.1016/j.cels.2019.07.003_bib92) 2013; 6
Kochańczyk (10.1016/j.cels.2019.07.003_bib95) 2017; 7
Kalluri (10.1016/j.cels.2019.07.003_bib88) 2016; 16
Cheung (10.1016/j.cels.2019.07.003_bib33) 2013; 155
Nguyen (10.1016/j.cels.2019.07.003_bib142) 2013; 126
Waclaw (10.1016/j.cels.2019.07.003_bib202) 2015; 525
Massagué (10.1016/j.cels.2019.07.003_bib129) 2016; 529
Newton (10.1016/j.cels.2019.07.003_bib141) 2012; 7
Qutaish (10.1016/j.cels.2019.07.003_bib152) 2018; 2018
Seidel (10.1016/j.cels.2019.07.003_bib170) 2011; 6
Walsh (10.1016/j.cels.2019.07.003_bib203) 2017; 20
Wheeler (10.1016/j.cels.2019.07.003_bib209) 2014; 111
Zervantonakis (10.1016/j.cels.2019.07.003_bib219) 2012; 109
Samek (10.1016/j.cels.2019.07.003_bib164) 2017
Bahado-Singh (10.1016/j.cels.2019.07.003_bib7) 2017; 7
Seo (10.1016/j.cels.2019.07.003_bib172) 2015; 7
Ronaldson-Bouchard (10.1016/j.cels.2019.07.003_bib159) 2018; 22
Garcia (10.1016/j.cels.2019.07.003_bib52) 2012; 28
Lopez (10.1016/j.cels.2019.07.003_bib121) 2013; 9
Whittle (10.1016/j.cels.2019.07.003_bib210) 2015; 17
Villani (10.1016/j.cels.2019.07.003_bib201) 2017; 356
Diehl (10.1016/j.cels.2019.07.003_bib41) 2008; 14
Senft (10.1016/j.cels.2019.07.003_bib171) 2016; 2
Zhang (10.1016/j.cels.2019.07.003_bib220) 2015; 527
Shamir (10.1016/j.cels.2019.07.003_bib174) 2016; 5
10.1016/j.cels.2019.07.003_bib40
Saengwimol (10.1016/j.cels.2019.07.003_bib163) 2018; 8
Fluegen (10.1016/j.cels.2019.07.003_bib48) 2017; 19
Tirosh (10.1016/j.cels.2019.07.003_bib194) 2016; 352
Li (10.1016/j.cels.2019.07.003_bib112) 2010; 17
Robinson (10.1016/j.cels.2019.07.003_bib157) 2017; 548
Aceto (10.1016/j.cels.2019.07.003_bib1) 2014; 158
Shirure (10.1016/j.cels.2019.07.003_bib178) 2018; 18
Hoshino (10.1016/j.cels.2019.07.003_bib71) 2015; 527
Teschendorff (10.1016/j.cels.2019.07.003_bib192) 2010; 4
Jia (10.1016/j.cels.2019.07.003_bib82) 2014; 10
Tape (10.1016/j.cels.2019.07.003_bib188) 2016; 34
Moncada (10.1016/j.cels.2019.07.003_bib136) 2019
Cancer Genome Atlas Research (10.1016/j.cels.2019.07.003_bib23) 2014; 513
Chandler (10.1016/j.cels.2019.07.003_bib27) 2012; 109
König (10.1016/j.cels.2019.07.003_bib97) 2012; 28
Ahmad (10.1016/j.cels.2019.07.003_bib4) 2012; 45
Hatzikirou (10.1016/j.cels.2019.07.003_bib65) 2012; 29
Nagrath (10.1016/j.cels.2019.07.003_bib139) 2007; 450
Han (10.1016/j.cels.2019.07.003_bib62) 2014; 5
Blinov (10.1016/j.cels.2019.07.003_bib15) 2017; 113
Gierahn (10.1016/j.cels.2019.07.003_bib56) 2017; 14
Shin (10.1016/j.cels.2019.07.003_bib177) 2017; 8
Zhang (10.1016/j.cels.2019.07.003_bib221) 2019; 9
Speer (10.1016/j.cels.2019.07.003_bib182) 1984; 44
Zanoni (10.1016/j.cels.2019.07.003_bib218) 2016; 6
Heilmann (10.1016/j.cels.2019.07.003_bib66) 2015; 75
Jeon (10.1016/j.cels.2019.07.003_bib79) 2014; 6
Olivença (10.1016/j.cels.2019.07.003_bib143) 2018; 8
Meyer (10.1016/j.cels.2019.07.003_bib131) 2014; 15
Cheung (10.1016/j.cels.2019.07.003_bib32) 2016; 352
Ghaffarizadeh (10.1016/j.cels.2019.07.003_bib54) 2018; 14
Neelakantan (10.1016/j.cels.2019.07.003_bib140) 2017; 8
Xue (10.1016/j.cels.2019.07.003_bib213) 2015; 8
Schubert (10.1016/j.cels.2019.07.003_bib168) 2015; 18
Koush (10.1016/j.cels.2019.07.003_bib99) 2019; 184
Bush (10.1016/j.cels.2019.07.003_bib21) 2017; 8
Brown (10.1016/j.cels.2019.07.003_bib20) 2017; 12
Scott (10.1016/j.cels.2019.07.003_bib169) 2013; 10
West (10.1016/j.cels.2019.07.003_bib208) 2012; 2
Robertson-Tessi (10.1016/j.cels.2019.07.003_bib156) 2015; 75
Heinrich (10.1016/j.cels.2019.07.003_bib67) 2002; 9
Poleszczuk (10.1016/j.cels.2019.07.003_bib150) 2015; 11
Klein (10.1016/j.cels.2019.07.003_bib93) 1999; 96
Muzumdar (10.1016/j.cels.2019.07.003_bib138) 2016; 7
Rhee (10.1016/j.cels.2019.07.003_bib154) 2018
Singh (10.1016/j.cels.2019.07.003_bib180) 2018; 4
Becker (10.1016/j.cels.2019.07.003_bib11) 2016; 30
Brannon (10.1016/j.cels.2019.07.003_bib18) 2013; 123
Te Boekhorst (10.1016/j.cels.2019.07.003_bib191) 2016; 132
Brady (10.1016/j.cels.2019.07.003_bib17) 2017; 8
Herzog (10.1016/j.cels.2019.07.003_bib69) 2013; 123
Letort (10.1016/j.cels.2019.07.003_bib110) 2019; 35
Lambert (10.1016/j.cels.2019.07.003_bib103) 2017; 168
Malaney (10.1016/j.cels.2019.07.003_bib125) 2014; 344
Leung (10.1016/j.cels.2019.07.003_bib111) 2017; 27
Becker (10.1016/j.cels.2019.07.003_bib12) 2007; 2
Uhl (10.1016/j.cels.2019.07.003_bib196) 2018; 12
Vennin (10.1016/j.cels.2019.07.003_bib200) 2016; 5
Yu (10.1016/j.cels.2019.07.003_bib215) 2013; 339
Chen (10.1016/j.cels.2019.07.003_bib30) 2014; 159
Morales (10.1016/j.cels.2019.07.003_bib137) 2014; 6
Lehmann (10.1016/j.cels.2019.07.003_bib108) 2017; 27
Ting (10.1016/j.cels.2019.07.003_bib193) 2014; 8
Hofschröer (10.1016/j.cels.2019.07.003_bib70) 2017; 7
Paull (10.1016/j.cels.2019.07.003_bib146) 2013; 29
Schillaci (10.1016/j.cels.2019.07.003_bib166) 2017; 7
Camacho (10.1016/j.cels.2019.07.003_bib22) 2018; 173
Pradeep (10.1016/j.cels.2019.07.003_bib151) 2014; 26
Enokida (10.1016/j.cels.2019.07.003_bib43) 2005; 11
Wu (10.1016/j.cels.2019.07.003_bib212) 2017; 13
Bettegowda (10.1016/j.cels.2019.07.003_bib13) 2014; 6
Ye (10.1016/j.cels.2019.07.003_bib214) 2015; 525
Zangooei (10.1016/j.cels.2019.07.003_bib217) 2017; 12
Wang (10.1016/j.cels.2019.07.003_bib206
References_xml – volume: 19
  start-page: 524
  year: 2003
  end-page: 531
  ident: bib73
  article-title: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
  publication-title: Bioinformatics
– volume: 118
  start-page: 1726
  year: 2012
  end-page: 1737
  ident: bib76
  article-title: Predictive clinical outcome of the intratumoral CD66b-positive neutrophil-to-CD8-positive T-cell ratio in patients with resectable nonsmall cell lung cancer
  publication-title: Cancer
– volume: 17
  start-page: 1158
  year: 2016
  end-page: 1170
  ident: bib197
  article-title: 10 year survival after breast-conserving surgery plus radiotherapy compared with mastectomy in early breast cancer in the Netherlands: a population-based study
  publication-title: Lancet Oncol.
– volume: 113
  start-page: 1365
  year: 2017
  end-page: 1372
  ident: bib15
  article-title: Compartmental and spatial rule-based modeling with virtual cell
  publication-title: Biophys. J.
– volume: 109
  start-page: 13515
  year: 2012
  end-page: 13520
  ident: bib219
  article-title: Three-dimensional microfluidic model for tumor cell intravasation and endothelial barrier function
  publication-title: Proc. Natl. Acad. Sci. USA
– volume: 7
  start-page: 601
  year: 2000
  end-page: 620
  ident: bib50
  article-title: Using Bayesian networks to analyze expression data
  publication-title: J. Comput. Biol.
– volume: 40
  start-page: 41
  year: 2016
  end-page: 48
  ident: bib183
  article-title: Impact of the physical microenvironment on tumor progression and metastasis
  publication-title: Curr. Opin. Biotechnol.
– volume: 8
  start-page: 1905
  year: 2014
  end-page: 1918
  ident: bib193
  article-title: Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells
  publication-title: Cell Rep.
– volume: 9
  start-page: 893
  year: 2007
  end-page: 904
  ident: bib211
  article-title: Multi-step pericellular proteolysis controls the transition from individual to collective cancer cell invasion
  publication-title: Nat. Cell Biol.
– volume: 6
  start-page: 26286
  year: 2016
  ident: bib118
  article-title: Deep learning as a tool for increased accuracy and efficiency of histopathological diagnosis
  publication-title: Sci. Rep.
– volume: 15
  start-page: 1491
  year: 2015
  end-page: 1504
  ident: bib39
  article-title: Improving pancreatic cancer diagnosis using circulating tumor cells: prospects for staging and single-cell analysis
  publication-title: Expert Rev. Mol. Diagn.
– volume: 525
  start-page: 256
  year: 2015
  end-page: 260
  ident: bib214
  article-title: Distinct EMT programs control normal mammary stem cells and tumour-initiating cells
  publication-title: Nature
– volume: 529
  start-page: 298
  year: 2016
  end-page: 306
  ident: bib129
  article-title: Metastatic colonization by circulating tumour cells
  publication-title: Nature
– volume: 290
  start-page: 2351
  year: 2015
  end-page: 2367
  ident: bib130
  article-title: The Mycobacterium tuberculosis Clp gene regulator is required for in vitro reactivation from hypoxia-induced dormancy
  publication-title: J. Biol. Chem.
– volume: 130
  start-page: 1147
  year: 2008
  end-page: 1154
  ident: bib6
  article-title: Dynamic imaging of cancer growth and invasion: a modified skin-fold chamber model
  publication-title: Histochem. Cell Biol.
– volume: 14
  start-page: 985
  year: 2008
  end-page: 990
  ident: bib41
  article-title: Circulating mutant DNA to assess tumor dynamics
  publication-title: Nat. Med.
– volume: 15
  start-page: 290
  year: 2018
  end-page: 298
  ident: bib123
  article-title: Using deep learning to model the hierarchical structure and function of a cell
  publication-title: Nat. Methods
– volume: 7
  start-page: 12685
  year: 2016
  ident: bib138
  article-title: Clonal dynamics following p53 loss of heterozygosity in Kras-driven cancers
  publication-title: Nat. Commun.
– volume: 11
  start-page: dmm034330
  year: 2018
  ident: bib77
  article-title: Intravital microscopy of collective invasion plasticity in breast cancer
  publication-title: Dis. Model Mech.
– volume: 29
  start-page: 49
  year: 2012
  end-page: 65
  ident: bib65
  article-title: 'Go or grow': the key to the emergence of invasion in tumor progression?
  publication-title: Math. Med. Biol.
– volume: 11
  start-page: 417
  year: 2014
  end-page: 422
  ident: bib58
  article-title: Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
  publication-title: Nat. Methods
– volume: 16
  start-page: 160
  year: 2015
  ident: bib109
  article-title: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer
  publication-title: Genome Biol.
– volume: 73
  start-page: 3811
  year: 2013
  end-page: 3816
  ident: bib207
  article-title: The dormancy dilemma: quiescence versus balanced proliferation
  publication-title: Cancer Res.
– volume: 11
  start-page: 16
  year: 2018
  ident: bib223
  article-title: PD-1 axis expression in musculoskeletal tumors and antitumor effect of nivolumab in osteosarcoma model of humanized mouse
  publication-title: J. Hematol. Oncol.
– volume: 3
  start-page: 515
  year: 2006
  end-page: 526
  ident: bib72
  article-title: Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways
  publication-title: J. R. Soc. Interface
– volume: 149
  start-page: 780
  year: 2012
  end-page: 794
  ident: bib107
  article-title: Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks
  publication-title: Cell
– reference: Pennisi, M., Pappalardo, F., and Motta, S. (2009). Agent based modeling of lung metastasis-immune system competition. Lecture Notes in Computer Science. Paper presented at: International Conference on Artificial Immune Systems (Springer), 1–3.
– volume: 114
  start-page: E5589
  year: 2017
  end-page: E5598
  ident: bib68
  article-title: Notch1 maintains dormancy of olfactory horizontal basal cells, a reserve neural stem cell
  publication-title: Proc. Natl. Acad. Sci. USA
– volume: 8
  start-page: 17535
  year: 2018
  ident: bib104
  article-title: Development and characterization of a spontaneously metastatic patient-derived xenograft model of human prostate cancer
  publication-title: Sci. Rep.
– volume: 25
  start-page: 1318
  year: 2018
  end-page: 1331.e4
  ident: bib89
  article-title: Patient-derived xenografts for prognostication and personalized treatment for head and neck squamous cell carcinoma
  publication-title: Cell Rep.
– volume: 165
  start-page: 910
  year: 2016
  end-page: 920
  ident: bib189
  article-title: Oncogenic KRAS regulates tumor cell signaling via stromal reciprocation
  publication-title: Cell
– volume: 67
  start-page: 275
  year: 1996
  end-page: 282
  ident: bib57
  article-title: Dichotomy of astrocytoma migration and proliferation
  publication-title: Int. J. Cancer
– volume: 450
  start-page: 1235
  year: 2007
  end-page: 1239
  ident: bib139
  article-title: Isolation of rare circulating tumour cells in cancer patients by microchip technology
  publication-title: Nature
– volume: 18
  start-page: 96
  year: 2015
  end-page: 108
  ident: bib168
  article-title: Absolute proteome composition and dynamics during dormancy and resuscitation of Mycobacterium tuberculosis
  publication-title: Cell Host Microbe
– volume: 14
  start-page: e1005991
  year: 2018
  ident: bib54
  article-title: PhysiCell: an open source physics-based cell simulator for 3-D multicellular systems
  publication-title: PLoS Comput. Biol.
– volume: 3
  start-page: 035002
  year: 2017
  ident: bib78
  article-title: Development of metastatic brain disease involves progression through lung metastases in EGFR mutated non-small cell lung cancer
  publication-title: Converg. Sci. Phys. Oncol.
– volume: 128
  start-page: 65
  year: 2017
  end-page: 77
  ident: bib44
  article-title: Time-lapsed, large-volume, high-resolution intravital imaging for tissue-wide analysis of single cell dynamics
  publication-title: Methods
– volume: 567
  start-page: 249
  year: 2019
  end-page: 252
  ident: bib106
  article-title: Hepatocytes direct the formation of a pro-metastatic niche in the liver
  publication-title: Nature
– volume: 17
  start-page: 619
  year: 2018
  end-page: 630
  ident: bib36
  article-title: A model of dormant-emergent metastatic breast cancer progression enabling exploration of biomarker signatures
  publication-title: Mol. Cell. Proteomics
– volume: 2018
  start-page: 9780349
  year: 2018
  ident: bib152
  article-title: Cryo-imaging and software platform for analysis of molecular MR imaging of micrometastases
  publication-title: Int. J. Biomed. Imaging
– volume: 513
  start-page: 559
  year: 2014
  end-page: 563
  ident: bib37
  article-title: Functional polarization of tumour-associated macrophages by tumour-derived lactic acid
  publication-title: Nature
– year: 2016
  ident: bib91
  article-title: Semi-supervised classification with graph convolutional networks
  publication-title: arXiv
– volume: 184
  start-page: 101
  year: 2019
  end-page: 108
  ident: bib99
  article-title: Functional MRS with J-edited lactate in human motor cortex at 4T
  publication-title: Neuroimage
– volume: 11
  start-page: 6582
  year: 2005
  end-page: 6588
  ident: bib43
  article-title: Multigene methylation analysis for detection and staging of prostate cancer
  publication-title: Clin. Cancer Res.
– volume: 27
  start-page: 392
  year: 2017
  end-page: 400
  ident: bib108
  article-title: Hypoxia induces a HIF-1-dependent transition from collective-to-amoeboid dissemination in epithelial cancer cells
  publication-title: Curr. Biol.
– volume: 34
  start-page: 627
  year: 2016
  end-page: 637
  ident: bib188
  article-title: Systems biology analysis of heterocellular signaling
  publication-title: Trends Biotechnol.
– volume: 18
  start-page: 1131
  year: 2004
  end-page: 1143
  ident: bib199
  article-title: Snail blocks the cell cycle and confers resistance to cell death
  publication-title: Genes Dev.
– volume: 17
  start-page: 816
  year: 2015
  end-page: 826
  ident: bib38
  article-title: Pancreatic cancer exosomes initiate pre-metastatic niche formation in the liver
  publication-title: Nat. Cell Biol.
– volume: 352
  start-page: 167
  year: 2016
  end-page: 169
  ident: bib32
  article-title: A collective route to metastasis: seeding by tumor cell clusters
  publication-title: Science
– volume: 540
  start-page: 588
  year: 2016
  end-page: 592
  ident: bib64
  article-title: Mechanism of early dissemination and metastasis in Her2+ mammary cancer
  publication-title: Nature
– volume: 1293
  start-page: 213
  year: 2015
  end-page: 220
  ident: bib128
  article-title: Modeling the breast cancer bone metastatic niche in complex three-dimensional cocultures
  publication-title: Methods Mol. Biol.
– volume: 755
  start-page: 291
  year: 2011
  end-page: 300
  ident: bib85
  article-title: Laser-capture microdissection and transcriptional profiling in archival FFPE tissue in prostate cancer
  publication-title: Methods Mol. Biol.
– volume: 14
  start-page: 573
  year: 2017
  end-page: 576
  ident: bib176
  article-title: Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions
  publication-title: Nat. Methods
– volume: 113
  start-page: E854
  year: 2016
  end-page: E863
  ident: bib34
  article-title: Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters
  publication-title: Proc. Natl. Acad. Sci. USA
– volume: 5
  start-page: 932
  year: 2015
  end-page: 943
  ident: bib63
  article-title: Real-time Imaging reveals local, transient vascular permeability, and tumor cell intravasation stimulated by TIE2hi macrophage-derived VEGFA
  publication-title: Cancer Discov.
– volume: 109
  start-page: 9786
  year: 2012
  end-page: 9791
  ident: bib27
  article-title: Implanted adipose progenitor cells as physicochemical regulators of breast cancer
  publication-title: Proc. Natl. Acad. Sci. USA
– volume: 77
  start-page: 2242
  year: 2017
  end-page: 2254
  ident: bib75
  article-title: Defining cancer subpopulations by adaptive strategies rather than molecular properties provides novel insights into intratumoral evolution
  publication-title: Cancer Res.
– volume: 19
  start-page: 518
  year: 2017
  end-page: 529
  ident: bib100
  article-title: The EMT-activator Zeb1 is a key factor for cell plasticity and promotes metastasis in pancreatic cancer
  publication-title: Nat. Cell Biol.
– volume: 15
  start-page: 807
  year: 2013
  end-page: 817
  ident: bib55
  article-title: The perivascular niche regulates breast tumour dormancy
  publication-title: Nat. Cell Biol.
– volume: 11
  start-page: 838
  year: 2015
  ident: bib162
  article-title: Frequency modulation of ERK activation dynamics rewires cell fate
  publication-title: Mol. Syst. Biol.
– volume: 30
  start-page: 825
  year: 2016
  end-page: 826
  ident: bib144
  article-title: Dormancy stems the tide of chemotherapy
  publication-title: Cancer Cell
– volume: 114
  start-page: E717
  year: 2017
  end-page: E726
  ident: bib153
  article-title: Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish
  publication-title: Proc. Natl. Acad. Sci. USA
– volume: 13
  start-page: 954
  year: 2017
  ident: bib61
  article-title: From word models to executable models of signaling networks using automated assembly
  publication-title: Mol. Syst. Biol.
– volume: 3
  start-page: 453
  year: 2003
  end-page: 458
  ident: bib46
  article-title: The pathogenesis of cancer metastasis: the 'seed and soil' hypothesis revisited
  publication-title: Nat. Rev. Cancer
– volume: 7
  start-page: 4711
  year: 2017
  ident: bib166
  article-title: Exosomes from metastatic cancer cells transfer amoeboid phenotype to non-metastatic cells and increase endothelial permeability: their emerging role in tumor heterogeneity
  publication-title: Sci. Rep.
– volume: 7
  start-page: e1700903
  year: 2018
  ident: bib2
  article-title: Biomaterial scaffolds as pre-metastatic niche mimics systemically alter the primary tumor and tumor microenvironment
  publication-title: Adv. Healthc. Mater.
– volume: 17
  start-page: 17
  year: 2015
  ident: bib210
  article-title: Patient-derived xenograft models of breast cancer and their predictive power
  publication-title: Breast Cancer Res.
– volume: 165
  start-page: 45
  year: 2016
  end-page: 60
  ident: bib126
  article-title: Metastatic latency and immune evasion through autocrine inhibition of WNT
  publication-title: Cell
– volume: 34
  start-page: 1163
  year: 2016
  end-page: 1176
  ident: bib3
  article-title: Metabolic reprogramming and dependencies associated with epithelial cancer stem cells independent of the epithelial-mesenchymal transition program
  publication-title: Stem Cells
– volume: 158
  start-page: 1110
  year: 2014
  end-page: 1122
  ident: bib1
  article-title: Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis
  publication-title: Cell
– volume: 513
  start-page: 202
  year: 2014
  end-page: 209
  ident: bib23
  article-title: Comprehensive molecular characterization of gastric adenocarcinoma
  publication-title: Nature
– volume: 5
  start-page: 3963
  year: 2014
  ident: bib62
  article-title: The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes
  publication-title: Nat. Commun.
– volume: 9
  start-page: 957
  year: 2002
  end-page: 970
  ident: bib67
  article-title: Mathematical models of protein kinase signal transduction
  publication-title: Mol. Cell
– year: 2019
  ident: bib136
  article-title: Building a tumor atlas: integrating single-cell RNA-seq data with spatial transcriptomics in pancreatic ductal adenocarcinoma
  publication-title: bioRxiv
– volume: 20
  start-page: 1329
  year: 2017
  end-page: 1341
  ident: bib35
  article-title: AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma
  publication-title: Nat. Neurosci.
– volume: 527
  start-page: 100
  year: 2015
  end-page: 104
  ident: bib220
  article-title: Microenvironment-induced PTEN loss by exosomal microRNA primes brain metastasis outgrowth
  publication-title: Nature
– volume: 123
  start-page: 1988
  year: 2013
  end-page: 1998
  ident: bib69
  article-title: Lactate preserves neuronal metabolism and function following antecedent recurrent hypoglycemia
  publication-title: J. Clin. Invest.
– volume: 6
  start-page: e28074
  year: 2011
  ident: bib170
  article-title: The oogenic germline starvation response in C. elegans
  publication-title: PLoS One
– year: 2017
  ident: bib164
  article-title: Explainable artificial intelligence: understanding, visualizing and interpreting deep learning models
  publication-title: arXiv
– volume: 4
  start-page: 1014
  year: 2014
  end-page: 1021
  ident: bib5
  article-title: Synthetic lethality in ATM-deficient RAD50-mutant tumors underlies outlier response to cancer therapy
  publication-title: Cancer Discov.
– volume: 7
  start-page: 8823
  year: 2017
  ident: bib19
  article-title: Machine learning quantum phases of matter beyond the fermion sign problem
  publication-title: Sci. Rep.
– volume: 78
  start-page: 3755
  year: 2018
  end-page: 3760
  ident: bib134
  article-title: Metabolic imaging of the human brain with hyperpolarized (13)C pyruvate demonstrates (13)C lactate production in brain tumor patients
  publication-title: Cancer Res.
– volume: 548
  start-page: 297
  year: 2017
  end-page: 303
  ident: bib157
  article-title: Integrative clinical genomics of metastatic cancer
  publication-title: Nature
– volume: 155
  start-page: 1639
  year: 2013
  end-page: 1651
  ident: bib33
  article-title: Collective invasion in breast cancer requires a conserved basal epithelial program
  publication-title: Cell
– volume: 114
  start-page: E5750
  year: 2017
  end-page: E5759
  ident: bib145
  article-title: Mechanochemical feedback underlies coexistence of qualitatively distinct cell polarity patterns within diverse cell populations
  publication-title: Proc. Natl. Acad. Sci. USA
– volume: 525
  start-page: 261
  year: 2015
  end-page: 264
  ident: bib202
  article-title: A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity
  publication-title: Nature
– volume: 7
  start-page: 16189
  year: 2017
  ident: bib7
  article-title: Integrated proteomic and metabolomic prediction of Term preeclampsia
  publication-title: Sci. Rep.
– volume: 6
  start-page: 555
  year: 2014
  end-page: 563
  ident: bib79
  article-title: Generation of 3D functional microvascular networks with human mesenchymal stem cells in microfluidic systems
  publication-title: Integr. Biol. (Camb.)
– volume: 13
  start-page: 1838
  year: 2018
  end-page: 1843
  ident: bib94
  article-title: Photophysical tuning of N-oxide-based probes enables ratiometric photoacoustic imaging of tumor hypoxia
  publication-title: ACS Chem. Biol.
– volume: 9
  start-page: 646
  year: 2013
  ident: bib121
  article-title: Programming biological models in Python using PySB
  publication-title: Mol. Syst. Biol.
– volume: 8
  start-page: 1231
  year: 2017
  ident: bib17
  article-title: Combating subclonal evolution of resistant cancer phenotypes
  publication-title: Nat. Commun.
– volume: 34
  start-page: 637
  year: 2016
  end-page: 645
  ident: bib173
  article-title: Wishbone identifies bifurcating developmental trajectories from single-cell data
  publication-title: Nat. Biotechnol.
– volume: 5
  start-page: 1989
  year: 2016
  end-page: 1999
  ident: bib158
  article-title: Epithelial-mesenchymal transition, proliferation, and angiogenesis in locally advanced cervical cancer treated with chemoradiotherapy
  publication-title: Cancer Med.
– volume: 2
  start-page: 727
  year: 2007
  end-page: 738
  ident: bib12
  article-title: Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
  publication-title: Nat. Protoc.
– volume: 6
  start-page: 224ra224
  year: 2014
  ident: bib13
  article-title: Detection of circulating tumor DNA in early- and late-stage human malignancies
  publication-title: Sci. Transl. Med.
– volume: 35
  start-page: 1211
  year: 2017
  ident: bib160
  article-title: Corrigendum: development and function of human innate immune cells in a humanized mouse model
  publication-title: Nat. Biotechnol.
– volume: 7
  start-page: 38244
  year: 2017
  ident: bib95
  article-title: Relaxation oscillations and hierarchy of feedbacks in MAPK signaling
  publication-title: Sci. Rep.
– volume: 4
  start-page: 12
  year: 2016
  ident: bib90
  article-title: In vitro tumor models: advantages, disadvantages, variables, and selecting the right platform
  publication-title: Front. Bioeng. Biotechnol.
– volume: 95
  start-page: 245134
  year: 2017
  ident: bib167
  article-title: Probing many-body localization with neural networks
  publication-title: Phys. Rev. B
– volume: 12
  start-page: 379
  year: 2017
  end-page: 389
  ident: bib20
  article-title: Zebrafish xenograft models of cancer and metastasis for drug discovery
  publication-title: Expert Opin. Drug Discov.
– volume: 4
  start-page: 104
  year: 2010
  ident: bib192
  article-title: Increased entropy of signal transduction in the cancer metastasis phenotype
  publication-title: BMC Syst. Biol.
– volume: 12
  start-page: 014101
  year: 2018
  ident: bib196
  article-title: Biomimetic microfluidic platform for the quantification of transient endothelial monolayer permeability and therapeutic transport under mimicked cancerous conditions
  publication-title: Biomicrofluidics
– volume: 8
  start-page: 707
  year: 2017
  ident: bib80
  article-title: Clinical responses to adoptive T-cell transfer can be modeled in an autologous immune-humanized mouse model
  publication-title: Nat. Commun.
– volume: 8
  start-page: 1376
  year: 2018
  end-page: 1388
  ident: bib175
  article-title: Cancer-associated fibroblasts enhance tumor (18)F-FDG uptake and contribute to the intratumor heterogeneity of PET-CT
  publication-title: Theranostics
– volume: 120
  start-page: 461
  year: 2010
  end-page: 467
  ident: bib16
  article-title: Detection of PIK3CA mutations in circulating free DNA in patients with breast cancer
  publication-title: Breast Cancer Res. Treat.
– volume: 353
  start-page: 78
  year: 2016
  end-page: 82
  ident: bib184
  article-title: Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
  publication-title: Science
– year: 2018
  ident: bib124
  article-title: AffinityNet: semi-supervised few-shot learning for disease type prediction
  publication-title: arXiv
– volume: 22
  start-page: 1339
  year: 2012
  end-page: 1355
  ident: bib14
  article-title: Global secretome analysis identifies novel mediators of bone metastasis
  publication-title: Cell Res.
– volume: 62
  start-page: 1129
  year: 2016
  end-page: 1139
  ident: bib53
  article-title: A study of hypermethylated circulating tumor DNA as a universal colorectal cancer biomarker
  publication-title: Clin. Chem.
– volume: 361
  year: 2018
  ident: bib87
  article-title: Developmental barcoding of whole mouse via homing CRISPR
  publication-title: Science
– volume: 11
  start-page: e1004025
  year: 2015
  ident: bib150
  article-title: Evolution and phenotypic selection of cancer stem cells
  publication-title: PLoS Comput. Biol.
– volume: 8
  start-page: 227
  year: 2005
  end-page: 239
  ident: bib165
  article-title: Genomic analysis of single cytokeratin-positive cells from bone marrow reveals early mutational events in breast cancer
  publication-title: Cancer Cell
– volume: 173
  start-page: 1562
  year: 2018
  end-page: 1565
  ident: bib216
  article-title: Visible machine learning for biomedicine
  publication-title: Cell
– volume: 173
  start-page: 1581
  year: 2018
  end-page: 1592
  ident: bib22
  article-title: Next-generation machine learning for biological networks
  publication-title: Cell
– volume: 19
  start-page: 1063
  year: 2013
  end-page: 1070
  ident: bib190
  article-title: Modeling boundary conditions for balanced proliferation in metastatic latency
  publication-title: Clin. Cancer Res.
– volume: 6
  start-page: 865
  year: 2014
  end-page: 881
  ident: bib137
  article-title: RARRES3 suppresses breast cancer lung metastasis by regulating adhesion and differentiation
  publication-title: EMBO Mol. Med.
– volume: 7
  start-page: 27067
  year: 2016
  end-page: 27084
  ident: bib84
  article-title: Stability of the hybrid epithelial/mesenchymal phenotype
  publication-title: Oncotarget
– volume: 159
  start-page: 402
  year: 2014
  end-page: 414
  ident: bib30
  article-title: Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks
  publication-title: Cell
– volume: 161
  start-page: 83
  year: 2017
  end-page: 94
  ident: bib204
  article-title: Longitudinally collected CTCs and CTC-clusters and clinical outcomes of metastatic breast cancer
  publication-title: Breast Cancer Res. Treat.
– volume: 8
  start-page: 3904
  year: 2018
  ident: bib143
  article-title: A mathematical model of the phosphoinositide pathway
  publication-title: Sci. Rep.
– volume: 123
  start-page: 4568
  year: 2013
  end-page: 4570
  ident: bib18
  article-title: "N of 1" case reports in the era of whole-genome sequencing
  publication-title: J. Clin. Invest.
– volume: 10
  start-page: 20130011
  year: 2013
  ident: bib169
  article-title: A mathematical model of tumour self-seeding reveals secondary metastatic deposits as drivers of primary tumour growth
  publication-title: J. R. Soc. Interface
– volume: 15
  start-page: 709
  year: 2014
  end-page: 721
  ident: bib131
  article-title: Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
  publication-title: Nat. Rev. Genet.
– volume: 8
  start-page: 15773
  year: 2017
  ident: bib140
  article-title: EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells
  publication-title: Nat. Commun.
– volume: 527
  start-page: 525
  year: 2015
  end-page: 530
  ident: bib224
  article-title: Epithelial-to-mesenchymal transition is dispensable for metastasis but induces chemoresistance in pancreatic cancer
  publication-title: Nature
– volume: 6
  start-page: 15639
  year: 2015
  end-page: 15651
  ident: bib83
  article-title: Comprehensive characterization of chemotherapeutic efficacy on metastases in the established gastric neuroendocrine cancer patient derived xenograft model
  publication-title: Oncotarget
– volume: 45
  start-page: 350
  year: 2012
  end-page: 362
  ident: bib4
  article-title: The inference of breast cancer metastasis through gene regulatory networks
  publication-title: J. Biomed. Inform.
– volume: 34
  start-page: D689
  year: 2006
  end-page: D691
  ident: bib105
  article-title: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
  publication-title: Nucleic Acids Res.
– volume: 114
  start-page: 2934
  year: 2017
  end-page: 2939
  ident: bib26
  article-title: Metabolic origins of spatial organization in the tumor microenvironment
  publication-title: Proc. Natl. Acad. Sci. USA
– volume: 118
  start-page: 3237
  year: 2017
  end-page: 3248
  ident: bib25
  article-title: Metastatic breast cancer cells enter Into dormant state and express cancer stem cells phenotype under chronic hypoxia
  publication-title: J. Cell. Biochem.
– volume: 6
  start-page: 382
  year: 2016
  end-page: 399
  ident: bib133
  article-title: Reduced proteolytic shedding of receptor tyrosine kinases is a post-translational mechanism of kinase inhibitor resistance
  publication-title: Cancer Discov.
– volume: 29
  start-page: 2757
  year: 2013
  end-page: 2764
  ident: bib146
  article-title: Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
  publication-title: Bioinformatics
– volume: 168
  start-page: 670
  year: 2017
  end-page: 691
  ident: bib103
  article-title: Emerging biological principles of metastasis
  publication-title: Cell
– volume: 344
  start-page: 1
  year: 2014
  end-page: 12
  ident: bib125
  article-title: One mouse, one patient paradigm: new avatars of personalized cancer therapy
  publication-title: Cancer Lett.
– volume: 8
  start-page: 1270
  year: 2017
  ident: bib177
  article-title: Percolation transition of cooperative mutational effects in colorectal tumorigenesis
  publication-title: Nat. Commun.
– volume: 9
  start-page: 2997
  year: 2018
  ident: bib149
  article-title: Systems analysis of intracellular pH vulnerabilities for cancer therapy
  publication-title: Nat. Commun.
– volume: 8
  start-page: ra59
  year: 2015
  ident: bib213
  article-title: Analysis of single-cell cytokine secretion reveals a role for paracrine signaling in coordinating macrophage responses to TLR4 stimulation
  publication-title: Sci. Signal.
– volume: 527
  start-page: 329
  year: 2015
  end-page: 335
  ident: bib71
  article-title: Tumour exosome integrins determine organotropic metastasis
  publication-title: Nature
– volume: 10
  start-page: e0118060
  year: 2015
  ident: bib51
  article-title: Lung epithelial cells induce both phenotype alteration and senescence in breast cancer cells
  publication-title: PLoS One
– volume: 111
  start-page: 2342
  year: 2014
  end-page: 2350
  ident: bib209
  article-title: Spontaneous dormancy of metastatic breast cancer cells in an all human liver microphysiologic system
  publication-title: Br. J. Cancer
– volume: 428
  start-page: 328
  year: 2017
  end-page: 337
  ident: bib186
  article-title: From good to bad: intravital imaging of the hijack of physiological processes by cancer cells
  publication-title: Dev. Biol.
– volume: 20
  start-page: 1623
  year: 2017
  end-page: 1640
  ident: bib203
  article-title: An integrated systems biology approach identifies TRIM25 as a key determinant of breast cancer metastasis
  publication-title: Cell Rep.
– volume: 13
  start-page: e1005618
  year: 2017
  ident: bib212
  article-title: Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a
  publication-title: PLoS Comput. Biol.
– volume: 7
  year: 2017
  ident: bib10
  article-title: Homeostasis back and forth: an ecoevolutionary perspective of cancer
  publication-title: Cold Spring Harb. Perspect. Med.
– volume: 14
  start-page: 395
  year: 2017
  end-page: 398
  ident: bib56
  article-title: Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
  publication-title: Nat. Methods
– volume: 541
  start-page: 331
  year: 2017
  end-page: 338
  ident: bib187
  article-title: Scaling single-cell genomics from phenomenology to mechanism
  publication-title: Nature
– volume: 17
  start-page: 5247
  year: 2018
  end-page: 5257
  ident: bib222
  article-title: Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease
  publication-title: Mol. Med. Rep.
– volume: 19
  start-page: 360
  year: 2008
  end-page: 368
  ident: bib42
  article-title: Equation discovery for systems biology: finding the structure and dynamics of biological networks from time course data
  publication-title: Curr. Opin. Biotechnol.
– volume: 10
  start-page: e1003460
  year: 2014
  ident: bib82
  article-title: VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data
  publication-title: PLoS Comput. Biol.
– volume: 9
  start-page: 21
  year: 2018
  ident: bib117
  article-title: Macrophages orchestrate breast cancer early dissemination and metastasis
  publication-title: Nat. Commun.
– volume: 734
  start-page: 73
  year: 2013
  end-page: 89
  ident: bib181
  article-title: Regulation of tumor cell dormancy by tissue microenvironments and autophagy
  publication-title: Adv. Exp. Med. Biol.
– volume: 352
  start-page: 189
  year: 2016
  end-page: 196
  ident: bib194
  article-title: Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
  publication-title: Science
– volume: 10
  start-page: 1061
  year: 2017
  end-page: 1074
  ident: bib60
  article-title: Mouse models of metastasis: progress and prospects
  publication-title: Dis. Model Mech.
– volume: 35
  start-page: 1188
  year: 2019
  end-page: 1196
  ident: bib110
  article-title: PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling
  publication-title: Bioinformatics
– volume: 16
  start-page: 582
  year: 2016
  end-page: 598
  ident: bib88
  article-title: The biology and function of fibroblasts in cancer
  publication-title: Nat. Rev. Cancer
– volume: 7
  start-page: 22031
  year: 2016
  end-page: 22049
  ident: bib114
  article-title: In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins
  publication-title: Oncotarget
– volume: 17
  start-page: E1151
  year: 2016
  ident: bib115
  article-title: A Mini-Review for cancer immunotherapy: molecular understanding of PD-1/PD-L1 pathway & translational blockade of immune checkpoints
  publication-title: Int. J. Mol. Sci.
– volume: 18
  start-page: 3687
  year: 2018
  end-page: 3702
  ident: bib178
  article-title: Tumor-on-a-chip platform to investigate progression and drug sensitivity in cell lines and patient-derived organoids
  publication-title: Lab Chip
– volume: 74
  start-page: 5963
  year: 2014
  end-page: 5977
  ident: bib185
  article-title: Network modeling of TGFbeta signaling in hepatocellular carcinoma epithelial-to-mesenchymal transition reveals joint sonic hedgehog and Wnt pathway activation
  publication-title: Cancer Res.
– volume: 96
  start-page: 4494
  year: 1999
  end-page: 4499
  ident: bib93
  article-title: Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells
  publication-title: Proc. Natl. Acad. Sci. USA
– volume: 7
  start-page: e34637
  year: 2012
  ident: bib141
  article-title: A stochastic Markov chain model to describe lung cancer growth and metastasis
  publication-title: PLoS One
– volume: 18
  start-page: 851
  year: 2017
  end-page: 869
  ident: bib135
  article-title: Deep learning in bioinformatics
  publication-title: Brief. Bioinform.
– volume: 19
  start-page: 120
  year: 2017
  end-page: 132
  ident: bib48
  article-title: Phenotypic heterogeneity of disseminated tumour cells is preset by primary tumour hypoxic microenvironments
  publication-title: Nat. Cell Biol.
– volume: 8
  start-page: 1669
  year: 2017
  ident: bib179
  article-title: Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis
  publication-title: Nat. Commun.
– volume: 356
  start-page: eaah4573
  year: 2017
  ident: bib201
  article-title: Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
  publication-title: Science
– volume: 19
  start-page: 285
  year: 2019
  end-page: 289
  ident: bib59
  article-title: Next generation sequencing-based validation of the revised international staging system for multiple myeloma: an analysis of the MMRF CoMMpass study
  publication-title: Clin. Lymphoma Myeloma Leuk.
– volume: 553
  start-page: 96
  year: 2018
  end-page: 100
  ident: bib132
  article-title: Senescence-associated reprogramming promotes cancer stemness
  publication-title: Nature
– year: 2016
  ident: bib205
  article-title: Deep learning for identifying metastatic breast cancer
  publication-title: arXiv
– volume: 4
  start-page: 281
  year: 2018
  end-page: 291
  ident: bib180
  article-title: Beyond tissue stiffness and Bioadhesivity: advanced biomaterials to model tumor microenvironments and drug resistance
  publication-title: Trends Cancer
– reference: Defferrard, M., Bresson, X., and Vandergheynst, P. (2016). Convolutional neural networks on graphs with fast localized spectral filtering. Paper presented at Advances in Neural Information Processing Systems.
– volume: 7
  start-page: 301ra130
  year: 2015
  ident: bib172
  article-title: Obesity-dependent changes in interstitial ECM mechanics promote breast tumorigenesis
  publication-title: Sci. Transl. Med.
– volume: 4
  start-page: 121490
  year: 2019
  ident: bib113
  article-title: Human primary liver cancer organoids reveal intratumor and interpatient drug response heterogeneity
  publication-title: JCI Insight
– volume: 2
  start-page: e975027
  year: 2015
  ident: bib102
  article-title: Caenorhabditis elegans as a model for cancer research
  publication-title: Mol. Cell. Oncol.
– volume: 49
  start-page: 1571
  year: 2009
  end-page: 1582
  ident: bib195
  article-title: MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma
  publication-title: Hepatology
– volume: 26
  start-page: 77
  year: 2014
  end-page: 91
  ident: bib151
  article-title: Hematogenous metastasis of ovarian cancer: rethinking mode of spread
  publication-title: Cancer Cell
– volume: 17
  start-page: 1917
  year: 2010
  end-page: 1926
  ident: bib112
  article-title: CpG island methylator phenotype associated with tumor recurrence in tumor-node-metastasis stage I hepatocellular carcinoma
  publication-title: Ann. Surg. Oncol.
– volume: 123
  start-page: 189
  year: 2013
  end-page: 205
  ident: bib28
  article-title: Hypoxia-inducible factor-dependent breast cancer-mesenchymal stem cell bidirectional signaling promotes metastasis
  publication-title: J. Clin. Invest.
– volume: 9
  start-page: 138
  year: 2019
  ident: bib221
  article-title: Seeking for correlative genes and signaling pathways With bone metastasis From breast cancer by integrated analysis
  publication-title: Front. Oncol.
– volume: 7
  start-page: 42369
  year: 2017
  ident: bib70
  article-title: Extracellular protonation modulates cell-cell interaction mechanics and tissue invasion in human melanoma cells
  publication-title: Sci. Rep.
– volume: 28
  start-page: 2402
  year: 2012
  end-page: 2403
  ident: bib97
  article-title: CySBML: a cytoscape plugin for SBML
  publication-title: Bioinformatics
– volume: 126
  start-page: 1454
  year: 2013
  end-page: 1463
  ident: bib142
  article-title: A dynamic model of the hypoxia-inducible factor 1alpha (HIF-1alpha) network
  publication-title: J. Cell Sci.
– volume: 75
  start-page: 4272
  year: 2015
  end-page: 4282
  ident: bib66
  article-title: A quantitative system for studying metastasis using transparent zebrafish
  publication-title: Cancer Res.
– volume: 12
  start-page: e0183810
  year: 2017
  ident: bib217
  article-title: Hybrid multiscale modeling and prediction of cancer cell behavior
  publication-title: PLoS One
– volume: 148
  start-page: 349
  year: 2012
  end-page: 361
  ident: bib155
  article-title: EMT and dissemination precede pancreatic tumor formation
  publication-title: Cell
– volume: 6
  start-page: ra68
  year: 2013
  ident: bib92
  article-title: Computational modeling of ERBB2-amplified breast cancer identifies combined ErbB2/3 blockade as superior to the combination of MEK and AKT inhibitors
  publication-title: Sci. Signal.
– volume: 97
  start-page: 107
  year: 2016
  end-page: 117
  ident: bib198
  article-title: Studying cancer metastasis: existing models, challenges and future perspectives
  publication-title: Crit. Rev. Oncol. Hematol.
– volume: 19
  start-page: 147
  year: 2017
  end-page: 149
  ident: bib45
  article-title: Pulling cells out of tumours
  publication-title: Nat. Cell Biol.
– volume: 2
  start-page: 802
  year: 2012
  ident: bib208
  article-title: Differential network entropy reveals cancer system hallmarks
  publication-title: Sci. Rep.
– volume: 5
  year: 2016
  ident: bib200
  article-title: Intravital imaging reveals new ancillary mechanisms co-opted by cancer cells to drive tumor progression
  publication-title: F1000Res.
– volume: 22
  start-page: 310
  year: 2018
  end-page: 324
  ident: bib159
  article-title: Organs-on-a-Chip: a fast track for engineered human tissues in drug development
  publication-title: Cell Stem Cell
– volume: 23
  start-page: 1241
  year: 2018
  end-page: 1250
  ident: bib29
  article-title: The rise of deep learning in drug discovery
  publication-title: Drug Discov. Today
– volume: 287
  start-page: 33533
  year: 2012
  end-page: 33544
  ident: bib116
  article-title: Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis
  publication-title: J. Biol. Chem.
– start-page: 3527
  year: 2018
  end-page: 3534
  ident: bib154
  article-title: Hybrid approach of relation network and localized graph convolutional filtering for breast cancer subtype classification
  publication-title: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence
– volume: 160
  start-page: 1246
  year: 2015
  end-page: 1260
  ident: bib31
  article-title: Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis
  publication-title: Cell
– volume: 8
  start-page: 15078
  year: 2017
  ident: bib96
  article-title: Image-guided genomics of phenotypically heterogeneous populations reveals vascular signalling during symbiotic collective cancer invasion
  publication-title: Nat. Commun.
– volume: 339
  start-page: 580
  year: 2013
  end-page: 584
  ident: bib215
  article-title: Circulating breast tumor cells exhibit dynamic changes in epithelial and mesenchymal composition
  publication-title: Science
– volume: 67
  start-page: 1995
  year: 2018
  end-page: 2005
  ident: bib9
  article-title: Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer
  publication-title: Gut
– volume: 1
  start-page: 2
  year: 2017
  ident: bib81
  article-title: Distinguishing mechanisms underlying EMT tristability
  publication-title: Cancer Converg.
– volume: 164
  start-page: 293
  year: 2016
  end-page: 309
  ident: bib127
  article-title: Functional genomic landscape of human breast cancer drivers, vulnerabilities, and resistance
  publication-title: Cell
– volume: 2
  start-page: 429
  year: 2016
  end-page: 442
  ident: bib171
  article-title: Adaptive stress responses During tumor metastasis and dormancy
  publication-title: Trends Cancer
– volume: 10
  start-page: 445
  year: 2009
  end-page: 457
  ident: bib49
  article-title: Collective cell migration in morphogenesis, regeneration and cancer
  publication-title: Nat. Rev. Mol. Cell Biol.
– volume: 4
  start-page: 636
  year: 2017
  end-page: 644.e9
  ident: bib119
  article-title: Time-resolved proteomics extends ribosome profiling-based measurements of protein synthesis dynamics
  publication-title: Cell Syst.
– volume: 4
  year: 2015
  ident: bib98
  article-title: Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells
  publication-title: Elife
– volume: 17
  start-page: 498
  year: 2016
  ident: bib147
  article-title: A methodological approach for using high-level Petri Nets to model the immune system response
  publication-title: BMC Bioinformatics
– volume: 132
  start-page: 209
  year: 2016
  end-page: 264
  ident: bib191
  article-title: Plasticity of cancer cell invasion-mechanisms and implications for therapy
  publication-title: Adv. Cancer Res.
– volume: 27
  start-page: 1287
  year: 2017
  end-page: 1299
  ident: bib111
  article-title: Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
  publication-title: Genome Res.
– volume: 8
  start-page: 105
  year: 2017
  ident: bib21
  article-title: PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens
  publication-title: Nat. Commun.
– volume: 527
  start-page: 472
  year: 2015
  end-page: 476
  ident: bib47
  article-title: Epithelial-to-mesenchymal transition is not required for lung metastasis but contributes to chemoresistance
  publication-title: Nature
– volume: 8
  start-page: 15664
  year: 2018
  ident: bib163
  article-title: A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of advanced human retinoblastoma
  publication-title: Sci. Rep.
– volume: 26
  start-page: 65
  year: 2007
  end-page: 76
  ident: bib74
  article-title: Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues
  publication-title: Oncogene
– volume: 292
  start-page: 342
  year: 2009
  end-page: 351
  ident: bib161
  article-title: 3D cryo-imaging: a very high-resolution view of the whole mouse
  publication-title: Anat. Rec. (Hoboken)
– volume: 30
  start-page: 836
  year: 2016
  end-page: 848
  ident: bib11
  article-title: Extracellular vesicles in cancer: cell-to-cell mediators of metastasis
  publication-title: Cancer Cell
– volume: 44
  start-page: 4124
  year: 1984
  end-page: 4130
  ident: bib182
  article-title: A stochastic numerical model of breast cancer growth that simulates clinical data
  publication-title: Cancer Res.
– volume: 553
  start-page: 467
  year: 2018
  end-page: 472
  ident: bib8
  article-title: Chromosomal instability drives metastasis through a cytosolic DNA response
  publication-title: Nature
– year: 2019
  ident: bib101
  article-title: The evolution of placental invasion and cancer metastasis are causally linked
  publication-title: bioRxiv
– volume: 5
  start-page: 1216
  year: 2016
  end-page: 1228
  ident: bib174
  article-title: Twist1-positive epithelial cells retain adhesive and proliferative capacity throughout dissemination
  publication-title: Biol. Open
– volume: 111
  start-page: 1541
  year: 2016
  end-page: 1552
  ident: bib24
  article-title: A chemomechanical model for nuclear morphology and stresses during cell transendothelial migration
  publication-title: Biophys. J.
– volume: 30
  start-page: 70
  year: 2015
  end-page: 78
  ident: bib206
  article-title: Simulating cancer growth with multiscale agent-based modeling
  publication-title: Semin. Cancer Biol.
– volume: 8
  start-page: 109
  year: 2015
  ident: bib86
  article-title: Comprehensive serial molecular profiling of an "N of 1" exceptional non-responder with metastatic prostate cancer progressing to small cell carcinoma on treatment
  publication-title: J. Hematol. Oncol.
– volume: 75
  start-page: 1567
  year: 2015
  end-page: 1579
  ident: bib156
  article-title: Impact of metabolic heterogeneity on tumor growth, invasion, and treatment outcomes
  publication-title: Cancer Res.
– volume: 356
  start-page: 800
  year: 2007
  end-page: 808
  ident: bib225
  article-title: DNA synthesis and repair genes RRM1 and ERCC1 in lung cancer
  publication-title: N. Engl. J. Med.
– volume: 28
  start-page: 672
  year: 2012
  end-page: 678
  ident: bib52
  article-title: Interactome-transcriptome integration for predicting distant metastasis in breast cancer
  publication-title: Bioinformatics
– volume: 12
  start-page: e0185844
  year: 2017
  ident: bib120
  article-title: A deep convolutional neural network-based automatic delineation strategy for multiple brain metastases stereotactic radiosurgery
  publication-title: PLoS One
– volume: 5
  start-page: 14739
  year: 2015
  ident: bib122
  article-title: Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets
  publication-title: Sci. Rep.
– volume: 6
  start-page: 19103
  year: 2016
  ident: bib218
  article-title: 3D tumor spheroid models for in vitro therapeutic screening: a systematic approach to enhance the biological relevance of data obtained
  publication-title: Sci. Rep.
– volume: 148
  start-page: 349
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib155
  article-title: EMT and dissemination precede pancreatic tumor formation
  publication-title: Cell
  doi: 10.1016/j.cell.2011.11.025
– volume: 7
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib10
  article-title: Homeostasis back and forth: an ecoevolutionary perspective of cancer
  publication-title: Cold Spring Harb. Perspect. Med.
  doi: 10.1101/cshperspect.a028332
– volume: 11
  start-page: dmm034330
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib77
  article-title: Intravital microscopy of collective invasion plasticity in breast cancer
  publication-title: Dis. Model Mech.
  doi: 10.1242/dmm.034330
– volume: 4
  start-page: 104
  year: 2010
  ident: 10.1016/j.cels.2019.07.003_bib192
  article-title: Increased entropy of signal transduction in the cancer metastasis phenotype
  publication-title: BMC Syst. Biol.
  doi: 10.1186/1752-0509-4-104
– volume: 11
  start-page: e1004025
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib150
  article-title: Evolution and phenotypic selection of cancer stem cells
  publication-title: PLoS Comput. Biol.
  doi: 10.1371/journal.pcbi.1004025
– volume: 22
  start-page: 310
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib159
  article-title: Organs-on-a-Chip: a fast track for engineered human tissues in drug development
  publication-title: Cell Stem Cell
  doi: 10.1016/j.stem.2018.02.011
– volume: 8
  start-page: 1669
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib179
  article-title: Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-017-01666-2
– volume: 7
  start-page: 22031
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib114
  article-title: In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins
  publication-title: Oncotarget
  doi: 10.18632/oncotarget.8247
– volume: 30
  start-page: 825
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib144
  article-title: Dormancy stems the tide of chemotherapy
  publication-title: Cancer Cell
  doi: 10.1016/j.ccell.2016.11.014
– volume: 356
  start-page: eaah4573
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib201
  article-title: Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
  publication-title: Science
  doi: 10.1126/science.aah4573
– start-page: 3527
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib154
  article-title: Hybrid approach of relation network and localized graph convolutional filtering for breast cancer subtype classification
  publication-title: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence
– volume: 11
  start-page: 838
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib162
  article-title: Frequency modulation of ERK activation dynamics rewires cell fate
  publication-title: Mol. Syst. Biol.
  doi: 10.15252/msb.20156458
– volume: 7
  start-page: 16189
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib7
  article-title: Integrated proteomic and metabolomic prediction of Term preeclampsia
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-017-15882-9
– volume: 8
  start-page: 15078
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib96
  article-title: Image-guided genomics of phenotypically heterogeneous populations reveals vascular signalling during symbiotic collective cancer invasion
  publication-title: Nat. Commun.
  doi: 10.1038/ncomms15078
– volume: 8
  start-page: 15664
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib163
  article-title: A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of advanced human retinoblastoma
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-018-34037-y
– volume: 5
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib200
  article-title: Intravital imaging reveals new ancillary mechanisms co-opted by cancer cells to drive tumor progression
  publication-title: F1000Res.
  doi: 10.12688/f1000research.8090.1
– volume: 165
  start-page: 45
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib126
  article-title: Metastatic latency and immune evasion through autocrine inhibition of WNT
  publication-title: Cell
  doi: 10.1016/j.cell.2016.02.025
– volume: 7
  start-page: 8823
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib19
  article-title: Machine learning quantum phases of matter beyond the fermion sign problem
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-017-09098-0
– volume: 111
  start-page: 1541
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib24
  article-title: A chemomechanical model for nuclear morphology and stresses during cell transendothelial migration
  publication-title: Biophys. J.
  doi: 10.1016/j.bpj.2016.08.011
– volume: 15
  start-page: 709
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib131
  article-title: Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
  publication-title: Nat. Rev. Genet.
  doi: 10.1038/nrg3788
– volume: 4
  start-page: 636
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib119
  article-title: Time-resolved proteomics extends ribosome profiling-based measurements of protein synthesis dynamics
  publication-title: Cell Syst.
  doi: 10.1016/j.cels.2017.05.001
– volume: 541
  start-page: 331
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib187
  article-title: Scaling single-cell genomics from phenomenology to mechanism
  publication-title: Nature
  doi: 10.1038/nature21350
– volume: 118
  start-page: 3237
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib25
  article-title: Metastatic breast cancer cells enter Into dormant state and express cancer stem cells phenotype under chronic hypoxia
  publication-title: J. Cell. Biochem.
  doi: 10.1002/jcb.25972
– volume: 16
  start-page: 582
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib88
  article-title: The biology and function of fibroblasts in cancer
  publication-title: Nat. Rev. Cancer
  doi: 10.1038/nrc.2016.73
– volume: 1293
  start-page: 213
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib128
  article-title: Modeling the breast cancer bone metastatic niche in complex three-dimensional cocultures
  publication-title: Methods Mol. Biol.
  doi: 10.1007/978-1-4939-2519-3_12
– volume: 292
  start-page: 342
  year: 2009
  ident: 10.1016/j.cels.2019.07.003_bib161
  article-title: 3D cryo-imaging: a very high-resolution view of the whole mouse
  publication-title: Anat. Rec. (Hoboken)
  doi: 10.1002/ar.20849
– volume: 155
  start-page: 1639
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib33
  article-title: Collective invasion in breast cancer requires a conserved basal epithelial program
  publication-title: Cell
  doi: 10.1016/j.cell.2013.11.029
– volume: 73
  start-page: 3811
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib207
  article-title: The dormancy dilemma: quiescence versus balanced proliferation
  publication-title: Cancer Res.
  doi: 10.1158/0008-5472.CAN-13-0356
– volume: 6
  start-page: 555
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib79
  article-title: Generation of 3D functional microvascular networks with human mesenchymal stem cells in microfluidic systems
  publication-title: Integr. Biol. (Camb.)
  doi: 10.1039/C3IB40267C
– volume: 26
  start-page: 77
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib151
  article-title: Hematogenous metastasis of ovarian cancer: rethinking mode of spread
  publication-title: Cancer Cell
  doi: 10.1016/j.ccr.2014.05.002
– volume: 130
  start-page: 1147
  year: 2008
  ident: 10.1016/j.cels.2019.07.003_bib6
  article-title: Dynamic imaging of cancer growth and invasion: a modified skin-fold chamber model
  publication-title: Histochem. Cell Biol.
  doi: 10.1007/s00418-008-0529-1
– volume: 114
  start-page: E717
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib153
  article-title: Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1620755114
– volume: 123
  start-page: 189
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib28
  article-title: Hypoxia-inducible factor-dependent breast cancer-mesenchymal stem cell bidirectional signaling promotes metastasis
  publication-title: J. Clin. Invest.
  doi: 10.1172/JCI69244
– volume: 173
  start-page: 1562
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib216
  article-title: Visible machine learning for biomedicine
  publication-title: Cell
  doi: 10.1016/j.cell.2018.05.056
– volume: 35
  start-page: 1188
  year: 2019
  ident: 10.1016/j.cels.2019.07.003_bib110
  article-title: PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bty766
– volume: 2
  start-page: e975027
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib102
  article-title: Caenorhabditis elegans as a model for cancer research
  publication-title: Mol. Cell. Oncol.
  doi: 10.4161/23723556.2014.975027
– volume: 15
  start-page: 807
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib55
  article-title: The perivascular niche regulates breast tumour dormancy
  publication-title: Nat. Cell Biol.
  doi: 10.1038/ncb2767
– volume: 20
  start-page: 1329
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib35
  article-title: AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma
  publication-title: Nat. Neurosci.
  doi: 10.1038/nn.4620
– volume: 4
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib98
  article-title: Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells
  publication-title: Elife
  doi: 10.7554/eLife.04640
– volume: 9
  start-page: 2997
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib149
  article-title: Systems analysis of intracellular pH vulnerabilities for cancer therapy
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-018-05261-x
– volume: 352
  start-page: 189
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib194
  article-title: Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
  publication-title: Science
  doi: 10.1126/science.aad0501
– volume: 553
  start-page: 96
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib132
  article-title: Senescence-associated reprogramming promotes cancer stemness
  publication-title: Nature
  doi: 10.1038/nature25167
– year: 2019
  ident: 10.1016/j.cels.2019.07.003_bib136
  article-title: Building a tumor atlas: integrating single-cell RNA-seq data with spatial transcriptomics in pancreatic ductal adenocarcinoma
  publication-title: bioRxiv
– volume: 5
  start-page: 932
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib63
  article-title: Real-time Imaging reveals local, transient vascular permeability, and tumor cell intravasation stimulated by TIE2hi macrophage-derived VEGFA
  publication-title: Cancer Discov.
  doi: 10.1158/2159-8290.CD-15-0012
– volume: 12
  start-page: e0183810
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib217
  article-title: Hybrid multiscale modeling and prediction of cancer cell behavior
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0183810
– volume: 19
  start-page: 360
  year: 2008
  ident: 10.1016/j.cels.2019.07.003_bib42
  article-title: Equation discovery for systems biology: finding the structure and dynamics of biological networks from time course data
  publication-title: Curr. Opin. Biotechnol.
  doi: 10.1016/j.copbio.2008.07.002
– volume: 19
  start-page: 285
  year: 2019
  ident: 10.1016/j.cels.2019.07.003_bib59
  article-title: Next generation sequencing-based validation of the revised international staging system for multiple myeloma: an analysis of the MMRF CoMMpass study
  publication-title: Clin. Lymphoma Myeloma Leuk.
  doi: 10.1016/j.clml.2019.01.003
– volume: 78
  start-page: 3755
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib134
  article-title: Metabolic imaging of the human brain with hyperpolarized (13)C pyruvate demonstrates (13)C lactate production in brain tumor patients
  publication-title: Cancer Res.
  doi: 10.1158/0008-5472.CAN-18-0221
– volume: 527
  start-page: 525
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib224
  article-title: Epithelial-to-mesenchymal transition is dispensable for metastasis but induces chemoresistance in pancreatic cancer
  publication-title: Nature
  doi: 10.1038/nature16064
– volume: 7
  start-page: 301ra130
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib172
  article-title: Obesity-dependent changes in interstitial ECM mechanics promote breast tumorigenesis
  publication-title: Sci. Transl. Med.
  doi: 10.1126/scitranslmed.3010467
– volume: 9
  start-page: 138
  year: 2019
  ident: 10.1016/j.cels.2019.07.003_bib221
  article-title: Seeking for correlative genes and signaling pathways With bone metastasis From breast cancer by integrated analysis
  publication-title: Front. Oncol.
  doi: 10.3389/fonc.2019.00138
– volume: 428
  start-page: 328
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib186
  article-title: From good to bad: intravital imaging of the hijack of physiological processes by cancer cells
  publication-title: Dev. Biol.
  doi: 10.1016/j.ydbio.2017.04.015
– volume: 18
  start-page: 1131
  year: 2004
  ident: 10.1016/j.cels.2019.07.003_bib199
  article-title: Snail blocks the cell cycle and confers resistance to cell death
  publication-title: Genes Dev.
  doi: 10.1101/gad.294104
– volume: 29
  start-page: 2757
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib146
  article-title: Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btt471
– volume: 165
  start-page: 910
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib189
  article-title: Oncogenic KRAS regulates tumor cell signaling via stromal reciprocation
  publication-title: Cell
  doi: 10.1016/j.cell.2016.03.029
– volume: 35
  start-page: 1211
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib160
  article-title: Corrigendum: development and function of human innate immune cells in a humanized mouse model
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt1217-1211c
– volume: 567
  start-page: 249
  year: 2019
  ident: 10.1016/j.cels.2019.07.003_bib106
  article-title: Hepatocytes direct the formation of a pro-metastatic niche in the liver
  publication-title: Nature
  doi: 10.1038/s41586-019-1004-y
– volume: 356
  start-page: 800
  year: 2007
  ident: 10.1016/j.cels.2019.07.003_bib225
  article-title: DNA synthesis and repair genes RRM1 and ERCC1 in lung cancer
  publication-title: N. Engl. J. Med.
  doi: 10.1056/NEJMoa065411
– volume: 27
  start-page: 392
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib108
  article-title: Hypoxia induces a HIF-1-dependent transition from collective-to-amoeboid dissemination in epithelial cancer cells
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2016.11.057
– volume: 353
  start-page: 78
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib184
  article-title: Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
  publication-title: Science
  doi: 10.1126/science.aaf2403
– volume: 123
  start-page: 4568
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib18
  article-title: "N of 1" case reports in the era of whole-genome sequencing
  publication-title: J. Clin. Invest.
  doi: 10.1172/JCI70935
– year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib124
  article-title: AffinityNet: semi-supervised few-shot learning for disease type prediction
  publication-title: arXiv
– volume: 11
  start-page: 6582
  year: 2005
  ident: 10.1016/j.cels.2019.07.003_bib43
  article-title: Multigene methylation analysis for detection and staging of prostate cancer
  publication-title: Clin. Cancer Res.
  doi: 10.1158/1078-0432.CCR-05-0658
– volume: 8
  start-page: 105
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib21
  article-title: PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-017-00136-z
– volume: 6
  start-page: 15639
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib83
  article-title: Comprehensive characterization of chemotherapeutic efficacy on metastases in the established gastric neuroendocrine cancer patient derived xenograft model
  publication-title: Oncotarget
  doi: 10.18632/oncotarget.3712
– volume: 20
  start-page: 1623
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib203
  article-title: An integrated systems biology approach identifies TRIM25 as a key determinant of breast cancer metastasis
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2017.07.052
– volume: 30
  start-page: 836
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib11
  article-title: Extracellular vesicles in cancer: cell-to-cell mediators of metastasis
  publication-title: Cancer Cell
  doi: 10.1016/j.ccell.2016.10.009
– volume: 10
  start-page: 445
  year: 2009
  ident: 10.1016/j.cels.2019.07.003_bib49
  article-title: Collective cell migration in morphogenesis, regeneration and cancer
  publication-title: Nat. Rev. Mol. Cell Biol.
  doi: 10.1038/nrm2720
– volume: 553
  start-page: 467
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib8
  article-title: Chromosomal instability drives metastasis through a cytosolic DNA response
  publication-title: Nature
  doi: 10.1038/nature25432
– volume: 755
  start-page: 291
  year: 2011
  ident: 10.1016/j.cels.2019.07.003_bib85
  article-title: Laser-capture microdissection and transcriptional profiling in archival FFPE tissue in prostate cancer
  publication-title: Methods Mol. Biol.
  doi: 10.1007/978-1-61779-163-5_24
– volume: 10
  start-page: 20130011
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib169
  article-title: A mathematical model of tumour self-seeding reveals secondary metastatic deposits as drivers of primary tumour growth
  publication-title: J. R. Soc. Interface
  doi: 10.1098/rsif.2013.0011
– volume: 17
  start-page: 17
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib210
  article-title: Patient-derived xenograft models of breast cancer and their predictive power
  publication-title: Breast Cancer Res.
  doi: 10.1186/s13058-015-0523-1
– volume: 5
  start-page: 3963
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib62
  article-title: The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes
  publication-title: Nat. Commun.
  doi: 10.1038/ncomms4963
– volume: 113
  start-page: E854
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib34
  article-title: Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1508541113
– volume: 118
  start-page: 1726
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib76
  article-title: Predictive clinical outcome of the intratumoral CD66b-positive neutrophil-to-CD8-positive T-cell ratio in patients with resectable nonsmall cell lung cancer
  publication-title: Cancer
  doi: 10.1002/cncr.26456
– ident: 10.1016/j.cels.2019.07.003_bib148
  doi: 10.1007/978-3-642-03246-2_1
– volume: 2
  start-page: 429
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib171
  article-title: Adaptive stress responses During tumor metastasis and dormancy
  publication-title: Trends Cancer
  doi: 10.1016/j.trecan.2016.06.004
– volume: 160
  start-page: 1246
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib31
  article-title: Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis
  publication-title: Cell
  doi: 10.1016/j.cell.2015.02.038
– volume: 123
  start-page: 1988
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib69
  article-title: Lactate preserves neuronal metabolism and function following antecedent recurrent hypoglycemia
  publication-title: J. Clin. Invest.
  doi: 10.1172/JCI65105
– volume: 5
  start-page: 1989
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib158
  article-title: Epithelial-mesenchymal transition, proliferation, and angiogenesis in locally advanced cervical cancer treated with chemoradiotherapy
  publication-title: Cancer Med.
  doi: 10.1002/cam4.751
– volume: 17
  start-page: 1917
  year: 2010
  ident: 10.1016/j.cels.2019.07.003_bib112
  article-title: CpG island methylator phenotype associated with tumor recurrence in tumor-node-metastasis stage I hepatocellular carcinoma
  publication-title: Ann. Surg. Oncol.
  doi: 10.1245/s10434-010-0921-7
– volume: 62
  start-page: 1129
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib53
  article-title: A study of hypermethylated circulating tumor DNA as a universal colorectal cancer biomarker
  publication-title: Clin. Chem.
  doi: 10.1373/clinchem.2015.253609
– volume: 28
  start-page: 2402
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib97
  article-title: CySBML: a cytoscape plugin for SBML
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts432
– volume: 19
  start-page: 147
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib45
  article-title: Pulling cells out of tumours
  publication-title: Nat. Cell Biol.
  doi: 10.1038/ncb3484
– volume: 450
  start-page: 1235
  year: 2007
  ident: 10.1016/j.cels.2019.07.003_bib139
  article-title: Isolation of rare circulating tumour cells in cancer patients by microchip technology
  publication-title: Nature
  doi: 10.1038/nature06385
– volume: 49
  start-page: 1571
  year: 2009
  ident: 10.1016/j.cels.2019.07.003_bib195
  article-title: MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma
  publication-title: Hepatology
  doi: 10.1002/hep.22806
– volume: 8
  start-page: 1376
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib175
  article-title: Cancer-associated fibroblasts enhance tumor (18)F-FDG uptake and contribute to the intratumor heterogeneity of PET-CT
  publication-title: Theranostics
  doi: 10.7150/thno.22717
– volume: 126
  start-page: 1454
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib142
  article-title: A dynamic model of the hypoxia-inducible factor 1alpha (HIF-1alpha) network
  publication-title: J. Cell Sci.
  doi: 10.1242/jcs.119974
– year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib91
  article-title: Semi-supervised classification with graph convolutional networks
  publication-title: arXiv
– volume: 6
  start-page: 865
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib137
  article-title: RARRES3 suppresses breast cancer lung metastasis by regulating adhesion and differentiation
  publication-title: EMBO Mol. Med.
  doi: 10.15252/emmm.201303675
– volume: 734
  start-page: 73
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib181
  article-title: Regulation of tumor cell dormancy by tissue microenvironments and autophagy
  publication-title: Adv. Exp. Med. Biol.
  doi: 10.1007/978-1-4614-1445-2_5
– volume: 161
  start-page: 83
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib204
  article-title: Longitudinally collected CTCs and CTC-clusters and clinical outcomes of metastatic breast cancer
  publication-title: Breast Cancer Res. Treat.
  doi: 10.1007/s10549-016-4026-2
– volume: 12
  start-page: 014101
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib196
  article-title: Biomimetic microfluidic platform for the quantification of transient endothelial monolayer permeability and therapeutic transport under mimicked cancerous conditions
  publication-title: Biomicrofluidics
  doi: 10.1063/1.5000377
– volume: 75
  start-page: 4272
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib66
  article-title: A quantitative system for studying metastasis using transparent zebrafish
  publication-title: Cancer Res.
  doi: 10.1158/0008-5472.CAN-14-3319
– volume: 18
  start-page: 3687
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib178
  article-title: Tumor-on-a-chip platform to investigate progression and drug sensitivity in cell lines and patient-derived organoids
  publication-title: Lab Chip
  doi: 10.1039/C8LC00596F
– volume: 12
  start-page: e0185844
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib120
  article-title: A deep convolutional neural network-based automatic delineation strategy for multiple brain metastases stereotactic radiosurgery
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0185844
– volume: 17
  start-page: 5247
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib222
  article-title: Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease
  publication-title: Mol. Med. Rep.
– volume: 15
  start-page: 290
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib123
  article-title: Using deep learning to model the hierarchical structure and function of a cell
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.4627
– volume: 18
  start-page: 96
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib168
  article-title: Absolute proteome composition and dynamics during dormancy and resuscitation of Mycobacterium tuberculosis
  publication-title: Cell Host Microbe
  doi: 10.1016/j.chom.2015.06.001
– volume: 540
  start-page: 588
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib64
  article-title: Mechanism of early dissemination and metastasis in Her2+ mammary cancer
  publication-title: Nature
  doi: 10.1038/nature20609
– volume: 527
  start-page: 472
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib47
  article-title: Epithelial-to-mesenchymal transition is not required for lung metastasis but contributes to chemoresistance
  publication-title: Nature
  doi: 10.1038/nature15748
– volume: 8
  start-page: 15773
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib140
  article-title: EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells
  publication-title: Nat. Commun.
  doi: 10.1038/ncomms15773
– volume: 149
  start-page: 780
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib107
  article-title: Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks
  publication-title: Cell
  doi: 10.1016/j.cell.2012.03.031
– volume: 513
  start-page: 559
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib37
  article-title: Functional polarization of tumour-associated macrophages by tumour-derived lactic acid
  publication-title: Nature
  doi: 10.1038/nature13490
– volume: 27
  start-page: 1287
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib111
  article-title: Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
  publication-title: Genome Res.
  doi: 10.1101/gr.209973.116
– volume: 8
  start-page: 1231
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib17
  article-title: Combating subclonal evolution of resistant cancer phenotypes
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-017-01174-3
– volume: 67
  start-page: 275
  year: 1996
  ident: 10.1016/j.cels.2019.07.003_bib57
  article-title: Dichotomy of astrocytoma migration and proliferation
  publication-title: Int. J. Cancer
  doi: 10.1002/(SICI)1097-0215(19960717)67:2<275::AID-IJC20>3.0.CO;2-9
– volume: 44
  start-page: 4124
  year: 1984
  ident: 10.1016/j.cels.2019.07.003_bib182
  article-title: A stochastic numerical model of breast cancer growth that simulates clinical data
  publication-title: Cancer Res.
– volume: 40
  start-page: 41
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib183
  article-title: Impact of the physical microenvironment on tumor progression and metastasis
  publication-title: Curr. Opin. Biotechnol.
  doi: 10.1016/j.copbio.2016.02.007
– volume: 8
  start-page: 3904
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib143
  article-title: A mathematical model of the phosphoinositide pathway
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-018-22226-8
– volume: 344
  start-page: 1
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib125
  article-title: One mouse, one patient paradigm: new avatars of personalized cancer therapy
  publication-title: Cancer Lett.
  doi: 10.1016/j.canlet.2013.10.010
– volume: 18
  start-page: 851
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib135
  article-title: Deep learning in bioinformatics
  publication-title: Brief. Bioinform.
– volume: 34
  start-page: D689
  year: 2006
  ident: 10.1016/j.cels.2019.07.003_bib105
  article-title: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkj092
– volume: 13
  start-page: e1005618
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib212
  article-title: Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a
  publication-title: PLoS Comput. Biol.
  doi: 10.1371/journal.pcbi.1005618
– volume: 168
  start-page: 670
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib103
  article-title: Emerging biological principles of metastasis
  publication-title: Cell
  doi: 10.1016/j.cell.2016.11.037
– volume: 13
  start-page: 1838
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib94
  article-title: Photophysical tuning of N-oxide-based probes enables ratiometric photoacoustic imaging of tumor hypoxia
  publication-title: ACS Chem. Biol.
  doi: 10.1021/acschembio.8b00099
– volume: 3
  start-page: 035002
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib78
  article-title: Development of metastatic brain disease involves progression through lung metastases in EGFR mutated non-small cell lung cancer
  publication-title: Converg. Sci. Phys. Oncol.
  doi: 10.1088/2057-1739/aa7a8d
– volume: 7
  start-page: 42369
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib70
  article-title: Extracellular protonation modulates cell-cell interaction mechanics and tissue invasion in human melanoma cells
  publication-title: Sci. Rep.
  doi: 10.1038/srep42369
– volume: 114
  start-page: E5750
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib145
  article-title: Mechanochemical feedback underlies coexistence of qualitatively distinct cell polarity patterns within diverse cell populations
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1700054114
– volume: 109
  start-page: 13515
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib219
  article-title: Three-dimensional microfluidic model for tumor cell intravasation and endothelial barrier function
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1210182109
– volume: 113
  start-page: 1365
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib15
  article-title: Compartmental and spatial rule-based modeling with virtual cell
  publication-title: Biophys. J.
  doi: 10.1016/j.bpj.2017.08.022
– volume: 5
  start-page: 14739
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib122
  article-title: Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets
  publication-title: Sci. Rep.
  doi: 10.1038/srep14739
– volume: 6
  start-page: 224ra224
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib13
  article-title: Detection of circulating tumor DNA in early- and late-stage human malignancies
  publication-title: Sci. Transl. Med.
  doi: 10.1126/scitranslmed.3007094
– volume: 13
  start-page: 954
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib61
  article-title: From word models to executable models of signaling networks using automated assembly
  publication-title: Mol. Syst. Biol.
  doi: 10.15252/msb.20177651
– volume: 19
  start-page: 518
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib100
  article-title: The EMT-activator Zeb1 is a key factor for cell plasticity and promotes metastasis in pancreatic cancer
  publication-title: Nat. Cell Biol.
  doi: 10.1038/ncb3513
– volume: 7
  start-page: 27067
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib84
  article-title: Stability of the hybrid epithelial/mesenchymal phenotype
  publication-title: Oncotarget
  doi: 10.18632/oncotarget.8166
– volume: 8
  start-page: ra59
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib213
  article-title: Analysis of single-cell cytokine secretion reveals a role for paracrine signaling in coordinating macrophage responses to TLR4 stimulation
  publication-title: Sci. Signal.
  doi: 10.1126/scisignal.aaa2155
– volume: 7
  start-page: 4711
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib166
  article-title: Exosomes from metastatic cancer cells transfer amoeboid phenotype to non-metastatic cells and increase endothelial permeability: their emerging role in tumor heterogeneity
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-017-05002-y
– volume: 14
  start-page: e1005991
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib54
  article-title: PhysiCell: an open source physics-based cell simulator for 3-D multicellular systems
  publication-title: PLoS Comput. Biol.
  doi: 10.1371/journal.pcbi.1005991
– volume: 14
  start-page: 573
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib176
  article-title: Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.4225
– volume: 7
  start-page: 601
  year: 2000
  ident: 10.1016/j.cels.2019.07.003_bib50
  article-title: Using Bayesian networks to analyze expression data
  publication-title: J. Comput. Biol.
  doi: 10.1089/106652700750050961
– volume: 114
  start-page: E5589
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib68
  article-title: Notch1 maintains dormancy of olfactory horizontal basal cells, a reserve neural stem cell
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1701333114
– volume: 158
  start-page: 1110
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib1
  article-title: Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis
  publication-title: Cell
  doi: 10.1016/j.cell.2014.07.013
– volume: 527
  start-page: 329
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib71
  article-title: Tumour exosome integrins determine organotropic metastasis
  publication-title: Nature
  doi: 10.1038/nature15756
– volume: 2018
  start-page: 9780349
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib152
  article-title: Cryo-imaging and software platform for analysis of molecular MR imaging of micrometastases
  publication-title: Int. J. Biomed. Imaging
  doi: 10.1155/2018/9780349
– volume: 525
  start-page: 261
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib202
  article-title: A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity
  publication-title: Nature
  doi: 10.1038/nature14971
– volume: 4
  start-page: 281
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib180
  article-title: Beyond tissue stiffness and Bioadhesivity: advanced biomaterials to model tumor microenvironments and drug resistance
  publication-title: Trends Cancer
  doi: 10.1016/j.trecan.2018.01.008
– volume: 132
  start-page: 209
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib191
  article-title: Plasticity of cancer cell invasion-mechanisms and implications for therapy
  publication-title: Adv. Cancer Res.
  doi: 10.1016/bs.acr.2016.07.005
– volume: 5
  start-page: 1216
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib174
  article-title: Twist1-positive epithelial cells retain adhesive and proliferative capacity throughout dissemination
  publication-title: Biol. Open
  doi: 10.1242/bio.019703
– volume: 11
  start-page: 417
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib58
  article-title: Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.2869
– volume: 6
  start-page: e28074
  year: 2011
  ident: 10.1016/j.cels.2019.07.003_bib170
  article-title: The oogenic germline starvation response in C. elegans
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0028074
– volume: 361
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib87
  article-title: Developmental barcoding of whole mouse via homing CRISPR
  publication-title: Science
  doi: 10.1126/science.aat9804
– volume: 28
  start-page: 672
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib52
  article-title: Interactome-transcriptome integration for predicting distant metastasis in breast cancer
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts025
– volume: 184
  start-page: 101
  year: 2019
  ident: 10.1016/j.cels.2019.07.003_bib99
  article-title: Functional MRS with J-edited lactate in human motor cortex at 4T
  publication-title: Neuroimage
  doi: 10.1016/j.neuroimage.2018.09.008
– volume: 30
  start-page: 70
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib206
  article-title: Simulating cancer growth with multiscale agent-based modeling
  publication-title: Semin. Cancer Biol.
  doi: 10.1016/j.semcancer.2014.04.001
– volume: 548
  start-page: 297
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib157
  article-title: Integrative clinical genomics of metastatic cancer
  publication-title: Nature
  doi: 10.1038/nature23306
– volume: 34
  start-page: 1163
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib3
  article-title: Metabolic reprogramming and dependencies associated with epithelial cancer stem cells independent of the epithelial-mesenchymal transition program
  publication-title: Stem Cells
  doi: 10.1002/stem.2286
– volume: 8
  start-page: 109
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib86
  article-title: Comprehensive serial molecular profiling of an "N of 1" exceptional non-responder with metastatic prostate cancer progressing to small cell carcinoma on treatment
  publication-title: J. Hematol. Oncol.
  doi: 10.1186/s13045-015-0204-7
– volume: 10
  start-page: e0118060
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib51
  article-title: Lung epithelial cells induce both phenotype alteration and senescence in breast cancer cells
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0118060
– volume: 12
  start-page: 379
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib20
  article-title: Zebrafish xenograft models of cancer and metastasis for drug discovery
  publication-title: Expert Opin. Drug Discov.
  doi: 10.1080/17460441.2017.1297416
– volume: 17
  start-page: E1151
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib115
  article-title: A Mini-Review for cancer immunotherapy: molecular understanding of PD-1/PD-L1 pathway & translational blockade of immune checkpoints
  publication-title: Int. J. Mol. Sci.
  doi: 10.3390/ijms17071151
– volume: 7
  start-page: 12685
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib138
  article-title: Clonal dynamics following p53 loss of heterozygosity in Kras-driven cancers
  publication-title: Nat. Commun.
  doi: 10.1038/ncomms12685
– volume: 120
  start-page: 461
  year: 2010
  ident: 10.1016/j.cels.2019.07.003_bib16
  article-title: Detection of PIK3CA mutations in circulating free DNA in patients with breast cancer
  publication-title: Breast Cancer Res. Treat.
  doi: 10.1007/s10549-010-0747-9
– volume: 7
  start-page: 38244
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib95
  article-title: Relaxation oscillations and hierarchy of feedbacks in MAPK signaling
  publication-title: Sci. Rep.
  doi: 10.1038/srep38244
– volume: 287
  start-page: 33533
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib116
  article-title: Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis
  publication-title: J. Biol. Chem.
  doi: 10.1074/jbc.M112.392332
– volume: 513
  start-page: 202
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib23
  article-title: Comprehensive molecular characterization of gastric adenocarcinoma
  publication-title: Nature
  doi: 10.1038/nature13480
– volume: 19
  start-page: 120
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib48
  article-title: Phenotypic heterogeneity of disseminated tumour cells is preset by primary tumour hypoxic microenvironments
  publication-title: Nat. Cell Biol.
  doi: 10.1038/ncb3465
– volume: 109
  start-page: 9786
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib27
  article-title: Implanted adipose progenitor cells as physicochemical regulators of breast cancer
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1121160109
– volume: 9
  start-page: 957
  year: 2002
  ident: 10.1016/j.cels.2019.07.003_bib67
  article-title: Mathematical models of protein kinase signal transduction
  publication-title: Mol. Cell
  doi: 10.1016/S1097-2765(02)00528-2
– volume: 527
  start-page: 100
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib220
  article-title: Microenvironment-induced PTEN loss by exosomal microRNA primes brain metastasis outgrowth
  publication-title: Nature
  doi: 10.1038/nature15376
– volume: 7
  start-page: e34637
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib141
  article-title: A stochastic Markov chain model to describe lung cancer growth and metastasis
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0034637
– volume: 8
  start-page: 227
  year: 2005
  ident: 10.1016/j.cels.2019.07.003_bib165
  article-title: Genomic analysis of single cytokeratin-positive cells from bone marrow reveals early mutational events in breast cancer
  publication-title: Cancer Cell
  doi: 10.1016/j.ccr.2005.08.003
– volume: 77
  start-page: 2242
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib75
  article-title: Defining cancer subpopulations by adaptive strategies rather than molecular properties provides novel insights into intratumoral evolution
  publication-title: Cancer Res.
  doi: 10.1158/0008-5472.CAN-16-2844
– volume: 6
  start-page: ra68
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib92
  article-title: Computational modeling of ERBB2-amplified breast cancer identifies combined ErbB2/3 blockade as superior to the combination of MEK and AKT inhibitors
  publication-title: Sci. Signal.
  doi: 10.1126/scisignal.2004008
– volume: 75
  start-page: 1567
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib156
  article-title: Impact of metabolic heterogeneity on tumor growth, invasion, and treatment outcomes
  publication-title: Cancer Res.
  doi: 10.1158/0008-5472.CAN-14-1428
– volume: 4
  start-page: 121490
  year: 2019
  ident: 10.1016/j.cels.2019.07.003_bib113
  article-title: Human primary liver cancer organoids reveal intratumor and interpatient drug response heterogeneity
  publication-title: JCI Insight
  doi: 10.1172/jci.insight.121490
– volume: 8
  start-page: 1270
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib177
  article-title: Percolation transition of cooperative mutational effects in colorectal tumorigenesis
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-017-01171-6
– volume: 8
  start-page: 17535
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib104
  article-title: Development and characterization of a spontaneously metastatic patient-derived xenograft model of human prostate cancer
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-018-35695-8
– volume: 19
  start-page: 524
  year: 2003
  ident: 10.1016/j.cels.2019.07.003_bib73
  article-title: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btg015
– volume: 529
  start-page: 298
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib129
  article-title: Metastatic colonization by circulating tumour cells
  publication-title: Nature
  doi: 10.1038/nature17038
– volume: 7
  start-page: e1700903
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib2
  article-title: Biomaterial scaffolds as pre-metastatic niche mimics systemically alter the primary tumor and tumor microenvironment
  publication-title: Adv. Healthc. Mater.
  doi: 10.1002/adhm.201700903
– volume: 4
  start-page: 12
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib90
  article-title: In vitro tumor models: advantages, disadvantages, variables, and selecting the right platform
  publication-title: Front. Bioeng. Biotechnol.
  doi: 10.3389/fbioe.2016.00012
– volume: 111
  start-page: 2342
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib209
  article-title: Spontaneous dormancy of metastatic breast cancer cells in an all human liver microphysiologic system
  publication-title: Br. J. Cancer
  doi: 10.1038/bjc.2014.533
– volume: 290
  start-page: 2351
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib130
  article-title: The Mycobacterium tuberculosis Clp gene regulator is required for in vitro reactivation from hypoxia-induced dormancy
  publication-title: J. Biol. Chem.
  doi: 10.1074/jbc.M114.615534
– volume: 14
  start-page: 395
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib56
  article-title: Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.4179
– volume: 26
  start-page: 65
  year: 2007
  ident: 10.1016/j.cels.2019.07.003_bib74
  article-title: Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues
  publication-title: Oncogene
  doi: 10.1038/sj.onc.1209755
– volume: 9
  start-page: 21
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib117
  article-title: Macrophages orchestrate breast cancer early dissemination and metastasis
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-017-02481-5
– volume: 16
  start-page: 160
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib109
  article-title: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer
  publication-title: Genome Biol.
  doi: 10.1186/s13059-015-0700-7
– volume: 17
  start-page: 619
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib36
  article-title: A model of dormant-emergent metastatic breast cancer progression enabling exploration of biomarker signatures
  publication-title: Mol. Cell. Proteomics
  doi: 10.1074/mcp.RA117.000370
– volume: 114
  start-page: 2934
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib26
  article-title: Metabolic origins of spatial organization in the tumor microenvironment
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1700600114
– volume: 6
  start-page: 382
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib133
  article-title: Reduced proteolytic shedding of receptor tyrosine kinases is a post-translational mechanism of kinase inhibitor resistance
  publication-title: Cancer Discov.
  doi: 10.1158/2159-8290.CD-15-0933
– volume: 159
  start-page: 402
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib30
  article-title: Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks
  publication-title: Cell
  doi: 10.1016/j.cell.2014.09.021
– volume: 96
  start-page: 4494
  year: 1999
  ident: 10.1016/j.cels.2019.07.003_bib93
  article-title: Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.96.8.4494
– volume: 10
  start-page: e1003460
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib82
  article-title: VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data
  publication-title: PLoS Comput. Biol.
  doi: 10.1371/journal.pcbi.1003460
– volume: 10
  start-page: 1061
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib60
  article-title: Mouse models of metastasis: progress and prospects
  publication-title: Dis. Model Mech.
  doi: 10.1242/dmm.030403
– year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib164
  article-title: Explainable artificial intelligence: understanding, visualizing and interpreting deep learning models
  publication-title: arXiv
– volume: 17
  start-page: 816
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib38
  article-title: Pancreatic cancer exosomes initiate pre-metastatic niche formation in the liver
  publication-title: Nat. Cell Biol.
  doi: 10.1038/ncb3169
– volume: 2
  start-page: 727
  year: 2007
  ident: 10.1016/j.cels.2019.07.003_bib12
  article-title: Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
  publication-title: Nat. Protoc.
  doi: 10.1038/nprot.2007.99
– volume: 29
  start-page: 49
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib65
  article-title: 'Go or grow': the key to the emergence of invasion in tumor progression?
  publication-title: Math. Med. Biol.
  doi: 10.1093/imammb/dqq011
– volume: 1
  start-page: 2
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib81
  article-title: Distinguishing mechanisms underlying EMT tristability
  publication-title: Cancer Converg.
  doi: 10.1186/s41236-017-0005-8
– volume: 97
  start-page: 107
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib198
  article-title: Studying cancer metastasis: existing models, challenges and future perspectives
  publication-title: Crit. Rev. Oncol. Hematol.
  doi: 10.1016/j.critrevonc.2015.08.009
– volume: 3
  start-page: 453
  year: 2003
  ident: 10.1016/j.cels.2019.07.003_bib46
  article-title: The pathogenesis of cancer metastasis: the 'seed and soil' hypothesis revisited
  publication-title: Nat. Rev. Cancer
  doi: 10.1038/nrc1098
– volume: 8
  start-page: 1905
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib193
  article-title: Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2014.08.029
– volume: 164
  start-page: 293
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib127
  article-title: Functional genomic landscape of human breast cancer drivers, vulnerabilities, and resistance
  publication-title: Cell
  doi: 10.1016/j.cell.2015.11.062
– volume: 15
  start-page: 1491
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib39
  article-title: Improving pancreatic cancer diagnosis using circulating tumor cells: prospects for staging and single-cell analysis
  publication-title: Expert Rev. Mol. Diagn.
  doi: 10.1586/14737159.2015.1091311
– volume: 19
  start-page: 1063
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib190
  article-title: Modeling boundary conditions for balanced proliferation in metastatic latency
  publication-title: Clin. Cancer Res.
  doi: 10.1158/1078-0432.CCR-12-3180
– volume: 3
  start-page: 515
  year: 2006
  ident: 10.1016/j.cels.2019.07.003_bib72
  article-title: Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways
  publication-title: J. R. Soc. Interface
  doi: 10.1098/rsif.2005.0109
– volume: 22
  start-page: 1339
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib14
  article-title: Global secretome analysis identifies novel mediators of bone metastasis
  publication-title: Cell Res.
  doi: 10.1038/cr.2012.89
– volume: 95
  start-page: 245134
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib167
  article-title: Probing many-body localization with neural networks
  publication-title: Phys. Rev. B
  doi: 10.1103/PhysRevB.95.245134
– volume: 34
  start-page: 627
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib188
  article-title: Systems biology analysis of heterocellular signaling
  publication-title: Trends Biotechnol.
  doi: 10.1016/j.tibtech.2016.02.016
– volume: 339
  start-page: 580
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib215
  article-title: Circulating breast tumor cells exhibit dynamic changes in epithelial and mesenchymal composition
  publication-title: Science
  doi: 10.1126/science.1228522
– volume: 67
  start-page: 1995
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib9
  article-title: Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer
  publication-title: Gut
  doi: 10.1136/gutjnl-2016-313372
– ident: 10.1016/j.cels.2019.07.003_bib40
– volume: 4
  start-page: 1014
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib5
  article-title: Synthetic lethality in ATM-deficient RAD50-mutant tumors underlies outlier response to cancer therapy
  publication-title: Cancer Discov.
  doi: 10.1158/2159-8290.CD-14-0380
– volume: 23
  start-page: 1241
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib29
  article-title: The rise of deep learning in drug discovery
  publication-title: Drug Discov. Today
  doi: 10.1016/j.drudis.2018.01.039
– volume: 8
  start-page: 707
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib80
  article-title: Clinical responses to adoptive T-cell transfer can be modeled in an autologous immune-humanized mouse model
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-017-00786-z
– volume: 9
  start-page: 646
  year: 2013
  ident: 10.1016/j.cels.2019.07.003_bib121
  article-title: Programming biological models in Python using PySB
  publication-title: Mol. Syst. Biol.
  doi: 10.1038/msb.2013.1
– volume: 352
  start-page: 167
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib32
  article-title: A collective route to metastasis: seeding by tumor cell clusters
  publication-title: Science
  doi: 10.1126/science.aaf6546
– volume: 525
  start-page: 256
  year: 2015
  ident: 10.1016/j.cels.2019.07.003_bib214
  article-title: Distinct EMT programs control normal mammary stem cells and tumour-initiating cells
  publication-title: Nature
  doi: 10.1038/nature14897
– volume: 6
  start-page: 26286
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib118
  article-title: Deep learning as a tool for increased accuracy and efficiency of histopathological diagnosis
  publication-title: Sci. Rep.
  doi: 10.1038/srep26286
– volume: 74
  start-page: 5963
  year: 2014
  ident: 10.1016/j.cels.2019.07.003_bib185
  article-title: Network modeling of TGFbeta signaling in hepatocellular carcinoma epithelial-to-mesenchymal transition reveals joint sonic hedgehog and Wnt pathway activation
  publication-title: Cancer Res.
  doi: 10.1158/0008-5472.CAN-14-0225
– volume: 173
  start-page: 1581
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib22
  article-title: Next-generation machine learning for biological networks
  publication-title: Cell
  doi: 10.1016/j.cell.2018.05.015
– year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib205
  article-title: Deep learning for identifying metastatic breast cancer
  publication-title: arXiv
– volume: 2
  start-page: 802
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib208
  article-title: Differential network entropy reveals cancer system hallmarks
  publication-title: Sci. Rep.
  doi: 10.1038/srep00802
– volume: 25
  start-page: 1318
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib89
  article-title: Patient-derived xenografts for prognostication and personalized treatment for head and neck squamous cell carcinoma
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2018.10.004
– volume: 6
  start-page: 19103
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib218
  article-title: 3D tumor spheroid models for in vitro therapeutic screening: a systematic approach to enhance the biological relevance of data obtained
  publication-title: Sci. Rep.
  doi: 10.1038/srep19103
– year: 2019
  ident: 10.1016/j.cels.2019.07.003_bib101
  article-title: The evolution of placental invasion and cancer metastasis are causally linked
  publication-title: bioRxiv
– volume: 34
  start-page: 637
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib173
  article-title: Wishbone identifies bifurcating developmental trajectories from single-cell data
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt.3569
– volume: 128
  start-page: 65
  year: 2017
  ident: 10.1016/j.cels.2019.07.003_bib44
  article-title: Time-lapsed, large-volume, high-resolution intravital imaging for tissue-wide analysis of single cell dynamics
  publication-title: Methods
  doi: 10.1016/j.ymeth.2017.07.019
– volume: 45
  start-page: 350
  year: 2012
  ident: 10.1016/j.cels.2019.07.003_bib4
  article-title: The inference of breast cancer metastasis through gene regulatory networks
  publication-title: J. Biomed. Inform.
  doi: 10.1016/j.jbi.2011.11.015
– volume: 14
  start-page: 985
  year: 2008
  ident: 10.1016/j.cels.2019.07.003_bib41
  article-title: Circulating mutant DNA to assess tumor dynamics
  publication-title: Nat. Med.
  doi: 10.1038/nm.1789
– volume: 17
  start-page: 498
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib147
  article-title: A methodological approach for using high-level Petri Nets to model the immune system response
  publication-title: BMC Bioinformatics
  doi: 10.1186/s12859-016-1361-6
– volume: 9
  start-page: 893
  year: 2007
  ident: 10.1016/j.cels.2019.07.003_bib211
  article-title: Multi-step pericellular proteolysis controls the transition from individual to collective cancer cell invasion
  publication-title: Nat. Cell Biol.
  doi: 10.1038/ncb1616
– volume: 17
  start-page: 1158
  year: 2016
  ident: 10.1016/j.cels.2019.07.003_bib197
  article-title: 10 year survival after breast-conserving surgery plus radiotherapy compared with mastectomy in early breast cancer in the Netherlands: a population-based study
  publication-title: Lancet Oncol.
  doi: 10.1016/S1470-2045(16)30067-5
– volume: 11
  start-page: 16
  year: 2018
  ident: 10.1016/j.cels.2019.07.003_bib223
  article-title: PD-1 axis expression in musculoskeletal tumors and antitumor effect of nivolumab in osteosarcoma model of humanized mouse
  publication-title: J. Hematol. Oncol.
  doi: 10.1186/s13045-018-0560-1
SSID ssj0001492402
Score 2.5828109
SecondaryResourceType review_article
Snippet Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully...
Cancer metastasis is no longer viewed as a linear cascade of events, but rather as a series of concurrent, partially overlapping processes, as successfully...
SourceID pubmedcentral
proquest
pubmed
crossref
elsevier
SourceType Open Access Repository
Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 109
SubjectTerms Animals
Disease Progression
Humans
Neoplasm Metastasis - genetics
Neoplasm Metastasis - pathology
Neoplasms - metabolism
Neoplasms - pathology
Signal Transduction
Systems Biology - methods
Title Systems Biology of Cancer Metastasis
URI https://dx.doi.org/10.1016/j.cels.2019.07.003
https://www.ncbi.nlm.nih.gov/pubmed/31465728
https://www.proquest.com/docview/2283110677
https://pubmed.ncbi.nlm.nih.gov/PMC6716621
Volume 9
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1ba9swFBZb-rKXsbJbdike9C042LJ80WMIK6VhY4x2657MkSyRZMMZjctgv35HlmQ76VrWvZggS8byd6LzSedGyHEkkSSAoGEMlIesUBACFyxUVGWpZBw1trHofviYnV6ws8v00peEd9EljZjK33-NK_kfVLENcTVRsvdAtnsoNuBvxBeviDBe_wljl27cFZR0sVaIoknN0wDyvu1qO2Sfc3NQtx3kKG-tQUuw58DfsHvnqjsHm1zAFMLdTD5NffsXqGFtw8hWV71kLRCaX3IJ37234WQ2HR4omBimwgdot-sO6vg0RJ21s0jygSzQwYIXR3ygO2Mb539jWbYnBOupRH1v3Ol4mzA1Snol5A3ve7qp8xj0zmjr0jyjNM8oI2M6Tx6SA4pbBDoiB7PF56-L_oSNcWM6MtUF_Yxc1JR18Nt_mduYyc2dx74D7YCRnD8hj91WIphZuTgkD1T9lBw7mQicTAQbHViZCHqZeEYuTt6fz09DVwkjlCxNm7BSrBCC60pwkKIQWhVQMVnhgluBULyiOuKAXDARuchN7SGAypS6kFLnOq2S52RUb2r1kgQ4JCuA6Qy5G0t0hfsVmmnFYqVVBHkxJrH_CqV0aeJNtZIf5e0QjMmkG_PTJkm5s3fqP27paJ6lbyWKy53j3nkkSlwDjWELarW5xk7IkeM2F-KYvLDIdO-RIBVIc4rzyncw6zqY_Oq7d-rVss2znuVxltH41b1m95o86v9Ub8ioubpWb5G3NuLICegfiFOXUA
linkProvider Library Specific Holdings
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Systems+Biology+of+Cancer+Metastasis&rft.jtitle=Cell+systems&rft.au=Suhail%2C+Yasir&rft.au=Cain%2C+Margo+P.&rft.au=Vanaja%2C+Kiran&rft.au=Kurywchak%2C+Paul+A.&rft.date=2019-08-28&rft.issn=2405-4712&rft.volume=9&rft.issue=2&rft.spage=109&rft.epage=127&rft_id=info:doi/10.1016%2Fj.cels.2019.07.003&rft.externalDBID=n%2Fa&rft.externalDocID=10_1016_j_cels_2019_07_003
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2405-4712&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2405-4712&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2405-4712&client=summon