scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data
Alquicira-Hernandez, Jose, Sathe, Anuja, Ji, Hanlee P, Nguyen, Quan, Powell, Joseph E
Published in Genome Biology (12.12.2019)
Published in Genome Biology (12.12.2019)
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Journal Article
Genomic Instability in Cancer: Teetering on the Limit of Tolerance
Andor, Noemi, Maley, Carlo C, Ji, Hanlee P
Published in Cancer research (Chicago, Ill.) (01.05.2017)
Published in Cancer research (Chicago, Ill.) (01.05.2017)
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Journal Article
Single-Cell Genomic Characterization Reveals the Cellular Reprogramming of the Gastric Tumor Microenvironment
Sathe, Anuja, Grimes, Susan M, Lau, Billy T, Chen, Jiamin, Suarez, Carlos, Huang, Robert J, Poultsides, George, Ji, Hanlee P
Published in Clinical cancer research (01.06.2020)
Published in Clinical cancer research (01.06.2020)
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Journal Article
Pan-cancer analysis of the extent and consequences of intratumor heterogeneity
Andor, Noemi, Graham, Trevor A, Jansen, Marnix, Xia, Li C, Aktipis, C Athena, Petritsch, Claudia, Ji, Hanlee P, Maley, Carlo C
Published in Nature medicine (01.01.2016)
Published in Nature medicine (01.01.2016)
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Journal Article
Single-cell analysis can define distinct evolution of tumor sites in follicular lymphoma
Haebe, Sarah, Shree, Tanaya, Sathe, Anuja, Day, Grady, Czerwinski, Debra K., Grimes, Susan M., Lee, HoJoon, Binkley, Michael S., Long, Steven R., Martin, Brock, Ji, Hanlee P., Levy, Ronald
Published in Blood (27.05.2021)
Published in Blood (27.05.2021)
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Journal Article
Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture
Li, Xingnan, Nadauld, Lincoln, Ootani, Akifumi, Corney, David C, Pai, Reetesh K, Gevaert, Olivier, Cantrell, Michael A, Rack, Paul G, Neal, James T, Chan, Carol W-M, Yeung, Trevor, Gong, Xue, Yuan, Jenny, Wilhelmy, Julie, Robine, Sylvie, Attardi, Laura D, Plevritis, Sylvia K, Hung, Kenneth E, Chen, Chang-Zheng, Ji, Hanlee P, Kuo, Calvin J
Published in Nature medicine (01.07.2014)
Published in Nature medicine (01.07.2014)
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Journal Article
Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay
Hernández Bustos, Adrián, Martiny, Elisa, Bom Pedersen, Nadia, Parvathaneni, Rohith Pavan, Hansen, Jonas, Ji, Hanlee P., Astakhova, Kira
Published in Analytical chemistry (Washington) (23.05.2023)
Published in Analytical chemistry (Washington) (23.05.2023)
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Journal Article
KmerKeys: a web resource for searching indexed genome assemblies and variants
Pavlichin, Dmitri S, Lee, HoJoon, Greer, Stephanie U, Grimes, Susan M, Weissman, Tsachy, Ji, Hanlee P
Published in Nucleic acids research (05.07.2022)
Published in Nucleic acids research (05.07.2022)
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Journal Article
Performance comparison of whole-genome sequencing platforms
LAM, Hugo Y. K, CLARK, Michael J, BUTTE, Atul J, JI, Hanlee P, SNYDER, Michael, RUI CHEN, RONG CHEN, NATSOULIS, Georges, O'HUALLACHAIN, Maeve, DEWEY, Frederick E, HABEGGER, Lukas, ASHLEY, Euan A, GERSTEIN, Mark B
Published in Nature biotechnology (01.01.2012)
Published in Nature biotechnology (01.01.2012)
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Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
Mason, Kaishu, Sathe, Anuja, Hess, Paul R, Rong, Jiazhen, Wu, Chi-Yun, Furth, Emma, Susztak, Katalin, Levinsohn, Jonathan, Ji, Hanlee P, Zhang, Nancy
Published in Genome Biology (12.01.2024)
Published in Genome Biology (12.01.2024)
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Journal Article
Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing
Kim, Heon Seok, Grimes, Susan M, Hooker, Anna C, Lau, Billy T, Ji, Hanlee P
Published in Genome Biology (06.12.2021)
Published in Genome Biology (06.12.2021)
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Journal Article
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Zlitni, Soumaya, Bishara, Alex, Moss, Eli L, Tkachenko, Ekaterina, Kang, Joyce B, Culver, Rebecca N, Andermann, Tessa M, Weng, Ziming, Wood, Christina, Handy, Christine, Ji, Hanlee P, Batzoglou, Serafim, Bhatt, Ami S
Published in Genome medicine (29.05.2020)
Published in Genome medicine (29.05.2020)
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Journal Article
Ultrasensitive detection of rare mutations using next-generation targeted resequencing
Flaherty, Patrick, Natsoulis, Georges, Muralidharan, Omkar, Winters, Mark, Buenrostro, Jason, Bell, John, Brown, Sheldon, Holodniy, Mark, Zhang, Nancy, Ji, Hanlee P.
Published in Nucleic acids research (01.01.2012)
Published in Nucleic acids research (01.01.2012)
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Journal Article
CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis
Shin, GiWon, Grimes, Susan M, Lee, HoJoon, Lau, Billy T, Xia, Li C, Ji, Hanlee P
Published in Nature communications (07.02.2017)
Published in Nature communications (07.02.2017)
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Journal Article
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
Lau, Billy T, Almeda, Alison, Schauer, Marie, McNamara, Madeline, Bai, Xiangqi, Meng, Qingxi, Partha, Mira, Grimes, Susan M, Lee, HoJoon, Heestand, Gregory M, Ji, Hanlee P
Published in Genome medicine (03.05.2023)
Published in Genome medicine (03.05.2023)
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Journal Article
GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers
Sathe, Anuja, Ayala, Carlos, Bai, Xiangqi, Grimes, Susan M, Lee, Byrne, Kin, Cindy, Shelton, Andrew, Poultsides, George, Ji, Hanlee P
Published in Genome medicine (26.11.2023)
Published in Genome medicine (26.11.2023)
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Journal Article
Tumor-associated microbiome features of metastatic colorectal cancer and clinical implications
An, Ho Jung, Partha, Mira A, Lee, HoJoon, Lau, Billy T, Pavlichin, Dmitri S, Almeda, Alison, Hooker, Anna C, Shin, Giwon, Ji, Hanlee P
Published in Frontiers in oncology (18.01.2024)
Published in Frontiers in oncology (18.01.2024)
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