GRAND: a database of gene regulatory network models across human conditions
Ben Guebila, Marouen, Lopes-Ramos, Camila M, Weighill, Deborah, Sonawane, Abhijeet Rajendra, Burkholz, Rebekka, Shamsaei, Behrouz, Platig, John, Glass, Kimberly, Kuijjer, Marieke L, Quackenbush, John
Published in Nucleic acids research (07.01.2022)
Published in Nucleic acids research (07.01.2022)
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Journal Article
Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism
Lopes-Ramos, Camila M, Kuijjer, Marieke L, Ogino, Shuji, Fuchs, Charles S, DeMeo, Dawn L, Glass, Kimberly, Quackenbush, John
Published in Cancer research (Chicago, Ill.) (01.10.2018)
Published in Cancer research (Chicago, Ill.) (01.10.2018)
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Journal Article
lionessR: single sample network inference in R
Kuijjer, Marieke L, Hsieh, Ping-Han, Quackenbush, John, Glass, Kimberly
Published in BMC cancer (25.10.2019)
Published in BMC cancer (25.10.2019)
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Journal Article
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas
van IJzendoorn, David G P, Szuhai, Karoly, Briaire-de Bruijn, Inge H, Kostine, Marie, Kuijjer, Marieke L, Bovée, Judith V M G
Published in PLoS computational biology (01.02.2019)
Published in PLoS computational biology (01.02.2019)
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Journal Article
Modulation of the osteosarcoma expression phenotype by microRNAs
Namløs, Heidi M, Meza-Zepeda, Leonardo A, Barøy, Tale, Østensen, Ingrid H G, Kresse, Stine H, Kuijjer, Marieke L, Serra, Massimo, Bürger, Horst, Cleton-Jansen, Anne-Marie, Myklebost, Ola
Published in PloS one (25.10.2012)
Published in PloS one (25.10.2012)
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Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma
Wong, Kim, van der Weyden, Louise, Schott, Courtney R., Foote, Alastair, Constantino-Casas, Fernando, Smith, Sionagh, Dobson, Jane M., Murchison, Elizabeth P., Wu, Hong, Yeh, Iwei, Fullen, Douglas R., Joseph, Nancy, Bastian, Boris C., Patel, Rajiv M., Martincorena, Inigo, Robles-Espinoza, Carla Daniela, Iyer, Vivek, Kuijjer, Marieke L., Arends, Mark J., Brenn, Thomas, Harms, Paul W., Wood, Geoffrey A., Adams, David J.
Published in Nature communications (21.01.2019)
Published in Nature communications (21.01.2019)
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Journal Article
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
Ben Guebila, Marouen, Wang, Tian, Lopes-Ramos, Camila M, Fanfani, Viola, Weighill, Des, Burkholz, Rebekka, Schlauch, Daniel, Paulson, Joseph N, Altenbuchinger, Michael, Shutta, Katherine H, Sonawane, Abhijeet R, Lim, James, Calderer, Genis, van IJzendoorn, David G P, Morgan, Daniel, Marin, Alessandro, Chen, Cho-Yi, Song, Qi, Saha, Enakshi, DeMeo, Dawn L, Padi, Megha, Platig, John, Kuijjer, Marieke L, Glass, Kimberly, Quackenbush, John
Published in Genome Biology (09.03.2023)
Published in Genome Biology (09.03.2023)
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Journal Article
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Paulson, Joseph N, Chen, Cho-Yi, Lopes-Ramos, Camila M, Kuijjer, Marieke L, Platig, John, Sonawane, Abhijeet R, Fagny, Maud, Glass, Kimberly, Quackenbush, John
Published in BMC bioinformatics (03.10.2017)
Published in BMC bioinformatics (03.10.2017)
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Journal Article
Regulatory network changes between cell lines and their tissues of origin
Lopes-Ramos, Camila M, Paulson, Joseph N, Chen, Cho-Yi, Kuijjer, Marieke L, Fagny, Maud, Platig, John, Sonawane, Abhijeet R, DeMeo, Dawn L, Quackenbush, John, Glass, Kimberly
Published in BMC genomics (12.09.2017)
Published in BMC genomics (12.09.2017)
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Journal Article
The Variable Genomic Landscape During Osteosarcoma Progression: Insights From a Longitudinal WGS Analysis
Meijer, Debora M., Ruano, Dina, Briaire‐de Bruijn, Inge H., Wijers‐Koster, Pauline M., Sande, Michiel A. J., Gelderblom, Hans, Cleton‐Jansen, Anne‐Marie, Miranda, Noel F. C. C., Kuijjer, Marieke L., Bovée, Judith V. M. G.
Published in Genes chromosomes & cancer (01.07.2024)
Published in Genes chromosomes & cancer (01.07.2024)
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Journal Article
Heterogeneity in the gene regulatory landscape of leiomyosarcoma
Belova, Tatiana, Biondi, Nicola, Hsieh, Ping-Han, Lutsik, Pavlo, Chudasama, Priya, Kuijjer, Marieke L
Published in NAR cancer (01.09.2023)
Published in NAR cancer (01.09.2023)
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Journal Article
Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data
Kuijjer, Marieke L., Rydbeck, Halfdan, Kresse, Stine H., Buddingh, Emilie P., Lid, Ana B., Roelofs, Helene, Bürger, Horst, Myklebost, Ola, Hogendoorn, Pancras C. W., Meza-Zepeda, Leonardo A., Cleton-Jansen, Anne-Marie
Published in Genes chromosomes & cancer (01.07.2012)
Published in Genes chromosomes & cancer (01.07.2012)
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Journal Article
IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma
Kuijjer, Marieke L, Peterse, Elisabeth F P, van den Akker, Brendy E W M, Briaire-de Bruijn, Inge H, Serra, Massimo, Meza-Zepeda, Leonardo A, Myklebost, Ola, Hassan, A Bassim, Hogendoorn, Pancras C W, Cleton-Jansen, Anne-Marie
Published in BMC cancer (20.05.2013)
Published in BMC cancer (20.05.2013)
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Journal Article
An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets
Hill, Katherine E, Kelly, Andrew D, Kuijjer, Marieke L, Barry, William, Rattani, Ahmed, Garbutt, Cassandra C, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark C, Arredouani, Mohamed S, Cote, Greg, Hornicek, Francis, Choy, Edwin, Duan, Zhenfeng, Quackenbush, John, Haibe-Kains, Benjamin, Spentzos, Dimitrios
Published in Journal of hematology and oncology (15.05.2017)
Published in Journal of hematology and oncology (15.05.2017)
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Journal Article
Kinome and mRNA expression profiling of high-grade osteosarcoma cell lines implies Akt signaling as possible target for therapy
Kuijjer, Marieke L, van den Akker, Brendy E W M, Hilhorst, Riet, Mommersteeg, Monique, Buddingh, Emilie P, Serra, Massimo, Bürger, Horst, Hogendoorn, Pancras C W, Cleton-Jansen, Anne-Marie
Published in BMC medical genomics (21.01.2014)
Published in BMC medical genomics (21.01.2014)
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Journal Article
Improving bioinformatics software quality through teamwork
Ferenc, Katalin, Rauluseviciute, Ieva, Hovan, Ladislav, Kumar, Vipin, Kuijjer, Marieke L, Mathelier, Anthony
Published in Bioinformatics (Oxford, England) (01.11.2024)
Published in Bioinformatics (Oxford, England) (01.11.2024)
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