RNA-Seq analysis in MeV
Howe, Eleanor A., Sinha, Raktim, Schlauch, Daniel, Quackenbush, John
Published in Bioinformatics (15.11.2011)
Published in Bioinformatics (15.11.2011)
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Journal Article
Using graph convolutional neural networks to learn a representation for glycans
Burkholz, Rebekka, Quackenbush, John, Bojar, Daniel
Published in Cell reports (Cambridge) (15.06.2021)
Published in Cell reports (Cambridge) (15.06.2021)
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Journal Article
Biologically informed NeuralODEs for genome-wide regulatory dynamics
Hossain, Intekhab, Fanfani, Viola, Fischer, Jonas, Quackenbush, John, Burkholz, Rebekka
Published in Genome Biology (21.05.2024)
Published in Genome Biology (21.05.2024)
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Journal Article
Genome-Wide Sex and Gender Differences in Cancer
Lopes-Ramos, Camila M, Quackenbush, John, DeMeo, Dawn L
Published in Frontiers in oncology (23.11.2020)
Published in Frontiers in oncology (23.11.2020)
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Journal Article
Understanding Tissue-Specific Gene Regulation
Sonawane, Abhijeet Rajendra, Platig, John, Fagny, Maud, Chen, Cho-Yi, Paulson, Joseph Nathaniel, Lopes-Ramos, Camila Miranda, DeMeo, Dawn Lisa, Quackenbush, John, Glass, Kimberly, Kuijjer, Marieke Lydia
Published in Cell reports (Cambridge) (24.10.2017)
Published in Cell reports (Cambridge) (24.10.2017)
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Journal Article
Challenges and emerging directions in single-cell analysis
Yuan, Guo-Cheng, Cai, Long, Elowitz, Michael, Enver, Tariq, Fan, Guoping, Guo, Guoji, Irizarry, Rafael, Kharchenko, Peter, Kim, Junhyong, Orkin, Stuart, Quackenbush, John, Saadatpour, Assieh, Schroeder, Timm, Shivdasani, Ramesh, Tirosh, Itay
Published in Genome Biology (08.05.2017)
Published in Genome Biology (08.05.2017)
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Journal Article
Somatic Mutations Drive Distinct Imaging Phenotypes in Lung Cancer
Rios Velazquez, Emmanuel, Parmar, Chintan, Liu, Ying, Coroller, Thibaud P, Cruz, Gisele, Stringfield, Olya, Ye, Zhaoxiang, Makrigiorgos, Mike, Fennessy, Fiona, Mak, Raymond H, Gillies, Robert, Quackenbush, John, Aerts, Hugo J W L
Published in Cancer research (Chicago, Ill.) (15.07.2017)
Published in Cancer research (Chicago, Ill.) (15.07.2017)
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Journal Article
survcomp: an R/Bioconductor package for performance assessment and comparison of survival models
Schröder, Markus S., Culhane, Aedín C., Quackenbush, John, Haibe-Kains, Benjamin
Published in Bioinformatics (15.11.2011)
Published in Bioinformatics (15.11.2011)
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Journal Article
Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes
PARKER, Joel S, MULLINS, Michael, QUACKENBUSH, John F, STIJLEMAN, Inge J, PALAZZO, Juan, MARRON, J. S, NOBEL, Andrew B, MARDIS, Elaine, NIELSEN, Torsten O, ELLIS, Matthew J, PEROU, Charles M, BERNARD, Philip S, CHEANG, Maggie C. U, LEUNG, Samuel, VODUC, David, VICKERY, Tammi, DAVIES, Sherri, FAURON, Christiane, XIAPING HE, ZHIYUAN HU
Published in Journal of clinical oncology (10.03.2009)
Published in Journal of clinical oncology (10.03.2009)
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Journal Article
Data Analysis Strategies in Medical Imaging
Parmar, Chintan, Barry, Joseph D, Hosny, Ahmed, Quackenbush, John, Aerts, Hugo J W L
Published in Clinical cancer research (01.08.2018)
Published in Clinical cancer research (01.08.2018)
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Journal Article
A Three-Gene Model to Robustly Identify Breast Cancer Molecular Subtypes
Haibe-Kains, Benjamin, Desmedt, Christine, Loi, Sherene, Culhane, Aedin C., Bontempi, Gianluca, Quackenbush, John, Sotiriou, Christos
Published in JNCI : Journal of the National Cancer Institute (22.02.2012)
Published in JNCI : Journal of the National Cancer Institute (22.02.2012)
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Journal Article
Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology
Wu, Weimiao, Parmar, Chintan, Grossmann, Patrick, Quackenbush, John, Lambin, Philippe, Bussink, Johan, Mak, Raymond, Aerts, Hugo J W L
Published in Frontiers in oncology (30.03.2016)
Published in Frontiers in oncology (30.03.2016)
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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
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV
Sathirapongsasuti, Jarupon Fah, Lee, Hane, Horst, Basil A. J., Brunner, Georg, Cochran, Alistair J., Binder, Scott, Quackenbush, John, Nelson, Stanley F.
Published in Bioinformatics (01.10.2011)
Published in Bioinformatics (01.10.2011)
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Journal Article
Estimating Sample-Specific Regulatory Networks
Kuijjer, Marieke Lydia, Tung, Matthew George, Yuan, GuoCheng, Quackenbush, John, Glass, Kimberly
Published in iScience (26.04.2019)
Published in iScience (26.04.2019)
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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