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37 p, 20.5 MB |
Epigenetic regulation during cancer transitions across 11 tumour types
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Terekhanova, Nadezhda V. (Washington University in St Louis) ;
Karpova, Alla (Washington University in St Louis) ;
Liang, Wen Wei (Washington University in St Louis) ;
Strzalkowski, Alexander (Department of Computer Science. Princeton University) ;
Chen, Siqi (Washington University in St Louis) ;
Li, Yize (Washington University in St Louis) ;
Southard-Smith, Austin N. (Washington University in St Louis) ;
Iglesia, Michael D. (Washington University in St Louis) ;
Wendl, Michael C. (Washington University in St Louis) ;
Jayasinghe, Reyka G. (Washington University in St Louis) ;
Liu, Jingxian (Washington University in St Louis) ;
Song, Yizhe (Washington University in St Louis) ;
Cao, Song (Washington University in St Louis) ;
Houston, Andrew (Washington University in St Louis) ;
Liu, Xiuting (Department of Medicine. Washington University in St Louis) ;
Wyczalkowski, Michael A. (Washington University in St Louis) ;
Lu, Rita Jui-Hsien (Washington University in St Louis) ;
Caravan, Wagma (Washington University in St Louis) ;
Shinkle, Andrew (Department of Medicine. Washington University in St Louis) ;
Naser Al Deen, Nataly (Washington University in St Louis) ;
Herndon, John M. (Washington University in St Louis) ;
Mudd, Jacqueline (Department of Surgery. Washington University in St Louis) ;
Ma, Cong (Department of Computer Science. Princeton University) ;
Sarkar, Hirak (Department of Computer Science. Princeton University) ;
Sato, Kazuhito (Washington University in St Louis) ;
Ibrahim, Omar.M. (Washington University in St Louis) ;
Mo, Chia-Kuei (Washington University in St Louis) ;
Chasnoff, Sara E. (Washington University in St Louis) ;
Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Held, Jasson M. (Washington University in St Louis) ;
Pachynski, Russell (Washington University in St Louis) ;
Schwarz, Julie K. (Department of Radiation Oncology. Washington University in St Louis) ;
Gillanders, William E. (Washington University in St Louis) ;
Kim, Albert H. (Department of Neurological Surgery. Washington University in St Louis) ;
Vij, Ravi (Washington University in St Louis) ;
DiPersio, John.F. (Washington University in St Louis) ;
Puram, Sidharth V. (Department of Otolaryngology-Head & Neck Surgery. Washington University in St Louis) ;
Chheda, Milan G. (Washington University in St Louis) ;
Fuh, Katherine C. (Department of Obstetrics and Gynecology. Washington University in St Louis) ;
DeNardo, David G. (Washington University in St Louis) ;
Fields, Ryan C. (Washington University in St Louis) ;
Chen, Feng (Washington University in St Louis) ;
Raphael, Benjamin J. (Department of Computer Science. Princeton University) ;
Ding, Li (Department of Genetics. Washington University in St Louis)
Chromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis. [...]
2023 -  10.1038/s41586-023-06682-5
Nature, Vol. 623 Núm. 7986 (september 2023) , p. 432-441
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50 p, 28.5 MB |
Pan-cancer proteogenomics connects oncogenic drivers to functional states
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Li, Yize (Washington University in St. Louis) ;
Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Tokheim, Collin (Harvard T.H. Chan School of Public Health) ;
Bailey, Matthew H. (Brigham Young University) ;
Yaron, Tomer (Weill Cornell Medicine) ;
Stathias, Vasileios (University of Miami Miller School of Medicine) ;
Geffen, Yifat (Massachusetts General Hospital) ;
Imbach, Kathleen (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Cao, Song (McDonnell Genome Institute) ;
Anand, Shankara (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Akiyama, Yo (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Liu, Wenke (NYU Grossman School of Medicine) ;
Wyczalkowski, Matthew A. (McDonnell Genome Institute) ;
Song, Yizhe (McDonnell Genome Institute) ;
Storrs, Erik P. (McDonnell Genome Institute) ;
Wendl, Michael C. (Washington University in St. Louis) ;
Zhang, Wubing (Dana-Farber Cancer Institute (Boston, Estats Units)) ;
Sibai, Mustafa (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ruiz-Serra, Victoria (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Liang, Wen-Wei (McDonnell Genome Institute) ;
Terekhanova, Nadezhda V. (McDonnell Genome Institute) ;
Martins Rodrigues, Fernanda (McDonnell Genome Institute) ;
Clauser, Karl R. (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Heiman, David I. (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Zhang, Qing (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Aguet, Francois (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Calinawan, Anna Pamela (Icahn School of Medicine at Mount Sinai) ;
Dhanasekaran, Saravana Mohan (University of Michigan) ;
Birger, Chet (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Satpathy, Shankha (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Zhou, Daniel Cui (McDonnell Genome Institute) ;
Wang, Liang-Bo (McDonnell Genome Institute) ;
Baral, Jessika (McDonnell Genome Institute) ;
Johnson, Jared L. (Weill Cornell Medicine) ;
Huntsman, Emily M. (Weill Cornell Medicine) ;
Pugliese, Pietro (University of Sannio (Benevento, Itàlia)) ;
Colaprico, Antonio (University of Miami Miller School of Medicine) ;
Iavarone, Antonio (University of Miami Miller School of Medicine) ;
Chheda, Milan G. (Washington University in St. Louis) ;
Ricketts, Christopher J. (National Institutes of Health) ;
Fenyö, David (NYU Grossman School of Medicine) ;
Payne, Samuel H. (Brigham Young University) ;
Rodriguez, Henry (Office of Cancer Clinical Proteomics Research) ;
Robles, Ana I. (Office of Cancer Clinical Proteomics Research) ;
Gillette, Michael A. (Harvard Medical School) ;
Kumar-Sinha, Chandan (University of Michigan) ;
Lazar, Alexander (The University of Texas MD Anderson Cancer Center) ;
Cantley, Lewis (Weill Cornell Medicine) ;
Getz, Gad A. (Harvard Medical School) ;
Ding, Li (Siteman Cancer Center) ;
An, Eunkyung ;
Anurag, Meenakshi ;
Bavarva, Jasmin ;
Birrer, Michael J. ;
Ceccarelli, Michele ;
Chan, Daniel W. ;
Chinnaiyan, Arul M. ;
Cho, Hanbyul ;
Chowdhury, Shrabanti ;
Cieslik, Marcin P. ;
da Veiga Leprevost, Felipe ;
Day, Corbin ;
Domagalski, Marcin J. ;
Dou, Yongchao ;
Druker, Brian J. ;
Edwards, Nathan ;
Ellis, Matthew J. ;
Selvan, Myvizhi Esai ;
Foltz, Steven M. ;
Francis, Alicia ;
Gonzalez Robles, Tania J. ;
Gosline, Sara J. C. ;
Gümüş, Zeynep H. ;
Hiltke, Tara ;
Hong, Runyu ;
Hostetter, Galen ;
Hu, Yingwei ;
Huang, Chen ;
Huntsman, Emily ;
Jaehnig, Eric J. ;
Jewel, Scott D. ;
Ji, Jiayi ;
Jiang, Wen ;
Katsnelson, Lizabeth ;
Ketchum, Karen A. ;
Kolodziejczak, Iga ;
Lei, Jonathan T. ;
Liao, Yuxing ;
Lindgren, Caleb M. ;
Liu, Tao ;
Ma, Weiping ;
McKerrow, Wilson ;
Nesvizhskii, Alexey I. ;
Newton, Chelsea ;
Oldroyd, Robert ;
Omenn, Gilbert S. ;
Paulovich, Amanda G. ;
Petralia, Francesca ;
Reva, Boris ;
Rodland, Karin D. ;
Ruggles, Kelly V. ;
Rykunov, Dmitry ;
Savage, Sara R. ;
Schadt, Eric E. ;
Schnaubelt, Michael ;
Schraink, Tobias ;
Shi, Zhiao ;
Smith, Richard D. ;
Song, Xiaoyu ;
Tan, Jimin ;
Thangudu, Ratna R. ;
Tignor, Nicole ;
Wang, Joshua M. ;
Wang, Pei ;
Wang, Ying Cindy ;
Wen, Bo ;
Wiznerowicz, Maciej ;
Yi, Xinpei ;
Zhang, Bing ;
Zhang, Hui ;
Zhang, Xu ;
Zhang, Zhen ;
Universitat Autònoma de Barcelona
Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying their significant cis-effects and distal trans-effects quantified at the RNA, protein, and phosphoprotein levels. [...]
2023 - 10.1016/j.cell.2023.07.014
Cell, Vol. 186 Núm. 18 (31 2023) , p. 3921-3944.e25
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27 p, 8.1 MB |
Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin
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Liang, Wen-Wei (Washington University in St. Louis) ;
Lu, Rita Jui-Hsien Lu (Washington University in St. Louis) ;
Jayasinghe, Reyka G. (Washington University in St. Louis) ;
Foltz, Steven M. (Washington University in St. Louis) ;
Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Geffen, Yifat (Massachusetts General Hospital) ;
Wendl, Michael C. (Department of Mathematics. Washington University in St. Louis) ;
Lazcano, Rossana (Departments of Pathology & Genomic Medicine. The University of Texas MD Anderson Cancer Center) ;
Kolodziejczak, Iga (Medical University of Warsaw) ;
Song, Yizhe (Washington University in St. Louis) ;
Govindan, Akshay (Washington University in St. Louis) ;
Demicco, Elisabeth G. (University of Toronto) ;
Li, Xiang (Washington University in St. Louis) ;
Li, Yize (Washington University in St. Louis) ;
Sethuraman, Sunantha (Washington University in St. Louis) ;
Payne, Samuel H. (Department of Biology. Brigham Young University) ;
Fenyö, David (Department of Biochemistry and Molecular Pharmacology. NYU Grossman School of Medicine) ;
Rodriguez, Henry (Office of Cancer Clinical Proteomics Research. National Cancer Institute) ;
Wiznerowicz, Maciej (Poznań University of Medical Sciences) ;
Shen, Hui (Van Andel Research Institute) ;
Mani, D.R. (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Rodland, Karin D. (Developmental. and Cancer Biology. Oregon Health & Science University) ;
Lazar, Alexander J. (Departments of Pathology & Genomic Medicine. The University of Texas MD Anderson Cancer Center) ;
Robles, Ana I. (Office of Cancer Clinical Proteomics Research) ;
Ding, Li (Washington University in St. Louis) ;
Universitat Autònoma de Barcelona
DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development and is closely intertwined with other genetic alterations. [...]
2023 - 10.1016/j.ccell.2023.07.013
Cancer Cell, Vol. 41 Núm. 9 (november 2023) , p. 1567-1585.e7
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11 p, 1.3 MB |
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools
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García-Prieto, Carlos A (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Martínez Jiménez, Francisco (Institute for Research in Biomedicine (IRB Barcelona)) ;
Valencia, Alfonso (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Motivation: The analysis of cancer genomes provides fundamental information about its etiology, the processes driving cell transformation or potential treatments. While researchers and clinicians are often only interested in the identification of oncogenic mutations, actionable variants or mutational signatures, the first crucial step in the analysis of any tumor genome is the identification of somatic variants in cancer cells (i. [...]
2022 - 10.1093/bioinformatics/btac306
Bioinformatics, Vol. 38 Núm. 12 (15 2022) , p. 3181-3191
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17 p, 1.6 MB |
The structural coverage of the human proteome before and after AlphaFold
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Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ruiz-Serra, Victoria (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Valentini, Samuel (University of Trento) ;
Valencia, Alfons (Institució Catalana de Recerca i Estudis Avançats) ;
Universitat Autònoma de Barcelona
The protein structure field is experiencing a revolution. From the increased throughput of techniques to determine experimental structures, to developments such as cryo-EM that allow us to find the structures of large protein complexes or, more recently, the development of artificial intelligence tools, such as AlphaFold, that can predict with high accuracy the folding of proteins for which the availability of homology templates is limited. [...]
2022 - 10.1371/journal.pcbi.1009818
PLoS computational biology, Vol. 18 Núm. 1 (january 2022) , p. e1009818
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