Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images
Khosravi, Pegah, Kazemi, Ehsan, Imielinski, Marcin, Elemento, Olivier, Hajirasouliha, Iman
Published in EBioMedicine (01.01.2018)
Published in EBioMedicine (01.01.2018)
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Journal Article
Fusion oncogenes-genetic musical chairs
Imielinski, Marcin, Ladanyi, Marc
Published in Science (American Association for the Advancement of Science) (31.08.2018)
Published in Science (American Association for the Advancement of Science) (31.08.2018)
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Journal Article
Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
Campbell, Joshua D, Alexandrov, Anton, Kim, Jaegil, Wala, Jeremiah, Berger, Alice H, Pedamallu, Chandra Sekhar, Shukla, Sachet A, Guo, Guangwu, Brooks, Angela N, Murray, Bradley A, Imielinski, Marcin, Hu, Xin, Ling, Shiyun, Akbani, Rehan, Rosenberg, Mara, Cibulskis, Carrie, Ramachandran, Aruna, Collisson, Eric A, Kwiatkowski, David J, Lawrence, Michael S, Weinstein, John N, Verhaak, Roel G W, Wu, Catherine J, Hammerman, Peter S, Cherniack, Andrew D, Getz, Gad, Artyomov, Maxim N, Schreiber, Robert, Govindan, Ramaswamy, Meyerson, Matthew
Published in Nature genetics (01.06.2016)
Published in Nature genetics (01.06.2016)
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Journal Article
SvABA: genome-wide detection of structural variants and indels by local assembly
Wala, Jeremiah A, Bandopadhayay, Pratiti, Greenwald, Noah F, O'Rourke, Ryan, Sharpe, Ted, Stewart, Chip, Schumacher, Steve, Li, Yilong, Weischenfeldt, Joachim, Yao, Xiaotong, Nusbaum, Chad, Campbell, Peter, Getz, Gad, Meyerson, Matthew, Zhang, Cheng-Zhong, Imielinski, Marcin, Beroukhim, Rameen
Published in Genome research (01.04.2018)
Published in Genome research (01.04.2018)
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Journal Article
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
Butler, Daniel, Mozsary, Christopher, Meydan, Cem, Foox, Jonathan, Rosiene, Joel, Shaiber, Alon, Danko, David, Afshinnekoo, Ebrahim, MacKay, Matthew, Sedlazeck, Fritz J., Ivanov, Nikolay A., Sierra, Maria, Pohle, Diana, Zietz, Michael, Gisladottir, Undina, Ramlall, Vijendra, Sholle, Evan T., Schenck, Edward J., Westover, Craig D., Hassan, Ciaran, Ryon, Krista, Young, Benjamin, Bhattacharya, Chandrima, Ng, Dianna L., Granados, Andrea C., Santos, Yale A., Servellita, Venice, Federman, Scot, Ruggiero, Phyllis, Fungtammasan, Arkarachai, Chin, Chen-Shan, Pearson, Nathaniel M., Langhorst, Bradley W., Tanner, Nathan A., Kim, Youngmi, Reeves, Jason W., Hether, Tyler D., Warren, Sarah E., Bailey, Michael, Gawrys, Justyna, Meleshko, Dmitry, Xu, Dong, Couto-Rodriguez, Mara, Nagy-Szakal, Dorottya, Barrows, Joseph, Wells, Heather, O’Hara, Niamh B., Rosenfeld, Jeffrey A., Chen, Ying, Steel, Peter A. D., Shemesh, Amos J., Xiang, Jenny, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Iftner, Angelika, Bezdan, Daniela, Sanchez, Elizabeth, Campion, Thomas R., Sipley, John, Cong, Lin, Craney, Arryn, Velu, Priya, Melnick, Ari M., Shapira, Sagi, Hajirasouliha, Iman, Borczuk, Alain, Iftner, Thomas, Salvatore, Mirella, Loda, Massimo, Westblade, Lars F., Cushing, Melissa, Wu, Shixiu, Levy, Shawn, Chiu, Charles, Schwartz, Robert E., Tatonetti, Nicholas, Rennert, Hanna, Imielinski, Marcin, Mason, Christopher E.
Published in Nature communications (12.03.2021)
Published in Nature communications (12.03.2021)
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Journal Article
Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression
Paulson, Thomas G., Galipeau, Patricia C., Oman, Kenji M., Sanchez, Carissa A., Kuhner, Mary K., Smith, Lucian P., Hadi, Kevin, Shah, Minita, Arora, Kanika, Shelton, Jennifer, Johnson, Molly, Corvelo, Andre, Maley, Carlo C., Yao, Xiaotong, Sanghvi, Rashesh, Venturini, Elisa, Emde, Anne-Katrin, Hubert, Benjamin, Imielinski, Marcin, Robine, Nicolas, Reid, Brian J., Li, Xiaohong
Published in Nature communications (28.04.2022)
Published in Nature communications (28.04.2022)
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Journal Article
The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
Huang, Linda, Fernandes, Helen, Zia, Hamid, Tavassoli, Peyman, Rennert, Hanna, Pisapia, David, Imielinski, Marcin, Sboner, Andrea, Rubin, Mark A, Kluk, Michael, Elemento, Olivier
Published in Journal of the American Medical Informatics Association : JAMIA (01.05.2017)
Published in Journal of the American Medical Informatics Association : JAMIA (01.05.2017)
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Journal Article
High-throughput Phenotyping of Lung Cancer Somatic Mutations
Berger, Alice H., Brooks, Angela N., Wu, Xiaoyun, Shrestha, Yashaswi, Chouinard, Candace, Piccioni, Federica, Bagul, Mukta, Kamburov, Atanas, Imielinski, Marcin, Hogstrom, Larson, Zhu, Cong, Yang, Xiaoping, Pantel, Sasha, Sakai, Ryo, Watson, Jacqueline, Kaplan, Nathan, Campbell, Joshua D., Singh, Shantanu, Root, David E., Narayan, Rajiv, Natoli, Ted, Lahr, David L., Tirosh, Itay, Tamayo, Pablo, Getz, Gad, Wong, Bang, Doench, John, Subramanian, Aravind, Golub, Todd R., Meyerson, Matthew, Boehm, Jesse S.
Published in Cancer cell (08.08.2016)
Published in Cancer cell (08.08.2016)
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Journal Article
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47
Anderson, Carl A, Boucher, Gabrielle, Lees, Charlie W, Franke, Andre, D'Amato, Mauro, Lee, James C, Goyette, Philippe, Latiano, Anna, Lagace, Caroline, Scott, Regan, Amininejad, Leila, Bumpstead, Suzannah, Baidoo, Leonard, Baldassano, Robert N, Brand, Stephan, Buning, Carsten, Colombel, Jean-Frederic, Denson, Lee A, DEVOS, Martine, Dubinsky, Marla, Edwards, Cathryn, Ellinghaus, David, Fehrmann, Rudolf S N, Florin, Timothy, Franchimont, Denis, Franke, Lude, Georges, Michel, Glas, Jurgen, Glazer, Nicole L, Guthery, Stephen L, Haritunians, Talin, Hayward, Nicholas K, Hugot, Jean-Pierre, Jobin, Gilles, Laukens, Debby, Lawrance, Ian, Lemann, Marc, Levine, Arie, LIBIOULLE, Cécile, Louis, Edouard, McGovern, Dermot P, Montgomery, Grant W, Morley, Katherine I, Mowat, Craig, Ng, Aylwin, Newman, William, Ophoff, Roel A, Papi, Laura, Palmieri, Orazio, Peyrin-Biroulet, Laurent, Panes, Julian, Phillips, Anne, Proctor, Deborah D, Roberts, Rebecca, Russell, Richard, Rutgeerts, Paul, Sanderson, Jeremy, Sans, Miquel, Sharma, Yashoda, Simms, Lisa A, Seielstad, Mark, Steinhart, A Hillary, Targan, Stephan R, van den Berg, Leonard H, Vatn, Morten, Walters, Thomas, Wijmenga, Cisca, Wilson, David C, Westra, Harm-Jan, Xavier, Ramnik J, Zhao, Zhen Z, Ponsioen, Cyriel Y, Andersen, Vibeke, Torkvist, Leif, Gazouli, Maria, Anagnou, Nicholas P, Sventoraityte, Jurgita, Mansfield, John C, Kugathasan, Subra, Silverberg, Mark S, Halfvarson, Jonas, Rotter, Jerome I, Mathew, Christopher G, Griffiths, Anne M, Gearry, Richard, Ahmad, Tariq, Brant, Steven R, Chamaillard, Mathias, Satsangi, Jack, Schreiber, Stefan, Daly, Mark J, Barrett, Jeffrey C, Parkes, Miles, Annese, Vito, Hakonarson, Hakon, Radford-Smith, Graham, Duerr, Richard H, Vermeire, Severine, Weersma, Rinse K, Rioux, John D
Published in Nature genetics (01.03.2011)
Published in Nature genetics (01.03.2011)
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A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events
Brooks, Angela N, Choi, Peter S, de Waal, Luc, Sharifnia, Tanaz, Imielinski, Marcin, Saksena, Gordon, Pedamallu, Chandra Sekhar, Sivachenko, Andrey, Rosenberg, Mara, Chmielecki, Juliann, Lawrence, Michael S, DeLuca, David S, Getz, Gad, Meyerson, Matthew
Published in PloS one (31.01.2014)
Published in PloS one (31.01.2014)
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A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci
Bradfield, Jonathan P, Qu, Hui-Qi, Wang, Kai, Zhang, Haitao, Sleiman, Patrick M, Kim, Cecilia E, Mentch, Frank D, Qiu, Haijun, Glessner, Joseph T, Thomas, Kelly A, Frackelton, Edward C, Chiavacci, Rosetta M, Imielinski, Marcin, Monos, Dimitri S, Pandey, Rahul, Bakay, Marina, Grant, Struan F A, Polychronakos, Constantin, Hakonarson, Hakon
Published in PLoS genetics (01.09.2011)
Published in PLoS genetics (01.09.2011)
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Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2
Greulich, Heidi, Kaplan, Bethany, Mertins, Philipp, Chen, Tzu-Hsiu, Tanaka, Kumiko E, Yun, Cai-Hong, Zhang, Xiaohong, Lee, Se-Hoon, Cho, Jeonghee, Ambrogio, Lauren, Liao, Rachel, Imielinski, Marcin, Banerji, Shantanu, Berger, Alice H, Lawrence, Michael S, Zhang, Jinghui, Pho, Nam H, Walker, Sarah R, Winckler, Wendy, Getz, Gad, Frank, David, Hahn, William C, Eck, Michael J, Mani, D. R, Jaffe, Jacob D, Carr, Steven A, Wong, Kwok-Kin, Meyerson, Matthew
Published in Proceedings of the National Academy of Sciences - PNAS (04.09.2012)
Published in Proceedings of the National Academy of Sciences - PNAS (04.09.2012)
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Journal Article
SETD2 Haploinsufficiency Enhances Germinal Center-Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis
Leung, Wilfred, Teater, Matt, Durmaz, Ceyda, Meydan, Cem, Chivu, Alexandra G, Chadburn, Amy, Rice, Edward J, Muley, Ashlesha, Camarillo, Jeannie M, Arivalagan, Jaison, Li, Ziyi, Flowers, Christopher R, Kelleher, Neil L, Danko, Charles G, Imielinski, Marcin, Dave, Sandeep S, Armstrong, Scott A, Mason, Christopher E, Melnick, Ari M
Published in Cancer discovery (06.07.2022)
Published in Cancer discovery (06.07.2022)
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Journal Article
In Situ Proteomic Analysis of Human Breast Cancer Epithelial Cells Using Laser Capture Microdissection: Annotation by Protein Set Enrichment Analysis and Gene Ontology
Cha, Sangwon, Imielinski, Marcin B., Rejtar, Tomas, Richardson, Elizabeth A., Thakur, Dipak, Sgroi, Dennis C., Karger, Barry L.
Published in Molecular & cellular proteomics (01.11.2010)
Published in Molecular & cellular proteomics (01.11.2010)
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Journal Article
Genetic modifiers of EGFR dependence in non-small cell lung cancer
Sharifnia, Tanaz, Rusu, Victor, Piccioni, Federica, Bagul, Mukta, Imielinski, Marcin, Cherniack, Andrew D., Pedamallu, Chandra Sekhar, Wong, Bang, Wilson, Frederick H., Garraway, Levi A., Altshuler, David, Golub, Todd R., Root, David E., Subramanian, Aravind, Meyerson, Matthew
Published in Proceedings of the National Academy of Sciences - PNAS (30.12.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (30.12.2014)
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Journal Article
Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNP
Grant, Struan F A, Li, Mingyao, Bradfield, Jonathan P, Kim, Cecilia E, Annaiah, Kiran, Santa, Erin, Glessner, Joseph T, Casalunovo, Tracy, Frackelton, Edward C, Otieno, F George, Shaner, Julie L, Smith, Ryan M, Imielinski, Marcin, Eckert, Andrew W, Chiavacci, Rosetta M, Berkowitz, Robert I, Hakonarson, Hakon
Published in PloS one (12.03.2008)
Published in PloS one (12.03.2008)
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Journal Article
Abstract 5895: Whole-genome characterization of lung adenocarcinomas lacking alterations in RTK/RAS/RAF/MAPK pathway
Carrot-Zhang, Jian, Devarakonda, Siddhartha, Robine, Nicolas, Yao, Xiaotong, Silva, Tiago C., Damrauer, Jeff, Deshpande, Aditya, Tsao, Ming-Sound, Yao, Christina, Wong, Chris, Bao, Lisui, Choi, Hyo Young, Felau, Ina, Zenklusen, Jean C., Robertson, Gordon, Trieua, Tuan, Liang, Wei-Wei, Zhou, Meng, Rheinbay, Esther, Hayes, Neil, Khurana, Ekta, Ding, Li, Laird, Peter, Elemento, Olivier, Weinstein, John, Kwiatkowski, David, Benz, Chris, Stuart, Josh, Yang, Lixing, Castro, Mauro, Travis, William, Hoadley, Katherine, Berman, Ben, Meyerson, Matthew, Govindan, Ramaswamy, Imielinski, Marcin
Published in Cancer research (Chicago, Ill.) (15.08.2020)
Published in Cancer research (Chicago, Ill.) (15.08.2020)
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Journal Article
High-throughput Phenotyping of Lung Cancer Somatic Mutations
Berger, Alice H., Brooks, Angela N., Wu, Xiaoyun, Shrestha, Yashaswi, Chouinard, Candace, Piccioni, Federica, Bagul, Mukta, Kamburov, Atanas, Imielinski, Marcin, Hogstrom, Larson, Zhu, Cong, Yang, Xiaoping, Pantel, Sasha, Sakai, Ryo, Watson, Jacqueline, Kaplan, Nathan, Campbell, Joshua D., Singh, Shantanu, Root, David E., Narayan, Rajiv, Natoli, Ted, Lahr, David L., Tirosh, Itay, Tamayo, Pablo, Getz, Gad, Wong, Bang, Doench, John, Subramanian, Aravind, Golub, Todd R., Meyerson, Matthew, Boehm, Jesse S.
Published in Cancer cell (11.12.2017)
Published in Cancer cell (11.12.2017)
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Follow-Up Analysis of Genome-Wide Association Data Identifies Novel Loci for Type 1 Diabetes
GRANT, Struan F. A, QU, Hui-Qi, ANNAIAH, Kiran, LAWSON, Margaret L, OTIENO, F. George, SANTA, Erin, SHANER, Julie L, SMITH, Ryan M, SKRABAN, Robert, IMIELINSKI, Marcin, CHIAVACCI, Rosetta M, GRUNDMEIER, Robert W, BRADFIELD, Jonathan P, STANLEY, Charles A, KIRSCH, Susan E, WAGGOTT, Daryl, PATERSON, Andrew D, MONOS, Dimitri S, POLYCHRONAKOS, Constantin, HAKONARSON, Hakon, MARCHAND, Luc, KIM, Cecilia E, GLESSNER, Joseph T, GRABS, Rosemarie, TABACK, Shayne P, FRACKELTON, Edward C, ECKERT, Andrew W
Published in Diabetes (New York, N.Y.) (01.01.2009)
Published in Diabetes (New York, N.Y.) (01.01.2009)
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