An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
Jacobs, Frank M. J., Greenberg, David, Nguyen, Ngan, Haeussler, Maximilian, Ewing, Adam D., Katzman, Sol, Paten, Benedict, Salama, Sofie R., Haussler, David
Published in Nature (London) (11.12.2014)
Published in Nature (London) (11.12.2014)
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Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Pollen, Alex A., Bhaduri, Aparna, Andrews, Madeline G., Nowakowski, Tomasz J., Meyerson, Olivia S., Mostajo-Radji, Mohammed A., Di Lullo, Elizabeth, Alvarado, Beatriz, Bedolli, Melanie, Dougherty, Max L., Fiddes, Ian T., Kronenberg, Zev N., Shuga, Joe, Leyrat, Anne A., West, Jay A., Bershteyn, Marina, Lowe, Craig B., Pavlovic, Bryan J., Salama, Sofie R., Haussler, David, Eichler, Evan E., Kriegstein, Arnold R.
Published in Cell (07.02.2019)
Published in Cell (07.02.2019)
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Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis
Fiddes, Ian T., Lodewijk, Gerrald A., Mooring, Meghan, Bosworth, Colleen M., Ewing, Adam D., Mantalas, Gary L., Novak, Adam M., van den Bout, Anouk, Bishara, Alex, Rosenkrantz, Jimi L., Lorig-Roach, Ryan, Field, Andrew R., Haeussler, Maximilian, Russo, Lotte, Bhaduri, Aparna, Nowakowski, Tomasz J., Pollen, Alex A., Dougherty, Max L., Nuttle, Xander, Addor, Marie-Claude, Zwolinski, Simon, Katzman, Sol, Kriegstein, Arnold, Eichler, Evan E., Salama, Sofie R., Jacobs, Frank M.J., Haussler, David
Published in Cell (31.05.2018)
Published in Cell (31.05.2018)
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FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
Salama, Sofie R, Underwood, Jason G, Uzilov, Andrew V, Katzman, Sol, Onodera, Courtney S, Mainzer, Jacob E, Mathews, David H, Lowe, Todd M, Haussler, David
Published in Nature methods (01.12.2010)
Published in Nature methods (01.12.2010)
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A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence
de Souza, Camila Ferreira, Sabedot, Thais S., Malta, Tathiane M., Stetson, Lindsay, Morozova, Olena, Sokolov, Artem, Laird, Peter W., Wiznerowicz, Maciej, Iavarone, Antonio, Snyder, James, deCarvalho, Ana, Sanborn, Zachary, McDonald, Kerrie L., Friedman, William A., Tirapelli, Daniela, Poisson, Laila, Mikkelsen, Tom, Carlotti, Carlos G., Kalkanis, Steven, Zenklusen, Jean, Salama, Sofie R., Barnholtz-Sloan, Jill S., Noushmehr, Houtan
Published in Cell reports (Cambridge) (10.04.2018)
Published in Cell reports (Cambridge) (10.04.2018)
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Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53
Wang, Ting, Zeng, Jue, Lowe, Craig B, Sellers, Robert G, Salama, Sofie R, Yang, Min, Burgess, Shawn M, Brachmann, Rainer K, Haussler, David
Published in Proceedings of the National Academy of Sciences - PNAS (20.11.2007)
Published in Proceedings of the National Academy of Sciences - PNAS (20.11.2007)
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TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
Newton, Yulia, Novak, Adam M, Swatloski, Teresa, McColl, Duncan C, Chopra, Sahil, Graim, Kiley, Weinstein, Alana S, Baertsch, Robert, Salama, Sofie R, Ellrott, Kyle, Chopra, Manu, Goldstein, Theodore C, Haussler, David, Morozova, Olena, Stuart, Joshua M
Published in Cancer research (Chicago, Ill.) (01.11.2017)
Published in Cancer research (Chicago, Ill.) (01.11.2017)
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Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids
Seiler, Spencer T., Mantalas, Gary L., Selberg, John, Cordero, Sergio, Torres-Montoya, Sebastian, Baudin, Pierre V., Ly, Victoria T., Amend, Finn, Tran, Liam, Hoffman, Ryan N., Rolandi, Marco, Green, Richard E., Haussler, David, Salama, Sofie R., Teodorescu, Mircea
Published in Scientific reports (23.11.2022)
Published in Scientific reports (23.11.2022)
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Double Minute Chromosomes in Glioblastoma Multiforme Are Revealed by Precise Reconstruction of Oncogenic Amplicons
SANBORN, J. Zachary, SALAMA, Sofie R, GRIFFORD, Mia, BRENNAN, Cameron W, MIKKELSEN, Tom, JHANWAR, Suresh, KATZMAN, Sol, CHIN, Lynda, HAUSSLER, David
Published in Cancer research (Chicago, Ill.) (01.10.2013)
Published in Cancer research (Chicago, Ill.) (01.10.2013)
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ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy
Rao, Arjun A, Madejska, Ada A, Pfeil, Jacob, Paten, Benedict, Salama, Sofie R, Haussler, David
Published in Frontiers in immunology (10.11.2020)
Published in Frontiers in immunology (10.11.2020)
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Human Genome Ultraconserved Elements Are Ultraselected
Katzman, Sol, Kern, Andrew D, Bejerano, Gill, Fewell, Ginger, Fulton, Lucinda, Wilson, Richard K, Salama, Sofie R, Haussler, David
Published in Science (American Association for the Advancement of Science) (17.08.2007)
Published in Science (American Association for the Advancement of Science) (17.08.2007)
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Forces shaping the fastest evolving regions in the human genome
Pollard, Katherine S, Salama, Sofie R, King, Bryan, Kern, Andrew D, Dreszer, Tim, Katzman, Sol, Siepel, Adam, Pedersen, Jakob S, Bejerano, Gill, Baertsch, Robert, Rosenbloom, Kate R, Kent, Jim, Haussler, David
Published in PLoS genetics (01.10.2006)
Published in PLoS genetics (01.10.2006)
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Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes
Field, Andrew R., Jacobs, Frank M.J., Fiddes, Ian T., Phillips, Alex P.R., Reyes-Ortiz, Andrea M., LaMontagne, Erin, Whitehead, Lila, Meng, Vincent, Rosenkrantz, Jimi L., Olsen, Mari, Hauessler, Max, Katzman, Sol, Salama, Sofie R., Haussler, David
Published in Stem cell reports (12.02.2019)
Published in Stem cell reports (12.02.2019)
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The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families
Fernandes, Jason D, Zamudio-Hurtado, Armando, Clawson, Hiram, Kent, W James, Haussler, David, Salama, Sofie R, Haeussler, Maximilian
Published in Mobile DNA (31.03.2020)
Published in Mobile DNA (31.03.2020)
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Regulation of Rugosity and Biofilm Formation in Vibrio cholerae: Comparison of VpsT and VpsR Regulons and Epistasis Analysis of vpsT, vpsR, and hapR
Beyhan, Sinem, Bilecen, Kivanc, Salama, Sofie R, Casper-Lindley, Catharina, Yildiz, Fitnat H
Published in Journal of Bacteriology (01.01.2007)
Published in Journal of Bacteriology (01.01.2007)
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Gamifying cell culture training: The ‘Seru-Otchi’ experience for undergraduates
T. Ly, Victoria, Ehrlich, Drew, Sevetson, Jess, Hoffman, Ryan N., Salama, Sofie R., Kurniawan, Sri, Teodorescu, Mircea
Published in Heliyon (15.05.2024)
Published in Heliyon (15.05.2024)
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Gene isoform specificity through enhancer-associated antisense transcription
Onodera, Courtney S, Underwood, Jason G, Katzman, Sol, Jacobs, Frank, Greenberg, David, Salama, Sofie R, Haussler, David
Published in PloS one (24.08.2012)
Published in PloS one (24.08.2012)
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A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations
Toor, Jugmohit S, Rao, Arjun A, McShan, Andrew C, Yarmarkovich, Mark, Nerli, Santrupti, Yamaguchi, Karissa, Madejska, Ada A, Nguyen, Son, Tripathi, Sarvind, Maris, John M, Salama, Sofie R, Haussler, David, Sgourakis, Nikolaos G
Published in Frontiers in immunology (30.01.2018)
Published in Frontiers in immunology (30.01.2018)
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Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures
Pfeil, Jacob, Sanders, Lauren M, Anastopoulos, Ioannis, Lyle, A Geoffrey, Weinstein, Alana S, Xue, Yuanqing, Blair, Andrew, Beale, Holly C, Lee, Alex, Leung, Stanley G, Dinh, Phuong T, Shah, Avanthi Tayi, Breese, Marcus R, Devine, W Patrick, Bjork, Isabel, Salama, Sofie R, Sweet-Cordero, E Alejandro, Haussler, David, Vaske, Olena Morozova
Published in PLoS computational biology (10.04.2020)
Published in PLoS computational biology (10.04.2020)
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