An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons von Jacobs, Frank M. J., Greenberg, David, Nguyen, Ngan, Haeussler, Maximilian, Ewing, Adam D., Katzman, Sol, Paten, Benedict, Salama, Sofie R., Haussler, David

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Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution von 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.

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Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis von 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

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A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence von 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

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FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing von Underwood, Jason G, Uzilov, Andrew V, Katzman, Sol, Onodera, Courtney S, Mainzer, Jacob E, Mathews, David H, Lowe, Todd M, Salama, Sofie R, Haussler, David

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Forces shaping the fastest evolving regions in the human genome von 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

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Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids von 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

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TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal von 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

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Cerebral Organoids as an Experimental Platform for Human Neurogenomics von Nowakowski, Tomasz J, Salama, Sofie R

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Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53 von Wang, Ting, Zeng, Jue, Lowe, Craig B, Sellers, Robert G, Salama, Sofie R, Yang, Min, Burgess, Shawn M, Brachmann, Rainer K, Haussler, David

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Double Minute Chromosomes in Glioblastoma Multiforme Are Revealed by Precise Reconstruction of Oncogenic Amplicons von SANBORN, J. Zachary, SALAMA, Sofie R, GRIFFORD, Mia, BRENNAN, Cameron W, MIKKELSEN, Tom, JHANWAR, Suresh, KATZMAN, Sol, CHIN, Lynda, HAUSSLER, David

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SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data von Poulsen, Line Dahl, Kielpinski, Lukasz Jan, Salama, Sofie R, Krogh, Anders, Vinther, Jeppe

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ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy von Rao, Arjun A, Madejska, Ada A, Pfeil, Jacob, Paten, Benedict, Salama, Sofie R, Haussler, David

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Human Genome Ultraconserved Elements Are Ultraselected von Katzman, Sol, Kern, Andrew D, Bejerano, Gill, Fewell, Ginger, Fulton, Lucinda, Wilson, Richard K, Salama, Sofie R, Haussler, David

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An RNA gene expressed during cortical development evolved rapidly in humans von Pollard, Katherine S., Salama, Sofie R., Lambert, Nelle, Lambot, Marie-Alexandra, Coppens, Sandra, Pedersen, Jakob S., Katzman, Sol, King, Bryan, Onodera, Courtney, Siepel, Adam, Kern, Andrew D., Dehay, Colette, Igel, Haller, Ares, Manuel, Vanderhaeghen, Pierre, Haussler, David

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A high-quality bonobo genome refines the analysis of hominid evolution von Mao, Yafei, Catacchio, Claudia R., Hillier, LaDeana W., Porubsky, David, Li, Ruiyang, Sulovari, Arvis, Fernandes, Jason D., Montinaro, Francesco, Gordon, David S., Storer, Jessica M., Haukness, Marina, Fiddes, Ian T., Murali, Shwetha Canchi, Dishuck, Philip C., Hsieh, PingHsun, Harvey, William T., Audano, Peter A., Mercuri, Ludovica, Piccolo, Ilaria, Antonacci, Francesca, Munson, Katherine M., Lewis, Alexandra P., Baker, Carl, Underwood, Jason G., Hoekzema, Kendra, Huang, Tzu-Hsueh, Sorensen, Melanie, Walker, Jerilyn A., Hoffman, Jinna, Thibaud-Nissen, Françoise, Salama, Sofie R., Pang, Andy W. C., Lee, Joyce, Hastie, Alex R., Paten, Benedict, Batzer, Mark A., Diekhans, Mark, Ventura, Mario, Eichler, Evan E.

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Gene isoform specificity through enhancer-associated antisense transcription von Onodera, Courtney S, Underwood, Jason G, Katzman, Sol, Jacobs, Frank, Greenberg, David, Salama, Sofie R, Haussler, David

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Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures von 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

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Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes von 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

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A distal enhancer and an ultraconserved exon are derived from a novel retroposon von Bejerano, Gill, Lowe, Craig B., Ahituv, Nadav, King, Bryan, Siepel, Adam, Salama, Sofie R., Rubin, Edward M., James Kent, W., Haussler, David

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