Improved data analysis for the MinION nanopore sequencer von Jain, Miten, Fiddes, Ian T, Miga, Karen H, Olsen, Hugh E, Paten, Benedict, Akeson, Mark

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Progressive Cactus is a multiple-genome aligner for the thousand-genome era von Armstrong, Joel, Hickey, Glenn, Diekhans, Mark, Fiddes, Ian T., Novak, Adam M., Deran, Alden, Fang, Qi, Xie, Duo, Feng, Shaohong, Stiller, Josefin, Genereux, Diane, Johnson, Jeremy, Marinescu, Voichita Dana, Alföldi, Jessica, Harris, Robert S., Lindblad-Toh, Kerstin, Haussler, David, Karlsson, Elinor, Jarvis, Erich D., Zhang, Guojie, Paten, Benedict

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The UCSC Genome Browser database: 2018 update von Casper, Jonathan, Zweig, Ann S, Villarreal, Chris, Tyner, Cath, Speir, Matthew L, Rosenbloom, Kate R, Raney, Brian J, Lee, Christopher M, Lee, Brian T, Karolchik, Donna, Hinrichs, Angie S, Haeussler, Maximilian, Guruvadoo, Luvina, Navarro Gonzalez, Jairo, Gibson, David, Fiddes, Ian T, Eisenhart, Christopher, Diekhans, Mark, Clawson, Hiram, Barber, Galt P, Armstrong, Joel, Haussler, David, Kuhn, Robert M, Kent, W James

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Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing von Replogle, Joseph M., Norman, Thomas M., Xu, Albert, Hussmann, Jeffrey A., Chen, Jin, Cogan, J. Zachery, Meer, Elliott J., Terry, Jessica M., Riordan, Daniel P., Srinivas, Niranjan, Fiddes, Ian T., Arthur, Joseph G., Alvarado, Luigi J., Pfeiffer, Katherine A., Mikkelsen, Tarjei S., Weissman, Jonathan S., Adamson, Britt

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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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A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing von Petti, Allegra A., Williams, Stephen R., Miller, Christopher A., Fiddes, Ian T., Srivatsan, Sridhar N., Chen, David Y., Fronick, Catrina C., Fulton, Robert S., Church, Deanna M., Ley, Timothy J.

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Nanopore sequencing and assembly of a human genome with ultra-long reads von Jain, Miten, Koren, Sergey, Miga, Karen H, Quick, Josh, Rand, Arthur C, Sasani, Thomas A, Tyson, John R, Beggs, Andrew D, Dilthey, Alexander T, Fiddes, Ian T, Malla, Sunir, Marriott, Hannah, Nieto, Tom, O'Grady, Justin, Olsen, Hugh E, Pedersen, Brent S, Rhie, Arang, Richardson, Hollian, Quinlan, Aaron R, Snutch, Terrance P, Tee, Louise, Paten, Benedict, Phillippy, Adam M, Simpson, Jared T, Loman, Nicholas J, Loose, Matthew

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Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation von Fiddes, Ian T, Armstrong, Joel, Diekhans, Mark, Nachtweide, Stefanie, Kronenberg, Zev N, Underwood, Jason G, Gordon, David, Earl, Dent, Keane, Thomas, Eichler, Evan E, Haussler, David, Stanke, Mario, Paten, Benedict

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Whole-Genome Alignment and Comparative Annotation von Armstrong, Joel, Fiddes, Ian T, Diekhans, Mark, Paten, Benedict

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Resolving the full spectrum of human genome variation using Linked-Reads von Marks, Patrick, Garcia, Sarah, Barrio, Alvaro Martinez, Belhocine, Kamila, Bernate, Jorge, Bharadwaj, Rajiv, Bjornson, Keith, Catalanotti, Claudia, Delaney, Josh, Fehr, Adrian, Fiddes, Ian T, Galvin, Brendan, Heaton, Haynes, Herschleb, Jill, Hindson, Christopher, Holt, Esty, Jabara, Cassandra B, Jett, Susanna, Keivanfar, Nikka, Kyriazopoulou-Panagiotopoulou, Sofia, Lek, Monkol, Lin, Bill, Lowe, Adam, Mahamdallie, Shazia, Maheshwari, Shamoni, Makarewicz, Tony, Marshall, Jamie, Meschi, Francesca, O'Keefe, Christopher J, Ordonez, Heather, Patel, Pranav, Price, Andrew, Royall, Ariel, Ruark, Elise, Seal, Sheila, Schnall-Levin, Michael, Shah, Preyas, Stafford, David, Williams, Stephen, Wu, Indira, Xu, Andrew Wei, Rahman, Nazneen, MacArthur, Daniel, Church, Deanna M

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Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution von Fiddes, Ian T., Pollen, Alex A., Davis, Jonathan M., Sikela, James M.

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Long-read sequence assembly of the gorilla genome von Gordon, David, Huddleston, John, Chaisson, Mark J. P., Hill, Christopher M., Kronenberg, Zev N., Munson, Katherine M., Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W., Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K., Haussler, David, Chin, Chen-Shan, Eichler, Evan E.

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The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain von Sarsani, Vishal Kumar, Raghupathy, Narayanan, Fiddes, Ian T, Armstrong, Joel, Thibaud-Nissen, Francoise, Zinder, Oraya, Bolisetty, Mohan, Howe, Kerstin, Hinerfeld, Doug, Ruan, Xiaoan, Rowe, Lucy, Barter, Mary, Ananda, Guruprasad, Paten, Benedict, Weinstock, George M, Churchill, Gary A, Wiles, Michael V, Schneider, Valerie A, Srivastava, Anuj, Reinholdt, Laura G

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scHLAcount: allele-specific HLA expression from single-cell gene expression data von Darby, Charlotte A, Stubbington, Michael J T, Marks, Patrick J, Martínez Barrio, Álvaro, Fiddes, Ian T

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Author Correction: A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing von Petti, Allegra A., Williams, Stephen R., Miller, Christopher A., Fiddes, Ian T., Srivatsan, Sridhar N., Chen, David Y., Fronick, Catrina C., Fulton, Robert S., Church, Deanna M., Ley, Timothy J.

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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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Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells von Tunstall, Tate, Kock, Richard, Vahala, Jiri, Diekhans, Mark, Fiddes, Ian, Armstrong, Joel, Paten, Benedict, Ryder, Oliver A, Steiner, Cynthia C

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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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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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Transcriptional activity and strain-specific history of mouse pseudogenes von Sisu, Cristina, Muir, Paul, Frankish, Adam, Fiddes, Ian, Diekhans, Mark, Thybert, David, Odom, Duncan T., Flicek, Paul, Keane, Thomas M., Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark

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