PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions von Lin, Michael F., Jungreis, Irwin, Kellis, Manolis

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Variation graph toolkit improves read mapping by representing genetic variation in the reference von Garrison, Erik, Sirén, Jouni, Novak, Adam M, Hickey, Glenn, Eizenga, Jordan M, Dawson, Eric T, Jones, William, Garg, Shilpa, Markello, Charles, Lin, Michael F, Paten, Benedict, Durbin, Richard

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Accurate, scalable cohort variant calls using DeepVariant and GLnexus von Yun, Taedong, Li, Helen, Chang, Pi-Chuan, Lin, Michael F, Carroll, Andrew, McLean, Cory Y

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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis von Pauli, Andrea, Valen, Eivind, Lin, Michael F, Garber, Manuel, Vastenhouw, Nadine L, Levin, Joshua Z, Fan, Lin, Sandelin, Albin, Rinn, John L, Regev, Aviv, Schier, Alexander F

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Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters von Wong, David J, Chang, Howard Y, Hung, Tiffany, Wang, Yulei, Lin, Michael F, Koegel, Ashley K, Kotake, Yojiro, Grant, Gavin D, Horlings, Hugo M, Shah, Nilay, Umbricht, Christopher, Wang, Pei, Wang, Yu, Kong, Benjamin, Langerød, Anita, Børresen-Dale, Anne-Lise, Kim, Seung K, van de Vijver, Marc, Sukumar, Saraswati, Whitfield, Michael L, Kellis, Manolis, Xiong, Yue

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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals von Kellis, Manolis, Feldser, David, Cassady, John P, Amit, Ido, Lander, Eric S, Zuk, Or, Lin, Michael F, Carey, Bryce W, Garber, Manuel, Mikkelsen, Tarjei S, Jacks, Tyler, Hacohen, Nir, Guttman, Mitchell, French, Courtney, Cabili, Moran N, Huarte, Maite, Regev, Aviv, Rinn, John L, Jaenisch, Rudolf, Bernstein, Bradley E

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Evolutionary Dynamics of Abundant Stop Codon Readthrough von Jungreis, Irwin, Chan, Clara S, Waterhouse, Robert M, Fields, Gabriel, Lin, Michael F, Kellis, Manolis

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Distinguishing protein-coding and noncoding genes in the human genome von Clamp, Michele, Fry, Ben, Kamal, Mike, Xie, Xiaohui, Cuff, James, Lin, Michael F, Kellis, Manolis, Lindblad-Toh, Kerstin, Lander, Eric S

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Evidence of abundant stop codon readthrough in Drosophila and other metazoa von Jungreis, Irwin, Lin, Michael F, Spokony, Rebecca, Chan, Clara S, Negre, Nicolas, Victorsen, Alec, White, Kevin P, Kellis, Manolis

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The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes von Pruitt, Kim D, Harrow, Jennifer, Harte, Rachel A, Wallin, Craig, Diekhans, Mark, Maglott, Donna R, Searle, Steve, Farrell, Catherine M, Loveland, Jane E, Ruef, Barbara J, Hart, Elizabeth, Suner, Marie-Marthe, Landrum, Melissa J, Aken, Bronwen, Ayling, Sarah, Baertsch, Robert, Fernandez-Banet, Julio, Cherry, Joshua L, Curwen, Val, Dicuccio, Michael, Kellis, Manolis, Lee, Jennifer, Lin, Michael F, Schuster, Michael, Shkeda, Andrew, Amid, Clara, Brown, Garth, Dukhanina, Oksana, Frankish, Adam, Hart, Jennifer, Maidak, Bonnie L, Mudge, Jonathan, Murphy, Michael R, Murphy, Terence, Rajan, Jeena, Rajput, Bhanu, Riddick, Lillian D, Snow, Catherine, Steward, Charles, Webb, David, Weber, Janet A, Wilming, Laurens, Wu, Wenyu, Birney, Ewan, Haussler, David, Hubbard, Tim, Ostell, James, Durbin, Richard, Lipman, David

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Berichtigung: A Supramolecular Complex in Small-Molecule Solar Cells based on Contorted Aromatic Molecules von Kang, Seok Ju, Kim, Jong Bok, Chiu, Chien-Yang, Ahn, Seokhoon, Schiros, Theanne, Lee, Stephanie S., Yager, Kevin G., Toney, Michael F., Loo, Yueh-Lin, Nuckolls, Colin

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A Supramolecular Complex in Small‐Molecule Solar Cells based on Contorted Aromatic Molecules von Kang, Seok Ju, Kim, Jong Bok, Chiu, Chien‐Yang, Ahn, Seokhoon, Schiros, Theanne, Lee, Stephanie S., Yager, Kevin G., Toney, Michael F., Loo, Yueh‐Lin, Nuckolls, Colin

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Error and error mitigation in low-coverage genome assemblies von Hubisz, Melissa J, Lin, Michael F, Kellis, Manolis, Siepel, Adam

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Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone von Park, Daniel J., Dudas, Gytis, Wohl, Shirlee, Goba, Augustine, Whitmer, Shannon L.M., Andersen, Kristian G., Sealfon, Rachel S., Ladner, Jason T., Kugelman, Jeffrey R., Matranga, Christian B., Winnicki, Sarah M., Qu, James, Gire, Stephen K., Gladden-Young, Adrianne, Jalloh, Simbirie, Nosamiefan, Dolo, Yozwiak, Nathan L., Moses, Lina M., Jiang, Pan-Pan, Lin, Aaron E., Schaffner, Stephen F., Bird, Brian, Towner, Jonathan, Mamoh, Mambu, Gbakie, Michael, Kanneh, Lansana, Kargbo, David, Massally, James L.B., Kamara, Fatima K., Konuwa, Edwin, Sellu, Josephine, Jalloh, Abdul A., Mustapha, Ibrahim, Foday, Momoh, Yillah, Mohamed, Erickson, Bobbie R., Sealy, Tara, Blau, Dianna, Paddock, Christopher, Brault, Aaron, Amman, Brian, Basile, Jane, Bearden, Scott, Belser, Jessica, Bergeron, Eric, Campbell, Shelley, Chakrabarti, Ayan, Dodd, Kimberly, Flint, Mike, Gibbons, Aridth, Goodman, Christin, Klena, John, McMullan, Laura, Morgan, Laura, Russell, Brandy, Salzer, Johanna, Sanchez, Angela, Wang, David, Jungreis, Irwin, Tomkins-Tinch, Christopher, Kislyuk, Andrey, Lin, Michael F., Chapman, Sinead, MacInnis, Bronwyn, Matthews, Ashley, Bochicchio, James, Hensley, Lisa E., Kuhn, Jens H., Nusbaum, Chad, Schieffelin, John S., Birren, Bruce W., Forget, Marc, Nichol, Stuart T., Palacios, Gustavo F., Ndiaye, Daouda, Happi, Christian, Gevao, Sahr M., Vandi, Mohamed A., Kargbo, Brima, Holmes, Edward C., Bedford, Trevor, Gnirke, Andreas, Ströher, Ute, Rambaut, Andrew, Garry, Robert F., Sabeti, Pardis C.

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Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes von Lin, Michael F, Deoras, Ameya N, Rasmussen, Matthew D, Kellis, Manolis

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Sparse Project VCF: efficient encoding of population genotype matrices von Lin, Michael F, Bai, Xiaodong, Salerno, William J, Reid, Jeffrey G

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IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring von Kalantar, Katrina L, Carvalho, Tiago, de Bourcy, Charles F A, Dimitrov, Boris, Dingle, Greg, Egger, Rebecca, Han, Julie, Holmes, Olivia B, Juan, Yun-Fang, King, Ryan, Kislyuk, Andrey, Lin, Michael F, Mariano, Maria, Morse, Todd, Reynoso, Lucia V, Cruz, David Rissato, Sheu, Jonathan, Tang, Jennifer, Wang, James, Zhang, Mark A, Zhong, Emily, Ahyong, Vida, Lay, Sreyngim, Chea, Sophana, Bohl, Jennifer A, Manning, Jessica E, Tato, Cristina M, DeRisi, Joseph L

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A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved] von Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter A, Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne E, Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas A, Markello, Charles J, Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard R, Lin, Michael F, Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Monlong, Jean, Musunuri, Rajeeva L, Sagayaradj, Sagayamary, Novak, Adam M, Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz J, Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki T, Zeng, Qiandong, Zook, Justin M, Paten, Benedict, Busby, Ben

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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE von Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V, Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L, Landolin, Jane M, Bristow, Christopher A, Ma, Lijia, Lin, Michael F, Washietl, Stefan, Arshinoff, Bradley I, Ay, Ferhat, Meyer, Patrick E, Robine, Nicolas, Washington, Nicole L, Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D, Candeias, Rogerio, Carlson, Joseph W, Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y, Will, Sebastian, Alekseyenko, Artyom A, Artieri, Carlo, Booth, Benjamin W, Brooks, Angela N, Dai, Qi, Davis, Carrie A, Duff, Michael O, Feng, Xin, Gorchakov, Andrey A, Gu, Tingting, Henikoff, Jorja G, Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K, Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K, Riddle, Nicole C, Sakai, Akiko, Samsonova, Anastasia, Sandler, Jeremy E, Schwartz, Yuri B, Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H, Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E, Brent, Michael R, Cherbas, Lucy, Elgin, Sarah C.R, Gingeras, Thomas R, Grossman, Robert, Hoskins, Roger A, Kaufman, Thomas C, Kent, William, Kuroda, Mitzi I, Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W, Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R, Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J, Celniker, Susan E, Henikoff, Steven, Karpen, Gary H, Lai, Eric C, MacAlpine, David M, Stein, Lincoln D, White, Kevin P, Kellis, Manolis

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A strategy for building and using a human reference pangenome [version 1; peer review: 1 approved, 1 approved with reservations] von Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter A, Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne E, Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas A, Markello, Charles J, Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard R, Lin, Michael F, Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Monlong, Jean, Musunuri, Rajeeva L, Sagayaradj, Sagayamary, Novak, Adam M, Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz J, Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki T, Zeng, Qiandong, Zook, Justin M, Paten, Benedict, Busby, Ben

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