PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

por Lin, Michael F., Jungreis, Irwin, Kellis, Manolis
Publicado 2011

Error and Error Mitigation in Low-Coverage Genome Assemblies

por Hubisz, Melissa J., Lin, Michael F., Kellis, Manolis, Siepel, Adam
Publicado 2011

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

por Lin, Michael F., Deoras, Ameya N., Rasmussen, Matthew D., Kellis, Manolis
Publicado 2008

Sparse Project VCF: efficient encoding of population genotype matrices

por Lin, Michael F, Bai, Xiaodong, Salerno, William J, Reid, Jeffrey G
Publicado 2020

Evolutionary Dynamics of Abundant Stop Codon Readthrough

por Jungreis, Irwin, Chan, Clara S., Waterhouse, Robert M., Fields, Gabriel, Lin, Michael F., Kellis, Manolis
Publicado 2016

FRESCo: finding regions of excess synonymous constraint in diverse viruses

por Sealfon, Rachel S, Lin, Michael F, Jungreis, Irwin, Wolf, Maxim Y, Kellis, Manolis, Sabeti, Pardis C
Publicado 2015

Accurate, scalable cohort variant calls using DeepVariant and GLnexus

por Yun, Taedong, Li, Helen, Chang, Pi-Chuan, Lin, Michael F, Carroll, Andrew, McLean, Cory Y
Publicado 2021

Variation graph toolkit improves read mapping by representing genetic variation in the reference

por 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
Publicado 2018

Extensive and coordinated transcription of noncoding RNAs within cell cycle promoters

por 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, Langerod, Anita, Børresen-Dale, Anne-Lise, Kim, Seung K., van de Vijver, Marc, Sukumar, Saraswati, Whitfield, Michael L., Kellis, Manolis, Xiong, Yue, Wong, David J., Chang, Howard Y.
Publicado 2011

IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

por 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
Publicado 2020

A strategy for building and using a human reference pangenome

por 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
Publicado 2021

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

por Butler, Geraldine, Rasmussen, Matthew D., Lin, Michael F., Santos, Manuel A.S., Sakthikumar, Sharadha, Munro, Carol A., Rheinbay, Esther, Grabherr, Manfred, Forche, Anja, Reedy, Jennifer L., Agrafioti, Ino, Arnaud, Martha B., Bates, Steven, Brown, Alistair J.P., Brunke, Sascha, Costanzo, Maria C., Fitzpatrick, David A., de Groot, Piet W. J., Harris, David, Hoyer, Lois L., Hube, Bernhard, Klis, Frans M., Kodira, Chinnappa, Lennard, Nicola, Logue, Mary E., Martin, Ronny, Neiman, Aaron M., Nikolaou, Elissavet, Quail, Michael A., Quinn, Janet, Santos, Maria C., Schmitzberger, Florian F., Sherlock, Gavin, Shah, Prachi, Silverstein, Kevin, Skrzypek, Marek S., Soll, David, Staggs, Rodney, Stansfield, Ian, Stumpf, Michael P H, Sudbery, Peter E., Thyagarajan, Srikantha, Zeng, Qiandong, Berman, Judith, Berriman, Matthew, Heitman, Joseph, Gow, Neil A. R., Lorenz, Michael C., Birren, Bruce W., Kellis, Manolis, Cuomo, Christina A.
Publicado 2009

A high-resolution map of human evolutionary constraint using 29 mammals

por Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F., Parker, Brian J., Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D., Lowe, Craig B., Holloway, Alisha K., Clamp, Michele, Gnerre, Sante, Alfoldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B., Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J., Rasmussen, Matthew D., Robinson, Jim, Stark, Alexander, Vilella, Albert J., Wen, Jiayu, Xie, Xiaohui, Zody, Michael C., Worley, Kim C., Kovar, Christie L., Muzny, Donna M., Gibbs, Richard A., Warren, Wesley C., Mardis, Elaine R, Weinstock, George M., Wilson, Richard K., Birney, Ewan, Margulies, Elliott H., Herrero, Javier, Green, Eric D., Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S., Pedersen, Jakob S., Lander, Eric S., Kellis, Manolis
Publicado 2011

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

por 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.
Publicado 2015

GA4GH: International policies and standards for data sharing across genomic research and healthcare

por Rehm, Heidi L., Page, Angela J.H., Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J.S., Beck, Tim, Beckmann, Jacques S., Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K., Boughtwood, Tiffany F., Bourque, Guillaume, Bowers, Sarion R., Brookes, Anthony J., Brudno, Michael, Brush, Matthew H., Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, L. Jonathan, Dyke, Stephanie O.M., Eddy, James A., Eilbeck, Karen, Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M., Ho, Calvin W.L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jené, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J.M., Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M., Kekesi-Lafrance, Kristina, Kelleher, Jerome, Kerry, Giselle, Khor, Seik-Soon, Knoppers, Bartha M., Konopko, Melissa A., Kosaki, Kenjiro, Kuba, Martin, Lawson, Jonathan, Leinonen, Rasko, Li, Stephanie, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Liyanage, Isuru Udara, Lopez, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Metke-Jimenez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Munoz-Torres, Monica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura A.D., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Rodriguez, Laura Lyman, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos, Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Guimera, Roman Valls, Vamathevan, Jessica, Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, North, Kathryn, Birney, Ewan
Publicado 2021