V-Phaser 2: variant inference for viral populations

by Yang, Xiao, Charlebois, Patrick, Macalalad, Alex, Henn, Matthew R, Zody, Michael C
Published 2013

Conpair: concordance and contamination estimator for matched tumor–normal pairs

by Bergmann, Ewa A., Chen, Bo-Juen, Arora, Kanika, Vacic, Vladimir, Zody, Michael C.
Published 2016

Correction: Closing gaps in the human genome using sequencing by synthesis

by Garber, Manuel, Zody, Michael C, Arachchi, Harindra C, Berlin, Aaron, Gnerre, Sante, Green, Lisa M, Lennon, Niall, Nusbaum, Chad
Published 2011

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

by Liu, Chang, Yang, Xiao, Duffy, Brian, Mohanakumar, Thalachallour, Mitra, Robi D., Zody, Michael C., Pfeifer, John D.
Published 2013

De novo assembly of highly diverse viral populations

by Yang, Xiao, Charlebois, Patrick, Gnerre, Sante, Coole, Matthew G, Lennon, Niall J, Levin, Joshua Z, Qu, James, Ryan, Elizabeth M, Zody, Michael C, Henn, Matthew R
Published 2012

Novel origins of copy number variation in the dog genome

by Berglund, Jonas, Nevalainen, Elisa M, Molin, Anna-Maja, Perloski, Michele, André, Catherine, Zody, Michael C, Sharpe, Ted, Hitte, Christophe, Lindblad-Toh, Kerstin, Lohi, Hannes, Webster, Matthew T
Published 2012

Exploiting Nucleotide Composition to Engineer Promoters

by Grabherr, Manfred G., Pontiller, Jens, Mauceli, Evan, Ernst, Wolfgang, Baumann, Martina, Biagi, Tara, Swofford, Ross, Russell, Pamela, Zody, Michael C., Di Palma, Federica, Lindblad-Toh, Kerstin, Grabherr, Reingard M.
Published 2011

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

by Malboeuf, Christine M., Yang, Xiao, Charlebois, Patrick, Qu, James, Berlin, Aaron M., Casali, Monica, Pesko, Kendra N., Boutwell, Christian L., DeVincenzo, John P., Ebel, Gregory D., Allen, Todd M., Zody, Michael C., Henn, Matthew R., Levin, Joshua Z.
Published 2013

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

by Macalalad, Alexander R., Zody, Michael C., Charlebois, Patrick, Lennon, Niall J., Newman, Ruchi M., Malboeuf, Christine M., Ryan, Elizabeth M., Boutwell, Christian L., Power, Karen A., Brackney, Doug E., Pesko, Kendra N., Levin, Joshua Z., Ebel, Gregory D., Allen, Todd M., Birren, Bruce W., Henn, Matthew R.
Published 2012

The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility

by Imsland, Freyja, Feng, Chungang, Boije, Henrik, Bed'hom, Bertrand, Fillon, Valérie, Dorshorst, Ben, Rubin, Carl-Johan, Liu, Ranran, Gao, Yu, Gu, Xiaorong, Wang, Yanqiang, Gourichon, David, Zody, Michael C., Zecchin, William, Vieaud, Agathe, Tixier-Boichard, Michèle, Hu, Xiaoxiang, Hallböök, Finn, Li, Ning, Andersson, Leif
Published 2012

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

by Bacharach, Eran, Mishra, Nischay, Briese, Thomas, Zody, Michael C., Kembou Tsofack, Japhette Esther, Zamostiano, Rachel, Berkowitz, Asaf, Ng, James, Nitido, Adam, Corvelo, André, Toussaint, Nora C., Abel Nielsen, Sandra Cathrine, Hornig, Mady, Del Pozo, Jorge, Bloom, Toby, Ferguson, Hugh, Eldar, Avi, Lipkin, W. Ian
Published 2016

The genomic basis of adaptive evolution in threespine sticklebacks

by Jones, Felicity C, Grabherr, Manfred G, Chan, Yingguang Frank, Russell, Pamela, Mauceli, Evan, Johnson, Jeremy, Swofford, Ross, Pirun, Mono, Zody, Michael C, White, Simon, Birney, Ewan, Searle, Stephen, Schmutz, Jeremy, Grimwood, Jane, Dickson, Mark C, Myers, Richard M, Miller, Craig T, Summers, Brian R, Knecht, Anne K, Brady, Shannon D, Zhang, Haili, Pollen, Alex A, Howes, Timothy, Amemiya, Chris, Lander, Eric S, Di Palma, Federica, Lindblad-Toh, Kerstin, Kingsley, David M
Published 2012

Comparison of Illumina and 454 Deep Sequencing in Participants Failing Raltegravir-Based Antiretroviral Therapy

by Li, Jonathan Z., Chapman, Brad, Charlebois, Patrick, Hofmann, Oliver, Weiner, Brian, Porter, Alyssa J., Samuel, Reshmi, Vardhanabhuti, Saran, Zheng, Lu, Eron, Joseph, Taiwo, Babafemi, Zody, Michael C., Henn, Matthew R., Kuritzkes, Daniel R., Hide, Winston, Wilson, Cara C., Berzins, Baiba I., Acosta, Edward P., Bastow, Barbara, Kim, Peter S., Read, Sarah W., Janik, Jennifer, Meres, Debra S., Lederman, Michael M., Mong-Kryspin, Lori, Shaw, Karl E., Zimmerman, Louis G., Leavitt, Randi, De La Rosa, Guy, Jennings, Amy
Published 2014

Mutations causing medullary cystic kidney disease type 1 (MCKD1) lie in a large VNTR in MUC1 missed by massively parallel sequencing

by Kirby, Andrew, Gnirke, Andreas, Jaffe, David B., Barešová, Veronika, Pochet, Nathalie, Blumenstiel, Brendan, Ye, Chun, Aird, Daniel, Stevens, Christine, Robinson, James T., Cabili, Moran N., Gat-Viks, Irit, Kelliher, Edward, Daza, Riza, DeFelice, Matthew, Hůlková, Helena, Sovová, Jana, Vylet’al, Petr, Antignac, Corinne, Guttman, Mitchell, Handsaker, Robert E., Perrin, Danielle, Steelman, Scott, Sigurdsson, Snaevar, Scheinman, Steven J., Sougnez, Carrie, Cibulskis, Kristian, Parkin, Melissa, Green, Todd, Rossin, Elizabeth, Zody, Michael C., Xavier, Ramnik J., Pollak, Martin R., Alper, Seth L., Lindblad-Toh, Kerstin, Gabriel, Stacey, Hart, P. Suzanne, Regev, Aviv, Nusbaum, Chad, Kmoch, Stanislav, Bleyer, Anthony J., Lander, Eric S., Daly, Mark J.
Published 2013

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

by 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
Published 2011

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

by Henn, Matthew R., Boutwell, Christian L., Charlebois, Patrick, Lennon, Niall J., Power, Karen A., Macalalad, Alexander R., Berlin, Aaron M., Malboeuf, Christine M., Ryan, Elizabeth M., Gnerre, Sante, Zody, Michael C., Erlich, Rachel L., Green, Lisa M., Berical, Andrew, Wang, Yaoyu, Casali, Monica, Streeck, Hendrik, Bloom, Allyson K., Dudek, Tim, Tully, Damien, Newman, Ruchi, Axten, Karen L., Gladden, Adrianne D., Battis, Laura, Kemper, Michael, Zeng, Qiandong, Shea, Terrance P., Gujja, Sharvari, Zedlack, Carmen, Gasser, Olivier, Brander, Christian, Hess, Christoph, Günthard, Huldrych F., Brumme, Zabrina L., Brumme, Chanson J., Bazner, Suzane, Rychert, Jenna, Tinsley, Jake P., Mayer, Ken H., Rosenberg, Eric, Pereyra, Florencia, Levin, Joshua Z., Young, Sarah K., Jessen, Heiko, Altfeld, Marcus, Birren, Bruce W., Walker, Bruce D., Allen, Todd M.
Published 2012