The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

by Adey, Andrew, Burton, Joshua N., Kitzman, Jacob O., Hiatt, Joseph B., Lewis, Alexandra P., Martin, Beth K., Qiu, Ruolan, Lee, Choli, Shendure, Jay
Published 2013

Recurrent Somatic Loss of TNFRSF14 in Classical Hodgkin Lymphoma

by Salipante, Stephen J., Adey, Andrew, Thomas, Anju, Lee, Choli, Liu, Yajuan J., Kumar, Akash, Lewis, Alexandra P., Wu, David, Fromm, Jonathan R., Shendure, Jay
Published in Genes Chromosomes Cancer (2015)

Whole genome prediction for preimplantation genetic diagnosis

by Kumar, Akash, Ryan, Allison, Kitzman, Jacob O, Wemmer, Nina, Snyder, Matthew W, Sigurjonsson, Styrmir, Lee, Choli, Banjevic, Milena, Zarutskie, Paul W, Lewis, Alexandra P, Shendure, Jay, Rabinowitz, Matthew
Published in Genome Med (2015)

Non-Invasive Fetal Genome Sequencing: Opportunities and Challenges

by Tabor, Holly K., Murray, Jeffrey C., Gammill, Hilary S., Kitzman, Jacob O., Snyder, Matthew W., Ventura, Mario, Lewis, Alexandra P., Qiu, Ruolan, Simmons, LaVone E., Rubens, Craig E., Santillan, Donna A., Eichler, Evan E., Bamshad, Michael J., Shendure, Jay
Published 2012

Non-invasive whole genome sequencing of a human fetus

by Kitzman, Jacob O., Snyder, Matthew W., Ventura, Mario, Lewis, Alexandra P., Qiu, Ruolan, Simmons, LaVone E., Gammill, Hilary S., Rubens, Craig E., Santillan, Donna A., Murray, Jeffrey C., Tabor, Holly K., Bamshad, Michael J., Eichler, Evan E., Shendure, Jay
Published 2012

Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes

by Hsieh, PingHsun, Vollger, Mitchell R., Dang, Vy, Porubsky, David, Baker, Carl, Cantsilieris, Stuart, Hoekzema, Kendra, Lewis, Alexandra P., Munson, Katherine M., Sorensen, Melanie, Kronenberg, Zev N., Murali, Shwetha, Nelson, Bradley J., Chiatante, Giorgia, Maggiolini, Flavia Angela Maria, Blanché, Hélène, Underwood, Jason G., Antonacci, Francesca, Deleuze, Jean-François, Eichler, Evan E.
Published in Science (2019)

Exome Sequencing Identifies Mutations in CCDC114 as a Cause of Primary Ciliary Dyskinesia

by Knowles, Michael R., Leigh, Margaret W., Ostrowski, Lawrence E., Huang, Lu, Carson, Johnny L., Hazucha, Milan J., Yin, Weining, Berg, Jonathan S., Davis, Stephanie D., Dell, Sharon D., Ferkol, Thomas W., Rosenfeld, Margaret, Sagel, Scott D., Milla, Carlos E., Olivier, Kenneth N., Turner, Emily H., Lewis, Alexandra P., Bamshad, Michael J., Nickerson, Deborah A., Shendure, Jay, Zariwala, Maimoona A.
Published 2013

A high-quality bonobo genome refines the analysis of hominid evolution

by 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.
Published in Nature (2021)

Mutations in SPAG1 Cause Primary Ciliary Dyskinesia Associated with Defective Outer and Inner Dynein Arms

by Knowles, Michael R., Ostrowski, Lawrence E., Loges, Niki T., Hurd, Toby, Leigh, Margaret W., Huang, Lu, Wolf, Whitney E., Carson, Johnny L., Hazucha, Milan J., Yin, Weining, Davis, Stephanie D., Dell, Sharon D., Ferkol, Thomas W., Sagel, Scott D., Olivier, Kenneth N., Jahnke, Charlotte, Olbrich, Heike, Werner, Claudius, Raidt, Johanna, Wallmeier, Julia, Pennekamp, Petra, Dougherty, Gerard W., Hjeij, Rim, Gee, Heon Yung, Otto, Edgar A., Halbritter, Jan, Chaki, Moumita, Diaz, Katrina A., Braun, Daniela A., Porath, Jonathan D., Schueler, Markus, Baktai, György, Griese, Matthias, Turner, Emily H., Lewis, Alexandra P., Bamshad, Michael J., Nickerson, Deborah A., Hildebrandt, Friedhelm, Shendure, Jay, Omran, Heymut, Zariwala, Maimoona A.
Published 2013

Sequence diversity analyses of an improved rhesus macaque genome enhances its biomedical utility

by Warren, Wesley C., Harris, R. Alan, Haukness, Marina, Fiddes, Ian T., Murali, Shwetha C., Fernandes, Jason, Dishuck, Philip C., Storer, Jessica M., Raveendran, Muthuswamy, Hillier, LaDeana W., Porubsky, David, Mao, Yafei, Gordon, David, Vollger, Mitchell R., Lewis, Alexandra P., Munson, Katherine M., DeVogelaere, Elizabeth, Armstrong, Joel, Diekhans, Mark, Walker, Jerilyn A., Tomlinson, Chad, Graves-Lindsay, Tina A., Kremitzki, Milinn, Salama, Sofie R., Audano, Peter A., Escalona, Merly, Maurer, Nicholas W., Antonacci, Francesca, Mercuri, Ludovica, Maggiolini, Flavia A.M., Catacchio, Claudia Rita, Underwood, Jason G., O’Connor, David H., Sanders, Ashley D., Korbel, Jan O., Ferguson, Betsy, Kubisch, H. Michael, Picker, Louis, Kalin, Ned H., Rosene, Douglas, Levine, Jon, Abbott, David H., Gray, Stanton B., Sanchez, Mar M., Kovacs-Balint, Zsofia A., Kemnitz, Joseph W., Thomasy, Sara M., Roberts, Jeffrey A., Kinnally, Erin L., Capitanio, John P., Skene, J.H. Pate, Platt, Michael, Cole, Shelley A., Green, Richard E., Ventura, Mario, Wiseman, Roger W., Paten, Benedict, Batzer, Mark A., Rogers, Jeffrey, Eichler, Evan E.
Published in Science (2020)

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

by Ebert, Peter, Audano, Peter A., Zhu, Qihui, Rodriguez-Martin, Bernardo, Porubsky, David, Bonder, Marc Jan, Sulovari, Arvis, Ebler, Jana, Zhou, Weichen, Mari, Rebecca Serra, Yilmaz, Feyza, Zhao, Xuefang, Hsieh, PingHsun, Lee, Joyce, Kumar, Sushant, Lin, Jiadong, Rausch, Tobias, Chen, Yu, Ren, Jingwen, Santamarina, Martin, Höps, Wolfram, Ashraf, Hufsah, Chuang, Nelson T., Yang, Xiaofei, Munson, Katherine M., Lewis, Alexandra P., Fairley, Susan, Tallon, Luke J., Clarke, Wayne E., Basile, Anna O., Byrska-Bishop, Marta, Corvelo, André, Evani, Uday S., Lu, Tsung-Yu, Chaisson, Mark J.P., Chen, Junjie, Li, Chong, Brand, Harrison, Wenger, Aaron M., Ghareghani, Maryam, Harvey, William T., Raeder, Benjamin, Hasenfeld, Patrick, Regier, Allison A., Abel, Haley J., Hall, Ira M., Flicek, Paul, Stegle, Oliver, Gerstein, Mark B., Tubio, Jose M.C., Mu, Zepeng, Li, Yang I., Shi, Xinghua, Hastie, Alex R., Ye, Kai, Chong, Zechen, Sanders, Ashley D., Zody, Michael C., Talkowski, Michael E., Mills, Ryan E., Devine, Scott E., Lee, Charles, Korbel, Jan O., Marschall, Tobias, Eichler, Evan E.
Published in Science (2021)