High-quality draft assemblies of mammalian genomes from massively parallel sequence data von Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J, Burton, Joshua N, Walker, Bruce J, Sharpe, Ted, Hall, Giles, Shea, Terrance P, Sykes, Sean, Berlin, Aaron M, Aird, Daniel, Costello, Maura, Daza, Riza, Williams, Louise, Nicol, Robert, Gnirke, Andreas, Nusbaum, Chad, Lander, Eric S, Jaffe, David B

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A direct characterization of human mutation based on microsatellites von Sun, James X, Helgason, Agnar, Masson, Gisli, Ebenesersdóttir, Sigríður Sunna, Li, Heng, Mallick, Swapan, Gnerre, Sante, Patterson, Nick, Kong, Augustine, Reich, David, Stefansson, Kari

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Genetic evidence for complex speciation of humans and chimpanzees von Patterson, Nick, Richter, Daniel J., Gnerre, Sante, Lander, Eric S., Reich, David

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Finished bacterial genomes from shotgun sequence data von Ribeiro, Filipe J, Przybylski, Dariusz, Yin, Shuangye, Sharpe, Ted, Gnerre, Sante, Abouelleil, Amr, Berlin, Aaron M, Montmayeur, Anna, Shea, Terrance P, Walker, Bruce J, Young, Sarah K, Russ, Carsten, Nusbaum, Chad, MacCallum, Iain, Jaffe, David B

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De novo assembly of highly diverse viral populations von 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

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The difficulty of avoiding false positives in genome scans for natural selection von Mallick, Swapan, Gnerre, Sante, Muller, Paul, Reich, David

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Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer von Janku, Filip, Zhang, Shile, Waters, Jill, Liu, Li, Huang, Helen J, Subbiah, Vivek, Hong, David S, Karp, Daniel D, Fu, Siqing, Cai, Xuyu, Ramzanali, Nishma M, Madwani, Kiran, Cabrilo, Goran, Andrews, Debra L, Zhao, Yue, Javle, Milind, Kopetz, E Scott, Luthra, Rajyalakshmi, Kim, Hyunsung J, Gnerre, Sante, Satya, Ravi Vijaya, Chuang, Han-Yu, Kruglyak, Kristina M, Toung, Jonathan, Zhao, Chen, Shen, Richard, Heymach, John V, Meric-Bernstam, Funda, Mills, Gordon B, Fan, Jian-Bing, Salathia, Neeraj S

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Initial sequence and comparative analysis of the cat genome von Pontius, Joan U, Mullikin, James C, Smith, Douglas R, Lindblad-Toh, Kerstin, Gnerre, Sante, Clamp, Michele, Chang, Jean, Stephens, Robert, Neelam, Beena, Volfovsky, Natalia, Schäffer, Alejandro A, Agarwala, Richa, Narfström, Kristina, Murphy, William J, Giger, Urs, Roca, Alfred L, Antunes, Agostinho, Menotti-Raymond, Marilyn, Yuhki, Naoya, Pecon-Slattery, Jill, Johnson, Warren E, Bourque, Guillaume, Tesler, Glenn, O'Brien, Stephen J

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Analysis of chimpanzee history based on genome sequence alignments von Caswell, Jennifer L, Mallick, Swapan, Richter, Daniel J, Neubauer, Julie, Schirmer, Christine, Gnerre, Sante, Reich, David

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Whole-genome sequence assembly for mammalian genomes: Arachne 2 von Jaffe, David B, Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, Lindblad-Toh, Kerstin, Mesirov, Jill P, Zody, Michael C, Lander, Eric S

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Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA von Liu, M.C., Klein, E.A., Swanton, C., Seiden, M.V., Klein, Eric A., Yeatman, Timothy J., Cohn, Allen L., Lapham, Rosanna, Parker, Alexander S., McIntyre, Kristi, Sekeres, Mikkael A., Siegel, Robert, Wang, Xuezhong, Cosgrove, David P., Trent, Jonathan, Thiel, David D., Garbo, Lawrence E., Giguere, Jeffrey K., Michels, Ross M., Harris, Ronald P., Richey, Stephen L., McCarthy, Timothy A., Couch, Fergus J., Wilks, Sharon T., Krie, Amy K., Balaraman, Rama, Rieger-Christ, Kimberly, Sullivan, Travis, Greenwald, Daniel R., Oh, William, Tsao, Che-Kai, Kennecke, Hagen F., Manhas, Atisha P., Ulrich, Brian K., Kovoor, Philip A., Stokoe, Christopher, Courtright, Jay G., Larson, Timothy G., Seiden, Michael V., Cummings, Steven R., Absalan, Farnaz, Alexander, Gregory, Allen, Brian, Aravanis, Alexander M., Beausang, John F., Berman, Jennifer, Bredno, Joerg, Calef, Robert, Cann, Gordon, Carter, Jeremy, Chen, Xiaoji, Chien, Tom C., Davydov, Konstantin, Demas, Vasiliki, Fields, Alexander P., Freese, Peter, Gnerre, Sante, Gross, Samuel, Hall, Megan P., Hartman, Anne-Renee, Hou, Chenlu, Hubbell, Earl, Jiang, Roger, Kim, TaeHyung, Klausner, Richard D., Kurtzman, Kathryn N., Lee, Mark, Lin, Wendy, Lipson, Jafi, Maddala, Tara, Maher, M. Cyrus, Melton, Collin, Mich, Andrea, Newman, Joshua, Nicula, Virgil, Nikolic, Ongjen, Patel, Shilpen, Rava, Richard, Schellenberger, Jan, Scott, Eric, Sehnert, Amy J., Shaknovich, Rita, Shanmugam, Avinash, Shashidhar, K.C., Shenoy, Archana, Shojaee, Seyedmehdi, Tang, Susan, Valouev, Anton, Venn, Oliver, Williams, Richard T., Wu, Tony, Yakym, Christopher, Yang, Xiao, Yecies, Jessica, Yip, Alexander S., Yue, Jeanne, Zhang, Lily, Zhang, Lori (Quan), Curtis, Christina, Berry, Donald A.

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High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants von Razavi, Pedram, Li, Bob T., Brown, David N., Jung, Byoungsok, Hubbell, Earl, Shen, Ronglai, Abida, Wassim, Juluru, Krishna, De Bruijn, Ino, Hou, Chenlu, Venn, Oliver, Lim, Raymond, Anand, Aseem, Maddala, Tara, Gnerre, Sante, Vijaya Satya, Ravi, Liu, Qinwen, Shen, Ling, Eattock, Nicholas, Yue, Jeanne, Blocker, Alexander W., Lee, Mark, Sehnert, Amy, Xu, Hui, Hall, Megan P., Santiago-Zayas, Angie, Novotny, William F., Isbell, James M., Rusch, Valerie W., Plitas, George, Heerdt, Alexandra S., Ladanyi, Marc, Hyman, David M., Jones, David R., Morrow, Monica, Riely, Gregory J., Scher, Howard I., Rudin, Charles M., Robson, Mark E., Diaz, Luis A., Solit, David B., Aravanis, Alexander M., Reis-Filho, Jorge S.

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The genomic substrate for adaptive radiation in African cichlid fish von Brawand, David, Wagner, Catherine E., Li, Yang I., Malinsky, Milan, Keller, Irene, Fan, Shaohua, Simakov, Oleg, Ng, Alvin Y., Lim, Zhi Wei, Bezault, Etienne, Turner-Maier, Jason, Johnson, Jeremy, Alcazar, Rosa, Noh, Hyun Ji, Russell, Pamela, Aken, Bronwen, Alföldi, Jessica, Amemiya, Chris, Azzouzi, Naoual, Baroiller, Jean-François, Barloy-Hubler, Frederique, Berlin, Aaron, Bloomquist, Ryan, Carleton, Karen L., Conte, Matthew A., D'Cotta, Helena, Eshel, Orly, Gaffney, Leslie, Galibert, Francis, Gante, Hugo F., Gnerre, Sante, Greuter, Lucie, Guyon, Richard, Haddad, Natalie S., Haerty, Wilfried, Harris, Rayna M., Hofmann, Hans A., Hourlier, Thibaut, Hulata, Gideon, Jaffe, David B., Lara, Marcia, Lee, Alison P., MacCallum, Iain, Mwaiko, Salome, Nikaido, Masato, Nishihara, Hidenori, Ozouf-Costaz, Catherine, Penman, David J., Przybylski, Dariusz, Rakotomanga, Michaelle, Renn, Suzy C. P., Ribeiro, Filipe J., Ron, Micha, Salzburger, Walter, Sanchez-Pulido, Luis, Santos, M. Emilia, Searle, Steve, Sharpe, Ted, Swofford, Ross, Tan, Frederick J., Williams, Louise, Young, Sarah, Yin, Shuangye, Okada, Norihiro, Kocher, Thomas D., Miska, Eric A., Lander, Eric S., Venkatesh, Byrappa, Fernald, Russell D., Meyer, Axel, Ponting, Chris P., Streelman, J. Todd, Lindblad-Toh, Kerstin, Seehausen, Ole, Di Palma, Federica

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Assemblathon 1: a competitive assessment of de novo short read assembly methods von Earl, Dent, Bradnam, Keith, St John, John, Darling, Aaron, Lin, Dawei, Fass, Joseph, Yu, Hung On Ken, Buffalo, Vince, Zerbino, Daniel R, Diekhans, Mark, Nguyen, Ngan, Ariyaratne, Pramila Nuwantha, Sung, Wing-Kin, Ning, Zemin, Haimel, Matthias, Simpson, Jared T, Fonseca, Nuno A, Birol, İnanç, Docking, T Roderick, Ho, Isaac Y, Rokhsar, Daniel S, Chikhi, Rayan, Lavenier, Dominique, Chapuis, Guillaume, Naquin, Delphine, Maillet, Nicolas, Schatz, Michael C, Kelley, David R, Phillippy, Adam M, Koren, Sergey, Yang, Shiaw-Pyng, Wu, Wei, Chou, Wen-Chi, Srivastava, Anuj, Shaw, Timothy I, Ruby, J Graham, Skewes-Cox, Peter, Betegon, Miguel, Dimon, Michelle T, Solovyev, Victor, Seledtsov, Igor, Kosarev, Petr, Vorobyev, Denis, Ramirez-Gonzalez, Ricardo, Leggett, Richard, MacLean, Dan, Xia, Fangfang, Luo, Ruibang, Li, Zhenyu, Xie, Yinlong, Liu, Binghang, Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J, Yin, Shuangye, Sharpe, Ted, Hall, Giles, Kersey, Paul J, Durbin, Richard, Jackman, Shaun D, Chapman, Jarrod A, Huang, Xiaoqiu, DeRisi, Joseph L, Caccamo, Mario, Li, Yingrui, Jaffe, David B, Green, Richard E, Haussler, David, Korf, Ian, Paten, Benedict

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Gibbon genome and the fast karyotype evolution of small apes von Carbone, Lucia, Alan Harris, R., Gnerre, Sante, Veeramah, Krishna R., Lorente-Galdos, Belen, Huddleston, John, Meyer, Thomas J., Herrero, Javier, Roos, Christian, Aken, Bronwen, Anaclerio, Fabio, Archidiacono, Nicoletta, Baker, Carl, Barrell, Daniel, Batzer, Mark A., Beal, Kathryn, Blancher, Antoine, Bohrson, Craig L., Brameier, Markus, Campbell, Michael S., Capozzi, Oronzo, Casola, Claudio, Chiatante, Giorgia, Cree, Andrew, Damert, Annette, de Jong, Pieter J., Dumas, Laura, Fernandez-Callejo, Marcos, Flicek, Paul, Fuchs, Nina V., Gut, Ivo, Gut, Marta, Hahn, Matthew W., Hernandez-Rodriguez, Jessica, Hillier, LaDeana W., Hubley, Robert, Ianc, Bianca, Izsvák, Zsuzsanna, Jablonski, Nina G., Johnstone, Laurel M., Karimpour-Fard, Anis, Konkel, Miriam K., Kostka, Dennis, Lazar, Nathan H., Lee, Sandra L., Lewis, Lora R., Liu, Yue, Locke, Devin P., Mallick, Swapan, Mendez, Fernando L., Muffato, Matthieu, Nazareth, Lynne V., Nevonen, Kimberly A., O’Bleness, Majesta, Ochis, Cornelia, Odom, Duncan T., Pollard, Katherine S., Quilez, Javier, Reich, David, Rocchi, Mariano, Schumann, Gerald G., Searle, Stephen, Sikela, James M., Skollar, Gabriella, Smit, Arian, Sonmez, Kemal, Hallers, Boudewijn ten, Terhune, Elizabeth, Thomas, Gregg W. C., Ullmer, Brygg, Ventura, Mario, Walker, Jerilyn A., Wall, Jeffrey D., Walter, Lutz, Ward, Michelle C., Wheelan, Sarah J., Whelan, Christopher W., White, Simon, Wilhelm, Larry J., Woerner, August E., Yandell, Mark, Zhu, Baoli, Hammer, Michael F., Marques-Bonet, Tomas, Eichler, Evan E., Fulton, Lucinda, Fronick, Catrina, Muzny, Donna M., Warren, Wesley C., Worley, Kim C., Rogers, Jeffrey, Wilson, Richard K., Gibbs, Richard A.

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

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ctDNA-based fusion detection for advanced colorectal cancer with a partner-agnostic assay von Barnett, Reagan, Gnerre, Sante, Willis, Jason, Overman, Michael J., Raghav, Kanwal Pratap Singh, Parseghian, Christine Megerdichian, Dasari, Arvind, Morelli, Maria Pia, Johnson, Benny, Eluri, Madhulika, Drusbosky, Leylah, Kopetz, Scott, Morris, Van K.

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Abstract 25: Reversion patterns in homologous recombination repair genes in metastatic cancer patients profiled by cell-free DNA von Fu, Yu, Yen, Jennifer, Aartyomenko, Alexander, Gnerre, Sante, Weiport, Caroline, Helman, Elena, Yablonovitch, Arielle, Pettitt, Stephen, Llord, Christopher, Tutt, Andrew, Nagy, Rebecca, Odegaard, Justin, Chudova, Darya, Talasaz, AmirAli

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Abstract 537: NTRK1 fusion detection from clinical cfDNA NGS using a de novo fusion caller von Yablonovitch, Arielle, Gnerre, Sante, Yen, Jennifer, Shell, Scott, Helman, Elena, Fairclough, Stephen, Nagy, Rebecca J., Odegaard, Justin, Chudova, Darya, Talasaz, AmirAli

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Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans von Haas, Brian J, Kamoun, Sophien, Zody, Michael C, Jiang, Rays H.Y, Handsaker, Robert E, Cano, Liliana M, Grabherr, Manfred, Kodira, Chinnappa D, Raffaele, Sylvain, Torto-Alalibo, Trudy, Bozkurt, Tolga O, Ah-Fong, Audrey M.V, Bollmann, Stephanie R, Grunwald, Niklaus J, Costanzo, Stefano, Jones, Richard W

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