Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

by Rodrigue, Sébastien, Malmstrom, Rex R., Berlin, Aaron M., Birren, Bruce W., Henn, Matthew R., Chisholm, Sallie W.
Published 2009

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

Pioglitazone is as effective as dexamethasone in a cockroach allergen-induced murine model of asthma

by Narala, Venkata R, Ranga, Rajesh, Smith, Monica R, Berlin, Aaron A, Standiford, Theodore J, Lukacs, Nicholas W, Reddy, Raju C
Published 2007

RNA-Seq methods for imperfect samples: development, evaluation and applications

by Adiconis, Xian, Fan, Lin, DeLuca, David, Sivachenko, Andrey, Pochet, Nathalie, Berlin, Aaron, Young, Sarah, Getz, Gad, Regev, Aviv, Nusbaum, Chad, Gnirke, Andreas, Levin, Joshua Z
Published 2011

The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations

by Keane, Michael, Craig, Thomas, Alföldi, Jessica, Berlin, Aaron M., Johnson, Jeremy, Seluanov, Andrei, Gorbunova, Vera, Di Palma, Federica, Lindblad-Toh, Kerstin, Church, George M., de Magalhães, João Pedro
Published 2014

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

Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

by Adiconis, Xian, Borges-Rivera, Diego, Satija, Rahul, DeLuca, David S., Busby, Michele A., Berlin, Aaron M., Sivachenko, Andrey, Thompson, Dawn Anne, Wysoker, Alec, Fennell, Timothy, Gnirke, Andreas, Pochet, Nathalie, Regev, Aviv, Levin, Joshua Z.
Published 2013

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

by Fisher, Sheila, Barry, Andrew, Abreu, Justin, Minie, Brian, Nolan, Jillian, Delorey, Toni M, Young, Geneva, Fennell, Timothy J, Allen, Alexander, Ambrogio, Lauren, Berlin, Aaron M, Blumenstiel, Brendan, Cibulskis, Kristian, Friedrich, Dennis, Johnson, Ryan, Juhn, Frank, Reilly, Brian, Shammas, Ramy, Stalker, John, Sykes, Sean M, Thompson, Jon, Walsh, John, Zimmer, Andrew, Zwirko, Zac, Gabriel, Stacey, Nicol, Robert, Nusbaum, Chad
Published 2011

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergen...

by Manning, Viola A., Pandelova, Iovanna, Dhillon, Braham, Wilhelm, Larry J., Goodwin, Stephen B., Berlin, Aaron M., Figueroa, Melania, Freitag, Michael, Hane, James K., Henrissat, Bernard, Holman, Wade H., Kodira, Chinnappa D., Martin, Joel, Oliver, Richard P., Robbertse, Barbara, Schackwitz, Wendy, Schwartz, David C., Spatafora, Joseph W., Turgeon, B. Gillian, Yandava, Chandri, Young, Sarah, Zhou, Shiguo, Zeng, Qiandong, Grigoriev, Igor V., Ma, Li-Jun, Ciuffetti, Lynda M.
Published 2013

An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

by Hoeppner, Marc P., Lundquist, Andrew, Pirun, Mono, Meadows, Jennifer R. S., Zamani, Neda, Johnson, Jeremy, Sundström, Görel, Cook, April, FitzGerald, Michael G., Swofford, Ross, Mauceli, Evan, Moghadam, Behrooz Torabi, Greka, Anna, Alföldi, Jessica, Abouelleil, Amr, Aftuck, Lynne, Bessette, Daniel, Berlin, Aaron, Brown, Adam, Gearin, Gary, Lui, Annie, Macdonald, J. Pendexter, Priest, Margaret, Shea, Terrance, Turner-Maier, Jason, Zimmer, Andrew, Lander, Eric S., di Palma, Federica, Lindblad-Toh, Kerstin, Grabherr, Manfred G.
Published 2014

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

by Matranga, Christian B, Andersen, Kristian G, Winnicki, Sarah, Busby, Michele, Gladden, Adrianne D, Tewhey, Ryan, Stremlau, Matthew, Berlin, Aaron, Gire, Stephen K, England, Eleina, Moses, Lina M, Mikkelsen, Tarjei S, Odia, Ikponmwonsa, Ehiane, Philomena E, Folarin, Onikepe, Goba, Augustine, Kahn, S Humarr, Grant, Donald S, Honko, Anna, Hensley, Lisa, Happi, Christian, Garry, Robert F, Malboeuf, Christine M, Birren, Bruce W, Gnirke, Andreas, Levin, Joshua Z, Sabeti, Pardis C
Published 2014

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

by Peng, Xinxia, Alföldi, Jessica, Gori, Kevin, Eisfeld, Amie J., Tyler, Scott R., Tisoncik-Go, Jennifer, Brawand, David, Law, G. Lynn, Skunca, Nives, Hatta, Masato, Gasper, David J., Kelly, Sara M., Chang, Jean, Thomas, Matthew J., Johnson, Jeremy, Berlin, Aaron M., Lara, Marcia, Russell, Pamela, Swofford, Ross, Turner-Maier, Jason, Young, Sarah, Hourlier, Thibaut, Aken, Bronwen, Searle, Steve, Sun, Xingshen, Yi, Yaling, Suresh, M., Tumpey, Terrence M., Siepel, Adam, Wisely, Samantha M., Dessimoz, Christophe, Kawaoka, Yoshihiro, Birren, Bruce W., Lindblad-Toh, Kerstin, Di Palma, Federica, Engelhardt, John F., Palermo, Robert E., Katze, Michael G.
Published 2014

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

The spotted gar genome illuminates vertebrate evolution and facilitates human-to-teleost comparisons

by Braasch, Ingo, Gehrke, Andrew R., Smith, Jeramiah J., Kawasaki, Kazuhiko, Manousaki, Tereza, Pasquier, Jeremy, Amores, Angel, Desvignes, Thomas, Batzel, Peter, Catchen, Julian, Berlin, Aaron M., Campbell, Michael S., Barrell, Daniel, Martin, Kyle J., Mulley, John F., Ravi, Vydianathan, Lee, Alison P., Nakamura, Tetsuya, Chalopin, Domitille, Fan, Shaohua, Wcisel, Dustin, Cañestro, Cristian, Sydes, Jason, Beaudry, Felix E. G., Sun, Yi, Hertel, Jana, Beam, Michael J., Fasold, Mario, Ishiyama, Mikio, Johnson, Jeremy, Kehr, Steffi, Lara, Marcia, Letaw, John H., Litman, Gary W., Litman, Ronda T., Mikami, Masato, Ota, Tatsuya, Saha, Nil Ratan, Williams, Louise, Stadler, Peter F., Wang, Han, Taylor, John S., Fontenot, Quenton, Ferrara, Allyse, Searle, Stephen M. J., Aken, Bronwen, Yandell, Mark, Schneider, Igor, Yoder, Jeffrey A., Volff, Jean-Nicolas, Meyer, Axel, Amemiya, Chris T., Venkatesh, Byrappa, Holland, Peter W. H., Guiguen, Yann, Bobe, Julien, Shubin, Neil H., Di Palma, Federica, Alföldi, Jessica, Lindblad-Toh, Kerstin, Postlethwait, John H.
Published 2016

Analysis of the African coelacanth genome sheds light on tetrapod evolution

by Amemiya, Chris T., Alföldi, Jessica, Lee, Alison P., Fan, Shaohua, Philippe, Hervé, MacCallum, Iain, Braasch, Ingo, Manousaki, Tereza, Schneider, Igor, Rohner, Nicolas, Organ, Chris, Chalopin, Domitille, Smith, Jeramiah J., Robinson, Mark, Dorrington, Rosemary A., Gerdol, Marco, Aken, Bronwen, Biscotti, Maria Assunta, Barucca, Marco, Baurain, Denis, Berlin, Aaron M., Blatch, Gregory L., Buonocore, Francesco, Burmester, Thorsten, Campbell, Michael S., Canapa, Adriana, Cannon, John P., Christoffels, Alan, De Moro, Gianluca, Edkins, Adrienne L., Fan, Lin, Fausto, Anna Maria, Feiner, Nathalie, Forconi, Mariko, Gamieldien, Junaid, Gnerre, Sante, Gnirke, Andreas, Goldstone, Jared V., Haerty, Wilfried, Hahn, Mark E., Hesse, Uljana, Hoffmann, Steve, Johnson, Jeremy, Karchner, Sibel I., Kuraku, Shigehiro, Lara, Marcia, Levin, Joshua Z., Litman, Gary W., Mauceli, Evan, Miyake, Tsutomu, Mueller, M. Gail, Nelson, David R., Nitsche, Anne, Olmo, Ettore, Ota, Tatsuya, Pallavicini, Alberto, Panji, Sumir, Picone, Barbara, Ponting, Chris P., Prohaska, Sonja J., Przybylski, Dariusz, Saha, Nil Ratan, Ravi, Vydianathan, Ribeiro, Filipe J., Sauka-Spengler, Tatjana, Scapigliati, Giuseppe, Searle, Stephen M. J., Sharpe, Ted, Simakov, Oleg, Stadler, Peter F., Stegeman, John J., Sumiyama, Kenta, Tabbaa, Diana, Tafer, Hakim, Turner-Maier, Jason, van Heusden, Peter, White, Simon, Williams, Louise, Yandell, Mark, Brinkmann, Henner, Volff, Jean-Nicolas, Tabin, Clifford J., Shubin, Neil, Schartl, Manfred, Jaffe, David, Postlethwait, John H., Venkatesh, Byrappa, Di Palma, Federica, Lander, Eric S., Meyer, Axel, Lindblad-Toh, Kerstin
Published 2013

The genomic substrate for adaptive radiation in African cichlid fish

by 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
Published 2014