Jalview Version 2—a multiple sequence alignment editor and analysis workbench von Waterhouse, Andrew M., Procter, James B., Martin, David M. A., Clamp, Michèle, Barton, Geoffrey J.

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Convergent regulatory evolution and loss of flight in paleognathous birds von Sackton, Timothy B., Grayson, Phil, Cloutier, Alison, Hu, Zhirui, Liu, Jun S., Wheeler, Nicole E., Gardner, Paul P., Clarke, Julia A., Baker, Allan J., Clamp, Michele, Edwards, Scott V.

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GeneWise and Genomewise von Birney, Ewan, Clamp, Michele, Durbin, Richard

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Identifying novel constrained elements by exploiting biased substitution patterns von Garber, Manuel, Guttman, Mitchell, Clamp, Michele, Zody, Michael C., Friedman, Nir, Xie, Xiaohui

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Distinguishing protein-coding and noncoding genes in the human genome von Clamp, Michele, Fry, Ben, Kamal, Mike, Xie, Xiaohui, Cuff, James, Lin, Michael F, Kellis, Manolis, Lindblad-Toh, Kerstin, Lander, Eric S

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The Jalview Java alignment editor von Clamp, Michele, Cuff, James, Searle, Stephen M., Barton, Geoffrey J.

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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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The Ensembl automatic gene annotation system von Curwen, Val, Eyras, Eduardo, Andrews, T Daniel, Clarke, Laura, Mongin, Emmanuel, Searle, Steven M J, Clamp, Michele

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ESTGenes: alternative splicing from ESTs in Ensembl von Eyras, Eduardo, Caccamo, Mario, Curwen, Val, Clamp, Michele

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The Ensembl analysis pipeline von Potter, Simon C, Clarke, Laura, Curwen, Val, Keenan, Stephen, Mongin, Emmanuel, Searle, Stephen M J, Stabenau, Arne, Storey, Roy, Clamp, Michele

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An Initial Strategy for the Systematic Identification of Functional Elements in the Human Genome by Low-Redundancy Comparative Sequencing von Margulies, Elliott H., Vinson, Jade P., NISC Comparative Sequencing Program, Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., Green, Eric D., Lander, Eric S., Mullikin, James C., Clamp, Michele

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Error, noise and bias in de novo transcriptome assemblies von Freedman, Adam H., Clamp, Michele, Sackton, Timothy B.

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Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure von Barros, Inês, Froufe, Hugo, Marnellos, George, Egas, Conceição, Delaney, Jennifer, Clamp, Michele, Santos, Ricardo Serrão, Bettencourt, Raul

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Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone von Cloutier, Alison, Sackton, Timothy B., Grayson, Phil, Clamp, Michele, Baker, Allan J., Edwards, Scott V.

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Biopipe: a flexible framework for protocol-based bioinformatics analysis von Hoon, Shawn, Ratnapu, Kiran Kumar, Chia, Jer-Ming, Kumarasamy, Balamurugan, Juguang, Xiao, Clamp, Michele, Stabenau, Arne, Potter, Simon, Clarke, Laura, Stupka, Elia

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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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Mining the draft human genome von Birney, Ewan, Bateman, Alex, Clamp, Michele E., Hubbard, Tim J.

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Three Periods of Regulatory Innovation During Vertebrate Evolution von Lowe, Craig B., Kellis, Manolis, Siepel, Adam, Raney, Brian J., Clamp, Michele, Salama, Sofie R., Kingsley, David M., Lindblad-Toh, Kerstin, Haussler, David

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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences von MIKKELSEN, Tarjei S, WAKEFIELD, Matthew J, JURKA, Jerzy, KAMAL, Michael, MAUCELI, Evan, SEARLE, Stephen M. J, SHARPE, Ted, BAKER, Michelle L, BATZER, Mark A, BENOS, Panayiotis V, BELOV, Katherine, CLAMP, Michele, AKEN, Bronwen, C, April, CUFF, James, DAS, Radhika, DAVIDOW, Lance, DEAKIN, Janine E, FAZZARI, Melissa J, GLASS, Jacob L, GRABHERR, Manfred, GREALLY, John M, WANJUN GU, AMEMIYA, Chris T, HORE, Timothy A, HUTTLEY, Gavin A, KLEBER, Michael, JIRTLE, Randy L, KOINA, Edda, LEE, Jeannie T, MAHONY, Shaun, MARRA, Marco A, MILLER, Robert D, NICHOLLS, Robert D, CHANG, Jean L, ODA, Mayumi, PAPENFUSS, Anthony T, PARRA, Zuly E, POLLOCK, David D, RAY, David A, SCHEIN, Jacqueline E, SPEED, Terence P, THOMPSON, Katherine, VANDEBERG, John L, WADE, Claire M, DUKE, Shannon, GARBER, Manuel, GENTLES, Andrew J, GOODSTADT, Leo, HEGER, Andreas

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Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10000 Vertebrate Species

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