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著者: Birney [70 articles]

Recent papers posted to CiteULike by the author Birney.
  • A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    Nature Biotechnology, Vol. 26, No. 7. (08 July 2008), pp. 779-785.
    by Thomas A Down, Vardhman K Rakyan, Daniel J Turner, Paul Flicek, Heng Li, Eugene Kulesha, Stefan Gräf, Nathan Johnson, Javier Herrero, Eleni M Tomazou, Natalie P Thorne, Liselotte Bäckdahl, Marlis Herberth, Kevin L Howe, David K Jackson, Marcos M Miretti, John C Marioni, Ewan Birney, Tim JP Hubbard, Richard Durbin, Simon Tavaré, Stephan Beck
    posted to no-tag by slevy03 on 2008-07-18 23:47:36 as ** along with 2 people bpcusack oelemento
  • Confounding between recombination and selection, and the Ped/Pop method for detecting selection
    Genome Res. (10 July 2008), gr.067181.107.
    by Paul F O'Reilly, Ewan Birney, David J Balding
    posted to selection recombination popgen by djkt on 2008-07-17 17:37:04 as **
  • The landscape of histone modifications across 1% of the human genome in five human cell lines
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 691-707.
    by Christoph M Koch, Robert M Andrews, Paul Flicek, Shane C Dillon, Ulas Karaoz, Gayle K Clelland, Sarah Wilcox, David M Beare, Joanna C Fowler, Phillippe Couttet, Keith D James, Gregory C Lefebvre, Alexander W Bruce, Oliver M Dovey, Peter D Ellis, Pawandeep Dhami, Cordelia F Langford, Zhiping Weng, Ewan Birney, Nigel P Carter, David Vetrie, Ian Dunham
  • The InterPro database, an integrated documentation resource for protein families, domains and functional sites
    Nucl. Acids Res., Vol. 29, No. 1. (1 January 2001), pp. 37-40.
    posted to no-tag by sgoetz on 2008-07-10 17:11:01 as ** along with 1 person alanrw
  • Levers and fulcrums: progress in cis-regulatory motif models
    Nature Methods, Vol. 5, No. 4., pp. 297-298.
    by Ewan Birney
  • The genome sequence of the malaria mosquito Anopheles gambiae.
    Science, Vol. 298, No. 5591. (4 October 2002), pp. 129-149.
    by RA Holt, GM Subramanian, A Halpern, GG Sutton, R Charlab, DR Nusskern, P Wincker, AG Clark, JM Ribeiro, R Wides, SL Salzberg, B Loftus, M Yandell, WH Majoros, DB Rusch, Z Lai, CL Kraft, JF Abril, V Anthouard, P Arensburger, PW Atkinson, H Baden, V de Berardinis, D Baldwin, V Benes, J Biedler, C Blass, R Bolanos, D Boscus, M Barnstead, S Cai, A Center, K Chaturverdi, GK Christophides, MA Chrystal, M Clamp, A Cravchik, V Curwen, A Dana, A Delcher, I Dew, CA Evans, M Flanigan, A Grundschober-Freimoser, L Friedli, Z Gu, P Guan, R Guigo, ME Hillenmeyer, SL Hladun, JR Hogan, YS Hong, J Hoover, O Jaillon, Z Ke, C Kodira, E Kokoza, A Koutsos, I Letunic, A Levitsky, Y Liang, JJ Lin, NF Lobo, JR Lopez, JA Malek, TC McIntosh, S Meister, J Miller, C Mobarry, E Mongin, SD Murphy, DA O'Brochta, C Pfannkoch, R Qi, MA Regier, K Remington, H Shao, MV Sharakhova, CD Sitter, J Shetty, TJ Smith, R Strong, J Sun, D Thomasova, LQ Ton, P Topalis, Z Tu, MF Unger, B Walenz, A Wang, J Wang, M Wang, X Wang, KJ Woodford, JR Wortman, M Wu, A Yao, EM Zdobnov, H Zhang, Q Zhao, S Zhao, SC Zhu, I Zhimulev, M Coluzzi, A della Torre, CW Roth, C Louis, F Kalush, RJ Mural, EW Myers, MD Adams, HO Smith, S Broder, MJ Gardner, CM Fraser, E Birney, P Bork, PT Brey, JC Venter, J Weissenbach, FC Kafatos, FH Collins, SL Hoffman
  • An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    Genome Res. (24 June 2008), gr.077479.108.
    by Vardhman Rakyan, Thomas Down, Natalie Thorne, Paul Flicek, Eugene Kulesha, Stefan Graf, Eleni Tomazou, Liselotte Backdahl, Nathan Johnson, Marils Herberth, Kevin Howe, David Jackson, Marcos Miretti, Heike Fiegler, John Marioni, Ewan Birney, Tim Hubbard, Nigel Carter, Simon Tavare, Stephan Beck
  • Update of the Anopheles gambiae PEST genome assembly
    Genome Biology, Vol. 8 (08 January 2007), R5.
    by Maria V Sharakhova, Martin P Hammond, Neil F Lobo, Jaroslaw Krzywinski, Maria F Unger, Maureen E Hillenmeyer, Robert V Bruggner, Ewan Birney, Frank H Collins
  • The Anopheles gambiae genome: an update.
    Trends in parasitology, Vol. 20, No. 2. (February 2004), pp. 49-52.
    by E Mongin, C Louis, RA Holt, E Birney, FH Collins
    posted to no-tag by nbesansk to the group Notre Dame Bioinformatics on 2008-06-27 19:53:40 as read
  • Using GeneWise in the Drosophila annotation experiment.
    Genome Res, Vol. 10, No. 4. (April 2000), pp. 547-548.
    by E Birney, R Durbin
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 22:52:25 as **
  • Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.
    Proceedings of the International Conference on Intelligent Systems for Molecular Biology, Vol. 5 (1997), pp. 56-64.
    by E Birney, R Durbin
    posted to 200806_prop by wenhan on 2008-06-24 22:51:45 as ** along with 1 person rabio
  • Comparative genomics of the eukaryotes.
    Science, Vol. 287, No. 5461. (24 March 2000), pp. 2204-2215.
    by GM Rubin, MD Yandell, JR Wortman, GL Gabor Miklos, CR Nelson, IK Hariharan, ME Fortini, PW Li, R Apweiler, W Fleischmann, JM Cherry, S Henikoff, MP Skupski, S Misra, M Ashburner, E Birney, MS Boguski, T Brody, P Brokstein, SE Celniker, SA Chervitz, D Coates, A Cravchik, A Gabrielian, RF Galle, WM Gelbart, RA George, LS Goldstein, F Gong, P Guan, NL Harris, BA Hay, RA Hoskins, J Li, Z Li, RO Hynes, SJ Jones, PM Kuehl, B Lemaitre, JT Littleton, DK Morrison, C Mungall, PH O'Farrell, OK Pickeral, C Shue, LB Vosshall, J Zhang, Q Zhao, XH Zheng, S Lewis
  • Patterns of somatic mutation in human cancer genomes
    Nature, Vol. 446, No. 7132., pp. 153-158.
    by Christopher Greenman, Philip Stephens, Raffaella Smith, Gillian L Dalgliesh, Christopher Hunter, Graham Bignell, Helen Davies, Jon Teague, Adam Butler, Claire Stevens, Sarah Edkins, Sarah O’meara, Imre Vastrik, Esther E Schmidt, Tim Avis, Syd Barthorpe, Gurpreet Bhamra, Gemma Buck, Bhudipa Choudhury, Jody Clements, Jennifer Cole, Ed Dicks, Simon Forbes, Kris Gray, Kelly Halliday, Rachel Harrison, Katy Hills, Jon Hinton, Andy Jenkinson, David Jones, Andy Menzies, Tatiana Mironenko, Janet Perry, Keiran Raine, Dave Richardson, Rebecca Shepherd, Alexandra Small, Calli Tofts, Jennifer Varian, Tony Webb, Sofie West, Sara Widaa, Andy Yates, Daniel P Cahill, David N Louis, Peter Goldstraw, Andrew G Nicholson, Francis Brasseur, Leendert Looijenga, Barbara L Weber, Yoke-Eng Chiew, Anna Defazio, Mel F Greaves, Anthony R Green, Peter Campbell, Ewan Birney, Douglas F Easton, Georgia Chenevix-Trench, Min-Han Tan, Sok K Khoo, Bin T Teh, Siu T Yuen, Suet Y Leung, Richard Wooster, Andrew P Futreal, Michael R Stratton
  • Ensembl 2008.
    Nucleic Acids Res (13 November 2007)
    by P Flicek, B L L Aken, K Beal, B Ballester, M Caccamo, Y Chen, L Clarke, G Coates, F Cunningham, T Cutts, T Down, S C C Dyer, T Eyre, S Fitzgerald, J Fernandez-Banet, S Gräf, S Haider, M Hammond, R Holland, K L L Howe, K Howe, N Johnson, A Jenkinson, A Kähäri, D Keefe, F Kokocinski, E Kulesha, D Lawson, I Longden, K Megy, P Meidl, B Overduin, A Parker, B Pritchard, A Prlic, S Rice, D Rios, M Schuster, I Sealy, G Slater, D Smedley, G Spudich, S Trevanion, A J J Vilella, J Vogel, S White, M Wood, E Birney, T Cox, V Curwen, R Durbin, X M M Fernandez-Suarez, J Herrero, T J P J Hubbard, A Kasprzyk, G Proctor, J Smith, A Ureta-Vidal, S Searle
  • Challenges and standards in integrating surveys of structural variation.
    Nat Genet, Vol. 39, No. 7 Suppl. (July 2007)
    by SW Scherer, C Lee, E Birney, DM Altshuler, EE Eichler, NP Carter, ME Hurles, L Feuk
  • The International Protein Index: an integrated database for proteomics experiments.
    Proteomics, Vol. 4, No. 7. (July 2004), pp. 1985-1988.
    posted to proteomics proteome ipi by dullhunk on 2008-06-09 15:05:27 as **
  • Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs
    Genome Res. (18 March 2008), gr.074492.107.
    by Daniel Zerbino, Ewan Birney
  • Picking pyknons out of the human genome.
    Cell, Vol. 125, No. 5. (2 June 2006), pp. 836-838.
    by A Meynert, E Birney
    posted to sirna rnai mirna by drajmo on 2008-06-08 22:33:02 as ****
  • The European Bioinformatics Institute's data resources
    Nucl. Acids Res., Vol. 31, No. 1. (1 January 2003), pp. 43-50.
    by Catherine Brooksbank, Evelyn Camon, Midori A Harris, Michele Magrane, Maria J Martin, Nicola Mulder, Claire O'Donovan, Helen Parkinson, Mary A Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron
    posted to no-tag by alanrw on 2008-06-08 17:08:10 as **
  • Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
    Nucl. Acids Res. (26 November 2007), gkm1018.
    by Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish Mcwilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim Hubbard, Ewan Birney
    posted to no-tag by alanrw on 2008-06-08 16:26:16 as **
  • Ensembl 2007.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
  • InterPro--an integrated documentation resource for protein families, domains and functional sites
    Bioinformatics, Vol. 16, No. 12. (1 December 2000), pp. 1145-1150.
    posted to no-tag by alanrw on 2008-06-04 16:59:17 as **
  • Dry work in a wet world: computation in systems biology
    Mol Syst Biol, Vol. 2 (4 July 2006)
    by Pascal Kahlem, Ewan Birney
    posted to no-tag by edvin on 2008-06-02 22:25:53 as ****
  • Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
    Nat Rev Genet, Vol. 9, No. 4. (April 2008), pp. 303-313.
    by Elliott H Margulies, Ewan Birney
    posted to no-tag by natstreet on 2008-05-28 14:12:08 as ** along with 5 people jyuh zwang mingzhi phoenixzxl ptrobajo
  • In vivo validation of a computationally predicted conserved Ath5 target gene set.
    PLoS genetics, Vol. 3, No. 9. (September 2007), pp. 1661-1671.
    posted to no-tag by isimpson on 2008-05-27 14:40:27 as *****
  • The Pfam protein families database.
    Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 276-280.
  • Reactome: a knowledgebase of biological pathways and processes
    Genome Biology, Vol. 8 (16 March 2007), R39.
    by Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein
  • Initial sequencing and comparative analysis of the mouse genome.
    Nature, Vol. 420, No. 6915. (5 December 2002), pp. 520-562.
    by RH Waterston, K Lindblad-Toh, E Birney, J Rogers, JF Abril, P Agarwal, R Agarwala, R Ainscough, M Alexandersson, P An, SE Antonarakis, J Attwood, R Baertsch, J Bailey, K Barlow, S Beck, E Berry, B Birren, T Bloom, P Bork, M Botcherby, N Bray, MR Brent, DG Brown, SD Brown, C Bult, J Burton, J Butler, RD Campbell, P Carninci, S Cawley, F Chiaromonte, AT Chinwalla, DM Church, M Clamp, C Clee, FS Collins, LL Cook, RR Copley, A Coulson, O Couronne, J Cuff, V Curwen, T Cutts, M Daly, R David, J Davies, KD Delehaunty, J Deri, ET Dermitzakis, C Dewey, NJ Dickens, M Diekhans, S Dodge, I Dubchak, DM Dunn, SR Eddy, L Elnitski, RD Emes, P Eswara, E Eyras, A Felsenfeld, GA Fewell, P Flicek, K Foley, WN Frankel, LA Fulton, RS Fulton, TS Furey, D Gage, RA Gibbs, G Glusman, S Gnerre, N Goldman, L Goodstadt, D Grafham, TA Graves, ED Green, S Gregory, R Guigó, M Guyer, RC Hardison, D Haussler, Y Hayashizaki, LW Hillier, A Hinrichs, W Hlavina, T Holzer, F Hsu, A Hua, T Hubbard, A Hunt, I Jackson, DB Jaffe, LS Johnson, M Jones, TA Jones, A Joy, M Kamal, EK Karlsson, D Karolchik, A Kasprzyk, J Kawai, E Keibler, C Kells, WJ Kent, A Kirby, DL Kolbe, I Korf, RS Kucherlapati, EJ Kulbokas, D Kulp, T Landers, JP Leger, S Leonard, I Letunic, R Levine, J Li, M Li, C Lloyd, S Lucas, B Ma, DR Maglott, ER Mardis, L Matthews, E Mauceli, JH Mayer, M McCarthy, WR McCombie, S McLaren, K McLay, JD McPherson, J Meldrim, B Meredith, JP Mesirov, W Miller, TL Miner, E Mongin, KT Montgomery, M Morgan, R Mott, JC Mullikin, DM Muzny, WE Nash, JO Nelson, MN Nhan, R Nicol, Z Ning, C Nusbaum, MJ O'Connor, Y Okazaki, K Oliver, E Overton-Larty, L Pachter, G Parra, KH Pepin, J Peterson, P Pevzner, R Plumb, CS Pohl, A Poliakov, TC Ponce, CP Ponting, S Potter, M Quail, A Reymond, BA Roe, KM Roskin, EM Rubin, AG Rust, R Santos, V Sapojnikov, B Schultz, J Schultz, MS Schwartz, S Schwartz, C Scott, S Seaman, S Searle, T Sharpe, A Sheridan, R Shownkeen, S Sims, JB Singer, G Slater, A Smit, DR Smith, B Spencer, A Stabenau, N Stange-Thomann, C Sugnet, M Suyama, G Tesler, J Thompson, D Torrents, E Trevaskis, J Tromp, C Ucla, A Ureta-Vidal, JP Vinson, AC Von Niederhausern, CM Wade, M Wall, RJ Weber, RB Weiss, MC Wendl, AP West, K Wetterstrand, R Wheeler, S Whelan, J Wierzbowski, D Willey, S Williams, RK Wilson, E Winter, KC Worley, D Wyman, S Yang, SP Yang, EM Zdobnov, MC Zody, ES Lander,
  • What everybody should know about the rat genome and its online resources
    Nat Genet, Vol. 40, No. 5. (May 2008), pp. 523-527.
    by Simon N Twigger, Kim D Pruitt, Xose M Fernandez-Suarez, Donna Karolchik, Kim C Worley, Donna R Maglott, Garth Brown, George Weinstock, Richard A Gibbs, Jim Kent, Ewan Birney, Howard J Jacob
    posted to rat-genetics by booker on 2008-05-15 03:29:09 as ** along with 1 person jyuh
  • The Bioperl Toolkit: Perl Modules for the Life Sciences
    Genome Res., Vol. 12, No. 10. (1 October 2002), pp. 1611-1618.
    by Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehvaslaiho, Chad Matsalla, Chris J Mungall, Brian I Osborne, Matthew R Pocock, Peter Schattner, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson, Ewan Birney
  • Reactome: a knowledgebase of biological pathways.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
  • The Ensembl genome database project
    Nucl. Acids Res., Vol. 30, No. 1. (1 January 2002), pp. 38-41.
    posted to hubbard-02 databases by CitoJam on 2008-04-26 19:23:34 as * along with 3 people incovoma kynn raylim
  • An overview of Ensembl.
    Genome Res, Vol. 14, No. 5. (May 2004), pp. 925-928.
  • Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
    Science, Vol. 316, No. 5822. (13 April 2007), pp. 222-234.
    by Rhesus, Richard A Gibbs, Jeffrey Rogers, Michael G Katze, Roger Bumgarner, George M Weinstock, Elaine R Mardis, Karin A Remington, Robert L Strausberg, Craig J Venter, Richard K Wilson, Mark A Batzer, Carlos D Bustamante, Evan E Eichler, Matthew W Hahn, Ross C Hardison, Kateryna D Makova, Webb Miller, Aleksandar Milosavljevic, Robert E Palermo, Adam Siepel, James M Sikela, Tony Attaway, Stephanie Bell, Kelly E Bernard, Christian J Buhay, Mimi N Chandrabose, Marvin Dao, Clay Davis, Kimberly D Delehaunty, Yan Ding, Huyen H Dinh, Shannon Dugan-Rocha, Lucinda A Fulton, Ramatu A Gabisi, Toni T Garner, Jennifer Godfrey, Alicia C Hawes, Judith Hernandez, Sandra Hines, Michael Holder, Jennifer Hume, Shalini N Jhangiani, Vandita Joshi, Ziad M Khan, Ewen F Kirkness, Andrew Cree, Gerald R Fowler, Sandra Lee, Lora R Lewis, Zhangwan Li, Yih-Shin Liu, Stephanie M Moore, Donna Muzny, Lynne V Nazareth, Dinh N Ngo, Geoffrey O Okwuonu, Grace Pai, David Parker, Heidie A Paul, Cynthia Pfannkoch, Craig S Pohl, Yu-Hui Rogers, San J Ruiz, Aniko Sabo, Jireh Santibanez, Brian W Schneider, Scott M Smith, Erica Sodergren, Amanda F Svatek, Teresa R Utterback, Selina Vattathil, Wesley Warren, Courtney S White, Asif T Chinwalla, Yucheng Feng, Aaron L Halpern, Ladeana W Hillier, Xiaoqiu Huang, Pat Minx, Joanne O Nelson, Kymberlie H Pepin, Xiang Qin, Granger G Sutton, Eli Venter, Brian P Walenz, John W Wallis, Kim C Worley, Shiaw-Pyng Yang, Steven M Jones, Marco A Marra, Mariano Rocchi, Jacqueline E Schein, Robert Baertsch, Laura Clarke, Miklos Csuros, Jarret Glasscock, Alan R Harris, Paul Havlak, Andrew R Jackson, Huaiyang Jiang, Yue