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stajich's Li [22 articles]

Recent papers posted to stajich's library by the author Li. You can also see everyone's Li.
  • Model-based Analysis of ChIP-Seq (MACS)
    Genome Biology, Vol. 9, No. 9. (2008)
    by Yong Zhang, Tao Liu, Clifford Meyer, Jerome Eeckhoute, David Johnson, Bradley Bernstein, Chad Nussbaum, Richard Myers, Myles Brown, Wei Li, Xiaole Liu
  • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Genome Research
    by Heng Li, J Ruan, R Durbin
  • Impact of whole genome amplification on analysis of copy number variants.
    Nucleic acids research, Vol. 36, No. 13. (August 2008)
    by TJ Pugh, AD Delaney, N Farnoud, S Flibotte, M Griffith, HI Li, H Qian, P Farinha, RD Gascoyne, MA Marra
  • Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Wei Sun, Shinsheng Yuan, Ker C Li
  • An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae.
    PLoS ONE, Vol. 2, No. 10. (2007)
    by I Lee, Z Li, EM Marcotte
  • Revisiting the Saccharomyces cerevisiae predicted ORFeome
    Genome Res. (23 May 2008), gr.076661.108.
    by Qian-Ru Li, Anne-Ruxandra Carvunis, Haiyuan Yu, Jing-Dong J Han, Quan Zhong, Nicolas Simonis, Stanley Tam, Tong Hao, Niels J Klitgord, Denis Dupuy, Danny Mou, Ilan Wapinski, Aviv Regev, David E Hill, Michael E Cusick, Marc Vidal
  • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    Genome Res. (7 February 2008), gr.7080508.
    by David S Johnson, Wei Li, Benjamin D Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S Carroll, Myles Brown, Paul Flicek, Christopher M Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J Farnham, Philipp Kapranov, David A Nix, Thomas R Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland Green, Jun S Song, Scott A Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M Myers, Jason D Lieb, Shirley X Liu
  • A nuclear receptor-like pathway regulating multidrug resistance in fungi
    Nature, Vol. 452, No. 7187., pp. 604-609.
    by Jitendra K Thakur, Haribabu Arthanari, Fajun Yang, Shih-Jung Pan, Xiaochun Fan, Julia Breger, Dominique P Frueh, Kailash Gulshan, Darrick K Li, Eleftherios Mylonakis, Kevin Struhl, Scott W Moye-Rowley, Brendan P Cormack, Gerhard Wagner, Anders M Näär
  • The Evolution of Combinatorial Gene Regulation in Fungi
    PLoS Biology, Vol. 6, No. 2. (1 February 2008), e38.
    by Brian B Tuch, David J Galgoczy, Aaron D Hernday, Hao Li, Alexander D Johnson
  • Intergeneric transfer of ribosomal genes between two fungi
    BMC Evolutionary Biology, Vol. 8 (18 March 2008), 87.
    by Jiatao Xie, Yanping Fu, Daohong Jiang, Guoqing Li, Junbin Huang, Bo Li, Tom Hsiang, Youliang Peng
  • 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,
  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
    Nature, Vol. 428, No. 6982. (1 April 2004), pp. 493-521.
    by RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, S Scherer, G Scott, D Steffen, KC Worley, PE Burch, G Okwuonu, S Hines, L Lewis, C DeRamo, O Delgado, S Dugan-Rocha, G Miner, M Morgan, A Hawes, R Gill, Celera, RA Holt, MD Adams, PG Amanatides, H Baden-Tillson, M Barnstead, S Chin, CA Evans, S Ferriera, C Fosler, A Glodek, Z Gu, D Jennings, CL Kraft, T Nguyen, CM Pfannkoch, C Sitter, GG Sutton, JC Venter, T Woodage, D Smith, HM Lee, E Gustafson, P Cahill, A Kana, L Doucette-Stamm, K Weinstock, K Fechtel, RB Weiss, DM Dunn, ED Green, RW Blakesley, GG Bouffard, PJ De Jong, K Osoegawa, B Zhu, M Marra, J Schein, I Bosdet, C Fjell, S Jones, M Krzywinski, C Mathewson, A Siddiqui, N Wye, J McPherson, S Zhao, CM Fraser, J Shetty, S Shatsman, K Geer, Y Chen, S Abramzon, WC Nierman, PH Havlak, R Chen, KJ Durbin, A Egan, Y Ren, XZ Song, B Li, Y Liu, X Qin, S Cawley, KC Worley, AJ Cooney, LM D'Souza, K Martin, JQ Wu, ML Gonzalez-Garay, AR Jackson, KJ Kalafus, MP McLeod, A Milosavljevic, D Virk, A Volkov, DA Wheeler, Z Zhang, JA Bailey, EE Eichler, E Tuzun, E Birney, E Mongin, A Ureta-Vidal, C Woodwark, E Zdobnov, P Bork, M Suyama, D Torrents, M Alexandersson, BJ Trask, JM Young, H Huang, H Wang, H Xing, S Daniels, D Gietzen, J Schmidt, K Stevens, U Vitt, J Wingrove, F Camara, M Mar Albà, JF Abril, R Guigo, A Smit, I Dubchak, EM Rubin, O Couronne, A Poliakov, N Hübner, D Ganten, C Goesele, O Hummel, T Kreitler, YA Lee, J Monti, H Schulz, H Zimdahl, H Himmelbauer, H Lehrach, HJ Jacob, S Bromberg, J Gullings-Handley, MI Jensen-Seaman, AE Kwitek, J Lazar, D Pasko, PJ Tonellato, S Twigger, CP Ponting, JM Duarte, S Rice, L Goodstadt, SA Beatson, RD Emes, EE Winter, C Webber, P Brandt, G Nyakatura, M Adetobi, F Chiaromonte, L Elnitski, P Eswara, RC Hardison, M Hou, D Kolbe, K Makova, W Miller, A Nekrutenko, C Riemer, S Schwartz, J Taylor, S Yang, Y Zhang, K Lindpaintner, TD Andrews, M Caccamo, M Clamp, L Clarke, V Curwen, R Durbin, E Eyras, SM Searle, GM Cooper, S Batzoglou, M Brudno, A Sidow, EA Stone, JC Venter, BA Payseur, G Bourque, C López-Otín, XS Puente, K Chakrabarti, S Chatterji, C Dewey, L Pachter, N Bray, VB Yap, A Caspi, G Tesler, PA Pevzner, D Haussler, KM Roskin, R Baertsch, H Clawson, TS Furey, AS Hinrichs, D Karolchik, WJ Kent, KR Rosenbloom, H Trumbower, M Weirauch, DN Cooper, PD Stenson, B Ma, M Brent, M Arumugam, D Shteynberg, RR Copley, MS Taylor, H Riethman, U Mudunuri, J Peterson, M Guyer, A Felsenfeld, S Old, S Mockrin, F Collins,
  • 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 Liu, David N Messina, Yufeng Shen, Henry X Song, Todd Wylie, Lan Zhang, Ewan Birney, Kyudong Han, Miriam K Konkel, Jungnam Lee, Arian F Smit, Brygg Ullmer, Hui Wang, Jinchuan Xing, Richard Burhans, Ze Cheng, John E Karro, Jian Ma, Brian Raney, Xinwei She, Michael J Cox, Jeffery P Demuth, Laura J Dumas, Sang-Gook Han, Janet Hopkins, Anis Karimpour-Fard, Young H Kim, Jonathan R Pollack, Tomas Vinar, Charles Addo-Quaye, Jeremiah Degenhardt, Alexandra Denby, Melissa J Hubisz, Amit Indap, Carolin Kosiol, Bruce T Lahn, Heather A Lawson, Alison Marklein, Rasmus Nielsen, Eric J Vallender, Andrew G Clark, Betsy Ferguson, Ryan D Hernandez, Kashif Hirani, Hildegard Kehrer-Sawatzki, Jessica Kolb, Shobha Patil, Ling-Ling Pu, Yanru Ren, David G Smith, David A Wheeler, Ian Schenck, Edward V Ball, Rui Chen, David N Cooper, Belinda Giardine, Fan Hsu, James W Kent, Arthur Lesk, David L Nelson, William E O'Brien, Kay Prufer, Peter D Stenson, James C Wallace, Hui Ke, Xiao-Ming Liu, Peng Wang, Andy P Xiang, Fan Yang, Galt P Barber, David Haussler, Donna Karolchik, Andy D Kern, Robert M Kuhn, Kayla E Smith, Ann S Zwieg
  • Genome Sequence of Aedes aegypti, a Major Arbovirus Vector.
    Science (17 May 2007)
    by Vishvanath Nene, Jennifer R R Wortman, Daniel Lawson, Brian Haas, Chinnappa Kodira, Zhijian Jake J Tu, Brendan Loftus, Zhijong Xi, Karyn Megy, Manfred Grabherr, Quinghu Ren, Evgeny M M Zdobnov, Neil F F Lobo, Kathryn S S Campbell, Susan E E Brown, Maria F F Bonaldo, Jingsong Zhu, Steven P P Sinkins, David G G Hogenkamp, Paulo Amedo, Peter Arsenburger, Peter W W Atkinson, Shelby Bidwell, Jim Biedler, Ewan Birney, Robert V V Bruggner, Javier Costas, Monique R R Coy, Jonathan Crabtree, Matt Crawford, Becky Debruyn, David Decaprio, Karin Eiglmeier, Eric Eisenstadt, Hamza El-Dorry, William M M Gelbart, Suely L L Gomes, Martin Hammond, Linda I I Hannick, James R R Hogan, Michael H H Holmes, David Jaffe, Spencer J J Johnston, Ryan C C Kennedy, Hean Koo, Saul Kravitz, Evgenia V V Kriventseva, David Kulp, Kurt Labutti, Edward Lee, Song Li, Diane D D Lovin, Chunhong Mao, Evan Mauceli, Carlos F M F Menck, Jason R R Miller, Philip Montgomery, Akio Mori, Ana L L Nascimento, Horacio F F Naveira, Chad Nusbaum, Sinéad B B O'leary, Joshua Orvis, Mihaela Pertea, Hadi Quesneville, Kyanne R R Reidenbach, Yu-Hui H Rogers, Charles W W Roth, Jennifer R R Schneider, Michael Schatz, Martin Shumway, Mario Stanke, Eric O O Stinson, Jose M C M Tubio, Janice P P Vanzee, Sergio Verjovski-Almeida, Doreen Werner, Owen White, Stefan Wyder, Qi Zeng, Qi Zhao, Yongmei Zhao, Catherine A A Hill, Alexander S S Raikhel, Marcelo B B Soares, Dennis L L Knudson, Norman H H Lee, James Galagan, Steven L L Salzberg, Ian T T Paulsen, George Dimopoulos, Frank H H Collins, Birren Bruce, Claire M M Fraser-Liggett, David W W Severson
  • The genome sequence of the rice blast fungus Magnaporthe grisea
    Nature, Vol. 434, No. 7036., pp. 980-986.
    by Ralph A Dean, Nicholas J Talbot, Daniel J Ebbole, Mark L Farman, Thomas K Mitchell, Marc J Orbach, Michael Thon, Resham Kulkarni, Jin-Rong Xu, Huaqin Pan, Nick D Read, Yong-Hwan Lee, Ignazio Carbone, Doug Brown, Yeon Y Oh, Nicole Donofrio, Jun S Jeong, Darren M Soanes, Slavica Djonovic, Elena Kolomiets, Cathryn Rehmeyer, Weixi Li, Michael Harding, Soonok Kim, Marc-Henri Lebrun, Heidi Bohnert, Sean Coughlan, Jonathan Butler, Sarah Calvo, Li-Jun Ma, Robert Nicol, Seth Purcell, Chad Nusbaum, James E Galagan, Bruce W Birren
  • The genome sequence of the filamentous fungus Neurospora crassa.
    Nature, Vol. 422, No. 6934. (24 April 2003), pp. 859-868.
  • Heterotrimeric G Protein Signaling in Filamentous Fungi.
    Annu Rev Microbiol (16 August 2006)
    by Liande Li, Sara J J Wright, Svetlana Krystofova, Gyungsoon Park, Katherine Borkovich
  • Targeted discovery of novel human exons by comparative genomics
    Genome Res. (7 November 2007), gr.7128207.
    by Adam Siepel, Mark Diekhans, Brona Brejova, Laura Langton, Michael Stevens, Charles L Comstock, Colleen Davis, Brent Ewing, Shelly Oommen, Christopher Lau, Hung-Chun Yu, Jianfeng Li, Bruce A Roe, Phil Green, Daniela S Gerhard, Gary Temple, David Haussler, Michael R Brent
  • The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
    PLoS Biology, Vol. 5, No. 3. (1 March 2007), e77.
    by Douglas B Rusch, Aaron L Halpern, Granger Sutton, Karla B Heidelberg, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A Eisen, Jeff M Hoffman, Karin Remington, Karen Beeson, Bao Tran, Hamilton Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freeman, Cynthia Andrews-Pfannkoch, Joseph E Venter, Kelvin Li, Saul Kravitz, John F Heidelberg, Terry Utterback, Yu-Hui Rogers, Luisa I Falcón, Valeria Souza, Germán Bonilla-Rosso, Luis E Eguiarte, David M Karl, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Victor Gallardo, Giselle Tamayo-Castillo, Michael R Ferrari, Robert L Strausberg, Kenneth Nealson, Robert Friedman, Marvin Frazier, Craig J Venter
  • A surprisingly large RNase P RNA in Candida glabrata
    RNA, Vol. 11, No. 7. (1 July 2005), pp. 1064-1072.
    by Rym Kachouri, Vilius Stribinskis, Yanglong Zhu, Kenneth S Ramos, Eric Westhof, Yong Li
    posted to rna_gene yeast by stajich on 2007-03-05 07:32:03 as **
  • Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods
    BMC Genomics, Vol. 7 (08 December 2006), 310.
    by Malali Gowda, Rc Venu, Mohan B Raghupathy, Kan Nobuta, Huameng Li, Eric Stahlberg, Rod Wing, Sean Coughlan, Christian D Haudenschild, Ralph Dean, Baek H Nahm, Blake C Meyers, Guo-Liang Wang
    posted to microarray magnaporthe gene_expression by stajich on 2007-02-07 01:40:20 as **
  • Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
    Nature, Vol. 444, No. 7115., pp. 97-101.
    by Jörg Kämper, Regine Kahmann, Michael Bölker, Li-Jun Ma, Thomas Brefort, Barry J Saville, Flora Banuett, James W Kronstad, Scott E Gold, Olaf Müller, Michael H Perlin, Han AB Wösten, Ronald de Vries, José Ruiz-Herrera, Cristina G Reynaga-Peña, Karen Snetselaar, Michael Mccann, José Pérez-Martín, Michael Feldbrügge, Christoph W Basse, Gero Steinberg, Jose I Ibeas, William Holloman, Plinio Guzman, Mark Farman, Jason E Stajich, Rafael Sentandreu, Juan M González-Prieto, John C Kennell, Lazaro Molina, Jan Schirawski, Artemio Mendoza-Mendoza, Doris Greilinger, Karin Münch, Nicole Rössel, Mario Scherer, Miroslav Vraneš, Oliver Ladendorf, Volker Vincon, Uta Fuchs, Björn Sandrock, Shaowu Meng, Eric CH Ho, Matt J Cahill, Kylie J Boyce, Jana Klose, Steven J Klosterman, Heine J Deelstra, Lucila Ortiz-Castellanos, Weixi Li, Patricia Sanchez-Alonso, Peter H Schreier, Isolde Häuser-Hahn, Martin Vaupel, Edda Koopmann, Gabi Friedrich, Hartmut Voss, Thomas Schlüter, Jonathan Margolis, Darren Platt, Candace Swimmer, Andreas Gnirke, Feng Chen, Valentina Vysotskaia, Gertrud Mannhaupt, Ulrich Güldener, Martin Münsterkötter, Dirk Haase, Matthias Oesterheld, Hans-Werner Mewes, Evan W Mauceli, David Decaprio, Claire M Wade, Jonathan Butler, Sarah Young, David B Jaffe, Sarah Calvo, Chad Nusbaum, James Galagan, Bruce W Birren
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