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neils genomics [41 articles]

Recent papers added to neils library classified by the tag genomics. You can also see everyone's genomics.
  • An online database for the detection of novel archaeal sequences in human ESTs.
    Bioinformatics (Oxford, England), Vol. 20, No. 15. (12 October 2004), pp. 2361-2362.
    by NF Saunders, PM Curmi, R Cavicchioli
    posted to pathogen genomics est database bioinformatics archaea by neils on 2008-05-11 10:26:19 as **
  • Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.
    Genome Res, Vol. 13, No. 7. (July 2003), pp. 1580-1588.
    by NF Saunders, T Thomas, PM Curmi, JS Mattick, E Kuczek, R Slade, J Davis, PD Franzmann, D Boone, K Rusterholtz, R Feldman, C Gates, S Bench, K Sowers, K Kadner, A Aerts, P Dehal, C Detter, T Glavina, S Lucas, P Richardson, F Larimer, L Hauser, M Land, R Cavicchioli
    posted to psychrophily methanogenium methanococcoides genomics bioinformatics antarctic by neils on 2008-05-11 10:24:46 as ** along with 1 person bpb
  • The minimum information about a genome sequence (MIGS) specification
    Nat Biotech, Vol. 26, No. 5. (May 2008), pp. 541-547.
    by Dawn Field, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J Allen, Samuel V Angiuoli, Michael Ashburner, Nelson Axelrod, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Peter Dawyndt, Paul De Vos, Claude Depamphilis, Robert Edwards, Nadeem Faruque, Robert Feldman, Jack Gilbert, Paul Gilna, Frank O Glockner, Philip Goldstein, Robert Guralnick, Dan Haft, David Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, Ian Joint, Leonid Kagan, Matthew Kane, Jessie Kennedy, George Kowalchuk, Renzo Kottmann, Eugene Kolker, Saul Kravitz, Nikos Kyrpides, Jim Leebens-Mack, Suzanna E Lewis, Kelvin Li, Allyson L Lister, Phillip Lord, Natalia Maltsev, Victor Markowitz, Jennifer Martiny, Barbara Methe, Ilene Mizrachi, Richard Moxon, Karen Nelson, Julian Parkhill, Lita Proctor, Owen White, Susanna-Assunta Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, David Ussery, Bob Vaughan, Naomi Ward, Trish Whetzel, Ingio San Gil, Gareth Wilson, Anil Wipat
    posted to standards sequencing information genomics bioinformatics by neils on 2008-05-09 00:35:47 as ** along with 1 person dullhunk
  • Genomics of an extreme psychrophile, Psychromonas ingrahamii
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Monica Riley, James Staley, Antoine Danchin, Tingzhang Wang, Thomas Brettin, Loren Hauser, Miriam Land, Linda Thompson
    posted to psychrophily psychromonas genomics genome bacteria by neils on 2008-05-06 15:00:02 as **
  • Vertebrate Genomes Code Excess Proteins with Charge Periodicity of 28 Residues
    J Biochem, Vol. 143, No. 5. (1 May 2008), pp. 661-665.
    by Runcong Ke, Noriyuki Sakiyama, Ryusuke Sawada, Masashi Sonoyama, Shigeki Mitaku
    posted to vertebrate sequences protein periodicity nuclear genomics charge by neils on 2008-05-06 14:13:37 as **
  • Evidence of a chimeric genome in the cyanobacterial ancestor of plastids
    BMC Evolutionary Biology, Vol. 8 (23 April 2008), 117.
    by Jeferson Gross, Jorg Meurer, Debashish Bhattacharya
    posted to plastid genomics evolution cyanobacteria chimera by neils on 2008-04-26 05:36:16 as **
  • The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
    Nature, Vol. 452, No. 7190. (24 April 2008), pp. 991-996.
    by Ray Ming, Shaobin Hou, Yun Feng, Qingyi Yu, Alexandre Dionne-Laporte, Jimmy H Saw, Pavel Senin, Wei Wang, Benjamin V Ly, Kanako L Lewis, Steven L Salzberg, Lu Feng, Meghan R Jones, Rachel L Skelton, Jan E Murray, Cuixia Chen, Wubin Qian, Junguo Shen, Peng Du, Moriah Eustice, Eric Tong, Haibao Tang, Eric Lyons, Robert E Paull, Todd P Michael, Kerr Wall, Danny W Rice, Henrik Albert, Ming-Li Wang, Yun J Zhu, Michael Schatz, Niranjan Nagarajan, Ricelle A Acob, Peizhu Guan, Andrea Blas, Ching M Wai, Christine M Ackerman, Yan Ren, Chao Liu, Jianmei Wang, Jianping Wang, Jong-Kuk Na, Eugene V Shakirov, Brian Haas, Jyothi Thimmapuram, David Nelson, Xiyin Wang, John E Bowers, Andrea R Gschwend, Arthur L Delcher, Ratnesh Singh, Jon Y Suzuki, Savarni Tripathi, Kabi Neupane, Hairong Wei, Beth Irikura, Maya Paidi, Ning Jiang, Wenli Zhang, Gernot Presting, Aaron Windsor, Rafael Navajas-Perez, Manuel J Torres, Alex F Feltus, Brad Porter, Yingjun Li, Max A Burroughs, Ming-Cheng Luo, Lei Liu, David A Christopher, Stephen M Mount, Paul H Moore, Tak Sugimura, Jiming Jiang, Mary A Schuler, Vikki Friedman, Thomas Mitchell-Olds, Dorothy E Shippen, Claude W Depamphilis, Jeffrey D Palmer, Michael Freeling, Andrew H Paterson, Dennis Gonsalves, Lei Wang, Maqsudul Alam
    posted to sequence plant papaya genomics genome by neils on 2008-04-24 00:39:40 as ** along with 2 people tanghaibao cmzmasek
  • Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
    Genome Res. (April 2008)
    by Nitin Gupta, Jamal Benhamida, Vipul Bhargava, Daniel Goodman, Elisabeth Kain, Ian Kerman, Ngan Nguyen, Noah Ollikainen, Jesse Rodriguez, Jian Wang, Mary S Lipton, Margaret Romine, Vineet Bafna, Richard D Smith, Pavel A Pevzner
    posted to comparative genomics mass proteomics spectrometry by neils on 2008-04-22 02:55:58 as ** along with 1 person brianb
  • Identification of the source of ancient remains through genomic sequencing
    Genome Res. (April 2008)
    by Matthew J Blow, Tao Zhang, Tanja Woyke, Camilla F Spelle, Andrei Krivoshapkin, Dongya Yang, Anatoly Derevianko, Edward M Rubin
    posted to dna genomics palaeontology sequencing by neils on 2008-04-22 02:53:55 as **
  • Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Wasna Viratyosin, Supawadee Ingsriswang, Eakasit Pacharawongsakda, Prasit Palittapongarnpim
    posted to bacteria bioinformatics genomics leptospira localisation membrane pathogen prediction protein scl secretion by neils on 2008-04-21 05:05:55 as ** along with 1 person sitake
  • Indicators from archaeal secretomes.
    Microbiological research (11 April 2008)
    by Mazen Saleh, Catharine Song, Sabah Nasserulla, L G G Leduc
    posted to analysis archaea bioinformatics genomics prediction secretion by neils on 2008-04-18 12:25:45 as **
  • Analysis of Aspergillus nidulans metabolism at the genome-scale
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Helga David, Ilknur Ozcelik, Gerald Hofmann, Jens Nielsen
    posted to aspergillus bioinformatics fungi genomics metabolomics orfan pathways by neils on 2008-04-11 10:07:46 as **
  • Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Shibu Yooseph, Weizhong Li, Granger Sutton
    posted to bioinformatics classification clustering genomics metagenomics microbial sequences by neils on 2008-04-11 01:50:41 as **
  • Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation
    Genome Biology, Vol. 9, No. 4. (2008)
    by Jonathan Berthon, Diego Cortez, Patrick Forterre
    posted to archaea comparative genomics replication translation by neils on 2008-04-09 12:02:55 as **
  • Molecular Signature of Hypersaline Adaptation: Insights from Genome and Proteome Composition of Halophilic Prokaryotes
    Genome Biology, Vol. 9, No. 4. (2008)
    by Sandip Paul, Sumit Bag, Sabyasachi Das, Eric Harvill, Chitra Dutta
    posted to adaptation bioinformatics comparative genomics halophile prokaryotes proteomics by neils on 2008-04-09 09:48:49 as ** along with 2 people Saby2000 rowenabrennavart
  • Large-Scale Analysis of Gene Clustering in Bacteria
    Genome Res. (2008)
    by Qingwu Yang, Sing H Sze
    posted to bacteria bioinformatics clustering genomics operon by neils on 2008-04-05 02:38:06 as **
  • Functional metagenomic profiling of nine biomes
    Nature (12 March 2008)
    by Elizabeth A Dinsdale, Robert A Edwards, Dana Hall, Florent Angly, Mya Breitbart, Jennifer M Brulc, Mike Furlan, Christelle Desnues, Matthew Haynes, Linlin Li, Lauren Mcdaniel, Mary A Moran, Karen E Nelson, Christina Nilsson, Robert Olson, John Paul, Beltran R Brito, Yijun Ruan, Brandon K Swan, Rick Stevens, David L Valentine, Rebecca V Thurber, Linda Wegley, Bryan A White, Forest Rohwer
    posted to biome genomics metagenomics profile sequencing by neils on 2008-04-04 00:55:51 as ** along with 9 people and 3 groups oelemento vaulot vrich jmeppley alexisfjdufresne bluto jyuh djkt kinestetika Papers recommended by the Roscoff Plankton Group Microbial-Ecology microbiology_nijmegen
  • Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset.
    Nucleic Acids Res (14 February 2008)
    by Jie Guo, Xiaomei Wu, Da-Yong Y Zhang, Kui Lin
    posted to dataset genomics interaction negative protein-protein quality yeast by neils on 2008-04-04 00:20:29 as ** along with 3 people tmmurali kluck stef_lise
  • An original SERPINA3 gene cluster: Elucidation of genomic organization and gene expression in the Bos taurus 21q24 region
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Patrick Pelissier, Didier Delourme, Agnes Germot, Xavier Blanchet, Samira Becila, Abderrahman Maftah, Hubert Leveziel, Ahmed Ouali, Laure Bremaud
    posted to bos-taurus cow expression genes genomics organisation serpin by neils on 2008-04-02 13:17:16 as **
  • LocateP: Genome-scale subcellular-location predictor for bacterial proteins
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Miaomiao Zhou, Jos Boekhorst, Christof Francke, Roland Siezen
    posted to bacterial bioinformatics genomics localisation prediction scl subcellular by neils on 2008-03-27 23:16:35 as **
  • PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Christine Fong, Laurence Rohmer, Matthew Radey, Michael Wasnick, Mitchell Brittnacher
    posted to bioinformatics conservation genomics neighbourhood prokaryotic synteny by neils on 2008-03-26 23:50:21 as ** along with 2 people treangen maximilianh
  • The impact of the neisserial DNA uptake sequences on genome evolution and stability
    Genome Biology, Vol. 9, No. 3. (2008)
    by Todd Treangen, Ole H Ambur, Tone Tonjum, Eduardo Rocha
    posted to dna dus evolution genomics neisseria uptake by neils on 2008-03-26 23:36:18 as ** along with 1 person treangen
  • PepLine: A Software Pipeline for High-Throughput Direct Mapping of Tandem Mass Spectrometry Data on Genomic Sequences
    J. Proteome Res. (19 March 2008)
    by Myriam Ferro, Marianne Tardif, Erwan Reguer, Romain Cahuzac, Christophe Bruley, Thierry Vermat, Estelle Nugues, Marielle Vigouroux, Yves Vandenbrouck, J&#xe9 Garin, R&#xf4, Me, Alain Viari
    posted to bioinformatics genomics mass pipeline proteomics software spectrometry by neils on 2008-03-19 13:49:21 as ** along with 1 person jyuh
  • The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Kirstin Replogle, Arthur Arnold, Gregory Ball, Mark Band, Staffan Bensch, Eliot Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia George, George Gong, Dennis Hasselquist, Alvaro Hernandez, Ryan Kim, Harris Lewin, Lei Liu, Peter Lovell, Claudio Mello, Sara Naurin, Sandra R Zas, Jyothi Thimmapuram, Juli Wade, David Clayton
    posted to annotation bioinformatics birds genome genomics zebrafinch by neils on 2008-03-19 00:15:14 as ** along with 2 people Schmidtc suizan
  • Protein production and purification.
    Nat Methods, Vol. 5, No. 2. (February 2008), pp. 135-146.
    by S Gräslund, P Nordlund, J Weigelt, J Bray, O Gileadi, S Knapp, U Oppermann, C Arrowsmith, R Hui, J Ming, S Dhe-Paganon, HW Park, A Savchenko, A Yee, A Edwards, R Vincentelli, C Cambillau, R Kim, SH Kim, Z Rao, Y Shi, TC Terwilliger, CY Kim, LW Hung, GS Waldo, Y Peleg, S Albeck, T Unger, O Dym, J Prilusky, JL Sussman, RC Stevens, SA Lesley, IA Wilson, A Joachimiak, F Collart, I Dementieva, MI Donnelly, WH Eschenfeldt, Y Kim, L Stols, R Wu, M Zhou, SK Burley, JS Emtage, JM Sauder, D Thompson, K Bain, J Luz, T Gheyi, F Zhang, S Atwell, SC Almo, JB Bonanno, A Fiser, S Swaminathan, FW Studier, MR Chance, A Sali, TB Acton, R Xiao, L Zhao, LC Ma, JF Hunt, L Tong, K Cunningham, M Inouye, S Anderson, H Janjua, R Shastry, CK Ho, D Wang, H Wang, M Jiang, GT Montelione, DI Stuart, RJ Owens, S Daenke, A Schütz, U Heinemann, S Yokoyama, K Büssow, KC Gunsalus
    posted to expression genomics proteins purification sg structure by neils on 2008-02-01 14:58:52 as ** along with 4 people hchmani Yanno jyuh dchughes
  • The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses.
    Proc Natl Acad Sci U S A, Vol. 102, No. 31. (2 August 2005), pp. 10913-10918.
    by BA Methé, KE Nelson, JW Deming, B Momen, E Melamud, X Zhang, J Moult, R Madupu, WC Nelson, RJ Dodson, LM Brinkac, SC Daugherty, AS Durkin, RT DeBoy, JF Kolonay, SA Sullivan, L Zhou, TM Davidsen, M Wu, AL Huston, M Lewis, B Weaver, JF Weidman, H Khouri, TR Utterback, TV Feldblyum, CM Fraser
    posted to colwellia for-thuber genome genomics psychrophily sequence by neils on 2008-01-25 06:53:04 as ** along with 4 people min013 bpb gilda MeganBarnett
  • Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis
    Gene, Vol. 297, No. 1-2. (4 September 2002), pp. 51-60.
    by Fredj Tekaia, Edouard Yeramian, Bernard Dujon
    posted to analysis composition correspondence evolution for-thuber genomics global proteins sequences thermophily by neils on 2008-01-25 06:51:06 as ** along with 1 person nagendranow
  • Identification of thermophilic species by the amino acid compositions deduced from their genomes.
    Nucleic Acids Res, Vol. 29, No. 7. (1 April 2001), pp. 1608-1615.
    by DP Kreil, CA Ouzounis
    posted to adaptation composition for-thuber genomics mesophily thermal thermophily by neils on 2008-01-25 06:47:54 as **
  • Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species
    PNAS, Vol. 96, No. 7. (30 March 1999), pp. 3578-3583.
    by Paul J Haney, Jonathan H Badger, Gerald L Buldak, Claudia I Reich, Carl R Woese, Gary J Olsen
    posted to adaptation for-thuber genomics hyperthermophily mesophily methanococcus methanogen thermal by neils on 2008-01-25 06:45:54 as ** along with 2 people bpb jmeppley
  • Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes.
    J Mol Evol, Vol. 44, No. 6. (June 1997), pp. 632-636.
    by N Galtier, JR Lobry
    posted to base composition dna for-thuber genomics ogt prokaryotes rna thermal by neils on 2008-01-25 06:30:02 as **
  • Structural and genomic correlates of hyperthermostability.
    J Biol Chem, Vol. 275, No. 42. (20 October 2000), pp. 32383-32386.
    by C Cambillau, JM Claverie
    posted to for-thuber genomics hyperthermophily structure thermal by neils on 2008-01-25 06:20:01 as **
  • Genomic correlates of hyperthermostability, an update.
    J Biol Chem, Vol. 278, No. 19. (9 May 2003), pp. 17198-17202.
    by K Suhre, JM Claverie
    posted to for-thuber genomics hyperthermophily protein structure by neils on 2008-01-25 06:11:08 as ** along with 1 person aalibes
  • Complete genome sequence of the myxobacterium Sorangium cellulosum
    Nature Biotechnology, Vol. 25, No. 11. (28 October 2007), pp. 1281-1289.
    by Susanne Schneiker, Olena Perlova, Olaf Kaiser, Klaus Gerth, Aysel Alici, Matthias O Altmeyer, Daniela Bartels, Thomas Bekel, Stefan Beyer, Edna Bode, Helge B Bode, Christoph J Bolten, Jomuna V Choudhuri, Sabrina Doss, Yasser A Elnakady, Bettina Frank, Lars Gaigalat, Alexander Goesmann, Carolin Groeger, Frank Gross, Lars Jelsbak, Lotte Jelsbak, Jörn Kalinowski, Carsten Kegler, Tina Knauber, Sebastian Konietzny, Maren Kopp, Lutz Krause, Daniel Krug, Bukhard Linke, Taifo Mahmud, Rosa Martinez-Arias, Alice C Mchardy, Michelle Merai, Folker Meyer, Sascha Mormann, Jose Muñoz-Dorado, Juana Perez, Silke Pradella, Shwan Rachid, Günter Raddatz, Frank Rosenau, Christian Rückert, Florenz Sasse, Maren Scharfe, Stephan C Schuster, Garret Suen, Anke Treuner-Lange, Gregory J Velicer, Frank-Jörg Vorhölter, Kira J Weissman, Roy D Welch, Silke C Wenzel, David E Whitworth, Susanne Wilhelm, Christoph Wittmann, Helmut Blöcker, Alfred Pühler, Rolf Müller
    posted to genome genomics kinases myxobacteria phosphoproteins by neils on 2008-01-06 03:03:22 as ** along with 3 people and 1 group zwang blobbybirdman kroos Myxo group
  • SMART 5: domains in the context of genomes and networks.
    Nucleic Acids Res, Vol. 34, No. Database issue. (Jan 2006), pp. D257-D260.
    by Ivica Letunic, Richard R Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork
    posted to alignment analysis article-nar article-pka-pkg article-predikin biological catalysis catalytic complexes databases domain genomics interface internet models multiprotein protein sequence structure tertiary user-computer by neils on 2007-12-04 03:22:13 as **
  • AgBase: a unified resource for functional analysis in agriculture.
    Nucleic Acids Res, Vol. 35, No. Database issue. (Jan 2007), pp. D599-D603.
    by Fiona M Mccarthy, Susan M Bridges, Nan Wang, Bryce G Magee, Paul W Williams, Dawn S Luthe, Shane C Burgess
    posted to agricultural agriculture animals crops databases domestic genetic genomics integration interface internet proteins proteomics systems user-computer article-pka-pkg by neils on 2007-12-04 01:53:38 as **
  • Classification and functional annotation of eukaryotic protein kinases.
    Proteins (7 June 2007)
    by Diego Miranda-Saavedra, Geoffrey J J Barton
    posted to annotation bioinformatics genomics kinase kinome by neils on 2007-12-02 07:26:39 as ** along with 1 person jyuh
  • Comparative kinomics of Plasmodium organisms: unity in diversity.
    Protein Pept Lett, Vol. 14, No. 6. (2007), pp. 509-517.
    by K Anamika, N Srinivasan
    posted to genomics kinase kinome plasmodium by neils on 2007-12-02 07:25:26 as **
  • The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe
    BMC Genomics, Vol. 8 (04 September 2007), 309.
    by Diego Miranda-Saavedra, Michael JR Stark, Jeremy C Packer, Christian P Vivares, Christian Doerig, Geoffrey J Barton
    posted to encephalitozoon genomics kinase kinome by neils on 2007-12-02 07:24:23 as **
  • A genomic perspective of protein kinases in Plasmodium falciparum.
    Proteins, Vol. 58, No. 1. (1 January 2005), pp. 180-189.
    by Anamika, N Srinivasan, A Krupa
    posted to genomics kinase kinome plasmodium by neils on 2007-12-02 07:22:34 as **
  • Analysis of the protein kinome of Entamoeba histolytica.
    Proteins (14 November 2007)
    by K Anamika, A Bhattacharya, N Srinivasan
    posted to entamoeba genomics kinase kinome by neils on 2007-12-02 07:21:18 as **
  • Distinguishing protein-coding and noncoding genes in the human genome
    Proceedings of the National Academy of Sciences (26 November 2007), 0709013104.
    by Michele Clamp, Ben Fry, Mike Kamal, Xiaohui Xie, James Cuff, Michael F Lin, Manolis Kellis, Kerstin Lindblad-Toh, Eric S Lander
    posted to bioinformatics genomics by neils on 2007-11-29 03:14:40 as ** along with 14 people and 3 groups tmmurali rvosa balicea sebastien_vigneau giovanni stajich cjeans cabbagezs maximilianh oelemento gjuggler slroberd renatomilani gracio EisenLab FAB-lab Berkeley Mycology
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