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neils sequence [42 articles]

Recent papers added to neils library classified by the tag sequence. You can also see everyone's sequence.
  • The cytochromes c-550 of Paracoccus denitrificans and Thiosphaera pantotropha: a need for re-evaluation of the history of Paracoccus cultures
    FEMS Microbiology Letters, Vol. 137, No. 1. (1996), pp. 95-101.
    by Celia F Goodhew, Graham W Pettigrew, Bart Devreese, Jozef Beeumen, Rob J Spanning, Simon C Baker, Neil Saunders, Stuart J Ferguson, Ian P Thompson
    posted to sequence paracoccus cytochrome analysis by neils on 2008-05-11 10:37:08 as **
  • Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution.
    Journal of molecular evolution, Vol. 59, No. 4. (October 2004), pp. 437-447.
    posted to serpin sequence evolution bioinformatics analysis by neils on 2008-05-11 10:11:58 as **
  • Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Steven Salzberg, Daniel Sommer, Michael Schatz, Adam Phillippy, Pablo Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna, Gopaljee Jha, Alok Pandey, Prabhu Patil, Hiromichi Ishihara, Damien Meyer, Boris Szurek, Valerie Verdier, Ralf Koebnik, Maxwell J Dow, Robert Ryan, Hisae Hirata, Shinji Tsuyumu, Sang W Lee, Pamela Ronald, Ramesh Sonti, Marie A Van Sluys, Jan Leach, Frank White, Adam Bogdanove
    posted to xanthomonas sequence rice pathogen genome evolution by neils on 2008-05-02 00:28:46 as **
  • SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Lukasz Kurgan, Krzysztof Cios, Ke Chen
    posted to structure sequence protein prediction bioinformatics by neils on 2008-05-02 00:27:57 as **
  • Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3635-3641.
    by JC Obenauer, LC Cantley, MB Yaffe
  • 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
  • ROC analysis: applications to the classification of biological sequences and 3D structures
    Brief Bioinform (11 January 2008), bbm064.
    by Paolo Sonego, Andras Kocsor, Sandor Pongor
  • Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis
    Genome Res. (2008)
    by Timothy P Stinear, Torsten Seemann, Paul F Harrison, Grant A Jenkin, John K Davies, Paul, Zahra Abdellah, Claire Arrowsmith, Tracey Chillingworth, Carol Churcher, Kay Clarke, Ann Cronin, Paul Davis, Ian Goodhead, Nancy Holroyd, Kay Jagels, Angela Lord, Sharon Moule, Karen Mungall, Halina Norbertczak, Michael A Quail, Ester Rabbinowitsch, Danielle Walker, Brian White, Sally Whitehead, Pamela, Roland Brosch, Lalita Ramakrishnan, Michael A Fischbach, Julian Parkhill, Stewart T Cole
    posted to genome marine mycobacterium pathogen sequence by neils on 2008-04-11 03:56:37 as **
  • Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches
    Bioinformatics (2008)
    by Marianne M Lee, Michael K Chan, Ralf Bundschuh
    posted to analysis bioinformatics psi-blast sequence statistics by neils on 2008-04-11 01:32:11 as **
  • Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses
    PLoS Comput Biol, Vol. 4, No. 3. (Mar 2008)
    by Feng J Sun, Gustavo C Anollés
    posted to archaea bioinformatics evolution phylogeny sequence structure trna viruses by neils on 2008-03-12 02:45:33 as **
  • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
    Nature, Vol. 452, No. 7183. (6 March 2008), pp. 88-92.
  • 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
  • Protein kinase specificity. A strategic collaboration between kinase peptide specificity and substrate recruitment.
    Cell Cycle, Vol. 4, No. 1. (Jan 2005), pp. 52-56.
    by Guozhi Zhu, Yin Liu, Stephen Shaw
  • GPS: a comprehensive www server for phosphorylation sites prediction.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (Jul 2005), pp. W184-W187.
    by Yu Xue, Fengfeng Zhou, Minjie Zhu, Kashif Ahmed, Guoliang Chen, Xuebiao Yao
  • PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory.
    BMC Bioinformatics, Vol. 7 (2006)
    by Yu Xue, Ao Li, Lirong Wang, Huanqing Feng, Xuebiao Yao
  • Centrosomal anchoring of the protein kinase CK1delta mediated by attachment to the large, coiled-coil scaffolding protein CG-NAP/AKAP450.
    J Mol Biol, Vol. 322, No. 4. (Sep 2002), pp. 785-797.
    by James E Sillibourne, Diane M Milne, Mikiko Takahashi, Yoshitaka Ono, David W Meek
  • Phosphorylation of p90 ribosomal S6 kinase (RSK) regulates extracellular signal-regulated kinase docking and RSK activity.
    Mol Cell Biol, Vol. 23, No. 14. (Jul 2003), pp. 4796-4804.
    by Philippe P Roux, Stephanie A Richards, John Blenis
  • A dimeric kinase assembly underlying autophosphorylation in the p21 activated kinases.
    J Mol Biol, Vol. 361, No. 2. (Aug 2006), pp. 312-326.
    by Michelle Pirruccello, Holger Sondermann, Jeffrey G Pelton, Patricia Pellicena, André Hoelz, Jonathan Chernoff, David E Wemmer, John Kuriyan
  • How do protein kinases recognize their substrates?
    Biochim Biophys Acta, Vol. 1314, No. 3. (Dec 1996), pp. 191-225.
    by LA Pinna, M Ruzzene
  • Identification of residues which regulate activity of the STE20-related kinase hMINK.
    Biochem Biophys Res Commun, Vol. 300, No. 3. (Jan 2003), pp. 694-698.
    by Jaeseung Lim, Andrew Lennard, Paul W Sheppard, Stuart Kellie
  • 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
  • The active conformation of the PAK1 kinase domain.
    Structure, Vol. 13, No. 5. (May 2005), pp. 769-778.
    by Ming Lei, Michael A Robinson, Stephen C Harrison
  • Structural modes of stabilization of permissive phosphorylation sites in protein kinases: distinct strategies in Ser/Thr and Tyr kinases.
    J Mol Biol, Vol. 339, No. 5. (Jun 2004), pp. 1025-1039.
  • Abscisic acid-activated SNRK2 protein kinases function in the gene-regulation pathway of ABA signal transduction by phosphorylating ABA response element-binding factors.
    Plant J, Vol. 44, No. 6. (Dec 2005), pp. 939-949.
    by Yuhko Kobayashi, Michiharu Murata, Hideyuki Minami, Shuhei Yamamoto, Yasuaki Kagaya, Tokunori Hobo, Akiko Yamamoto, Tsukaho Hattori
  • Prediction of phosphorylation sites using SVMs.
    Bioinformatics, Vol. 20, No. 17. (Nov 2004), pp. 3179-3184.
    by Jong H Kim, Juyoung Lee, Bermseok Oh, Kuchan Kimm, Insong Koh
  • Biochemical characterization of the tobacco 42-kD protein kinase activated by osmotic stress.
    Plant Physiol, Vol. 136, No. 2. (Oct 2004), pp. 3255-3265.
    by Anna Kelner, Izabela Pekala, Szymon Kaczanowski, Grazyna Muszynska, Grahame D Hardie, Grazyna Dobrowolska
  • C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats.
    J Biol Chem, Vol. 279, No. 24. (Jun 2004), pp. 24957-24964.
    by Janice C Jones, Hemali P Phatnani, Timothy A Haystead, Justin A Macdonald, Munir S Alam, Arno L Greenleaf
  • KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (Jul 2005), pp. W226-W229.
    by Hsien Da Huang, Tzong Y Lee, Shih W Tzeng, Jorng T Horng
  • Amino acid substitution matrices from protein blocks.
    Proc Natl Acad Sci U S A, Vol. 89, No. 22. (Nov 1992), pp. 10915-10919.
  • BRSK2 is activated by cyclic AMP-dependent protein kinase A through phosphorylation at Thr260.
    Biochem Biophys Res Commun, Vol. 347, No. 4. (Sep 2006), pp. 867-871.
    by Zekun Guo, Wenwen Tang, Jian Yuan, Xinya Chen, Bo Wan, Xiuting Gu, Kuntian Luo, Yingli Wang, Long Yu
  • Characterization of cyclin L2, a novel cyclin with an arginine/serine-rich domain: phosphorylation by DYRK1A and colocalization with splicing factors.
    J Biol Chem, Vol. 279, No. 6. (Feb 2004), pp. 4612-4624.
    by Katrin de Graaf, Paul Hekerman, Oliver Spelten, Andreas Herrmann, Len C Packman, Konrad Büssow, Gerhard M Newen, Walter Becker
  • Pfam: clans, web tools and services.
    Nucleic Acids Res, Vol. 34, No. Database issue. (Jan 2006), pp. D247-D251.
    by Robert D Finn, Jaina Mistry, Benjamin S Böckler, Sam G Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R Eddy, Erik LL Sonnhammer, Alex Bateman
  • Profile hidden Markov models.
    Bioinformatics, Vol. 14, No. 9. (1998), pp. 755-763.
    by SR Eddy
  • ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (Jul 2006), pp. W362-W365.
    by Edouard de Castro, Christian JA Sigrist, Alexandre Gattiker, Virginie Bulliard, Petra, Elisabeth Gasteiger, Amos Bairoch, Nicolas Hulo
  • A kinase sequence database: sequence alignments and family assignment.
    Bioinformatics, Vol. 18, No. 9. (Sep 2002), pp. 1274-1275.
    by Oleksandr Buzko, Kevan M Shokat
  • Protein kinases associated with the yeast phosphoproteome.
    BMC Bioinformatics, Vol. 7 (2006)
    by Ross I Brinkworth, Alan L Munn, Bostjan Kobe
  • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.
    J Mol Biol, Vol. 294, No. 5. (Dec 1999), pp. 1351-1362.
  • Scoring of predicted GRK2 phosphorylation sites in Nedd4-2.
    Bioinformatics, Vol. 22, No. 18. (Sep 2006), pp. 2192-2195.
    by Jonathan W Arthur, Angeles S Perez, David I Cook
  • The protein kinase complement of the human genome.
    Science, Vol. 298, No. 5600. (Dec 2002), pp. 1912-1934.
  • The importance of intrinsic disorder for protein phosphorylation.
    Nucleic Acids Res, Vol. 32, No. 3. (2004), pp. 1037-1049.
    by Lilia M Iakoucheva, Predrag Radivojac, Celeste J Brown, Timothy R O'Connor, Jason G Sikes, Zoran Obradovic, Keith A Dunker
  • The Gene Ontology (GO) project in 2006.
    Nucleic Acids Res, Vol. 34, No. Database issue. (Jan 2006), pp. D322-D326.
    by gene O Consortium
  • Proteomic and computational analysis of secreted proteins with type I signal peptides from the Antarctic archaeon Methanococcoides burtonii.
    J Proteome Res, Vol. 5, No. 9. (Sep 2006), pp. 2457-2464.
    by Neil FW Saunders, Charmaine Ng, Mark Raftery, Michael Guilhaus, Amber Goodchild, Ricardo Cavicchioli
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