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neils's library [336 articles]

Recent papers added to neils's library.
  • 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 **
  • 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 **
  • Pathogenic archaea: do they exist?
    BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 25, No. 11. (November 2003), pp. 1119-1128.
    by R Cavicchioli, PM Curmi, N Saunders, T Thomas
    posted to review pathogen archaea by neils on 2008-05-11 10:25:26 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 NosX and NirX proteins of Paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase.
    Journal of bacteriology, Vol. 182, No. 18. (September 2000), pp. 5211-5217.
    by NF Saunders, JJ Hornberg, WN Reijnders, HV Westerhoff, S de Vries, RJ van Spanning
    posted to reductase paracoccus oxide nosx nitrous nirx maturation enzyme by neils on 2008-05-11 10:24:14 as **
  • Transcriptional analysis of the nirS gene, encoding cytochrome cd1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63.
    Microbiology (Reading, England), Vol. 146 ( Pt 2) (February 2000), pp. 509-516.
    by NF Saunders, SJ Ferguson, SC Baker
    posted to transcription reductase paracoccus nitrite nirs cytochrome by neils on 2008-05-11 10:23:18 as **
  • Transcription regulation of the nir gene cluster encoding nitrite reductase of Paracoccus denitrificans involves NNR and NirI, a novel type of membrane protein.
    Molecular microbiology, Vol. 34, No. 1. (October 1999), pp. 24-36.
    by NF Saunders, EN Houben, S Koefoed, S de Weert, WN Reijnders, HV Westerhoff, AP De Boer, RJ Van Spanning
    posted to transcription regulation reductase paracoccus nnr nitrite nir by neils on 2008-05-11 10:21:36 as **
  • Nitric oxide is a signal for NNR-mediated transcription activation in Paracoccus denitrificans.
    Journal of bacteriology, Vol. 181, No. 13. (July 1999), pp. 4129-4132.
    by RJ Van Spanning, E Houben, WN Reijnders, S Spiro, HV Westerhoff, N Saunders
    posted to transcription regulation paracoccus oxide nnr nitric by neils on 2008-05-11 10:20:52 as **
  • Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds.
    Journal of molecular biology, Vol. 269, No. 3. (13 June 1997), pp. 440-455.
    by SC Baker, NF Saunders, AC Willis, SJ Ferguson, J Hajdu, V Fülöp
    posted to structure reductase protein nitrite haem cytochrome beta-propeller by neils on 2008-05-11 10:19:58 as **
  • Structural characterization of Paracoccus denitrificans cytochrome c peroxidase and assignment of the low and high potential heme sites.
    Biochemistry, Vol. 36, No. 26. (1 July 1997), pp. 7958-7966.
    by W Hu, G Van Driessche, B Devreese, CF Goodhew, DF McGinnity, N Saunders, V Fulop, GW Pettigrew, JJ Van Beeumen
    posted to potential peroxidase paracoccus haem cytochrome calcium by neils on 2008-05-11 10:19:23 as **
  • Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme.
    Nature, Vol. 389, No. 6649. (25 September 1997), pp. 406-412.
    by PA Williams, V Fülöp, EF Garman, NF Saunders, SJ Ferguson, J Hajdu
    posted to structure reductase protein nitrite mechanism haem crystallography by neils on 2008-05-11 10:18:50 as **
  • Disruption of the Pseudomonas aeruginosa dipZ gene, encoding a putative protein-disulfide reductase, leads to partial pleiotropic deficiency in c-type cytochrome biogenesis.
    Microbiology (Reading, England), Vol. 143 ( Pt 10) (October 1997), pp. 3111-3122.
    by MD Page, NF Saunders, SJ Ferguson
    posted to pseudomonas disulphide dipz cytochrome biogenesis by neils on 2008-05-11 10:17:57 as **
  • A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii.
    Molecular microbiology, Vol. 53, No. 1. (July 2004), pp. 309-321.
    by A Goodchild, NF Saunders, H Ertan, M Raftery, M Guilhaus, PM Curmi, R Cavicchioli
    posted to psychrophily proteomics methanococcoides archaea antarctic by neils on 2008-05-11 10:12:36 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.
    by TH Roberts, J Hejgaard, NF Saunders, R Cavicchioli, PM Curmi
    posted to serpin sequence evolution bioinformatics analysis by neils on 2008-05-11 10:11:58 as **
  • Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry.
    Journal of proteome research, Vol. 3, No. 6. (c 2004), pp. 1164-1176.
    by A Goodchild, M Raftery, NF Saunders, M Guilhaus, R Cavicchioli
    posted to spectrometry psychrophily proteomics methanococcoides mass chromatography archaea antarctic by neils on 2008-05-11 10:11:12 as **
  • Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii.
    Journal of proteome research, Vol. 4, No. 2. (r 2005), pp. 464-472.
    by NF Saunders, A Goodchild, M Raftery, M Guilhaus, PM Curmi, R Cavicchioli
    posted to psychrophily proteins prediction methanococcoides function bioinformatics archaea antarctic by neils on 2008-05-11 10:09:25 as **
  • Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT.
    Journal of proteome research, Vol. 4, No. 2. (r 2005), pp. 473-480.
    by A Goodchild, M Raftery, NF Saunders, M Guilhaus, R Cavicchioli
    posted to psychrophily proteomics methanococcoides icat archaea antarctic by neils on 2008-05-11 10:08:25 as **
  • Improved success of sparse matrix protein crystallization screening with heterogeneous nucleating agents.
    PLoS ONE, Vol. 2, No. 10. (2007)
    by AS Thakur, G Robin, G Guncar, NF Saunders, J Newman, JL Martin, B Kobe
    posted to screening protein nucleation crystallography by neils on 2008-05-11 10:06:39 as **
  • Fibroblast growth factor receptor 2 phosphorylation on serine 779 couples to 14-3-3 and regulates cell survival and proliferation.
    Molecular and cellular biology, Vol. 28, No. 10. (May 2008), pp. 3372-3385.
    by A Lonic, EF Barry, C Quach, B Kobe, N Saunders, MA Guthridge
    posted to phosphorylation fibroblast fgfr 14-3-3 by neils on 2008-05-11 10:06:01 as **
  • notes Computational evidence for the catalytic mechanism of glutaminyl cyclase. A DFT investigation
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Matteo Calvaresi, Marco Garavelli, Andrea Bottoni
    posted to structure protein dft computational catalysis by neils on 2008-05-10 09:12:23 as **
  • Kemp elimination catalysts by computational enzyme design
    Nature (19 March 2008)
    by Daniela Röthlisberger, Olga Khersonsky, Andrew M Wollacott, Lin Jiang, Jason Dechancie, Jamie Betker, Jasmine L Gallaher, Eric A Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N Houk, Dan S Tawfik, David Baker
    posted to enzyme design computational catalysis by neils on 2008-05-10 03:10:52 as ** along with 3 people cactus jwm msuarezdiez
  • Discovering sequence motifs with arbitrary insertions and deletions.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by MC Frith, NF Saunders, B Kobe, TL Bailey
    posted to sequences motifs discovery bioinformatics by neils on 2008-05-09 13:29:46 as ** along with 1 person cabbagesofdoom
  • Fast protein tertiary structure retrieval based on global surface shape similarity
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (xx 2008)
    by Lee Sael, Bin Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov, Daisuke Kihara
    posted to structure retrieval protein prediction bioinformatics by neils on 2008-05-09 10:19:56 as **
  • Protein Disorder Is Positively Correlated with Gene Expression in Escherichia coli
    J. Proteome Res. (9 May 2008)
    by Oleg Paliy, Shawn M Gargac, Yugong Cheng, Vladimir N Uversky, Keith A Dunker
    posted to structure protein expression ecoli disorder by neils on 2008-05-09 07:51:04 as **
  • Identification and Characterization of Sulfolobus solfataricus P2 Proteome Using Multidimensional Liquid Phase Protein Separations
    J. Proteome Res. (9 May 2008)
    by Bobby F Assiddiq, Ambrosius P Snijders, Poh K Chong, Phillip C Wright, Mark Dickman
    posted to sulfolobus spectrometry proteomics mass chromatography archaea by neils on 2008-05-09 07:49:31 as **
  • Crystal Structure of the FK506 Binding Domain of Plasmodium falciparum FKBP35 in Complex with FK506
    Biochemistry (9 May 2008)
    by Masayo Kotaka, Hong Ye, Reema Alag, Guangan Hu, Zbynek Bozdech, Peter R Preiser, Ho S Yoon, Julien Lescar
    posted to structure plasmodium ligand fkbp crystallography complexes by neils on 2008-05-09 06:57:49 as ** along with 1 person becarmson
  • 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 **
  • Phosphorylation of Retinoblastoma Protein by Viral Protein with Cyclin-Dependent Kinase Function
    Science, Vol. 320, No. 5877. (9 May 2008), pp. 797-799.
    by Adam J Hume, Jonathan S Finkel, Jeremy P Kamil, Donald M Coen, Michael R Culbertson, Robert F Kalejta
    posted to virus retinoblastoma phosphorylation kinase cyclin-dependent by neils on 2008-05-09 00:33:27 as ** along with 3 people Petersarkies mclarenv biomcgary
  • The Paradoxical Platypus
    BioScience, Vol. 49, No. 3. (1999), pp. 211-218.
    by Brian K Hall
    posted to platypus history ecology australia by neils on 2008-05-08 08:29:06 as **
  • Genome analysis of the platypus reveals unique signatures of evolution
    Nature, Vol. 453, No. 7192. (May 2008), pp. 175-183.
    posted to platypus genome evolution bioinformatics by neils on 2008-05-08 00:43:58 as ** along with 7 people hpaces lp2 natstreet ealloza cabbagesofdoom gjuggler fhsantanna
  • From the Cover: Extreme polyploidy in a large bacterium
    Proceedings of the National Academy of Sciences, Vol. 105, No. 18. (6 May 2008), pp. 6730-6734.
    by Jennifer E Mendell, Kendall D Clements, Howard J Choat, Esther R Angert
    posted to symbiosis polyploidy genome epulopiscium bacteria by neils on 2008-05-08 00:43:00 as **
  • The Leucine-Rich Repeat Domain of Internalin B Folds along a Polarized N-Terminal Pathway
    Structure, Vol. 16 (May 2008), pp. 705-714.
    by Naomi Courtemanche, Doug Barrick
    posted to repeat proteins protein pathway lrr leucine folding by neils on 2008-05-07 02:37:18 as **
  • Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis
    Mol Syst Biol, Vol. 4 (6 May 2008)
    by Naoyuki Sugiyama, Hirofumi Nakagami, Keiichi Mochida, Arsalan Daudi, Masaru Tomita, Ken Shirasu, Yasushi Ishihama
    posted to tyrosine spectrometry proteomics phosphorylation mass arabidopsis by neils on 2008-05-06 23:39:40 as ** along with 1 person zwang
  • 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 **
  • Structural Evidence for Direct Interactions between the BRCT Domains of Human BRCA1 and a Phospho-peptide from Human ACC1
    Biochemistry (2 May 2008)
    by Yang Shen, Liang Tong
    posted to no-tag by neils on 2008-05-02 07:56:46 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 **
  • Structural analysis of the essential self-cleaving type III secretion proteins EscU and SpaS
    Nature, Vol. 453, No. 7191., pp. 124-127.
    by Raz Zarivach, Wanyin Deng, Marija Vuckovic, Heather B Felise, Hai V Nguyen, Samuel I Miller, Brett B Finlay, Natalie CJ Strynadka
    posted to type-iii structure secretion cleavage bacteria by neils on 2008-05-01 02:25:46 as **
  • Life without RNase P
    Nature, Vol. 453, No. 7191., pp. 120-123.
    by Lennart Randau, Imke Schröder, Dieter Söll
    posted to trna synthesis rnasep ribonuclease nanoarcheum evolution archaea by neils on 2008-05-01 02:19:42 as ** along with 3 people and 2 groups kinestetika zwang stajich microbiology_nijmegen Berkeley Mycology
  • A Mechanism for Src Kinase-Dependent Signaling by Noncatalytic Receptors
    Biochemistry (30 April 2008)
    by Jonathan A Cooper, Hong Qian
    posted to src signaling receptor mechanism kinase by neils on 2008-04-30 08:52:26 as **
  • Calcium-Dependent Heme Structure in the Reduced Forms of the Bacterial Cytochrome c Peroxidase from Paracoccus pantotrophus
    Biochemistry (29 April 2008)
    by Sofia R Pauleta, Yi Lu, Celia F Goodhew, Isabel Moura, Graham W Pettigrew, John A Shelnutt
    posted to structure peroxidase paracoccus haem cytochrome calcium by neils on 2008-04-29 09:21:09 as **
  • A Quick Guide for Computer-Assisted Instruction in Computational Biology and Bioinformatics
    PLoS Comput Biol, Vol. 4, No. 4. (Apr 2008)
    by Manuel J Costa, Eduardo Galembeck, Guilherme A Marson, Bayardo B Torres
    posted to teaching computer-assisted bioinformatics by neils on 2008-04-28 06:38:52 as **
  • Deconstruction of Iterative Multidomain Polyketide Synthase Function
    Science, Vol. 320, No. 5873. (11 April 2008), pp. 243-246.
    by Jason M Crawford, Paul M Thomas, Jonathan R Scheerer, Anna L Vagstad, Neil L Kelleher, Craig A Townsend
    posted to secondary polyketide pks metabolism fungi by neils on 2008-04-28 00:15:24 as **
  • An evaluation of automated homology modelling methods at low target template sequence similarity
    Bioinformatics, Vol. 23, No. 15. (1 August 2007), pp. 1901-1908.
    by James A Dalton, Richard M Jackson
    posted to structure protein prediction modelling homology evaluation bioinformatics by neils on 2008-04-26 12:05:56 as ** along with 3 people pansapiens chad_davis biehl
  • 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 **
  • Constructing templates for protein structure prediction by simulation of protein folding pathways
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Ilona Kifer, Ruth Nussinov, Haim J Wolfson
    posted to structure simulation protein prediction modelling folding by neils on 2008-04-25 01:52:40 as **
  • NetworKIN: a resource for exploring cellular phosphorylation networks
    Nucl. Acids Res., Vol. 36 (2008), pp. D695-699.
    by Rune Linding, Lars J Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B Yaffe, Tony Pawson
    posted to transduction signal prediction phosphorylation networks bioinformatics by neils on 2008-04-24 16:22:01 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
    posted to transduction structure software sites signal sequence proteome proteins protein phosphorylation motifs internet databases binding article-predikin article-nar analysis amino algorithms by neils on 2008-04-24 16:16:06 as ** along with 1 person mloewer
  • Site-Specific Phosphorylation Profiling of Arabidopsis Proteins by Mass Spectrometry and Peptide Chip Analysis
    J. Proteome Res. (24 April 2008)
    by Sergio de la Fuente van Bentem, Dorothea Anrather, Ilse Dohnal, Elisabeth Roitinger, Edina Csaszar, Jos Joore, Joshua Buijnink, Alessandro Carreri, Celine Forzani, Zdravko J Lorkovic, Andrea Barta, David Lecourieux, Andreas Verhounig, Claudia Jonak, Heribert Hirt
    posted to spectrometry proteins plant phosphorylation peptide mass chip arabidopsis by neils on 2008-04-24 06:46:05 as ** along with 2 people brianb cjhall
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