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neils's library [438 articles]

Recent papers added to neils's library ordered by importance.
  • Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement
    Genome Res. (14 July 2008), gr.080119.108.
    by Andrew L Hufton, Detlef Groth, Martin Vingron, Hans Lehrach, Albert J Poustka, Georgia Panopoulou
    posted to vertebrate rearrangement genomics genome evolution duplication by neils on 2008-07-15 04:48:45 as ** along with 2 people and 1 group cisevol alhufton BergmanLab
  • Revealing unique properties of the ribosome using a network based analysis
    Nucl. Acids Res. (14 July 2008), gkn433.
    by Hilda David-Eden, Yael Mandel-Gutfreund
    posted to structure ribosome network modelling analysis by neils on 2008-07-15 04:45:46 as **
  • Global analysis of protein phosphorylation in yeast
    Nature, Vol. 438, No. 7068., pp. 679-684.
    by Jason Ptacek, Geeta Devgan, Gregory Michaud, Heng Zhu, Xiaowei Zhu, Joseph Fasolo, Hong Guo, Ghil Jona, Ashton Breitkreutz, Richelle Sopko, Rhonda R Mccartney, Martin C Schmidt, Najma Rachidi, Soo-Jung Lee, Angie S Mah, Lihao Meng, Michael JR Stark, David F Stern, Claudio De Virgilio, Mike Tyers, Brenda Andrews, Mark Gerstein, Barry Schweitzer, Paul F Predki, Michael Snyder
    posted to yeast proteomics phosphorylation analysis by neils on 2008-07-12 13:04:47 as ** along with 6 people and 1 group carlk tmmurali tuck balabu nickluscombe koller EBI-regulation
  • Revisiting the Saccharomyces cerevisiae predicted ORFeome
    Genome Res. (2008)
    by Qian R Li, Anne R Carvunis, Haiyuan Yu, Jing, 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
    posted to orfan transcript yeast prediction orfs genomics by neils on 2008-07-11 04:48:06 as **
  • Extracting sequence features to predict protein-DNA interactions: a comparative study
    Nucl. Acids Res., Vol. 36, No. 12. (1 July 2008), pp. 4137-4148.
    by Qing Zhou, Jun S Liu
    posted to sequence protein-dna prediction interaction bioinformatics by neils on 2008-07-11 00:31:23 as ** along with 1 person maximilianh
  • Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex
    Nucl. Acids Res., Vol. 36, No. 12. (1 July 2008), pp. 3993-4008.
    by Henri-Marc Bourbon
    posted to transcription phylogeny genomics evolution comparative by neils on 2008-07-11 00:30:15 as **
  • A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology
    Cell, Vol. 134, No. 1. (11 July 2008), pp. 112-123.
    by David J Pagliarini, Sarah E Calvo, Betty Chang, Sunil A Sheth, Scott B Vafai, Shao-En Ong, Geoffrey A Walford, Canny Sugiana, Avihu Boneh, William K Chen, David E Hill, Marc Vidal, James G Evans, David R Thorburn, Steven A Carr, Vamsi K Mootha
    posted to scl protein mitochondria localisation disease complex-i bioinformatics by neils on 2008-07-11 00:27:50 as ** along with 1 person ptrobajo
  • Immunomodulatory Effects of Polar Lichens on the Function of Macrophages In Vitro.
    Marine biotechnology (New York, N.Y.) (9 July 2008)
    by Hye-Sook S Choi, Joung H Yim, Hong K Lee, Suhkneung Pyo
    posted to phosphorylation pathway macrophage lichen immunology antarctic by neils on 2008-07-11 00:20:06 as **
  • Structural Relationships Among the Ribosomal Stalk Proteins from the Three Domains of Life.
    Journal of molecular evolution (9 July 2008)
    by Przemysław Grela, Pau Bernadó, Dmitri Svergun, Jan Kwiatowski, Dariusz Abramczyk, Nikodem Grankowski, Marek Tchórzewski
    posted to protein structure ribosome phylogeny evolution by neils on 2008-07-11 00:18:55 as **
  • The Crystal Structure of the Ran-Nup153ZnF2 Complex: a General Ran Docking Site at the Nuclear Pore Complex
    Structure, Vol. 16, No. 7. (9 July 2008), pp. 1116-1125.
    by Nils Schrader, Carolin Koerner, Katja Koessmeier, Jan-Amadé Bangert, Alfred Wittinghofer, Raphael Stoll, Ingrid R Vetter
    posted to structure ran nup nuclear npc complex by neils on 2008-07-10 04:38:13 as **
  • Protein-Protein Interactions in the Membrane: Sequence, Structural, and Biological Motifs
    Structure, Vol. 16, No. 7. (9 July 2008), pp. 991-1001.
    by David T Moore, Bryan W Berger, William F Degrado
    posted to review protein-protein motifs membrane interaction by neils on 2008-07-10 04:36:45 as ** along with 2 people jonsta247 zwang
  • The Structure of an Archaeal Pilus.
    Journal of molecular biology (12 June 2008)
    by Ying A A Wang, Xiong Yu, Sandy Y M Y Ng, Ken F F Jarrell, Edward H H Egelman
    posted to electron-microscopy cryo-em structure pilus methanococcus archaea by neils on 2008-07-09 12:51:38 as **
  • Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF
    Genome Biology, Vol. 9, No. 7. (2008)
    by Agathe Bourgogne, Danielle Garsin, Xiang Qin, Kavindra Singh, Jouko Sillanpaa, Shailaja Yerrapragada, Yan Ding, Shannon D Rocha, Christian Buhay, Hua Shen, Guan Chen, Gabrielle Williams, Donna Muzny, Arash Maadani, Kristina Fox, Jason Gioia, Lei Chen, Yue Shang, Cesar Arias, Sreedhar Nallapareddy, Meng Zhao, Vittal Prakash, Shahreen Chowdhury, Huaiyang Jiang, Richard Gibbs, Barbara Murray, Sarah Highlander, George Weinstock
    posted to virulence pathogen genomics enterococcus bacteria by neils on 2008-07-09 03:42:20 as **
  • Protein structure protection commits gene expression patterns
    Genome Biology, Vol. 9 (07 July 2008), R107.
    by Jianping Chen, Han Liang, Ariel Fernandez
    posted to structure protein gene expression disorder correlation by neils on 2008-07-08 01:55:18 as **
  • PhyloWidget: web-based visualizations for the tree of life
    Bioinformatics, Vol. 24, No. 14. (15 July 2008), pp. 1641-1642.
    by Gregory E Jordan, William H Piel
    posted to webserver visualisation software phylogeny by neils on 2008-07-07 14:14:43 as ** along with 1 person gjuggler
  • InteroPorc: Automated Inference of Highly Conserved Protein Interaction Networks.
    Bioinformatics (Oxford, England) (28 May 2008)
    by Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Franck Chauvat, Corinne Cassier-Chauvat, Jean-Christophe C Aude, Pierre Legrain
    posted to network protein-protein prediction interaction bioinformatics by neils on 2008-07-07 14:13:12 as ** along with 3 people cerca renatomilani cabbagesofdoom
  • 2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Jens Allmer, Sebastian Kuhlgert, Michael Hippler
    posted to mass-spec proteomics database bioinformatics by neils on 2008-07-07 14:10:41 as **
  • The ORFeome of Staphylococcus aureus v 1.1
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Christina Brandner, Richard Maier, Daryl Henderson, Helmut Hintner, Johann Bauer, Kamil Onder
    posted to staphylococcus orf library genomics bacteria by neils on 2008-07-07 14:09:43 as ** along with 1 person joaocarrico
  • Non-functional phosphorylations?
    Trends in Biochemical Sciences, Vol. In Press, Corrected Proof
    by Gustav E Lienhard
    posted to specificity phosphorylation hypothesis evolution by neils on 2008-07-06 07:44:14 as ** along with 1 person brianb
  • Food Idiosyncrasies: Beetroot and Asparagus
    Drug Metab Dispos, Vol. 29, No. 4. (1 April 2001), pp. 539-543.
    by SC Mitchell
    posted to review metabolism human genetics food by neils on 2008-07-06 05:08:10 as **
  • Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.
    Nature protocols, Vol. 3, No. 7. (June 2008), pp. 1171-1179.
    by Gerrit Langer, Serge X X Cohen, Victor S S Lamzin, Anastassis Perrakis
    posted to x-ray software protocol modelling crystallography by neils on 2008-07-06 01:25:43 as **
  • Contextual Specificity in Peptide-Mediated Protein Interactions
    PLoS ONE, Vol. 3, No. 7. (2 July 2008), e2524.
    by Amelie Stein, Patrick Aloy
    posted to specificity protein-protein peptide interaction energy context binding by neils on 2008-07-06 01:23:12 as ** along with 1 person zdai
  • Taxonomic distribution of large DNA viruses in the sea
    Genome Biology, Vol. 9, No. 7. (2008)
    by Adam Monier, Jean M Claverie, Hiroyuki Ogata
    posted to virus taxonomy phylogeny marine ecology by neils on 2008-07-04 00:31:19 as ** along with 1 person and 1 group djkt iSEEM
  • Deducing topology of protein-protein interaction networks from experimentally measured sub-networks
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Ling Yang, Thomas Vondriska, Zhangang Han, Robb Maclellan, James Weiss, Zhilin Qu
    posted to network topology protein-protein interaction bioinformatics by neils on 2008-07-04 00:29:49 as ** along with 2 people brianb renatomilani
  • Life Sciences and the web: a new era for collaboration
    Mol Syst Biol, Vol. 4 (1 July 2008)
    by Jonathan A Sagotsky, Le Zhang, Zhihui Wang, Sean Martin, Thomas S Deisboeck
    posted to wiki web20 review collaboration by neils on 2008-07-03 12:26:42 as ** along with 5 people renatomilani CameronNeylon tharris dullhunk reyez
  • The split genes of Nanoarchaeum equitans are an ancestral character.
    Gene (11 June 2008)
    by Massimo Di Giulio
    posted to nanoarcheum introns hyperthermophily evolution archaea by neils on 2008-07-02 14:31:36 as **
  • A General System for Studying Protein-Protein Interactions in Gram-Negative Bacteria
    J. Proteome Res. (1 July 2008)
    by Dale A Pelletier, Gregory B Hurst, Linda J Foote, Patricia K Lankford, Catherine K Mckeown, Tse-Yuan Lu, Denise D Schmoyer, Manesh B Shah, Judson W Hervey, Hayes W Mcdonald, Brian S Hooker, William R Cannon, Don S Daly, Jason M Gilmore, Steven H Wiley, Deanna L Auberry, Yisong Wang, Frank W Larimer, Stephen J Kennel, Mitchel J Doktycz, Jennifer L Morrell-Falvey, Elizabeth T Owens, Michelle V Buchanan
    posted to tag protein-protein interaction bacteria affinity by neils on 2008-07-01 13:24:33 as ** along with 1 person brianb
  • The topology of the bacterial co-conserved protein network and its implications for predicting protein function
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Anis K Fard, Sonia Leach, Lawrence Hunter, Ryan Gill
    posted to topology protein-protein network interaction bacteria by neils on 2008-07-01 00:32:28 as **
  • Insight into the proteome of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis: the major cytosolic and membrane proteins.
    Archives of microbiology (27 June 2008)
    by Tillmann Burghardt, Manfred Saller, Sonja Gürster, Daniel Müller, Carolin Meyer, Ulrike Jahn, Eduard Hochmuth, Rainer Deutzmann, Frank Siedler, Patrick Babinger, Reinhard Wirth, Harald Huber, Reinhard Rachel
    posted to proteomics membrane ignicoccus cytosol archaea by neils on 2008-06-29 04:48:48 as **
  • A protein functional leap: how a single mutation reverses the function of the transcription regulator TetR
    Nucl. Acids Res. (28 June 2008), gkn400.
    by Marcus Resch, Harald Striegl, Eva M Henssler, Madhumati Sevvana, Claudia Egerer-Sieber, Emile Schiltz, Wolfgang Hillen, Yves A Muller
    posted to tet structure-activity repressor protein mutation by neils on 2008-06-29 04:43:08 as **
  • Co-Evolving Motions at Protein-Protein Interfaces of Two-Component Signaling Systems Identified by Covariance Analysis
    Biochemistry (28 June 2008)
    by Hendrik Szurmant, Benjamin G Bobay, Robert A White, Daniel M Sullivan, Richele J Thompson, Terence Hwa, James A Hoch, John Cavanagh
    posted to two-component protein-protein nmr interaction dynamics covariance analysis by neils on 2008-06-28 09:02:46 as ** along with 3 people pansapiens marck paulschlesinger
  • Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences
    Nucl. Acids Res. (27 June 2008), gkn390.
    by S Pitre, C North, M Alamgir, M Jessulat, A Chan, X Luo, JR Green, M Dumontier, F Dehne, A Golshani
    posted to peptide yeast protein-protein prediction interaction bioinformatics by neils on 2008-06-28 03:28:18 as ** along with 3 people renatomilani brianb pansapiens
  • Protein complex identification by supervised graph local clustering
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i250-268.
    by Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph
    posted to complex protein-protein interaction graph clustering bioinformatics by neils on 2008-06-28 01:53:59 as ** along with 1 person chad_davis
  • Serine/threonine kinase (pk-1) is a component of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) very late gene transcription complex and it phosphorylates a 102kDa polypeptide of the complex.
    Virus research (21 June 2008)
    by Gourav Mishra, Pooja Chadha, Rakha H H Das
    posted to complex virus phosphorylation kinase autographa by neils on 2008-06-27 00:37:33 as **
  • A Phylogenomic Study of Birds Reveals Their Evolutionary History
    Science, Vol. 320, No. 5884. (27 June 2008), pp. 1763-1768.
    by Shannon J Hackett, Rebecca T Kimball, Sushma Reddy, Rauri C Bowie, Edward L Braun, Michael J Braun, Jena L Chojnowski, Andrew W Cox, Kin-Lan Han, John Harshman, Christopher J Huddleston, Ben D Marks, Kathleen J Miglia, William S Moore, Frederick H Sheldon, David W Steadman, Christopher C Witt, Tamaki Yuri
    posted to bird phylogeny nuclear evolution dna by neils on 2008-06-27 00:35:13 as ** along with 4 people and 1 group iBartomeus whym dchughes gulsacan behavior_flexibility
  • Assembly reflects evolution of protein complexes
    Nature (18 June 2008)
    by Emmanuel D Levy, Elisabetta B Erba, Carol V Robinson, Sarah A Teichmann
    posted to complex structure quaternary protein-protein interaction evolution assembly by neils on 2008-06-26 03:53:59 as ** along with 7 people phoenixzxl marck faion psique zwang jwm paulschlesinger
  • Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection
    BMC Genomics, Vol. 9 (25 June 2008), 301.
    by M Navajas, A Migeon, C Alaux, Ml, GE Robinson, JD Evans, S Cros-Arteil, D Crauser, Y Le Conte
    posted to bee parasitism mites microarray expression differential apis by neils on 2008-06-26 02:18:23 as **
  • What makes pathogens pathogenic
    Genome Biology, Vol. 9, No. 6. (2008)
    by Garth Ehrlich, Luisa N Hiller, Fen Hu
    posted to review pathogen genetics environment by neils on 2008-06-25 01:16:06 as ** along with 1 person marck
  • Federated repositories of X-ray diffraction images
    Acta Crystallographica Section D, Vol. 64, No. 7. (Jul 2008), pp. 810-814.
    by Steve Androulakis, Jason Schmidberger, Mark A Bate, Ross Degori, Anthony Beitz, Cyrus Keong, Bob Cameron, Sheena Mcgowan, Corrine J Porter, Andrew Harrison, Jane Hunter, Jennifer L Martin, Bostjan Kobe, Renwick CJ Dobson, Michael W Parker, James C Whisstock, Joan Gray, Andrew Treloar, David Groenewegen, Neil Dickson, Ashley M Buckle
    posted to x-ray repository images database crystallography by neils on 2008-06-23 02:27:31 as **
  • GMODWeb: a web framework for the generic model organism database
    Genome Biology, Vol. 9, No. 6. (2008)
    by Brian O'Connor, Allen Day, Scott Cain, Olivier Arnaiz, Linda Sperling, Lincoln Stein
    posted to software perl gmod genomics framework bioinformatics by neils on 2008-06-21 03:05:23 as ** along with 4 people jyuh jamselem dullhunk tharris
  • The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity.
    The Journal of biological chemistry (17 June 2008)
    by Scott I I Hauenstein, Ya-Ming M Hou, John J J Perona
    posted to trna synthesis methanosarcinaceae enzymology activity by neils on 2008-06-20 00:46:10 as **
  • Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis
    J. Proteome Res. (19 June 2008)
    by Samuel H Payne, Margaret Yau, Marcus B Smolka, Stephen Tanner, Huilin Zhou, Vineet Bafna
    posted to phosphoprotein scoring proteome phosphorylation ms-ms bioinformatics by neils on 2008-06-19 09:14:49 as ** along with 1 person brianb
  • Global Impact of Oncogenic Src on a Phosphotyrosine Proteome
    J. Proteome Res. (19 June 2008)
    by Weifeng Luo, Robbert J Slebos, Salisha Hill, Ming Li, Jan Brábek, Ramars Amanchy, Raghothama Chaerkady, Akhilesh Pandey, Amy-Joan L Ham, Steven K Hanks
    posted to tyrosine src proteomics phosphorylation oncogene by neils on 2008-06-19 09:13:38 as **
  • Colander: A Probability-Based Support Vector Machine Algorithm for Automatic Screening for CID Spectra of Phosphopeptides Prior to Database Search
    J. Proteome Res. (19 June 2008)
    by Bingwen Lu, Cristian I Ruse, John R Yates
    posted to mass-spec svm phosphopeptides machine-learning database cid bioinformatics by neils on 2008-06-19 09:10:38 as **
  • The amphioxus genome and the evolution of the chordate karyotype
    Nature, Vol. 453, No. 7198. (19 June 2008), pp. 1064-1071.
    by Nicholas H Putnam, Thomas Butts, David E Ferrier, Rebecca F Furlong, Uffe Hellsten, Takeshi Kawashima, Marc Robinson-Rechavi, Eiichi Shoguchi, Astrid Terry, Jr-Kai Yu, E[grave]lia Benito-Gutierrez, Inna Dubchak, Jordi Garcia-Fernandez, Jeremy J Gibson-Brown, Igor V Grigoriev, Amy C Horton, Pieter J de Jong, Jerzy Jurka, Vladimir V Kapitonov, Yuji Kohara, Yoko Kuroki, Erika Lindquist, Susan Lucas, Kazutoyo Osoegawa, Len A Pennacchio, Asaf A Salamov, Yutaka Satou, Tatjana Sauka-Spengler, Jeremy Schmutz, Tadasu Shin-I, Atsushi Toyoda, Marianne Bronner-Fraser, Asao Fujiyama, Linda Z Holland, Peter W Holland, Nori Satoh, Daniel S Rokhsar
    posted to genome evolution chordate amphioxus by neils on 2008-06-19 00:52:46 as ** along with 1 person gulsacan
  • The Landscape of Human Proteins Interacting with Viruses and Other Pathogens
    PLoS Pathog, Vol. 4, No. 2. (Feb 2008)
    by Matthew D Dyer, Murali, Bruno W Sobral
    posted to virus protein-protein pathogen interaction human database bioinformatics by neils on 2008-06-18 13:51:04 as **
  • Snake Venomics of the Lancehead Pitviper Bothrops asper: Geographic, Individual, and Ontogenetic Variations
    J. Proteome Res. (17 June 2008)
    by Alberto Alape-Girón, Libia Sanz, José Escolano, Marietta Flores-Díaz, Marvin Madrigal, Mahmood Sasa, Juan J Calvete
    posted to venom snake proteomics evolution comparative by neils on 2008-06-18 01:41:35 as **
  • Isolation of microbes from Lake Vostok accretion ice.
    Applied and environmental microbiology (13 June 2008)
    by Tom D'Elia, Ram Veerapaneni, Scott O O Rogers
    posted to psychrophily lake-vostok isolation culture bacteria antarctic by neils on 2008-06-18 00:59:43 as **
  • Inferring modules of functionally interacting proteins using the Bond Energy Algorithm.
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Ryosuke Watanabe, Enrique Morett, Edgar Vallejo
    posted to algorithm protein-protein prediction interaction energy by neils on 2008-06-18 00:57:15 as **
  • PURE: a webserver for the prediction of domains in unassigned regions in proteins
    BMC Bioinformatics, Vol. 9 (14 June 2008), 281.
    by Chilamakuri CS Reddy, Shameer Khader, Bernard O Offmann, Ramanthan Sowdhamini
    posted to region webserver protein prediction domain bioinformatics by neils on 2008-06-15 10:50:02 as ** along with 1 person niallhaslam
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