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neils's library [465 articles]

Recent papers added to neils's library ordered by importance.
  • The structural basis for an essential subunit interaction in influenza virus RNA polymerase
    Nature (27 July 2008)
    by Eiji Obayashi, Hisashi Yoshida, Fumihiro Kawai, Naoya Shibayama, Atsushi Kawaguchi, Kyosuke Nagata, Jeremy RH Tame, Sam-Yong Park
    posted to virus subunit protein-protein polymerase interaction by neils on 2008-08-28 00:47:44 as **
  • Crystal structure of the polymerase PAC–PB1N complex from an avian influenza H5N1 virus
    Nature (09 July 2008)
    by Xiaojing He, Jie Zhou, Mark Bartlam, Rongguang Zhang, Jianyuan Ma, Zhiyong Lou, Xuemei Li, Jingjing Li, Andrzej Joachimiak, Zonghao Zeng, Ruowen Ge, Zihe Rao, Yingfang Liu
    posted to virus structure polymerase h5n1 crystallography complex avian by neils on 2008-08-28 00:46:13 as **
  • Alignment of protein structures in the presence of domain motions
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Roberto Mosca, Barbara Brannetti, Thomas Schneider
    posted to structure protein motion domain bioinformatics alignment by neils on 2008-08-28 00:46:10 as ** along with 2 people vinithepooh reyez
  • Identification and correction of abnormal, incomplete and mispredicted proteins in public databases
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Alinda Nagy, Hedi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, Laszlo Banyai, Laszlo Patthy
    posted to structure sequence protein prediction errors database bioinformatics by neils on 2008-08-28 00:42:01 as **
  • Discovering regulatory motifs in the Plasmodium genome using comparative genomics.
    Bioinformatics (Oxford, England) (8 July 2008)
    by Jie Wu, Douglas H H Sieglaff, Joshua Gervin, Xiaohui S S Xie
    posted to regulation plasmodium motifs genomics comparative by neils on 2008-08-25 13:48:34 as ** along with 2 people Neeperando semrich
  • Protein structure search and local structure characterization
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Shih Y Ku, Yuh J Hu
    posted to structure search protein bioinformatics alphabet by neils on 2008-08-23 02:16:28 as ** along with 1 person reyez
  • Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities
    PLoS ONE, Vol. 3, No. 8. (2008), e3042.
    by Jack A Gilbert, Dawn Field, Ying Huang, Rob Edwards, Weizhong Li, Paul Gilna, Ian Joint
    posted to transcriptomics sequencing microbiology metagenomics by neils on 2008-08-23 02:15:14 as **
  • High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
    Science (21 August 2008), 1158684.
    by Haiyuan Yu, Pascal Braun, Muhammed A Yildirim, Irma Lemmens, Kavitha Venkatesan, Julie Sahalie, Tomoko Hirozane-Kishikawa, Fana Gebreab, Na Li, Nicolas Simonis, Tong Hao, Jean-Francois Rual, Amelie Dricot, Alexei Vazquez, Ryan R Murray, Christophe Simon, Leah Tardivo, Stanley Tam, Nenad Svrzikapa, Changyu Fan, Anne-Sophie de Smet, Adriana Motyl, Michael E Hudson, Juyong Park, Xiaofeng Xin, Michael E Cusick, Troy Moore, Charlie Boone, Michael Snyder, Frederick P Roth, Albert-Laszlo Barabasi, Jan Tavernier, David E Hill, Marc Vidal
    posted to yeast protein-protein network map interactome binary by neils on 2008-08-22 13:14:11 as ** along with 1 person maralena
  • Significant contribution of Archaea to extant biomass in marine subsurface sediments
    Nature (20 July 2008)
    by Julius S Lipp, Yuki Morono, Fumio Inagaki, Kai-Uwe Hinrichs
    posted to marine ecology biomass archaea by neils on 2008-08-21 00:13:53 as ** along with 1 person and 1 group djkt iSEEM
  • Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
    Nat Rev Genet, Vol. 9, No. 9. (2008), pp. 678-688.
    by Lincoln D Stein
    posted to review infrastructure bioinformatics by neils on 2008-08-20 00:10:27 as ** along with 16 people and 4 groups srp33 alaninmcr druvus ilya carolh12 sjcockell thomaskelder fgibson jago GustavoLacerda jandot dansullivanblk mrochman stajich tharris dullhunk kpa-resources Knowledge_Economy_Reform Global_health_enterprise_architecture Berkeley Mycology
  • notes Predicting PDZ domain-peptide interactions from primary sequences
    Nat Biotech, Vol. advanced online publication (2008)
    by Jiunn R Chen, Bryan H Chang, John E Allen, Michael A Stiffler, Gavin Macbeath
    posted to protein-protein prediction peptide pdz interaction domain bioinformatics by neils on 2008-08-19 00:19:29 as **
  • Complete genome of Phenylobacterium zucineum - a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562
    BMC Genomics, Vol. 9 (13 August 2008), 386.
    by Yingfeng Luo, Xiaoli Xu, Zonghui Ding, Zhen Liu, Bing Zhang, Zhiyu Yan, Jie Sun, Songnian Hu, Xun Hu
    posted to symbiosis phenylobacterium genome bacteria by neils on 2008-08-17 08:00:31 as **
  • High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Evandro Novaes, Derek Drost, William Farmerie, Georgios Pappas, Dario Grattapaglia, Ronald Sederoff, Matias Kirst
    posted to snp plant genomics eucalyptus annotation by neils on 2008-08-17 07:57:24 as ** along with 3 people GustavoLacerda natstreet gpappas
  • Immobilized Metal Affinity Chromatography Revisited: pH/Acid Control toward High Selectivity in Phosphoproteomics
    J. Proteome Res. (16 August 2008)
    by Chia-Feng Tsai, Yi-Ting Wang, Yet-Ran Chen, Chen-Yu Lai, Pei-Yi Lin, Kuan-Ting Pan, Jeou-Yuan Chen, Kay-Hooi Khoo, Yu-Ju Chen
    posted to purification proteomics phosphopeptides chromatography by neils on 2008-08-16 12:07:38 as ** along with 1 person brianb
  • Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes
    Science, Vol. 321, No. 5891. (15 August 2008), pp. 960-964.
    by Stan J Brouns, Matthijs M Jore, Magnus Lundgren, Edze R Westra, Rik J Slijkhuis, Ambrosius P Snijders, Mark J Dickman, Kira S Makarova, Eugene V Koonin, John van der Oost
    posted to virus rna prokaryote defence crispr by neils on 2008-08-15 03:38:59 as ** along with 1 person zwang
  • The cis-regulatory map of Shewanella genomes
    Nucl. Acids Res. (13 August 2008), gkn515.
    by Jiajian Liu, Xing Xu, Gary D Stormo
    posted to shewanella regulation genomics bacteria by neils on 2008-08-14 08:37:37 as **
  • Penalized feature selection and classification in bioinformatics
    Brief Bioinform, Vol. 9, No. 5. (1 September 2008), pp. 392-403.
    by Shuangge Ma, Jian Huang
    posted to selection review feature classification bioinformatics by neils on 2008-08-13 23:49:44 as ** along with 1 person robertvandenberg
  • Impacts of protein-protein interaction domains on organism and network complexity
    Genome Res. (August 2008)
    by Kai Xia, Zheng Fu, Lei Hou, Jing
    posted to protein-protein network interaction domain complexity by neils on 2008-08-13 01:28:04 as **
  • Gain and loss of phosphorylation sites in human cancer
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i241-247.
    by Predrag Radivojac, Peter H Baenziger, Maricel G Kann, Matthew E Mort, Matthew W Hahn, Sean D Mooney
    posted to substrate phosphorylation mutation human cancer by neils on 2008-08-11 00:38:19 as ** along with 1 person brianb
  • Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i105-111.
    by Rafael Najmanovich, Natalja Kurbatova, Janet Thornton
    posted to structure similarity protein ligand discrimination binding by neils on 2008-08-11 00:37:28 as ** along with 2 people nickolay reyez
  • An integrative approach for predicting interactions of protein regions
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i35-41.
    by Sven-Eric Schelhorn, Thomas Lengauer, Mario Albrecht
    posted to protein-protein prediction interaction integration by neils on 2008-08-11 00:36:09 as ** along with 2 people kluck zwang
  • PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i14-20.
    by Chia-Ying Yang, Chao-Hui Chang, Ya-Ling Yu, Tsu-Chun E Lin, Sheng-An Lee, Chueh-Chuan Yen, Jinn-Moon Yang, Jin-Mei Lai, Yi-Ren Hong, Tzu-Ling Tseng, Kun-Mao Chao, Chi-Ying F Huang
    posted to phosphoprotein kinase interactome human database by neils on 2008-08-11 00:35:03 as ** along with 2 people brianb renatomilani
  • Annotation of metagenome short reads using proxygenes
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i7-13.
    by Daniel Dalevi, Natalia N Ivanova, Konstantinos Mavromatis, Sean D Hooper, Ernest Szeto, Philip Hugenholtz, Nikos C Kyrpides, Victor M Markowitz
    posted to metagenomics genome annotation 454 by neils on 2008-08-11 00:33:57 as **
  • A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing
    Cell, Vol. Vol 134 (August 2008), pp. 416-426.
    by Richard E Green, Anna, Johannes Krause, Adrian W Briggs, Philip LF Johnson, Caroline Uhler, Matthias Meyer, Jeffrey M Good, Tomislav Maricic, Udo Stenzel, Kay Prüfer, Michael Siebauer, Hernán A Burbano, Michael Ronan, Jonathan M Rothberg, Michael Egholm, Pavao Rudan, Dejana Brajković, Željko Kućan, Ivan Gušić, Mårten Wikström, Liisa Laakkonen, Janet Kelso, Montgomery Slatkin, Svante Pääbo
    posted to sequencing neandertal mitochondria dna ancient by neils on 2008-08-09 04:26:35 as **
  • Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution
    Nucl. Acids Res., Vol. 36, No. 14. (1 August 2008), pp. 4529-4548.
    by Nicolas J Tourasse, Anne-Brit Kolsto
    posted to introns genomics evolution bacteria bacillus by neils on 2008-08-08 02:10:27 as **
  • A protein-DNA docking benchmark
    Nucl. Acids Res., Vol. 36, No. 14. (1 August 2008), e88.
    by Marc van Dijk, Alexandre M Bonvin
    posted to protein-dna docking benchmark by neils on 2008-08-08 02:09:13 as ** along with 2 people boris_aguilar reyez
  • An evaluation of human protein-protein interaction data in the public domain
    BMC Bioinformatics, Vol. 7, No. Suppl 5. (2006)
    by Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, YL Ramachandra, Akhilesh Pandey
    posted to review protein-protein interaction human database by neils on 2008-08-06 05:27:51 as ** along with 7 people and 1 group zdai renatomilani frohike grahamc alwinpremanand lpfernandes hpaces Bioinformatics
  • 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 4 people mdstobbe brianb raiyar 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 ** along with 1 person daforerog
  • 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 2 people papamicd 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
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