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neils's bioinformatics [124 articles]

Recent papers added to neils's library classified by the tag bioinformatics. You can also see everyone's bioinformatics.
  • Apparently low reproducibility of true differential expression discoveries in microarray studies.
    Bioinformatics (Oxford, England) (16 July 2008)
    by Min Zhang, Chen Yao, Zheng Guo, Jinfeng Zou, Lin Zhang, Hui Xiao, Dong Wang, Da Yang, Xue Gong, Jing Zhu, Yanhui Li, Xia Li
    posted to statistics reproducibility microarray expression differential bioinformatics by neils on 2008-09-06 10:48:09 as ** along with 2 people GeeSharpMinor shigepong
  • Big data: The future of biocuration
    Nature, Vol. 455, No. 7209. (2008), pp. 47-50.
    by Doug Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P Hill, Renate Kania, Mary Schaeffer, Susan St Pierre, Simon Twigger, Owen White, Yon
    posted to review recommendation proposal database curation career bioinformatics by neils on 2008-09-04 05:44:55 as ** along with 3 people psique fgibson dullhunk
  • Prediction of Peptidase Category Based on Functional Domain Composition
    J. Proteome Res. (3 September 2008)
    by Xiaochun Xu, Dong Yu, Wei Fang, Yushao Cheng, Ziliang Qian, Wencong Lu, Yudong Cai, Kaiyan Feng
    posted to prediction peptidase function domain bioinformatics by neils on 2008-09-03 13:22:31 as **
  • notes Genome-Scale Computational Biology and Bioinformatics in Australia
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000068.
    by Mark A Ragan, Tim Littlejohn, Bruce Ross
    posted to australia bioinformatics genomics infrastructure review by neils on 2008-09-01 02:03:26 as ** along with 2 people barry AbnerCYH
  • TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model
    BMC Bioinformatics, Vol. 9 (31 August 2008), 358.
    by Mallika Veeramalai, Yuzhen Ye, Adam Godzik
    posted to alignment bioinformatics prediction software structural by neils on 2008-09-01 01:38:46 as ** along with 1 person reyez
  • Impact of residue accessible surface area on the prediction of protein secondary structures
    BMC Bioinformatics, Vol. 9 (31 August 2008), 357.
    by Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk, Sayed-Amir Marashi
    posted to accessibility bioinformatics prediction secondary structure surface by neils on 2008-09-01 01:31:22 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 alignment bioinformatics domain motion protein structure by neils on 2008-08-28 00:46:10 as ** along with 2 people reyez vinithepooh
  • 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 bioinformatics database errors prediction protein sequence structure by neils on 2008-08-28 00:42:01 as ** along with 2 people grahamc piergiorgioduca
  • Protein structure search and local structure characterization
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Shih Y Ku, Yuh J Hu
    posted to alphabet bioinformatics protein search structure by neils on 2008-08-23 02:16:28 as ** along with 2 people chad_davis reyez
  • 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 bioinformatics infrastructure review by neils on 2008-08-20 00:10:27 as ** along with 16 people and 4 groups carolh12 ilya alaninmcr druvus srp33 dullhunk tharris stajich mrochman dansullivanblk jandot GustavoLacerda jago fgibson thomaskelder sjcockell Berkeley Mycology Global_health_enterprise_architecture Knowledge_Economy_Reform kpa-resources
  • 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 bioinformatics domain interaction pdz peptide prediction protein-protein by neils on 2008-08-19 00:19:29 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 bioinformatics classification feature review selection by neils on 2008-08-13 23:49:44 as ** along with 1 person robertvandenberg
  • 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 bioinformatics interaction prediction protein-dna sequence by neils on 2008-07-11 00:31:23 as ** along with 1 person maximilianh
  • 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 bioinformatics complex-i disease localisation mitochondria protein scl by neils on 2008-07-11 00:27:50 as ** along with 4 people brianb ptrobajo raiyar mdstobbe
  • 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 bioinformatics interaction prediction protein-protein network by neils on 2008-07-07 14:13:12 as ** along with 3 people cabbagesofdoom renatomilani cerca
  • 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 bioinformatics database proteomics mass-spec by neils on 2008-07-07 14:10:41 as **
  • 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 bioinformatics interaction protein-protein topology network by neils on 2008-07-04 00:29:49 as ** along with 2 people renatomilani brianb
  • 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 bioinformatics interaction prediction protein-protein yeast peptide by neils on 2008-06-28 03:28:18 as ** along with 4 people brianb pansapiens renatomilani jyuh
  • 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 bioinformatics clustering graph interaction protein-protein complex by neils on 2008-06-28 01:53:59 as ** along with 1 person chad_davis
  • 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 bioinformatics framework genomics gmod perl software by neils on 2008-06-21 03:05:23 as ** along with 4 people tharris dullhunk jyuh jamselem
  • 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 bioinformatics ms-ms phosphorylation proteome scoring phosphoprotein by neils on 2008-06-19 09:14:49 as ** along with 1 person brianb
  • 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 bioinformatics cid database machine-learning phosphopeptides svm mass-spec by neils on 2008-06-19 09:10:38 as **
  • 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 bioinformatics database human interaction pathogen protein-protein virus by neils on 2008-06-18 13:51:04 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 bioinformatics domain prediction protein webserver region by neils on 2008-06-15 10:50:02 as ** along with 1 person niallhaslam
  • NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
    Nucl. Acids Res. (4 June 2008), gkn336.
    by Sylvain Brohee, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, Jacques van Helden
    posted to bioinformatics cluster pathways software webserver network by neils on 2008-06-05 02:58:50 as ** along with 2 people brianb balicea
  • Large-scale analysis of gene clustering in bacteria
    Genome Res., Vol. 18, No. 6. (1 June 2008), pp. 949-956.
    by Qingwu Yang, Sing-Hoi Sze
    posted to bacteria bioinformatics clustering genetics operon prediction by neils on 2008-06-03 02:29:35 as **
  • iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources
    PLoS ONE, Vol. 3, No. 5. (May 2008)
    by Ivo D Dinov, Daniel Rubin, William Lorensen, Jonathan Dugan, Jeff Ma, Shawn Murphy, Beth Kirschner, William Bug, Michael Sherman, Aris Floratos, David Kennedy, HV Jagadish, Jeanette Schmidt, Brian Athey, Andrea Califano, Mark Musen, Russ Altman, Ron Kikinis, Isaac Kohane, Scott Delp, Stott D Parker, Arthur W Toga
    posted to bioinformatics computational-biology framework software tools by neils on 2008-05-31 13:42:35 as **
  • poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Raghunandan Kainkaryam, Peter Woolf
    posted to bioinformatics drug prediction screen by neils on 2008-05-31 03:53:47 as ** along with 3 people reyez jyuh rmk
  • PROMALS3D web server for accurate multiple protein sequence and structure alignments
    Nucl. Acids Res. (24 May 2008), gkn322.
    by Jimin Pei, Ming Tang, Nick V Grishin
    posted to alignment bioinformatics protein sequence structure webserver by neils on 2008-05-29 04:29:21 as **
  • PIE: an online prediction system for protein-protein interactions from text
    Nucl. Acids Res. (28 May 2008), gkn281.
    by Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, Byoung-Tak Zhang
    posted to bioinformatics interaction prediction protein-protein text-mining webserver by neils on 2008-05-29 03:02:27 as ** along with 3 people satre tharris jyuh
  • ENDEAVOUR update: a web resource for gene prioritization in multiple species
    Nucl. Acids Res. (28 May 2008), gkn325.
    by Leon-Charles Tranchevent, Roland Barriot, Shi Yu, Steven V Vooren, Peter V Loo, Bert Coessens, Bart D Moor, Stein Aerts, Yves Moreau
    posted to bioinformatics candidate function selection webserver gene by neils on 2008-05-29 02:58:21 as ** along with 1 person jyuh
  • Unravelling the genomic mosaic of a ubiquitous genus of marine cyanobacteria
    Genome Biology, Vol. 9, No. 5. (2008)
    by Alexis Dufresne, Martin Ostrowski, David Scanlan, Laurence Garczarek, Sophie Mazard, Brian Palenik, Ian Paulsen, Nicole T de Marsac, Patrick Wincker, Carole Dossat, Steve Ferriera, Justin Johnson, Anton Post, Wolfgang Hess, Frederic Partensky
    posted to analysis bioinformatics comparative cyanobacteria genomics by neils on 2008-05-28 12:00:23 as ** along with 1 person bcondon
  • Prediction of enzyme function by combining sequence similarity and protein interactions
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Jordi Espadaler, Narayanan Eswar, Enric Querol, Francesc Aviles, Andrej Sali, Marc M Renom, Baldomero Oliva
    posted to bioinformatics enzyme function interaction prediction protein-protein sequence by neils on 2008-05-28 01:05:07 as ** along with 1 person and 1 group aprildh31 Proteasome
  • Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites
    BMC Bioinformatics, Vol. 9 (26 May 2008), 245.
    by Neil FW Saunders, Ross I Brinkworth, Thomas Huber, Bruce E Kemp, Bostjan Kobe
    posted to bioinformatics prediction predikin specificity substrate kinase by neils on 2008-05-27 05:06:18 as ** along with 1 person jyuh
  • The statistical significance of nucleotide position-weight matrix matches
    Comput. Appl. Biosci., Vol. 12, No. 5. (1 October 1996), pp. 431-439.
    by Jean-Michel Claverie, Stephane Audic
    posted to bioinformatics matrix nucleotide pwm statistics by neils on 2008-05-14 06:41:04 as ** along with 2 people and 2 groups samal bsmagic Bioinformatics bioinplant
  • Estimating the size of the human interactome
    Proceedings of the National Academy of Sciences (12 May 2008), 0708078105.
    by Michael P Stumpf, Thomas Thorne, Eric de Silva, Ronald Stewart, Hyeong J An, Michael Lappe, Carsten Wiuf
    posted to bioinformatics human interaction interactome network prediction protein-protein by neils on 2008-05-14 04:39:31 as ** along with 20 people zwang chrissp100 sanchezbuelna jyuh phoenixzxl tmmurali paolomarcatili mjoach xingxu Ema cabbagesofdoom balicea marck friendpine brianb roys Evangelia dragonrez chad_davis bpcusack
  • The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information
    Nucl. Acids Res. (13 May 2008), gkn279.
    by Neil F Saunders, Bostjan Kobe
    posted to bioinformatics peptide prediction predikin specificity webserver kinase by neils on 2008-05-14 03:57:42 as **
  • Biocomputational prediction of small non-coding RNAs in Streptomyces
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Josef Panek, Jan Bobek, Karel Mikulik, Marek Basler, Jiri Vohradsky
    posted to bacteria bioinformatics ncrna prediction streptomyces by neils on 2008-05-13 13:09:48 as **
  • notes In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Bolstad, Amy C Anderson
    posted to bioinformatics docking lead optimisation virtual screen by neils on 2008-05-13 09:16:16 as **
  • Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Andrew Bordner, Andrey Gorin
    posted to bioinformatics interaction interface pdb protein-protein complex by neils on 2008-05-13 00:10:20 as ** along with 2 people phoenixzxl bicko
  • 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 archaea bioinformatics database est genomics pathogen 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 antarctic bioinformatics genomics methanococcoides methanogenium psychrophily by neils on 2008-05-11 10:24:46 as ** along with 1 person bpb
  • 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 analysis bioinformatics evolution sequence serpin by neils on 2008-05-11 10:11:58 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 antarctic archaea bioinformatics function methanococcoides prediction psychrophily protein by neils on 2008-05-11 10:09:25 as **
  • 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 bioinformatics discovery glam2 motifs sequence by neils on 2008-05-09 13:29:46 as ** along with 6 people gjuggler Stew dquest cabbagesofdoom Ema Evangelia
  • 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 bioinformatics prediction protein retrieval structure by neils on 2008-05-09 10:19:56 as **
  • 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 bioinformatics genomics information sequencing standards by neils on 2008-05-09 00:35:47 as ** along with 6 people jmeppley dullhunk jyuh tharris jamselem jfr
  • Genome analysis of the platypus reveals unique signatures of evolution
    Nature, Vol. 453, No. 7192. (May 2008), pp. 175-183.
    posted to bioinformatics evolution genome platypus by neils on 2008-05-08 00:43:58 as ** along with 9 people pbull hpaces Tominator fhsantanna gjuggler cabbagesofdoom ealloza natstreet lp2
  • 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 bioinformatics prediction protein sequence structure by neils on 2008-05-02 00:27:57 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 bioinformatics computer-assisted teaching by neils on 2008-04-28 06:38:52 as **
    • Note: You may cite this page as: http://www.citeulike.org/user/neils/tag/bioinformatics

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