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Group: Bioinformatics - library [3518 articles]

Neue Artikel von Mitliedern der Gruppe Bioinformatics Gruppe
  • Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets
    BMC Genomics, Vol. 8 (28 June 2007), 200.
    by Sebastian Oeder, Joerg Mages, Paul Flicek, Roland Lang
    posted to nat expression antisense affymetrix by dswan to the group Bioinformatics on 2008-11-21 11:22:55 as *** along with 1 person jfr
  • Efficient de novo assembly of bacterial genomes using low coverage short read sequencing.
    Genome research (17 November 2008)
    by Josephine A A Reinhardt, David A A Baltrus, Marc T T Nishimura, William R R Jeck, Corbin D D Jones, Jeffery R R Dangl
    posted to ht_sequencing bacteria assembly 454 2008 by hpaces to the group Bioinformatics on 2008-11-21 09:46:47 as **
  • Computational prediction of host-pathogen protein protein interactions
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i159-166.
    by Matthew D Dyer, TM Murali, Bruno W Sobral
    posted to systems proteins pathomics pathogen networks malaria interactions host-pathogen computationalbiology by behindtherabbit to the group Bioinformatics on 2008-11-17 20:58:13 as read along with 4 people operon GustavoLacerda carlk cerca
  • PIG--the pathogen interaction gateway
    Nucl. Acids Res. (4 November 2008), gkn799.
    by Tim Driscoll, Matthew D Dyer, TM Murali, Bruno W Sobral
    posted to visualization proteins pathomics pathogen networks interactions database blast by behindtherabbit to the group Bioinformatics on 2008-11-17 20:47:54 as read
  • Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes
    PLoS ONE, Vol. 3, No. 11. (14 November 2008), e3727.
    by Hong Sun, Geir Skogerbø, Zhen Wang, Wei Liu, Yixue Li
    posted to structural motifs genes elements conserved by sameetmehta to the group Bioinformatics on 2008-11-15 01:52:53 as ***** along with 3 people hpaces bpcusack Ema
  • Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results
    PLoS ONE, Vol. 3, No. 11. (14 November 2008), e3724.
    by Hyuna Yang, Christina A Harrington, Kristina Vartanian, Christopher D Coldren, Rob Hall, Gary A Churchill
    posted to randomization microarray_analysis interesting by sameetmehta to the group Bioinformatics on 2008-11-14 17:13:53 as ***** along with 2 people rdiaz GeeSharpMinor
  • Creative elements: network-based predictions of active centres in proteins and cellular and social networks.
    Trends in biochemical sciences (20 October 2008)
    by Peter Csermely
    posted to small_world review networks by barry to the group Bioinformatics on 2008-10-25 18:28:13 as ** along with 2 people nilanjanroy cmmorel
  • Surface Sites for Engineering Allosteric Control in Proteins
    Science, Vol. 322, No. 5900. (17 October 2008), pp. 438-442.
    by Jeeyeon Lee, Madhusudan Natarajan, Vishal C Nashine, Michael Socolich, Tina Vo, William P Russ, Stephen J Benkovic, Rama Ranganathan
    posted to sca protein_design correlated_mutations allosteric by barry to the group Bioinformatics on 2008-10-17 03:06:03 as *** along with 5 people and 2 groups lflorez cactus marck i000 paulschlesinger structural_bioinformatics McCammon
  • Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines.
    Proceedings of the National Academy of Sciences of the United States of America (30 September 2008)
    by Mohammad Monirul M Islam, Shihori Sohya, Keiichi Noguchi, Masafumi Yohda, Yutaka Kuroda
    posted to protein_structure protein_design bpti by barry to the group Bioinformatics on 2008-10-05 19:12:36 as ** along with 2 groups structural_bioinformatics McCammon
  • A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.
    Proceedings of the National Academy of Sciences of the United States of America (1 October 2008)
    by Mingyang Lu, Jianpeng Ma
    posted to nma coarse_grain by barry to the group Bioinformatics on 2008-10-05 19:05:40 as ** along with 4 people and 3 groups apaydin ruvido agrossfield skoddet Nielsen group structural_bioinformatics McCammon
  • Exploring the functional landscape of gene expression: directed search of large microarray compendia.
    Bioinformatics (30 August 2007)
    by Matthew A A Hibbs, David C C Hess, Chad L L Myers, Curtis Huttenhower, Kai Li, Olga G G Troyanskaya
    posted to visualization microarray expression algorithm by tharris to the group Bioinformatics on 2008-10-03 17:02:48 as ** along with 3 people jyuh tmmurali rdiaz
  • Protein co-evolution, co-adaptation and interactions
    The EMBO Journal, Vol. aop, No. current. (25 September 2008)
    by Florencio Pazos, Alfonso Valencia
    posted to review protein_protein phylogeny correlated_mutations by barry to the group Bioinformatics on 2008-10-02 20:24:17 as ***** along with 3 people and 2 groups fhsantanna marti sjcockell structural_bioinformatics McCammon
  • Flexible ligand docking to multiple receptor conformations: a practical alternative.
    Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 178-184.
    by M Totrov, R Abagyan
    posted to review md_simulation docking by barry to the group Bioinformatics on 2008-10-02 19:48:14 as ** along with 1 person and 2 groups aqeel structural_bioinformatics McCammon
  • The structure of protein evolution and the evolution of protein structure
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Richard A Goldstein
    posted to review protein_structure protein_evolution fold_space by barry to the group Bioinformatics on 2008-10-02 19:46:30 as ** along with 3 people and 2 groups bpb zwang cmzmasek structural_bioinformatics McCammon
  • notes Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Anthony A Kossiakoff, Shohei Koide
    posted to review protein_protein protein_dynamics by barry to the group Bioinformatics on 2008-10-02 19:21:01 as ** along with 1 person and 2 groups paulschlesinger structural_bioinformatics McCammon
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816.
    posted to project human genome encode by pengchy to the group Bioinformatics on 2008-10-02 02:50:26 as ** along with 27 people and 3 groups polivares Eroslavochka timflutre raistrick jyuh cmmorel dpollard ilh djkt plofje ramensky joepickrell massivemayhem fishtank Garamonfok jmuhlich bioyang cabbagezs xingxu antonkratz mimulus_99 julianjonker gjuggler drbal maralena ep161302 jasonflannick JacksonLab EisenLab SorgerLab
  • A Specificity Map for the PDZ Domain Family
    PLoS Biology, Vol. 6, No. 9. (1 September 2008), e239.
    by Raffi Tonikian, Yingnan Zhang, Stephen L Sazinsky, Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A Held, Brent A Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C Chan, Somasekar Seshagiri, Laurence A Lasky, Chris Sander, Charles Boone, Gary D Bader, Sachdev S Sidhu
    posted to protein_protein pdz by barry to the group Bioinformatics on 2008-09-30 18:44:35 as *** along with 3 people and 2 groups markchen zwang cabbagesofdoom structural_bioinformatics McCammon
  • An information-based sequence distance and its application to whole mitochondrial genome phylogeny
    Bioinformatics, Vol. 17, No. 2. (1 February 2001), pp. 149-154.
    by Ming Li, Jonathan H Badger, Xin Chen, Sam Kwong, Paul Kearney, Haoyong Zhang
    posted to no-tag by isakemal to the group Bioinformatics on 2008-09-29 03:57:24 as ** along with 2 people balicea karipuf
  • notes An Inhibitor of FtsZ with Potent and Selective Anti-Staphylococcal Activity
    Science, Vol. 321, No. 5896. (19 September 2008), pp. 1673-1675.
    by David J Haydon, Neil R Stokes, Rebecca Ure, Greta Galbraith, James M Bennett, David R Brown, Patrick J Baker, Vladimir V Barynin, David W Rice, Sveta E Sedelnikova, Jonathan R Heal, Joseph M Sheridan, Sachin T Aiwale, Pramod K Chauhan, Anil Srivastava, Amit Taneja, Ian Collins, Jeff Errington, Lloyd G Czaplewski
    posted to tubulin ftsz drug_design cytoskeleton by barry to the group Bioinformatics on 2008-09-29 01:52:44 as read along with 2 people and 2 groups martainn madhadron structural_bioinformatics McCammon
  • Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000151.
    by Raja Mazumder, Sona Vasudevan
    posted to protein_structure protein_function by barry to the group Bioinformatics on 2008-09-26 21:48:09 as ** along with 9 people and 1 group i000 pengchy raik chad_davis zwang druvus reyez mdstobbe jameswasmuth structural_bioinformatics
  • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (2007), pp. 646-661.
    by Allison P Heath, Lydia E Kavraki, Cecilia Clementi
    posted to protein_structure coarse_grain by barry to the group Bioinformatics on 2008-09-26 18:14:38 as *** along with 2 people and 2 groups aqeel mijam structural_bioinformatics McCammon
  • Iterative signature algorithm for the analysis of large-scale gene expression data
    Physical Review E, Vol. 67, No. 3. (11 March 2003), 031902.
    by Sven Bergmann, Jan Ihmels, Naama Barkai
    posted to no-tag by tvdbulck to the group Bioinformatics on 2008-09-23 15:18:38 as **
  • Local Function Conservation in Sequence and Structure Space
    PLoS Comput Biol, Vol. 4, No. 7. (4 July 2008), e1000105.
    by Nils Weinhold, Oliver Sander, Francisco S Domingues, Thomas Lengauer, Ingolf Sommer
    posted to protein_structure protein_sequence function_prediction by barry to the group Bioinformatics on 2008-09-08 17:53:09 as read along with 2 people and 2 groups cabbagesofdoom Ema structural_bioinformatics McCammon
  • Enriched random forests.
    Bioinformatics (Oxford, England) (22 July 2008)
    by Dhammika Amaratunga, Javier Cabrera, Yung-Seop S Lee
    posted to random_forest by pengchy to the group Bioinformatics on 2008-09-06 09:03:38 as ** along with 3 people jfr jjrodriguez jyuh
  • Getting Started in Computational Immunology
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000128.
    by Steven H Kleinstein
    posted to review immunology by barry to the group Bioinformatics on 2008-09-05 21:58:23 as ** along with 8 people and 1 group Zephyrus nuin reyez dakelley GeeSharpMinor rebeccamancy AbnerCYH jjray Roswell Cancer Crosstalk
  • Gene Expression Profiles in the Brain Predict Behavior in Individual Honey Bees
    Science, Vol. 302, No. 5643. (10 October 2003), pp. 296-299.
    by Charles W Whitfield, Anne-Marie Cziko, Gene E Robinson
    posted to predict behavior by pengchy to the group Bioinformatics on 2008-09-02 07:14:41 as ***** along with 1 group bioNetwork_sysBio
  • An Enzymatic Atavist Revealed in Dual Pathways for Water Activation
    PLoS Biology, Vol. 6, No. 8. (1 August 2008), e206.
    by Donghong Min, Helen R Josephine, Hongzhi Li, Clemens Lakner, Iain S Macpherson, Gavin J Naylor, David Swofford, Lizbeth Hedstrom, Wei Yang
    posted to imp_dehydrogenase qm_mm by barry to the group Bioinformatics on 2008-08-26 18:45:20 as ***** along with 2 groups McCammon structural_bioinformatics
  • Fast embedding methods for clustering tens of thousands of sequences.
    Computational biology and chemistry, Vol. 32, No. 4. (August 2008), pp. 282-286.
    by G Blackshields, M Larkin, IM Wallace, A Wilm, DG Higgins
    posted to bioinf_methods clustering protein_sequence by barry to the group Bioinformatics on 2008-08-23 20:27:35 as **** along with 1 group structural_bioinformatics
  • A comparison of common programming languages used in bioinformatics
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Mathieu Fourment, Michael Gillings
    posted to programming review by barry to the group Bioinformatics on 2008-08-21 18:01:48 as * along with 15 people and 1 group treangen natstreet nlapalu druvus jamselem dullhunk laughcry ibuch urgi sci91078 renatomilani xili03 phoenixzxl jyuh chad_davis structural_bioinformatics
  • Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin
    Journal of Molecular Biology, Vol. 381, No. 5. (19 September 2008), pp. 1407-1420.
    by Yang Yang, Haibo Yu, Qiang Cui
    posted to md_simulation molecular_motors motor_model myosin qm by barry to the group Bioinformatics on 2008-08-18 20:21:10 as ** along with 1 group structural_bioinformatics
  • MetalDetector: a web server for predicting metal binding sites and disulfide bridges in proteins from sequence
    Bioinformatics (16 July 2008), btn371.
    by Marco Lippi, Andrea Passerini, Marco Punta, Burkhard Rost, Paolo Frasconi
    posted to biochemistry bioinformatics disulfide-bridges machine-learning metal-binding-sites prediction-servers protein-function protein-structure by paolo to the group Bioinformatics on 2008-08-14 13:59:31 as ***** along with 1 person druvus
  • Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins
    Structure, Vol. 16, No. 6. (11 June 2008), pp. 885-896.
    by Alemayehu A Gorfe, Barry J Grant, Andrew J Mccammon
    posted to md_simulation mine ntpases pca protein_dynamics protein_structure ras by barry to the group Bioinformatics on 2008-06-10 22:34:01 as read along with 1 group structural_bioinformatics
  • Microarray learning with ABC.
    Biostatistics (14 June 2007)
    by Dhammika Amaratunga, Javier Cabrera, Vladimir Kovtun
    posted to clustering microarrays by barry to the group Bioinformatics on 2008-06-09 22:24:20 as ** along with 2 people jfr jyuh
  • VisANT: an integrative framework for networks in systems biology
    Brief Bioinform (7 May 2008), bbn020.
    by Zhenjun Hu, Evan S Snitkin, Charles Delisi
    posted to biology graph systems visualization by sameetmehta to the group Bioinformatics on 2008-05-13 04:50:49 as ***** along with 7 people druvus jfr bootsy maralena jyuh maoxizeng srp33
  • A new pheromone trail-based genetic algorithm for comparative genome assembly
    Nucl. Acids Res. (29 April 2008), gkn168.
    by Fangqing Zhao, Fanggeng Zhao, Tao Li, Donald A Bryant
    posted to assembly bioinformatics genome genomics by fqzhao to the group Bioinformatics on 2008-05-07 21:28:04 as read
  • Darwinian Evolution on a Chip
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e85.
    by Brian M Paegel, Gerald F Joyce
    posted to directed_evolution journal_club by barry to the group Bioinformatics on 2008-04-29 20:13:18 as **** along with 11 people and 1 group stevanspringer operon xingxu Minty renatomilani TomQ phoenixzxl melting dlobo cfleet fdsayre GEB
  • A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e98.
    by Julian R Hughes, Ana M Meireles, Katherine H Fisher, Angel Garcia, Philip R Antrobus, Alan Wainman, Nicole Zitzmann, Charlotte Deane, Hiroyuki Ohkura, James G Wakefield
    posted to mts protein_protein tubulin by barry to the group Bioinformatics on 2008-04-29 19:37:04 as ** along with 1 person cdeane
  • Very fast empirical prediction and rationalization of protein pKa values.
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 704-721.
    by H Li, AD Robertson, JH Jensen
    posted to bioinf_methods md_simulation pka by barry to the group Bioinformatics on 2008-04-25 20:55:37 as ** along with 6 people RamuAnandakrishnan gisle bicko sim82 sunhwan mschofie
  • notes Tracing evolutionary pressure
    Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 908-915.
    by Kai Ye, Gert Vriend, Adriaan P Ijzerman
    posted to bioinf_methods phylogeny protein_evolution protein_sequence residue_annotation by barry to the group Bioinformatics on 2008-04-11 19:13:22 as *** along with 2 people and 1 group sunhwan gulkur structural_bioinformatics
  • Integration of microarray and textual data improves the prognosis prediction of breast, lung and ovarian cancer patients.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 279-290.
    by O Gevaert, S Van Vooren, B de Moor
    posted to bayesian integration literature microarray network text by frohike to the group Bioinformatics on 2008-04-07 14:49:29 as ** along with 2 people mitko jfr
  • A Framework for Elucidating Regulatory Networks Based on Prior Information and Expression Data
    Annals of the New York Academy of Sciences, Vol. 1115, No. 1. (December 2007), pp. 240-248.
    by Olivier Gevaert, VAN Vooren, N Steve, DE Moor, T Bar
    posted to bayesian dream integration microarray network prior protein by frohike to the group Bioinformatics on 2008-04-07 14:48:50 as ** along with 1 person jyuh
  • Expression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation
    BMC Cancer, Vol. 8 (22 January 2008), 18.
    by Olivier Gevaert, Frank De Smet, Toon Van Gorp, Nathalie Pochet, Kristof Engelen, Frederic Amant, Bart De Moor, Dirk Timmerman, Ignace Vergote
    posted to cancer microarray ovarian platin platinum by frohike to the group Bioinformatics on 2008-04-07 14:48:20 as ** along with 1 person jfr
  • Prediction of ectopic pregnancy in women with a pregnancy of unknown location
    Ultrasound in Obstetrics and Gynecology, Vol. 29, No. 6. (June 2007), pp. 680-687.
    by Condous, , Van Calster, , Kirk, , Haider, , Timmerman, , Van Huffel, , Bourne,
    posted to clinical logistic pul regression by frohike to the group Bioinformatics on 2008-04-07 14:45:30 as **
  • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    Mol Syst Biol, Vol. 3 (10 July 2007)
    by Robert Schuetz, Lars Kuepfer, Uwe Sauer
    posted to coli escherichia flux by robertvandenberg to the group Bioinformatics on 2008-04-06 12:27:04 as ** along with 5 people alexg fishtank zwang Ema michaelbarton
  • Assessment of PLSDA cross validation
    Metabolomics, Vol. 4, No. 1. (31 March 2008), pp. 81-89.
    by Johan Westerhuis, Huub Hoefsloot, Suzanne Smit, Daniel Vis, Age Smilde, Ewoud van Velzen, John van Duijnhoven, Ferdi van Dorsten
    posted to cross-validation plsda validation by robertvandenberg to the group Bioinformatics on 2008-04-06 12:12:48 as ** along with 1 person jyuh
  • A simple method for assessing sample sizes in microarray experiments.
    BMC Bioinformatics, Vol. 7 (2006)
    by R Tibshirani
    posted to microarray micro-array sample sampling size by robertvandenberg to the group Bioinformatics on 2008-04-05 10:15:21 as ** along with 4 people jen_drake gpalidwor ugengma bertelsen
  • A second generation human haplotype map of over 3.1 million SNPs
    Nature, Vol. 449, No. 7164. (18 October 2007), pp. 851-861.
    posted to genetic hapmap human snp variation by frohike to the group Bioinformatics on 2008-04-04 13:56:06 as ** along with 13 people and 1 group Hans45 misonneh gowtham psique jyuh dchughes djkt lp2 ryanraaum xingxu jasonflannick skumagai mfm11 parkinson's disease references
  • Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    Nucleic Acids Research, Vol. 33, No. 20. (2005), pp. e175-e175.
    by Manhong Dai, Pinglang Wang, Andrew D Boyd, Georgi Kostov, Brian Athey, Edward G Jones, William E Bunney, Richard M Myers, Terry P Speed, Huda Akil, Stanley J Watson, Fan Meng
    posted to cdf by frohike to the group Bioinformatics on 2008-04-04 10:34:14 as ** along with 9 people and 1 group giovenko pcahan1 incovoma nicholso heliopais Montrachet shikin bertelsen waszak GeneGo
  • Extending pathways based on gene lists using InterPro domain signatures
    BMC Bioinformatics, Vol. 9 (04 January 2008), 3.
    by Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, Tim Beissbarth
    posted to geneset gsea interpro by frohike to the group Bioinformatics on 2008-04-04 10:26:10 as ** along with 4 people ealloza renatomilani jyuh AlexanderPico
  • Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions.
    Nucleic Acids Res (16 March 2008)
    by Katleen De Preter, Roland Barriot, Frank Speleman, Jo Vandesompele, Yves Moreau
    posted to aberration chromosomal geneset gsea positional by frohike to the group Bioinformatics on 2008-04-04 10:20:24 as ** along with 4 people tmmurali bootsy inesdesantiago jfr
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