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Tag bioinfo [49 articles]

Recent papers classified by the tag bioinfo.
  • Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes.
    Genome Res (12 December 2005)
    by Kouichi Kimura, Ai Wakamatsu, Yutaka Suzuki, Toshio Ota, Tetsuo Nishikawa, Riu Yamashita, Jun-Ichi I Yamamoto, Mitsuo Sekine, Katsuki Tsuritani, Hiroyuki Wakaguri, Shizuko Ishii, Tomoyasu Sugiyama, Kaoru Saito, Yuko Isono, Ryotaro Irie, Norihiro Kushida, Takahiro Yoneyama, Rie Otsuka, Katsuhiro Kanda, Takahide Yokoi, Hiroshi Kondo, Masako Wagatsuma, Katsuji Murakawa, Shinichi Ishida, Tadashi Ishibashi, Asako Takahashi-Fujii, Tomoo Tanase, Keiichi Nagai, Hisashi Kikuchi, Kenta Nakai, Takao Isogai, Sumio Sugano
    posted to annotation bioinfo genome promoter by textoris on 2007-02-24 15:04:30 as read along with 7 people ujh troels_marstrand olympos nosada17 antonkratz bethsabrina yoanjacquemin
  • Validation and refinement of gene-regulatory pathways on a network of physical interactions.
    Genome Biol, Vol. 6, No. 7. (2005)
    by CH Yeang, HC Mak, S McCuine, C Workman, T Jaakkola, T Ideker
    posted to bioinfo reseaux by textoris on 2005-09-17 17:33:25 as ** along with 13 people and 1 group isimpson hplatero snuppepuppan abhik tmmurali wnpx noano koller ccr cdppublications AlexanderPico carlk jago CDP
  • Text mining for metabolic pathways, signaling cascades, and protein networks.
    Sci STKE, Vol. 2005, No. 283. (10 May 2005)
    by R Hoffmann, M Krallinger, E Andres, J Tamames, C Blaschke, A Valencia
    posted to bioinfo text_mining by textoris on 2005-09-17 17:12:17 as ** along with 6 people and 4 groups irenas matzke kuhn yas marcius fisherp dbk-lab T_lab BioinfoCIPF SGU-CIPF
  • Having a BLAST with bioinformatics (and avoiding BLASTphemy).
    Genome Biol, Vol. 2, No. 10. (2001)
    by A Pertsemlidis, JW Fondon
    posted to bioinfo blast by textoris on 2005-09-17 17:15:38 as read along with 8 people and 2 groups karbak ziquje prtmht shantanu cjeans sujaikumar scottstensland hpaces Bioinformatics MathBio
  • Systems biology: where it's at in 2005.
    Genome Biol, Vol. 6, No. 8. (2005)
    by B Lehner, J Tischler, AG Fraser
    posted to bioinfo biology system by textoris on 2005-09-17 17:19:38 as ** along with 4 people Borelli hammerle_dea biosv mangtronix
  • Statistical implications of pooling RNA samples for microarray experiments.
    BMC Bioinformatics, Vol. 4 (24 June 2003)
    by X Peng, CL Wood, EM Blalock, KC Chen, PW Landfield, AJ Stromberg
    posted to analyse bioinfo puces_adn stat by textoris on 2005-09-17 15:58:10 as **
  • The Vertebrate Genome Annotation (Vega) database.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by JL Ashurst, CK Chen, JG Gilbert, K Jekosch, S Keenan, P Meidl, SM Searle, J Stalker, R Storey, S Trevanion, L Wilming, T Hubbard
    posted to annotation bioinfo genome by textoris on 2007-02-24 14:55:43 as read
  • Self-correcting maps of molecular pathways.
    PLoS ONE, Vol. 1 (2006)
    by A Rzhetsky, T Zheng, C Weinreb
    posted to bioinfo network by textoris on 2007-02-24 15:15:48 as read along with 3 people massivemayhem equipediaz florianleitner
  • Text-mining and information-retrieval services for molecular biology.
    Genome Biol, Vol. 6, No. 7. (2005)
    by M Krallinger, A Valencia
    posted to bioinfo text_mining by textoris on 2005-09-17 17:11:08 as ** along with 10 people and 6 groups A_Hoogendam fisherp irenas Enro carlblesius yas caporaso shimah78us cjeans spinaltap526 dbk-lab Blog_and_Wiki_Research mgh-lcs hst-bmi T_lab biomedical-nlp
  • Viewing and annotating sequence data with Artemis.
    Brief Bioinform, Vol. 4, No. 2. (June 2003), pp. 124-132.
    by M Berriman, K Rutherford
    posted to annotation bioinfo genome by textoris on 2007-02-24 14:51:42 as read
  • Implementing the iHOP concept for navigation of biomedical literature.
    Bioinformatics, Vol. 21 Suppl 2 (1 September 2005)
    by R Hoffmann, A Valencia
    posted to bioinfo ihop modules network text_mining by textoris on 2007-02-24 15:23:03 as read along with 3 people and 4 groups yas marcius mroos T_lab BioinfoCIPF SGU-CIPF AID
  • The otter annotation system.
    Genome Res, Vol. 14, No. 5. (May 2004), pp. 963-970.
    by SM Searle, J Gilbert, V Iyer, M Clamp
    posted to annotation bioinfo genome by textoris on 2007-02-24 14:58:09 as read
  • ARTEMIS: a tool for displaying and annotating DNA sequence.
    Brief Bioinform, Vol. 1, No. 2. (May 2000), pp. 199-200.
    by RJ Mural
    posted to annotation bioinfo genome by textoris on 2007-02-24 14:50:53 as read
  • iHOPerator: User-scripting a personalized bioinformatics Web, starting with the iHOP website
    BMC Bioinformatics, Vol. 7 (15 December 2006), 534.
    by Benjamin M Good, Edward A Kawas, Byron Y Kuo, Mark D Wilkinson
    posted to bioinfo ihop modules network text_mining by textoris on 2007-02-24 15:18:54 as read along with 7 people jfr chad_davis dullhunk egonw equipediaz cerami jyuh
  • Text-mining approaches in molecular biology and biomedicine.
    Drug Discov Today, Vol. 10, No. 6. (15 March 2005), pp. 439-445.
    by M Krallinger, RA Erhardt, A Valencia
    posted to bioinfo text_mining by textoris on 2005-09-17 17:12:42 as *** along with 4 people and 1 group irenas kuhn josepe kallberg dbk-lab
  • Genome annotation past, present, and future: how to define an ORF at each locus.
    Genome Res, Vol. 15, No. 12. (December 2005), pp. 1777-1786.
    by MR Brent
    posted to annotation bioinfo genome by textoris on 2007-02-24 15:00:11 as read along with 3 people and 1 group Ayest indigoviolet wenhan EisenLab
  • VEGA, the genome browser with a difference.
    Brief Bioinform, Vol. 6, No. 2. (June 2005), pp. 189-193.
    by J Loveland
    posted to annotation bioinfo genome by textoris on 2007-02-24 14:54:46 as read
  • Interactive visualization and exploration of relationships between biological objects.
    Trends Biotechnol, Vol. 18, No. 12. (December 2000), pp. 487-494.
    by DR Gilbert, M Schroeder, J van Helden
    posted to 3d bioinfo reseaux by textoris on 2005-09-17 15:54:22 as read
  • PoooL: An efficient method for estimating haplotype frequencies from large DNA pools.
    Bioinformatics (Oxford, England) (23 June 2008)
    by Han Zhang, Hsin-Chou C Yang, Yaning Yang
    posted to bioinfo decode pooling by rmk on 2008-08-30 15:43:17 as *** along with 2 people APRegier jyuh
  • 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 bioinfo cgt design pooling quapo std by rmk on 2008-08-17 22:45:37 as read along with 3 people reyez neils jyuh
  • Directed acyclic graph kernels for structural RNA analysis
    BMC Bioinformatics, Vol. 9 (22 July 2008), 318.
    by Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
    posted to bioinfo by rmk on 2008-07-23 14:47:32 as ***
  • GBParsy: A GenBank flatfile parser library with high speed
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Tae H Lee, Yeon K Kim, Baek H Nahm
    posted to bioinfo by rmk on 2008-07-28 22:40:13 as ** along with 2 people and 1 group nuin stajich Berkeley Mycology
  • BioBayes: A Software Package for Bayesian Inference in Systems Biology
    Bioinformatics (16 July 2008), btn338.
    by Vladislav Vyshemirsky, Mark Girolami
    posted to bayes bioinfo code sysbio by rmk on 2008-08-30 15:44:01 as ** along with 4 people renatomilani nuin lemke jyuh
  • Machine learning based analyses on metabolic networks supports high-throughput knockout screens
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Kitiporn Plaimas, Jan P Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, Rainer Konig
    posted to bioinfo by rmk on 2008-07-24 13:14:16 as ** along with 1 person colinDotAIBN
  • Computational design of synthetic gene circuits with composable parts.
    Bioinformatics (Oxford, England) (25 June 2008)
    by M A A Marchisio, J Stelling
    posted to bioinfo synthbio by rmk on 2008-08-30 15:44:45 as ** along with 2 people austin lemke
  • A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification
    BMC Bioinformatics, Vol. 9 (22 July 2008), 319.
    by Alexander Statnikov, Lily Wang, Constantin F Aliferis
    posted to bioinfo by rmk on 2008-07-23 14:47:08 as *** along with 4 people jfr mdharsee provero chad_davis
  • Combining transcriptional datasets using the generalized singular value decomposition
    BMC Bioinformatics, Vol. 9 (08 August 2008), 335.
    by Andreas W Schreiber, Neil J Shirley, Rachel A Burton, Geoffrey B Fincher
    posted to bioinfo by rmk on 2008-08-08 21:47:38 as ** along with 3 people GeeSharpMinor shigepong dansullivanblk
  • Identification of genetic variants using bar-coded multiplexed sequencing
    Nat Meth, Vol. 5, No. 10. (October 2008), pp. 887-893.
    by David W Craig, John V Pearson, Szabolcs Szelinger, Aswin Sekar, Margot Redman, Jason J Corneveaux, Traci L Pawlowski, Trisha Laub, Gary Nunn, Dietrich A Stephan, Nils Homer, Matthew J Huentelman
    posted to ucla bioinfo bio algorithms by pwais on 2008-09-30 00:11:37 as ** along with 1 person matthewsuderman
  • Protein Structure Prediction with Large Neighborhood Constraint Programming Search
    Principles and Practice of Constraint Programming (2008), pp. 82-96.
    by Ivan Dotu, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote
    posted to search programming constraint bioinformatics bioinfo bio by pwais on 2008-10-04 21:20:48 as **
  • When is homology not homology?
    Curr Opin Genet Dev, Vol. 8, No. 6. (December 1998), pp. 675-680.
    by GA Wray, E Abouheif
    posted to bioinfo by neetiitr on 2008-06-06 02:49:23 as **** along with 2 people and 2 groups sangeetha anatiferous Bioinformatics insilicodrug
  • Basic local alignment search tool.
    J Mol Biol, Vol. 215, No. 3. (5 October 1990), pp. 403-410.
    by SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman
    posted to alignement bioinfo by hervelequere on 2008-03-11 15:23:21 as ** along with 45 people and 6 groups pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
  • Bioinformatics--principles and potential of a new multidisciplinary tool.
    Trends Biotechnol, Vol. 14, No. 8. (August 1996), pp. 261-272.
    by D Benton
    posted to bioinfo by greger_halltorp on 2005-02-12 15:41:12 as read
  • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680.
    by JD Thompson, DG Higgins, TJ Gibson
    posted to bioinfo by greger_halltorp on 2005-02-14 12:22:28 as read along with 24 people and 1 group usagi-kirin jmw jshapiro mercaptan evaf caldavis miguel onlyrey bjorns aprasad RMGraze moborg arcticrasta dullhunk caporaso ahanora Haggan BioNica leelarcombe timflutre adijr xingxu newton1234 Lombardo_7 biomedical-nlp
  • A statistical method for alignment-free comparison of regulatory sequences
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i249-255.
    by Miriam R Kantorovitz, Gene E Robinson, Saurabh Sinha
    posted to sequences regulatory bioinfo - by CharlesM on 2008-10-09 14:47:56 as ** along with 2 people and 1 group maximilianh cisevol cis-regulatory-evolution
  • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
    BMC Bioinformatics, Vol. 3 (24 October 2002)
    by N Rajewsky, M Vergassola, U Gaul, ED Siggia
    posted to algorithm bioinfo maximal-likelihood by ansobol on 2007-07-10 09:25:33 as ** along with 6 people and 1 group isimpson indigoviolet adepace koller Stew csdhwang EisenLab
  • Genetic Sequential Dynamical Systems
    (15 Mar 2006)
    by Maria A Avino-Diaz, Humberto Ortiz
    posted to bioinfo by ansobol on 2006-03-18 07:59:06 as **
  • The transposition distance for phylogenetic trees
    (18 Apr 2006)
    by Francesc Rossello, Gabriel Valiente
    posted to bioinfo phylogenomics tree by ansobol on 2006-04-20 08:00:37 as **
  • Faster Algorithms for Constructing a Galois Lattice, Enumerating All Maximal Bipartite Cliques and Closed Frequent Sets
    (19 Feb 2006)
    by Vicky Choi, Yang Huang
    posted to algorithm assignment bioinfo galois by ansobol on 2006-02-21 06:45:36 as **
  • notes Emergent Computation : Emphasizing Bioinformatics (Biological and Medical Physics, Biomedical Engineering)
    (07 January 2005)
    by Matthew Simon
    posted to bioinfo biology computation by ansobol on 2005-09-07 15:47:32 as **
  • Digital search trees and chaos game representation
    (29 May 2006)
    by Peggy Cénac, Brigitte Chauvin, Stéphane Ginouillac, Nicolas Pouyanne
    posted to bioinfo biology biomacromolecule dna markov by ansobol on 2006-05-30 20:57:11 as **
  • The Mathematics of Phylogenomics
    (27 Sep 2005)
    by Lior Pachter, Bernd Sturmfels
    posted to bioinfo phylogenomics by ansobol on 2005-09-28 19:50:25 as **
  • Hidden word statistics
    J. ACM, Vol. 53, No. 1. (January 2006), pp. 147-183.
    by Philippe Flajolet, Wojciech Szpankowski, Brigitte Vall&\#233;e
    posted to bioinfo biology clt combinatorics large-deviation by ansobol on 2006-04-01 20:18:00 as ** along with 1 person BarrosH
  • The Mystery of Two Straight Lines in Bacterial Genome Statistics
    (28 February 2005)
    by A Gorban, A Yu
    posted to bioinfo by ansobol on 2005-03-08 17:21:15 as **
  • Topology in Molecular Biology : DNA and Proteins (Biological and Medical Physics, Biomedical Engineering)
    (31 August 2005)
    by Michael I Monastyrsky
    posted to bioinfo biology dna protein topology by ansobol on 2005-09-07 15:44:33 as ** along with 1 person gane5h
  • Discrete differential geometry of proteins: a new method for encoding three-dimensional structures of proteins
    (5 June 2005)
    by Naoto Morikawa
    posted to bioinfo biology biomacromolecule biopolymer protein by ansobol on 2005-06-07 16:49:31 as **
  • Parametric Inference for Biological Sequence Analysis
    (26 January 2004)
    by Lior Pachter, Bernd Sturmfels
    posted to bioinfo statistical tropical by ansobol on 2005-03-30 08:21:09 as **
  • Solvable models of neighbor-dependent nucleotide substitution processes
    (3 Oct 2005)
    by Jean Bérard, Gouéré, Didier Piau
    posted to bioinfo by ansobol on 2005-10-04 16:48:30 as ** along with 1 person Ayest
  • Tropical Geometry of Statistical Models
    (26 January 2004)
    by Lior Pachter, Bernd Sturmfels
    posted to bioinfo statistical tropical by ansobol on 2005-03-08 12:17:00 as **
  • Algebraic Statistics for Computational Biology
    (22 August 2005)
    edited by L Pachter, B Sturmfels
    posted to algebra algorithm bioinfo statistics by ansobol on 2006-04-06 06:21:10 as ** along with 2 people and 1 group mdreid BarrosH Statistical Machine Learning
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