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hpaces bioinformatics [42 articles]

Recent papers added to hpaces library classified by the tag bioinformatics. You can also see everyone's bioinformatics.
  • Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons
    Human Mutation, Vol. 28, No. 2. (2007), pp. 99-130.
    by Hildegard Kehrer-Sawatzki, David N Cooper
    posted to review human comparative_genomics chimp bioinformatics 2006 by hpaces on 2008-07-09 10:58:00 as ** along with 6 people and 2 groups pradiptaray bpb balicea dchughes sebastien_vigneau jpdemuth G4ID Genetics-of-Gambling
  • KEGG for linking genomes to life and the environment
    Nucl. Acids Res. (12 December 2007), gkm882.
    by Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi
    posted to database bioinformatics 2008 by hpaces on 2008-05-19 10:00:42 as ** along with 9 people TheresaNiederberger natstreet massivemayhem irenas jyuh raiyar barriot renatomilani shung
  • Vir-Mir db: prediction of viral microRNA candidate hairpins.
    Nucleic acids research, Vol. 36, No. Database issue. (January 2008)
    by SC Li, CK Shiau, WC Lin
    posted to mirna database bioinformatics 2008 by hpaces on 2008-05-11 16:11:41 as **
  • Mapping and sequencing of structural variation from eight human genomes
    Nature, Vol. 453, No. 7191., pp. 56-64.
    by Jeffrey M Kidd, Gregory M Cooper, William F Donahue, Hillary S Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci, Eric Haugen, Troy Zerr, Alice N Yamada, Peter Tsang, Tera L Newman, Eray Tüzün, Ze Cheng, Heather M Ebling, Nadeem Tusneem, Robert David, Will Gillett, Karen A Phelps, Molly Weaver, David Saranga, Adrianne Brand, Wei Tao, Erik Gustafson, Kevin Mckernan, Lin Chen, Maika Malig, Joshua D Smith, Joshua M Korn, Steven A Mccarroll, David A Altshuler, Daniel A Peiffer, Michael Dorschner, John Stamatoyannopoulos, David Schwartz, Deborah A Nickerson, James C Mullikin, Richard K Wilson, Laurakay Bruhn, Maynard V Olson, Rajinder Kaul, Douglas R Smith, Evan E Eichler
    posted to human horizontal_transfer bioinformatics 2008 by hpaces on 2008-05-11 12:45:22 as read along with 15 people and 1 group jyuh chrisamiller maximilianh vplagnol kintoki chad_davis Ema aprasad kaniko psique shikin balicea djkt dchughes bpb GeneGo
  • Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity.
    Proc Natl Acad Sci U S A, Vol. 104, No. 18. (1 May 2007), pp. 7564-7569.
    by LH Saal, P Johansson, K Holm, SK Gruvberger-Saal, QB She, M Maurer, S Koujak, AA Ferrando, P Malmström, L Memeo, J Isola, PO Bendahl, N Rosen, H Hibshoosh, M Ringnér, A Borg, R Parsons
    posted to regulation gene_expression_array cancer bioinformatics array 2007 by hpaces on 2008-05-02 09:59:31 as **** along with 1 person jfr
  • What is principal component analysis?
    Nature Biotechnology, Vol. 26, No. 3., pp. 303-304.
    by Markus Ringnér
    posted to statistics review bioinformatics algorithm 2008 by hpaces on 2008-05-02 07:29:10 as ** along with 52 people and 3 groups mjoach ale rrbarb HugoMarcelo tharris rsantana kengg laharrin chrissp100 xingxu dekay23 rvosa i-stevenson dimka dayjm markusd ashko craigwilson06 abbie_riner quianominorleo bibay2004 jfr kristgy pavanghatty rchauhan waghsk adacier fryanpan sobolevnrm Yanno jyuh operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu FAB-lab Bioinformatics baker-group
  • Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts
    BMC Bioinformatics, Vol. 8 (26 June 2007), 221.
    by Joern Toedling, Oleg Sklyar, Wolfgang Huber
    posted to 2007 algorithm array bioinformatics software by hpaces on 2008-01-31 10:33:54 as ** along with 5 people inesdesantiago jyuh jfr ghattem caseybrown
  • Automated generation of heuristics for biological sequence comparison
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by Guy Slater, Ewan Birney
    posted to 2005 algorithm alignment bioinformatics software by hpaces on 2008-01-29 10:43:34 as **** along with 4 people and 1 group indigoviolet massivemayhem wenhan marti EisenLab
  • Chaos game representation for comparison of whole genomes
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Jijoy Joseph, Roschen Sasikumar
    posted to 2006 bioinformatics evolution genomics by hpaces on 2008-01-22 08:25:32 as ** along with 2 people operon skhadar
  • The ENCODE (ENCyclopedia Of DNA Elements) Project.
    Science, Vol. 306, No. 5696. (22 October 2004), pp. 636-640.
    by E Encode
    posted to 2007 bioinformatics genomics human by hpaces on 2007-12-20 13:23:33 as ** along with 8 people and 1 group setar balajis skhadar qfwills djkt frohike JeffR100 olympos Bioinformatics
  • Identification of disulfide reductases in Campylobacterales: a bioinformatics investigation.
    Antonie Van Leeuwenhoek, Vol. 92, No. 4. (November 2007), pp. 429-441.
    by NO Kaakoush, T Sterzenbach, WG Miller, S Suerbaum, GL Mendz
    posted to 2007 bacteria bioinformatics comparative_genomics genome by hpaces on 2007-12-11 09:02:55 as **
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to 2007 algorithm bioinformatics multiple_alignment review by hpaces on 2007-12-10 20:03:19 as ***** along with 3 people and 1 group skhadar sobolevnrm mingzhi baker-group
  • Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e230.
    by Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael Stumpf, Sylvia Richardson, Carsten Wiuf
    posted to 2007 bacteria bioinformatics evolution networks protein by hpaces on 2007-12-10 19:41:09 as ** along with 3 people zwang xingxu Ema
  • MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216.
    by Saurabh Sinha, Xin He
    posted to 2007 algorithm alignment bioinformatics hmm regulation software by hpaces on 2007-12-10 19:39:22 as ** along with 7 people and 2 groups ana dpollard cjeans zwang maximilianh Ema uwe EisenLab cis-regulatory-evolution
  • Detecting Coevolution in and among Protein Domains
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e211.
    by Chen-Hsiang Yeang, David Haussler
    posted to 2007 algorithm bioinformatics coevolution evolution protein by hpaces on 2007-12-10 18:37:49 as ** along with 11 people and 1 group pradiptaray balicea skhadar zwang sobolevnrm niallhaslam mingzhi Ema phoenixzxl penpen926 friendpine baker-group
  • A forest-based approach to identifying gene and gene gene interactions
    Proceedings of the National Academy of Sciences (28 November 2007), 0709868104.
    by Xiang Chen, Ching-Ti Liu, Meizhuo Zhang, Heping Zhang
    posted to 2007 bioinformatics gene_regulation by hpaces on 2007-12-09 09:08:20 as ** along with 5 people jyuh balicea cjeans zwang xingxu
  • Predicting protein function from sequence and structure
    Nat Rev Mol Cell Biol, Vol. 8, No. 12. (December 2007), pp. 995-1005.
    by David Lee, Oliver Redfern, Christine Orengo
    posted to 2007 bioinformatics function prediction protein review structure by hpaces on 2007-12-09 09:05:31 as ** along with 8 people kluck skhadar neils cjeans zwang Evangelia Ema renatomilani
  • Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
    Bioinformatics, Vol. 23, No. 1. (1 January 2007), pp. 127-128.
    by Letunic, Ivica, Bork, Peer
    posted to 2006 bacteria bioinformatics phylogeny software by hpaces on 2007-12-09 08:35:14 as ** along with 4 people and 2 groups jyuh marcius skhadar gjuggler BioinfoCIPF SGU-CIPF
  • EVOLUTION: Passages Found Through Labyrinth of Bacterial Evolution
    Science, Vol. 301, No. 5634. (8 August 2003), pp. 745a-746.
    by Elizabeth Pennisi
    posted to 2003 bacteria bioinformatics evolution genome horizontal_transfer by hpaces on 2007-12-09 08:02:02 as **
  • An efficient algorithm for large-scale detection of protein families.
    Nucleic Acids Res, Vol. 30, No. 7. (1 April 2002), pp. 1575-1584.
    by AJ Enright, S Van Dongen, CA Ouzounis
    posted to 2002 algorithm array bioinformatics clustering computational software by hpaces on 2007-11-28 07:13:01 as ** along with 12 people and 2 groups Borelli camster operon knaseanka indigoviolet skhadar nirfriedman dgront entropy gcalda GustavoLacerda RebeccaHamer dbk-lab EisenLab
  • Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Nature, Vol. 450, No. 7167., pp. 219-232.
    by Alexander Stark, Michael F Lin, Pouya Kheradpour, Jakob S Pedersen, Leopold Parts, Joseph W Carlson, Madeline A Crosby, Matthew D Rasmussen, Sushmita Roy, Ameya N Deoras, Graham J Ruby, Julius Brennecke, Harvard F Curators, Berkeley, Emily Hodges, Angie S Hinrichs, Anat Caspi, Benedict Paten, Seung-Won Park, Mira V Han, Morgan L Maeder, Benjamin J Polansky, Bryanne E Robson, Stein Aerts, Jacques van Helden, Bassem Hassan, Donald G Gilbert, Deborah A Eastman, Michael Rice, Michael Weir, Matthew W Hahn, Yongkyu Park, Colin N Dewey, Lior Pachter, James W Kent, David Haussler, Eric C Lai, David P Bartel, Gregory J Hannon, Thomas C Kaufman, Michael B Eisen, Andrew G Clark, Douglas Smith, Susan E Celniker, William M Gelbart, Manolis Kellis
    posted to 2007 bioinformatics comparative_genomics drosophila by hpaces on 2007-11-20 18:02:35 as **** along with 13 people and 2 groups shuzhens PetrovLab operon tmmurali djkt timflutre stajich lp2 cabbagezs nklee roys caseybrown gjuggler csb_journal_club_public Berkeley Mycology
  • Quantification of ortholog losses in insects and vertebrates.
    Genome Biology, Vol. 8 (16 November 2007), R242.
    by Stefan Wyder, Evgenia V Kriventseva, Reinhard Schroder, Tatsuhiko Kadowaki, Evgeny M Zdobnov
    posted to 2007 bioinformatics comparative_genomics evolution insect ortholog vertebrate by hpaces on 2007-11-20 08:02:22 as ** along with 3 people and 2 groups cjeans hlapp svdate Bioinformatics ParkinsonLab_at_MaRS
  • WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by R Zika, J Paces, A Pavlícek, V Paces
    posted to 2004 algorithm alignment bioinformatics my phylogeny software by hpaces on 2007-11-13 16:09:23 as read
  • Representing GC variation along eukaryotic chromosomes
    Gene, Vol. 333 (26 May 2004), pp. 135-141.
    by Jan Paces, Radek Zika, Vaclav Paces, Adam Pavlicek, Oliver Clay, Giorgio Bernardi
    posted to 2004 algorithm bioinformatics eukaryotic genomics my software by hpaces on 2007-11-13 16:07:02 as read
  • The Bioperl Toolkit: Perl Modules for the Life Sciences
    Genome Res., Vol. 12, No. 10. (1 October 2002), pp. 1611-1618.
    by Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehvaslaiho, Chad Matsalla, Chris J Mungall, Brian I Osborne, Matthew R Pocock, Peter Schattner, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson, Ewan Birney
    posted to 2002 algorithm bioinformatics software by hpaces on 2007-11-13 15:23:35 as ** along with 17 people and 2 groups ninch jmeppley chad_davis rvosa indigoviolet skhadar dullhunk dgront stajich noby incovoma glycine tyrosine threonine valine nklee sekmi EisenLab FAB-lab
  • Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study
    Genome Biology, Vol. 8 (08 November 2007), R236.
    by Arjun Bhutkar, William M Gelbart, Temple F Smith
    posted to 2007 bioinformatics computational gene_organisation genomics phylogeny by hpaces on 2007-11-13 15:21:26 as ** along with 5 people and 1 group isimpson indigoviolet dpollard balicea maximilianh EisenLab
  • The Global Landscape of Sequence Diversity
    Genome Biology, Vol. 8 (08 November 2007), R238.
    by Jose M Peregrin-Alvarez, John Parkinson
    posted to 2007 bioinformatics eukaryotic genomics phylogeny by hpaces on 2007-11-13 15:16:58 as *** along with 4 people skhadar gpalidwor cjeans ale
  • Executable cell biology
    Nat Biotech, Vol. 25, No. 11. (November 2007), pp. 1239-1249.
    by Jasmin Fisher, Thomas A Henzinger
    posted to 2007 bioinformatics computational review by hpaces on 2007-11-10 14:14:48 as ***** along with 9 people and 2 groups Doug tmmurali austin julius dbikard neils cjeans mircea tlandrain csb_journal_club_public Centre de Recherches Interdisciplinaires
  • Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e181.
    by Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Cenk S Sahinalp, Evan E Eichler
    posted to 2007 algorithm bioinformatics evolution genome genomics primate by hpaces on 2007-11-03 18:38:16 as ** along with 1 person and 1 group zwang Bioinformatics
  • A Computational Approach to the Functional Screening of Genomes
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e174.
    by Davide Chiarugi, Pierpaolo Degano, Roberto Marangoni
    posted to 2007 bioinformatics computational genomics by hpaces on 2007-11-02 11:03:40 as ** along with 3 people and 1 group cjeans zwang ale Bioinformatics
  • Structural motifs of biomolecules
    Proceedings of the National Academy of Sciences, Vol. 104, No. 44. (30 October 2007), pp. 17283-17286.
    by Jayanth R Banavar, Trinh X Hoang, John H Maddocks, Amos Maritan, Chiara Poletto, Andrzej Stasiak, Antonio Trovato
    posted to 2007 bioinformatics structure by hpaces on 2007-11-01 16:40:10 as ** along with 3 people and 1 group zwang sobolevnrm afenley baker-group
  • Mapping sequences by parts
    Algorithms for Molecular Biology, Vol. 2 (19 September 2007), 11.
    by Gilles Didier, Carito Guziolowski
    posted to 2007 algorithm alignment bioinformatics by hpaces on 2007-10-31 13:30:25 as **
  • Bayesian methods in bioinformatics and computational systems biology.
    Brief Bioinform (12 April 2007)
    by Darren J J Wilkinson
    posted to 2007 algorithm bayesian bioinformatics by hpaces on 2007-10-31 09:22:07 as ** along with 14 people and 1 group quianominorleo i-stevenson jyuh Borelli jfr wnpx neveaire zwang bertelsen cabbagezs julesyoo blobbybirdman vietanh0 waszak Bioinformatics
  • A reality check for alignments and trees
    Trends in Genetics, Vol. 23, No. 10. (October 2007), pp. 478-480.
    by William Martin, Mayo Roettger, Peter J Lockhart
    posted to 2007 algorithm alignment bioinformatics phylogeny by hpaces on 2007-10-31 08:49:56 as **
  • The entire organization of transcription units on the Bacillus subtilis genome
    BMC Genomics, Vol. 8 (28 June 2007), 197.
    by Hirokazu Kobayashi, Joe Akitomi, Nobuyuki Fujii, Kazuo Kobayashi, Md A Amin, Ken Kurokawa, Naotake Ogasawara, Shigehiko Kanaya
    posted to 2007 algorithm annotation bacteria bioinformatics genomics by hpaces on 2007-10-31 07:09:47 as **** along with 1 person Cortel
  • Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons.
    Mol Biol Evol, Vol. 22, No. 11. (November 2005), pp. 2198-2208.
    by BP Cusack, KH Wolfe
    posted to 2005 bioinformatics comparative_genomics evolution human mouse by hpaces on 2007-10-31 07:06:04 as ** along with 2 people Cortel radek
  • Simplified ontologies allowing comparison of developmental mammalian gene expression
    Genome Biology, Vol. 8 (25 October 2007), R229.
    by Adele Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide
    posted to 2007 bioinformatics comparative_genomics development ontology to_read by hpaces on 2007-10-31 07:00:57 as ** along with 1 person annacarina07
  • On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees
    Genome Biology, Vol. 8, No. 10. (2007)
    by Tomas M Bonet, Jesus S Ruiz, Lluis Armengol, Razi Khaja, Jaume Bertranpetit, Mariano Rocchi, Elodie Gazave, Nuria L Bigas, Arcadi Navarro
    posted to bioinformatics chimp comparative_genomics human by hpaces on 2007-10-31 06:53:37 as **** along with 2 people and 1 group djkt maximilianh Bioinformatics
  • Evaluation of clustering algorithms for protein-protein interaction networks
    BMC Bioinformatics, Vol. 7 (06 November 2006), 488.
    by Sylvain Brohee, Jacques van Helden
    posted to algorithm bioinformatics clustering networks to_read by hpaces on 2007-10-30 12:20:15 as ** along with 13 people and 1 group AbnerCYH Borelli carlk pdelosri jfr chad_davis balajis nirfriedman dquest grahamc cjeans Pao-Yang oktie EPFL_SB_ITP_LBS
  • Detection of DNA copy number alterations in cancer by array comparative genomic hybridization.
    Genet Med, Vol. 9, No. 9. (September 2007), pp. 574-584.
    by E Michels, K De Preter, N Van Roy, F Speleman
    posted to 2007 array bioinformatics comparative_genomics by hpaces on 2007-10-30 12:16:54 as ** along with 1 person and 1 group frohike Bioinformatics
  • Superparamagnetic Clustering of Data
    Physical Review Letters, Vol. 76, No. 18. (29 April 1996), 3251.
    by Marcelo Blatt, Shai Wiseman, Eytan Domany
    posted to algorithm bioinformatics clustering by hpaces on 2007-10-30 12:11:29 as ***
  • Having a BLAST with bioinformatics (and avoiding BLASTphemy).
    Genome Biol, Vol. 2, No. 10. (2001)
    by A Pertsemlidis, JW Fondon
    posted to algorithm bioinformatics blast similarity to_read by hpaces on 2007-10-30 12:02:32 as *** along with 8 people and 2 groups karbak ziquje prtmht textoris shantanu cjeans sujaikumar scottstensland MathBio Bioinformatics
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