Register | Log in | FAQ      [?] 
Recent | Recommended | Search | Authors | Tags | Export

Group: Berkeley Mycology - with tag bioinformatics [27 articles]

Recent papers posted by members of the Berkeley Mycology group with tag bioinformatics
  • PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.
    Nucleic acids research (2 October 2008)
    by Tim Hulsen, Peter M A M Groenen, Jacob de Vlieg, Wynand Alkema
    posted to phylogenetics methods comparative_genomics bioinformatics by stajich to the group Berkeley Mycology on 2008-10-10 20:43:20 as ** along with 1 person nuin
  • Model-based Analysis of ChIP-Seq (MACS)
    Genome Biology, Vol. 9, No. 9. (2008)
    by Yong Zhang, Tao Liu, Clifford Meyer, Jerome Eeckhoute, David Johnson, Bradley Bernstein, Chad Nussbaum, Richard Myers, Myles Brown, Wei Li, Xiaole Liu
    posted to solexa shortread methods computational_biology chipseq bioinformatics binding_site by stajich to the group Berkeley Mycology on 2008-09-26 16:02:11 as ** along with 7 people djkt mdperry fpattyn bcondon idonaldson caseybrown kengg
  • High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs.
    PLoS ONE, Vol. 3, No. 9. (2008)
    by J Livny, H Teonadi, M Livny, MK Waldor
    posted to rna noncoding_rna methods genome_annotation bioinformatics by stajich to the group Berkeley Mycology on 2008-09-25 00:21:43 as ** along with 2 people druvus eskay
  • The infinite sites model of genome evolution
    Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (2008), pp. 14254-14261.
    by Jian Ma, Aakrosh Ratan, Brian J Raney, Bernard B Suh, Webb Miller, David Haussler
    posted to population_genomics molecular_evolution genomics genome_evolution computational_biology bioinformatics by stajich to the group Berkeley Mycology on 2008-09-24 19:53:28 as ** along with 1 person stringertheory
  • Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
    BMC Evolutionary Biology, Vol. 8 (22 September 2008), 255.
    by Julien Dutheil, Bastien Boussau
    posted to software sequence_analysis library bioinformatics by stajich to the group Berkeley Mycology on 2008-09-23 19:09:15 as ** along with 2 people lptolik druvus
  • PLINK: a tool set for whole-genome association and population-based linkage analyses.
    American journal of human genetics, Vol. 81, No. 3. (September 2007), pp. 559-575.
    by S Purcell, B Neale, K Todd-Brown, L Thomas, MA Ferreira, D Bender, J Maller, P Sklar, PI de Bakker, MJ Daly, PC Sham
    posted to wga software population_genomics methods linkage bioinformatics by stajich to the group Berkeley Mycology on 2008-09-19 19:17:55 as ** along with 4 people and 2 groups vplagnol misonneh Zephyrus psique Roswell Cancer Crosstalk parkinson's disease references
  • Nested Containment List (NCList): A new algorithm for accelerating interval query of genome alignment and interval databases
    Bioinformatics (18 January 2007), btl647.
    by Alexander V Alekseyenko, Christopher J Lee
    posted to rangequery methods database bioinformatics by stajich to the group Berkeley Mycology on 2008-09-08 22:04:33 as ** along with 1 person dandaman
  • Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.
    Genome research (29 August 2008)
    by Vardges Ter-Hovhannisyan, Alexandre Lomsadze, Yury O O Chernoff, Mark Borodovsky
    posted to methods genome gene_prediction fungi bioinformatics annotation by stajich to the group Berkeley Mycology on 2008-09-07 20:19:51 as ** along with 1 person bcondon
  • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Genome Research
    by Heng Li, J Ruan, R Durbin
    posted to bioinformatics methods nextgensequencing shortread solexa by stajich to the group Berkeley Mycology on 2008-09-01 06:20:33 as ** along with 1 group EisenLab
  • 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 database genome informatics infrastructure by stajich to the group Berkeley Mycology on 2008-08-19 16:25:02 as ** along with 20 people and 3 groups nuin rdiaz bmaust jyuh carolh12 ilya alaninmcr druvus srp33 dullhunk tharris mrochman dansullivanblk neils jandot GustavoLacerda jago fgibson thomaskelder sjcockell Global_health_enterprise_architecture Knowledge_Economy_Reform kpa-resources
  • BranchClust: A phylogenetic algorithm for selecting gene families
    BMC Bioinformatics, Vol. 8 (10 April 2007), 120.
    by Maria S Poptsova, Peter J Gogarten
    posted to bioinformatics gene_tree methods orthology paralogs phylogenetics phylogenomics by stajich to the group Berkeley Mycology on 2008-08-17 18:17:13 as ** along with 2 people and 1 group dandaman rvosa FAB-lab
  • SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation
    Nucl. Acids Res., Vol. 36, No. 11. (1 June 2008), pp. 3819-3827.
    by Morten Kloster, Chao Tang
    posted to bioinformatics codon_bias methods by stajich to the group Berkeley Mycology on 2008-07-28 06:18:17 as ** along with 1 person GustavoLacerda
  • 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 bioinformatics methods parser by stajich to the group Berkeley Mycology on 2008-07-25 17:03:34 as ** along with 2 people nuin rmk
  • An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae.
    PLoS ONE, Vol. 2, No. 10. (2007)
    by I Lee, Z Li, EM Marcotte
    posted to bioinformatics gene_network saccharomyces by stajich to the group Berkeley Mycology on 2008-07-21 05:00:25 as **
  • Unraveling Protein Networks with Power Graph Analysis
    PLoS Comput Biol, Vol. 4, No. 7. (11 July 2008), e1000108.
    by Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder
    posted to bioinformatics graphics methods protein protein_interactions visualization by stajich to the group Berkeley Mycology on 2008-07-16 17:12:31 as ** along with 20 people and 1 group jfr jiny aramesh2 AbnerCYH jmuhlich MatthiasReimann royerloic Ema lptolik kengg roys reyez tmmurali nuin Borelli askrajiv renatomilani chad_davis sebk rsantana OPIG
  • Conditional Variable Importance for Random Forests
    BMC Bioinformatics, Vol. 9 (11 July 2008), 307.
    by Carolin Strobl, Anne-Laure Boulesteix, Thomas Kneib, Thomas Augustin, Achim Zeileis
    posted to bioinformatics methods randomforest by stajich to the group Berkeley Mycology on 2008-07-16 12:29:30 as ** along with 1 person jyuh
  • How Well Does the HoT Score Reflect Sequence Alignment Accuracy?
    Mol Biol Evol, Vol. 25, No. 8. (1 August 2008), pp. 1576-1580.
    by Barry G Hall
    posted to alignment bioinformatics methods molecular_evolution statistics by stajich to the group Berkeley Mycology on 2008-07-15 16:36:43 as ** along with 3 people gjuggler bpcusack cabbagesofdoom
  • The multiple gene duplication problem revisited.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by MS Bansal, O Eulenstein
    posted to bioinformatics gene_duplication genome methods by stajich to the group Berkeley Mycology on 2008-07-07 03:37:26 as ** along with 2 people bpcusack tharris
  • A max-margin model for efficient simultaneous alignment and folding of RNA sequences.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by CB Do, CS Foo, S Batzoglou
    posted to alignment bioinformatics folding methods rna by stajich to the group Berkeley Mycology on 2008-07-07 03:32:02 as ** along with 1 person bootsy
  • An Improved General Amino Acid Replacement Matrix
    Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1307-1320.
    by Si Q Le, Olivier Gascuel
    posted to bioinformatics evolution methods molecular_evolution phylogenetics protein_evolution by stajich to the group Berkeley Mycology on 2008-06-14 07:08:01 as ** along with 2 people friendpine dmp
  • Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome.
    Current biology : CB, Vol. 18, No. 10. (20 May 2008), pp. 758-762.
    by C Addo-Quaye, TW Eshoo, DP Bartel, MJ Axtell
    posted to bioinformatics illumina methods mirna sequencing sirna smallrna solexa by stajich to the group Berkeley Mycology on 2008-06-13 01:19:25 as **
  • Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends.
    Nature biotechnology (9 June 2008)
    by Marcelo A A German, Manoj Pillay, Dong-Hoon H Jeong, Amit Hetawal, Shujun Luo, Prakash Janardhanan, Vimal Kannan, Linda A A Rymarquis, Kan Nobuta, Rana German, Emanuele De Paoli, Cheng Lu, Gary Schroth, Blake C C Meyers, Pamela J J Green
    posted to bioinformatics htg methods mirna sequencing smallrna solexa by stajich to the group Berkeley Mycology on 2008-06-13 01:11:30 as ** along with 2 people jfr megraw
  • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    Genome Res. (11 June 2008), gr.079558.108.
    by John Marioni, Cristopher Mason, Shrikant Mane, Matthew Stephens, Yoav Gilad
    posted to bioinformatics gene_expression methods rnaseq sequencing solexa by stajich to the group Berkeley Mycology on 2008-06-11 21:57:15 as ** along with 16 people dakelley caseybrown Ema balicea vega lusk semrich vmarshal fpattyn giovanni ela503 Stew jyuh kengg shurjo GustavoLacerda
  • UniPrime: a workflow-based platform for improved universal primer design
    Nucl. Acids Res., Vol. 36, No. 10. (1 June 2008), e56.
    by Michael Bekaert, Emma C Teeling
    posted to bioinformatics primer_design by stajich to the group Berkeley Mycology on 2008-06-09 16:41:39 as ** along with 3 people jyuh tharris niallhaslam
  • GENOMEPOP: A program to simulate genomes in populations
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Antonio C Rodriguez
    posted to bioinformatics methods population_genomics simulation by stajich to the group Berkeley Mycology on 2008-04-30 19:51:51 as ** along with 3 people druvus tonia_schwartz jyuh
  • Hawkeye: a visual analytics tool for genome assemblies
    Genome Biology, Vol. 8 (09 March 2007), R34.
    by Michael C Schatz, Adam M Phillippy, Ben Shneiderman, Steven L Salzberg
    posted to assembly bioinformatics comparison genome by stajich to the group Berkeley Mycology on 2008-03-23 21:27:35 as ** along with 2 people and 1 group azazello Neeperando gatech-compgenomics
  • Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
    Genome Res. (19 February 2008), gr.7179508.
    by Ryan D Morin, Michael D O'Connor, Malachi Griffith, Florian Kuchenbauer, Allen Delaney, Anna-Liisa Prabhu, Yongjun Zhao, Helen Mcdonald, Thomas Zeng, Martin Hirst, Connie J Eaves, Marco A Marra
    posted to bioinformatics human mirna sequencing solexa by stajich to the group Berkeley Mycology on 2008-02-19 22:01:54 as ** along with 4 people maralena jfr caseybrown gdb
    • Note: You may cite this page as: http://www.citeulike.org/group/3565/tag/bioinformatics

    RIS BibTeX
    CiteULike organises scholarly (or academic) papers or literature and provides bibliographic (which means it makes bibliographies) for universities and higher education establishments. It helps undergraduates and postgraduates. People studying for PhDs or in postdoctoral (postdoc) positions. The service is similar in scope to EndNote or RefWorks or any other reference manager like BibTeX, but it is a social bookmarking service for scientists and humanities researchers.