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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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Genome Research
    by Heng Li, J Ruan, R Durbin
  • 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
  • BranchClust: A phylogenetic algorithm for selecting gene families
    BMC Bioinformatics, Vol. 8 (10 April 2007), 120.
    by Maria S Poptsova, Peter J Gogarten
  • 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
  • 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
  • The multiple gene duplication problem revisited.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
  • 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
  • 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
  • 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
  • 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
  • GENOMEPOP: A program to simulate genomes in populations
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Antonio C Rodriguez
  • 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
  • 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
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