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stajich methods [38 articles]

最近 stajich さんのライブラリに追加された論文の中から タグ methods. You can also see everyone's methods.
  • 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 parser methods bioinformatics by stajich on 2008-07-25 17:03:34 as ** along with 1 group Berkeley Mycology
  • Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Wei Sun, Shinsheng Yuan, Ker C Li
    posted to quantitative_genetics qtl methods eqtl by stajich on 2008-07-21 05:55:45 as ** along with 3 people and 1 group caseybrown ddunbar natstreet Berkeley Mycology
  • 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 visualization protein_interactions protein methods graphics bioinformatics by stajich on 2008-07-16 17:12:31 as ** along with 14 people and 1 group lptolik MatthiasReimann jmuhlich AbnerCYH royerloic tmmurali chad_davis renatomilani askrajiv Borelli nuin reyez kengg Ema Berkeley Mycology
  • 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 randomforest methods bioinformatics by stajich on 2008-07-16 12:29:30 as ** along with 1 person and 1 group jyuh Berkeley Mycology
  • 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 statistics molecular_evolution methods bioinformatics alignment by stajich on 2008-07-15 16:36:43 as ** along with 1 group Berkeley Mycology
  • Phylogenetic Signal in the Eukaryotic Tree of Life
    Science, Vol. 321, No. 5885. (4 July 2008), pp. 121-123.
    by Michael J Sanderson
    posted to phylogenetics phylogenetic_marker_selection methods by stajich on 2008-07-07 04:58:37 as ** along with 6 people and 1 group aprasad djkt gulsacan dchughes marck caseybrown Berkeley Mycology
  • The multiple gene duplication problem revisited.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by MS Bansal, O Eulenstein
    posted to methods genome gene_duplication bioinformatics by stajich on 2008-07-07 03:37:26 as ** along with 1 person and 1 group tharris Berkeley Mycology
  • 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 rna methods folding bioinformatics alignment by stajich on 2008-07-07 03:32:02 as ** along with 1 person and 1 group bootsy Berkeley Mycology
  • 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 protein_evolution phylogenetics molecular_evolution methods evolution bioinformatics by stajich on 2008-06-14 07:08:00 as ** along with 1 person and 1 group friendpine Berkeley Mycology
  • 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 solexa smallrna sirna sequencing mirna methods illumina bioinformatics by stajich on 2008-06-13 01:19:25 as ** along with 1 group Berkeley Mycology
  • 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 solexa smallrna sequencing mirna methods htg bioinformatics by stajich on 2008-06-13 01:11:30 as ** along with 1 group Berkeley Mycology
  • 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 solexa sequencing rnaseq methods gene_expression bioinformatics by stajich on 2008-06-11 21:57:14 as ** along with 11 people and 1 group Ema jyuh caseybrown vmarshal lusk fpattyn ela503 semrich balicea vega giovanni Berkeley Mycology
  • Malin: maximum likelihood analysis of intron evolution in eukaryotes.
    Bioinformatics (Oxford, England) (12 May 2008)
    by Miklós Csur Ös
    posted to methods intron_loss intron_gain intron_evolution by stajich on 2008-05-14 22:09:51 as ** along with 1 group Berkeley Mycology
  • DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony.
    Bioinformatics (Oxford, England) (12 May 2008)
    by André Wehe, Mukul S S Bansal, J Gordon G Burleigh, Oliver Eulenstein
    posted to phylogenetics methods gene_tree gene_duplication duplication by stajich on 2008-05-14 22:09:21 as ** along with 1 person and 1 group tharris Berkeley Mycology
  • An endogenous small interfering RNA pathway in Drosophila
    Nature (07 May 2008)
    by Benjamin Czech, Colin D Malone, Rui Zhou, Alexander Stark, Catherine Schlingeheyde, Monica Dus, Norbert Perrimon, Manolis Kellis, James A Wohlschlegel, Ravi Sachidanandam, Gregory J Hannon, Julius Brennecke
    posted to smallrna mirna methods drosophila by stajich on 2008-05-12 17:21:16 as ** along with 1 person and 1 group mtagaya Berkeley Mycology
  • The McDonald-Kreitman Test and Slightly Deleterious Mutations
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1007-1015.
    by Jane Charlesworth, Adam Eyre-Walker
    posted to population_genomics population_genetics molecular_evolution methods adaptation by stajich on 2008-05-10 01:44:49 as ** along with 4 people and 1 group gjuggler Stew cabbagesofdoom stevanspringer Berkeley Mycology
  • GENOMEPOP: A program to simulate genomes in populations
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Antonio C Rodriguez
    posted to simulation population_genomics methods bioinformatics by stajich on 2008-04-30 19:51:50 as ** along with 2 people and 1 group jyuh tonia_schwartz Berkeley Mycology
  • Discovering microRNAs from deep sequencing data using miRDeep
    Nature Biotechnology, Vol. 26, No. 4., pp. 407-415.
    by Marc R Friedländer, Wei Chen, Catherine Adamidi, Jonas Maaskola, Ralf Einspanier, Signe Knespel, Nikolaus Rajewsky
    posted to smallrna mirna methods evolution by stajich on 2008-04-25 23:40:15 as ** along with 3 people and 1 group jfr tmmurali giovanni Berkeley Mycology
  • The birth and death of microRNA genes in Drosophila.
    Nat Genet (17 February 2008)
    by Jian Lu, Yang Shen, Qingfa Wu, Supriya Kumar, Bin He, Suhua Shi, Richard W W Carthew, San Ming M Wang, Chung-I I Wu
    posted to smallrna mirna methods evolution drosophila by stajich on 2008-04-25 23:38:05 as ** along with 5 people and 1 group djkt bootsy emptyhb cellison megraw Berkeley Mycology
  • Statistical issues in the analysis of Illumina data
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Mark Dunning, Nuno B Morais, Andy Lynch, Simon Tavare, Matthew Ritchie
    posted to statistics shortread methods illumina array by stajich on 2008-04-25 16:11:11 as ** along with 4 people and 1 group srp33 neveaire RockHI thomaskelder Berkeley Mycology
  • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
    Mol Biol Evol, Vol. 17, No. 4. (April 2000), pp. 540-552.
    by J Castresana
    posted to alignment coccipaper methods phylogenetics by stajich on 2008-04-21 01:28:35 as ** along with 4 people and 1 group cmzmasek aprasad treangen ArtemPankin Berkeley Mycology
  • ProbCons: Probabilistic consistency-based multiple sequence alignment.
    Genome Res, Vol. 15, No. 2. (February 2005), pp. 330-340.
    by CB Do, MS Mahabhashyam, M Brudno, S Batzoglou
    posted to alignment coccipaper methods multiple_sequence_alignment by stajich on 2008-04-21 01:26:08 as ** along with 5 people and 1 group newton1234 bpb radek balajis olympos Berkeley Mycology
  • PAML: a program package for phylogenetic analysis by maximum likelihood.
    Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.
    by Z Yang
    posted to coccipaper codon_model methods molecular_evolution paml phylogenetics by stajich on 2008-04-19 21:34:23 as ** along with 11 people and 3 groups skumagai tharris bjorns chrn chad_davis indigoviolet penka BioNica pv usagi-kirin jmjimenez EisenLab Nie Berkeley Mycology
  • Levers and fulcrums: progress in cis-regulatory motif models
    Nature Methods, Vol. 5, No. 4., pp. 297-298.
    by Ewan Birney
    posted to cis-regulatory comparative_genomics methods motif prediction by stajich on 2008-04-07 16:11:40 as ** along with 3 people and 2 groups isimpson pradiptaray emptyhb EisenLab Berkeley Mycology
  • Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
    BMC Evolutionary Biology, Vol. 8 (26 March 2008), 95.
    by Stefanie Hartmann, Todd J Vision
    posted to methods phylogenomics by stajich on 2008-04-01 06:19:14 as ** along with 2 people and 1 group aprasad Patola Berkeley Mycology
  • Testing Congruence in Phylogenomic Analysis
    Systematic Biology, Vol. 57, No. 1. (2008), pp. 104-115.
    by Jessica W Leigh, Edward Susko, Manuela Baumgartner, Andrew J Roger
    posted to methods phylogenetics phylogenomics by stajich on 2008-03-14 21:08:27 as ** along with 1 group Berkeley Mycology
  • A phylogenomic investigation into the origin of Metazoa
    Mol Biol Evol (9 January 2008), msn006.
    by Inaki Ruiz-Trillo, Andrew J Roger, Gertraud Burger, Michael W Gray, Franz B Lang
    posted to evodevo evolution metazoa metazoan methods multicellular phylogenomics by stajich on 2008-03-05 17:54:57 as ** along with 2 people and 1 group cmzmasek renatomilani Berkeley Mycology
  • Searching for statistically significant regulatory modules.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by TL Bailey, WS Noble
    posted to cis-regulatory methods module motif by stajich on 2007-12-05 18:30:08 as ** along with 2 people and 2 groups xili03 indigoviolet EisenLab Berkeley Mycology
  • New Approaches to Phylogenetic Tree Search and Their Application to Large Numbers of Protein Alignments
    Systematic Biology, Vol. 56, No. 5. (2007), pp. 727-740.
    by Simon Whelan
    posted to methods phylogenetics phylogenomics by stajich on 2007-11-29 17:39:54 as ** along with 1 person and 1 group rvosa FAB-lab
  • An ant colony optimization algorithm for phylogenetic estimation under the minimum evolution principle
    BMC Evolutionary Biology, Vol. 7 (15 November 2007), 228.
    by Daniele Catanzaro, Raffaele Pesenti, Michel C Milinkovitch
    posted to methods phylogenetics by stajich on 2007-11-21 16:49:40 as **
  • MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
    Genome Res. (19 November 2007), gr.6743907.
    by Brandi L Cantarel, Ian Korf, Sofia M Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Sanchez, Mark Yandell
    posted to gene_finding genome_annotation methods by stajich on 2007-11-19 21:02:44 as ** along with 5 people jamselem tharris timflutre GustavoLacerda urgi
  • Detecting and overcoming systematic errors in genome-scale phylogenies.
    Syst Biol, Vol. 56, No. 3. (June 2007), pp. 389-399.
    by N Rodríguez-Ezpeleta, H Brinkmann, B Roure, N Lartillot, BF Lang, H Philippe
    posted to methods phylogenetics phylogenomics by stajich on 2007-11-16 20:15:16 as ** along with 3 people and 2 groups aprasad rvosa dandaman FAB-lab Berkeley Mycology
  • Evaluation of the models handling heterotachy in phylogenetic inference
    BMC Evolutionary Biology, Vol. 7 (01 November 2007), 206.
    by Yan Zhou, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe
    posted to heterotachy methods phylogenetics phylogenomics by stajich on 2007-11-07 04:18:59 as ** along with 1 group Berkeley Mycology
  • Improved Consensus Network Techniques for Genome-Scale Phylogeny
    Molecular Biology and Evolution, Vol. 23, No. 5. (15 May 2006), pp. 848-855.
    by Barbara R Holland, Lars S Jermiin, Vincent Moulton
    posted to genome_evolution methods phylogenetics phylogenomics by stajich on 2007-08-28 09:23:26 as ** along with 1 person and 1 group rvosa FAB-lab
  • Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments
    Mol Biol Evol, Vol. 24, No. 6. (1 June 2007), pp. 1380-1383.
    by Giddy Landan, Dan Graur
    posted to alignment methods multiple_sequence_alignment by stajich on 2007-05-29 16:23:12 as *** along with 7 people and 1 group aprasad rvosa BioNica cjeans zwang lilou mailund FAB-lab
  • notes Complex early genes.
    Proc Natl Acad Sci U S A, Vol. 102, No. 6. (8 February 2005), pp. 1986-1991.
    by SW Roy, W Gilbert
    posted to evolution intron intron_loss methods by stajich on 2007-05-22 06:33:07 as read
  • The pattern of intron loss
    PNAS, Vol. 102, No. 3. (18 January 2005), pp. 713-718.
    by Scott W Roy, Walter Gilbert
    posted to evolution intron intron_loss methods by stajich on 2007-05-22 06:32:37 as read along with 1 person zhlei
  • Lower Bounds on Multiple Sequence Alignment using Exact 3-way Alignment
    BMC Bioinformatics, Vol. 8 (30 April 2007), 140.
    by Charles J Colbourn, Sudhir Kumar
    posted to alignment methods by stajich on 2007-05-01 06:01:19 as **
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