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aprasads methods [66 articles]

Neue Publikationen in aprasads Bibliothek eingetragen unter dem Bezeichner: methods. You can also see everyone's methods.
  • Computational identification of transcriptional regulatory elements in DNA sequence
    Nucl. Acids Res., Vol. 34, No. 12. (19 July 2006), pp. 3585-3598.
    by Debraj Guhathakurta
    posted to review regulatory methods cns by aprasad on 2008-12-04 23:19:47 as ** along with 10 people and 1 group isimpson tmmurali jfr johncumbers reidy giovanni cabbagezs ankur_iitg vietanh0 xili03 GeschwindLab
  • Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap
    Systematic Biology, Vol. 57, No. 5. (October 2008), pp. 665-674.
    by Kim, Junhyong, Sanderson, Michael
    posted to phylogenetics partitioning model methods likelihood by aprasad on 2008-10-19 20:35:56 as ** along with 2 people skembel nuin
  • Motif Evaluation by Leave-one-out Scoring
    Computational Intelligence and Bioinformatics and Computational Biology, 2006. CIBCB '06. 2006 IEEE Symposium on (2006), pp. 1-7.
    by Audrey Girouard, Noah W Smith, Donna K Slonim
    posted to motif methods algorithm by aprasad on 2008-10-01 16:39:54 as **
  • Probabilistic Phylogenetic Inference with Insertions and Deletions
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000172.
    by Elena Rivas, Sean R Eddy
    posted to phylogenetics methods indel by aprasad on 2008-09-22 20:39:31 as ** along with 9 people and 1 group treangen pradiptaray zwang nuin timflutre druvus djkt gjuggler emptyhb iSEEM
  • Phylogenetic Inference Using Whole Genomes
    Annual Review of Genomics and Human Genetics, Vol. 9, No. 1. (2008), pp. 217-231.
    by Bruce Rannala, Ziheng Yang
    posted to review phylogenomics phylogenetics methods genomics congruence by aprasad on 2008-09-04 17:04:51 as ** along with 4 people treangen druvus gjuggler zwang
  • Segment-based multiple sequence alignment
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i187-192.
    by Tobias Rausch, Anne K Emde, David Weese, Andreas Doring, Cedric Notredame, Knut Reinert
    posted to alignment methods msa tools by aprasad on 2008-08-13 18:59:33 as ** along with 6 people Md_2007 zwang Ema APRegier djkt groepl
  • NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences.
    Genomics (27 May 2008)
    by Dominic Rose, Jana Hertel, Kristin Reiche, Peter FF Stadler, Jörg Hackermüller
    posted to alignment methods msa tools by aprasad on 2008-07-30 16:16:50 as ** along with 1 person maximilianh
  • Comparative physical mapping: Universal overgo hybridization probe design and BAC library hybridization.
    Methods in molecular biology (Clifton, N.J.), Vol. 422 (2008), pp. 119-132.
    by JW Thomas
    posted to bac_mapping methods overgo by aprasad on 2008-07-20 21:28:28 as **
  • jModelTest: Phylogenetic Model Averaging
    Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1253-1256.
    by David Posada
    posted to methods model_choice tools by aprasad on 2008-06-26 21:29:49 as **
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to alignment indel methods by aprasad on 2008-06-23 19:05:48 as ** along with 23 people and 3 groups pradiptaray alexeid marti bpcusack hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
  • primetv: A viewer for reconciled trees
    BMC Bioinformatics, Vol. 8 (07 May 2007), 148.
    by Bengt Sennblad, Eva Schreil, Ann, Jens Lagergren, Lars Arvestad
    posted to methods tools tree_visualization by aprasad on 2008-06-19 22:45:22 as ** along with 1 person gendlerk
  • Molecular phylogeny and divergence times of Malagasy tenrecs: influence of data partitioning and taxon sampling on dating analyses.
    BMC Evolutionary Biology, Vol. 8 (31 March 2008), 102.
    by Celine Poux, Ole Madsen, Julian Glos, Wilfried W de Jong, Miguel Vences
    posted to afrotheria methods time time_tree by aprasad on 2008-06-19 20:24:39 as **
  • Analysis of Sequence Conservation at Nucleotide Resolution
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e254.
    by Saurabh Asthana, Mikhail Roytberg, John Stamatoyannopoulos, Shamil Sunyaev
    posted to comparative_genomics conservation mcs methods by aprasad on 2008-05-13 15:42:29 as ** along with 4 people djkt GustavoLacerda nklee maximilianh
  • Genomic clocks and evolutionary timescales.
    Trends Genet, Vol. 19, No. 4. (April 2003), pp. 200-206.
    by Blair S Hedges, S Kumar
    posted to methods molecular_clock review by aprasad on 2008-05-13 01:20:45 as ** along with 1 person bandrewfox
  • Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae).
    Molecular phylogenetics and evolution, Vol. 46, No. 2. (February 2008), pp. 532-546.
    by AN Egan, KA Crandall
    posted to indel methods phylogenetics review by aprasad on 2008-05-07 19:35:44 as **
  • Computation and Analysis of Genomis Multi-Sequence Alignments.
    Annu Rev Genomics Hum Genet (9 May 2007)
    by Mathieu Blanchette
    posted to alignment methods review by aprasad on 2008-05-06 19:35:12 as ** along with 5 people and 1 group treangen dpollard lilou nklee maximilianh EisenLab
  • Phylogenetic Mixture Models Can Reduce Node-Density Artifacts
    Systematic Biology, Vol. 57, No. 2. (2008), pp. 286-293.
    by Chris Venditti, Andrew Meade, Mark Pagel
    posted to likelihood long_branch_attraction methods mixture_models phylogenetics simulation by aprasad on 2008-04-30 17:17:03 as ** along with 1 person and 1 group rvosa FAB-lab
  • A simulation study of the reliability of recombination detection methods.
    Molecular biology and evolution, Vol. 18, No. 10. (October 2001), pp. 1929-1939.
    by C Wiuf, T Christensen, J Hein
    posted to simulation recombination methods congruence bacteria by aprasad on 2008-04-28 16:35:34 as **
  • Influence Function for Robust Phylogenetic Reconstructions
    Mol Biol Evol, Vol. 25, No. 5. (1 May 2008), pp. 869-873.
    by Avner B Hen, Mahendra Mariadassou, Marie A Poursat, Philippe Vandenkoornhuyse
    posted to congruence likelihood methods phylogenetics by aprasad on 2008-04-26 13:55:27 as **
  • Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times
    Diversity & Distributions, Vol. 12, No. 1. (January 2006), pp. 35-48.
    by Frank Rutschmann
    posted to methods molecular_clock review time by aprasad on 2008-04-18 15:04:56 as ** along with 1 person akifumi
  • Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences.
    Syst Biol, Vol. 56, No. 6. (December 2007), pp. 988-1010.
    by DA Morrison
    posted to likelihood methods phylogenetics tools by aprasad on 2008-03-29 08:24:22 as ** along with 2 people druvus akifumi
  • Molecular phylogenetics: state-of-the-art methods for looking into the past.
    Trends Genet, Vol. 17, No. 5. (May 2001), pp. 262-272.
    by S Whelan, P Liò, N Goldman
    posted to methods model_selection phylogenetics review by aprasad on 2008-03-05 23:05:19 as ** along with 1 person gjuggler
  • Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects
    BMC Evolutionary Biology, Vol. 7 (28 August 2007), 147.
    by Johann W Waegele, Christoph Mayer
    posted to long_branch_attraction methods phylogenetics signal by aprasad on 2008-02-29 14:03:01 as **
  • Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods
    Systematic Biology, Vol. 54, No. 1. (February 2005), pp. 66-76.
    by Barbara Holland, Frederic Delsuc, Vincent Moulton
    posted to consensus mammal methods phylogenetics root tree by aprasad on 2008-02-29 04:45:59 as **
  • The relative performance of indel-coding methods in simulations
    Molecular Phylogenetics and Evolution, Vol. 44, No. 2. (August 2007), pp. 724-740.
    by Mark P Simmons, Kai Muller, Andrew P Norton
    posted to indel methods phylogenetics by aprasad on 2008-02-28 23:09:55 as ** along with 1 person druvus
  • Dating nodes on molecular phylogenies: a critique of molecular biogeography
    Cladistics, Vol. 21, No. 1. (2005), pp. 62-78.
    by Michael Heads
    posted to methods review time tree by aprasad on 2008-02-28 21:36:37 as **
  • Model use in phylogenetics: nine key questions
    Trends in Ecology & Evolution, Vol. 22, No. 2. (February 2007), pp. 87-94.
    by Scot A Kelchner, Michael A Thomas
    posted to methods model_choice model_selection phylogenetics review by aprasad on 2008-02-28 20:15:08 as ** along with 3 people and 2 groups dchughes russelld bpcusack G4ID Genetics-of-Gambling
  • Rocks and clocks: calibrating the Tree of Life using fossils and molecules
    Trends in Ecology & Evolution, Vol. 22, No. 8. (August 2007), pp. 424-431.
    by Philip C Donoghue, Michael J Benton
    posted to methods phylogenetics review time tree by aprasad on 2008-02-28 20:06:10 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
    Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 298-309.
    by Gerton Lunter, Andrea Rocco, Naila Mimouni, Andreas Heger, Alexandre Caldeira, Jotun Hein
    posted to alignment methods tools by aprasad on 2008-02-07 18:56:32 as ** along with 8 people brant treangen djkt grahamc dandaman mailund gjuggler AaronDarling
  • Alignment Uncertainty and Genomic Analysis
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.
    by Karen M Wong, Marc A Suchard, John P Huelsenbeck
    posted to alignment genomics methods phylogenetics by aprasad on 2008-01-26 18:15:23 as **** along with 27 people and 2 groups druvus treangen bpb dayjm pradiptaray dpollard tny djkt cjeans zwang lisa1 cactus biomcgary lilou kinestetika dandaman gjuggler renatomilani mclarenv youdon bpcusack guhjy jdelcampo adacier gracio timflutre jfr EisenLab microbiology_nijmegen
  • Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data.
    Genome Inform, Vol. 13 (2002), pp. 82-92.
    by PJ Waddell, H Kishino, R Ota
    posted to bayesian bootstrap consensus methods phylogenetics by aprasad on 2008-01-17 22:48:55 as **
  • The Bayesian Star Paradox Persists for Long Finite Sequences
    Molecular Biology and Evolution, Vol. 24, No. 4. (April 2007), pp. 1075-1079.
    by Steel, Mike, Matsen, A Frederick
    posted to bayesian bias methods star_paradox by aprasad on 2008-01-16 20:43:07 as **
  • Comment on "Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees"
    Science, Vol. 312, No. 5772. (21 April 2006), 367a.
    by Fredrik Ronquist, Bret Larget, John P Huelsenbeck, Joseph B Kadane, Donald Simon, Paul van der Mark
    posted to bayesian methods phylogenetics by aprasad on 2008-01-16 20:33:03 as ** along with 1 person AaronDarling
  • Tree disagreement: Measuring and testing incongruence in phylogenies
    Journal of Biomedical Informatics, Vol. 39, No. 1. (February 2006), pp. 86-102.
    by Paul J Planet
    posted to congruence likelihood methods parsimony phylogenetics review by aprasad on 2008-01-10 15:46:05 as ** along with 1 person akifumi
  • Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference.
    Nat Protoc, Vol. 2, No. 11. (2007), pp. 3022-3030.
    by WJ Murphy, SJ O'Brien
    posted to comparative_genomics map methods primer tools by aprasad on 2007-11-26 15:09:24 as **
  • Detecting and overcoming systematic errors in genome-scale phylogenies.
    Syst Biol, Vol. 56, No. 3. (June 2007), pp. 389-399.
    by Rodríguez N Ezpeleta, H Brinkmann, B Roure, N Lartillot, BF Lang, H Philippe
    posted to methods non-phylogenetic_signal phylogenetics phylogenomics by aprasad on 2007-09-27 21:07:39 as ** along with 3 people and 2 groups rvosa stajich dandaman FAB-lab Berkeley Mycology
  • INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events.
    Nucleic Acids Res (21 May 2007)
    by Feng, Chueng, Trees
    posted to indel methods tools by aprasad on 2007-09-13 22:20:10 as ** along with 5 people and 1 group natstreet druvus guhjy dpollard lilou EisenLab
  • Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model.
    PLoS Comput Biol, Vol. 2, No. 1. (13 January 2006)
    by Gerton Lunter, Chris PP Ponting, Jotun Hein
    posted to indel methods mutation_rate neutral selection by aprasad on 2007-09-13 20:48:39 as ** along with 10 people and 2 groups nklee eckart_bindewald eweaver lhonigberg acidwizard juliettecolinas bpcusack Stew cisevol mailund EisenLab cis-regulatory-evolution
  • Dog as an Outgroup to Human and Mouse
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e74.
    by Gerton Lunter
    posted to mammal methods phylogenetics rare_genomic_characters rodents transposon tree by aprasad on 2007-09-13 20:47:07 as **
  • Using evolutionary Expectation Maximization to estimate indel rates.
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2294-2300.
    by I Holmes
    posted to evolution indel methods mutation_rate by aprasad on 2007-09-02 13:29:54 as ** along with 2 people druvus nirfriedman
  • CONSEL: for assessing the confidence of phylogenetic tree selection.
    Bioinformatics, Vol. 17, No. 12. (December 2001), pp. 1246-1247.
    by H Shimodaira, M Hasegawa
    posted to consel likelihood methods tools by aprasad on 2007-08-31 21:55:04 as read along with 2 people druvus polpotak
  • Divergence of conserved non-coding sequences: rate estimates and relative rate tests.
    Mol Biol Evol, Vol. 21, No. 11. (November 2004), pp. 2116-2121.
    by GP Wagner, C Fried, SJ Prohaska, PF Stadler
    posted to cns genome_evolution methods mutation_rate by aprasad on 2007-08-28 13:45:31 as **
  • 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 by aprasad on 2007-08-09 21:11:14 as ** along with 9 people and 1 group treangen druvus rvosa BioNica stajich cjeans zwang lilou mailund FAB-lab
  • What is a hidden Markov model?
    Nat Biotechnol, Vol. 22, No. 10. (October 2004), pp. 1315-1316.
    by SR Eddy
    posted to hmm methods by aprasad on 2007-08-08 20:46:17 as ** along with 7 people and 1 group gulkur brian indigoviolet timflutre berthoums mailund dullhunk EisenLab
  • From pixels to picograms: a beginners' guide to genome quantification by Feulgen image analysis densitometry.
    J Histochem Cytochem, Vol. 50, No. 6. (June 2002), pp. 735-749.
    by DC Hardie, TR Gregory, PD Hebert
    posted to densitometry feulgen genome_size methods by aprasad on 2007-08-03 16:05:14 as **
  • An Empirical Codon Model for Protein Sequence Evolution
    Mol Biol Evol, Vol. 24, No. 7. (1 July 2007), pp. 1464-1479.
    by Carolin Kosiol, Ian Holmes, Nick Goldman
    posted to coding codon methods model phylogenetics by aprasad on 2007-07-31 14:46:33 as ** along with 3 people BioNica cjeans gjuggler
  • Fair-Balance Paradox, Star-Tree Paradox and Bayesian Phylogenetics.
    Mol Biol Evol (7 May 2007)
    by Ziheng Yang
    posted to bayesian bias methods phylogenetics star_paradox by aprasad on 2007-07-31 14:43:38 as ** along with 3 people akifumi cjeans ryanraaum
  • Exact and heuristic algorithms for the Indel Maximum Likelihood Problem.
    J Comput Biol, Vol. 14, No. 4. (May 2007), pp. 446-461.
    by AB Diallo, V Makarenkov, M Blanchette
    posted to algorithm evolution indel methods model phylogenetics by aprasad on 2007-07-21 21:34:52 as ** along with 2 people timflutre gjuggler
  • Profiling Phylogenetic Informativeness
    Systematic Biology, Vol. 56, No. 2. (2007), pp. 222-231.
    by Jeffrey P Townsend
    posted to methods phylogenetics by aprasad on 2007-07-20 16:26:16 as ** along with 4 people and 2 groups gjuggler rvosa stajich Jporci FAB-lab Berkeley Mycology
  • Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.
    Proc Natl Acad Sci U S A, Vol. 104, No. 17. (24 April 2007), pp. 7145-7150.
    by X Xie, TS Mikkelsen, A Gnirke, Lindblad K Toh, M Kellis, ES Lander
    posted to element functional mcs methods motif regulatory by aprasad on 2007-06-15 15:29:40 as ** along with 4 people xwbcn olympos rschulz bpcusack
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