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lilou's library [32 articles]

Recent papers added to lilou's library.
  • GENOMICS: Lining Up to Avoid Bias
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 416-417.
    by Antonis Rokas
    posted to alignment_comparison by lilou on 2008-02-05 09:06:48 as ** along with 7 people operon dayjm cjeans dandaman renatomilani bpcusack gjuggler
  • 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_comparison by lilou on 2008-02-05 09:04:41 as ** along with 25 people and 2 groups bpb aprasad dayjm pradiptaray dpollard tny djkt cjeans zwang lisa1 cactus biomcgary kinestetika dandaman gjuggler renatomilani mclarenv youdon bpcusack jyuh jdelcampo adacier gracio timflutre jfr EisenLab microbiology_nijmegen
  • MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution
    Genome Res., Vol. 14, No. 3. (1 March 2004), pp. 442-450.
    by Peter D Keightley, Toby Johnson
    posted to alignment alignment_comparison conserved_noncoding_seq by lilou on 2007-10-01 10:44:06 as ** along with 2 people and 1 group penka adijr Nie
  • Intron Length Evolution in Drosophila.
    Mol Biol Evol (21 August 2006)
    by Daven C C Presgraves
    posted to divergence drosophila evolution genome_size_intron by lilou on 2007-10-01 10:41:49 as ** along with 4 people and 1 group aprasad JAShapiro indigoviolet dpollard EisenLab
  • Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments.
    Mol Biol Evol (20 August 2007)
    by Tanya Golubchik, Michael J J Wise, Simon Easteal, Lars S S Jermiin
    posted to alignment_comparison indel occuracy by lilou on 2007-08-30 09:14:51 as ** along with 4 people druvus zwang dandaman caseybrown
  • 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_comparison by lilou on 2007-08-27 10:14:39 as ** along with 7 people and 1 group aprasad rvosa BioNica stajich cjeans zwang mailund FAB-lab
  • On the Incidence of Intron Loss and Gain in Paralogous Gene Families
    Mol Biol Evol (29 April 2007), msm082.
    by Scott W Roy, David Penny
    posted to gain intron loss by lilou on 2007-08-20 10:06:45 as ** along with 2 people and 1 group stajich jwestbrook King_Lab
  • Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics
    Molecular Phylogenetics and Evolution, Vol. 42, No. 3. (March 2007), pp. 827-837.
    by Conrad A Matthee, Geeta Eick, Sandi Willows-Munro, Claudine Montgelard, Amanda T Pardini, Terence J Robinson
    posted to evolution indel intron by lilou on 2007-07-05 15:17:05 as ** along with 1 person aprasad
  • Measuring the accuracy of genome-size multiple alignments
    Genome Biology, Vol. 8 (26 June 2007), R124.
    by Amol Prakash, Martin Tompa
    posted to alignment comparison occuracy by lilou on 2007-07-05 15:16:01 as ** along with 3 people and 2 groups dpollard AaronDarling stajich EisenLab Berkeley Mycology
  • What controls the length of noncoding DNA?
    Curr Opin Genet Dev, Vol. 11, No. 6. (December 2001), pp. 652-659.
    by JM Comeron
    posted to length noncoding by lilou on 2007-07-05 14:58:05 as ** along with 3 people and 1 group aprasad penka miniprep Nie
  • Patterns and rates of intron divergence between humans and chimpanzees
    Genome Biology, Vol. 8 (19 February 2007), R21.
    by Elodie Gazave, Tomas Marques-Bonet, Olga Fernando, Brian Charlesworth, Arcadi Navarro
    posted to divergence intron by lilou on 2007-06-28 15:56:40 as ** along with 3 people and 2 groups nickluscombe cisevol hdopazo EBI-regulation cis-regulatory-evolution
  • 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-Chi C Chen, Chueng-Jong J Chen, Trees-Juen J Chuang
    posted to indel by lilou on 2007-06-12 08:56:59 as ** along with 5 people and 1 group natstreet druvus jyuh aprasad dpollard EisenLab
  • SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools.
    BMC Bioinformatics, Vol. 7 (2006)
    by AC Shih, DT Lee, L Lin, CL Peng, SH Chen, YW Wu, CY Wong, MY Chou, TC Shiao, MF Hsieh
    posted to alignment_comparison by lilou on 2007-06-11 10:13:10 as ** along with 2 people aprasad chodar
  • PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
    PLoS Comput Biol, Vol. 1, No. 7. (December 2005)
    by R Siddharthan, ED Siggia, E van Nimwegen
    posted to motif by lilou on 2007-06-08 09:26:41 as ** along with 12 people and 3 groups druvus ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk idonaldson yevishere isimpson structural_bioinformatics Bioinformatics EBI-regulation
  • Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.
    BMC Bioinformatics, Vol. 7, No. 1. (16 March 2006)
    by Rahul Siddharthan
    posted to alignment noncoding by lilou on 2007-06-08 09:24:23 as ** along with 1 person and 1 group dpollard EisenLab
  • PIP: a database of potential intron polymorphism markers.
    Bioinformatics (1 June 2007)
    by Long Yang, Gulei Jin, Xiangqian Zhao, Yan Zheng, Zhaohua Xu, Weiren Wu
    posted to intron_polymorphism by lilou on 2007-06-06 12:39:43 as ** along with 1 person jyuh
  • Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.
    Genome Biol, Vol. 6, No. 8. (2005)
    by PR Haddrill, B Charlesworth, DL Halligan, P Andolfatto
    posted to drosophila intron by lilou on 2007-05-30 14:52:01 as ** along with 2 people and 2 groups penka cisevol Nie cis-regulatory-evolution
  • Evolutionary constraints in conserved nongenic sequences of mammals
    Genome Res., Vol. 15, No. 10. (1 October 2005), pp. 1373-1378.
    by Peter D Keightley, Gregory V Kryukov, Shamil Sunyaev, Daniel L Halligan, Daniel J Gaffney
    posted to conserved_noncoding_seq by lilou on 2007-05-30 14:50:09 as ** along with 3 people and 1 group penka miniprep ankur_iitg Nie
  • The Functions of Introns: From Junk DNA to Designed DNA
    posted to intron_function by lilou on 2007-05-30 14:48:59 as ** along with 1 person miniprep
  • Benchmarking tools for the alignment of functional noncoding DNA.
    BMC Bioinformatics, Vol. 5 (21 January 2004)
    by DA Pollard, CM Bergman, J Stoye, SE Celniker, MB Eisen
    posted to alignment conserved_noncoding_seq by lilou on 2007-05-30 14:45:01 as read along with 6 people and 1 group cap1 indigoviolet adijr idonaldson gjuggler nklee EisenLab
  • Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
    BMC Bioinformatics, Vol. 7 (14 August 2006), 376.
    by Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen
    posted to alignment conserved_seq by lilou on 2007-05-30 14:44:11 as ** along with 6 people and 2 groups aprasad dpollard lusk Garamonfok cisevol emptyhb EisenLab cis-regulatory-evolution
  • Intron Size and Exon Evolution in Drosophila
    Genetics, Vol. 170, No. 1. (1 May 2005), pp. 481-485.
    by Gabriel Marais, Pierre Nouvellet, Peter D Keightley, Brian Charlesworth
    posted to intron_size by lilou on 2007-05-30 14:36:45 as ** along with 1 person and 1 group penka Nie
  • Genome size and intron size in Drosophila.
    Mol Biol Evol, Vol. 15, No. 6. (June 1998), pp. 770-773.
    by EN Moriyama, DA Petrov, DL Hartl
    posted to genome_size_intron by lilou on 2007-05-30 14:35:04 as ** along with 2 people and 1 group brant penka Nie
  • "Genome design" model: Evidence from conserved intronic sequence in human-mouse comparison
    Genome Res., Vol. 16, No. 3. (1 March 2006), pp. 347-354.
    by Alexander E Vinogradov
    posted to genome_design by lilou on 2007-05-30 14:30:42 as read along with 5 people and 2 groups aprasad tuck indigoviolet penka miniprep EisenLab Nie
  • 'Genome design' model and multicellular complexity: golden middle.
    Nucleic Acids Res, Vol. 34, No. 20. (2006), pp. 5906-5914.
    by AE Vinogradov
    posted to genome_design by lilou on 2007-05-30 14:29:49 as read
  • The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes).
    Genes Genet Syst, Vol. 82, No. 2. (April 2007), pp. 135-144.
    by S Imai, T Sasaki, A Shimizu, S Asakawa, H Hori, N Shimizu
    posted to genome_size by lilou on 2007-05-30 14:26:42 as ** along with 1 person and 1 group jwestbrook King_Lab
  • Three distinct modes of intron dynamics in the evolution of eukaryotes.
    Genome Res (10 May 2007)
    by Liran Carmel, Yuri I I Wolf, Igor B B Rogozin, Eugene V V Koonin
    posted to intron_dynamic by lilou on 2007-05-30 14:22:57 as ** along with 6 people and 3 groups dchughes penka djkt jwestbrook cabbagezs seitentaisei G4ID King_Lab Genetics-of-Gambling
  • Evolutionarily conserved genes preferentially accumulate introns.
    Genome Res (10 May 2007)
    by Liran Carmel, Igor B B Rogozin, Yuri I I Wolf, Eugene V V Koonin
    posted to intron_dynamic by lilou on 2007-05-30 14:22:17 as ** along with 5 people and 2 groups balicea dchughes djkt cabbagezs xingxu G4ID Genetics-of-Gambling
  • A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing.
    Genome Res (24 May 2007)
    by Rodger B B Voelker, J Andrew A Berglund
    posted to conserved_noncoding_seq by lilou on 2007-05-30 14:21:13 as ** along with 4 people and 2 groups dchughes djkt olympos rvoelker G4ID Genetics-of-Gambling
  • The mode and tempo of genome size evolution in eukaryotes.
    Genome Res (9 April 2007)
    by Matthew J J Oliver, Dmitri Petrov, David Ackerly, Paul Falkowski, Oscar M M Schofield
    posted to genome_size by lilou on 2007-05-30 14:18:58 as ** along with 4 people and 3 groups aprasad dpollard dchughes diamantis EisenLab G4ID Genetics-of-Gambling
  • Intron-genome size relationship on a large evolutionary scale.
    J Mol Evol, Vol. 49, No. 3. (September 1999), pp. 376-384.
    by AE Vinogradov
    posted to genome_size_intron by lilou on 2007-05-30 14:15:59 as read along with 1 person and 1 group penka Nie
  • Computation and Analysis of Genomis Multi-Sequence Alignments.
    Annu Rev Genomics Hum Genet (9 May 2007)
    by Mathieu Blanchette
    posted to alignment large by lilou on 2007-05-30 14:13:48 as *** along with 4 people and 1 group dpollard nklee maximilianh aprasad EisenLab
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