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タグ: indel [69 articles]

Recent papers classified by the tag indel.
  • Discovering sequence motifs with arbitrary insertions and deletions.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by MC Frith, NF Saunders, B Kobe, TL Bailey
    posted to de-novo detection indel motif by Stew on 2008-05-13 10:24:59 as ** along with 6 people gjuggler dquest cabbagesofdoom neils Ema Evangelia
  • Transducers: an emerging probabilistic framework for modeling indels on trees
    Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3258-3262.
    by Robert K Bradley, Ian Holmes
    posted to indel phylogeny by ryanraaum on 2007-11-27 12:53:19 as ** along with 1 person djkt
  • Phylocomposer and phylodirector: analysis and visualization of transducer indel models
    Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3263-3264.
    by Ian Holmes
    posted to bio-tools indel phylogeny by ryanraaum on 2007-11-27 12:54:24 as ** along with 3 people balicea djkt smbe2008
  • Functional constraint and small insertions and deletions in the ENCODE regions of the human genome
    Genome Biology, Vol. 8 (04 September 2007), R180.
    by Taane G Clark, Toby Andrew, Gregory M Cooper, Elliot H Marguiles, James C Mullikin, David J Balding
    posted to encode estimate indel rate update-when-final by ryanraaum on 2007-09-14 12:51:29 as ** along with 2 people caseybrown aprasad
  • Human-specific insertions and deletions inferred from mammalian genome sequences
    Genome Res., Vol. 17, No. 1. (1 January 2007), pp. 16-22.
    by Feng-Chi Chen, Chueng-Jong Chen, Wen-Hsiung Li, Trees-Juen Chuang
    posted to comparative human indel by olympos on 2007-01-03 16:26:12 as read along with 2 people and 2 groups dchughes caseybrown G4ID Genetics-of-Gambling
  • Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins
    BMC Bioinformatics, Vol. 9 (25 June 2008), 293.
    by Michael Hsing, Artem Cherkasov
    posted to database indel by nuin on 2008-07-10 16:12:57 as ** along with 1 person druvus
  • 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
  • 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
  • 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
  • A universal algorithm for de novo decrypting of heterozygous indel sequences: A tool for personalized medicine.
    Clin Chim Acta (23 November 2007)
    by Ching-Wan W Lam
    posted to indel snp by jyuh on 2008-07-18 05:57:17 as ** along with 1 person brant
  • An initial map of insertion and deletion (INDEL) variation in the human genome.
    Genome Res, Vol. 16, No. 9. (September 2006), pp. 1182-1190.
    by Ryan E E Mills, Christopher T T Luttig, Christine E E Larkins, Adam Beauchamp, Circe Tsui, W Stephen S Pittard, Scott E E Devine
    posted to genome indel normal variation by jackjackjjj on 2006-09-26 03:56:58 as ***** along with 3 people and 2 groups bpb dpollard ealloza EisenLab BioinfoCIPF
  • MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
    BMC Bioinformatics, Vol. 7 (08 June 2006), 292.
    by Jun Wang, Peter D Keightley, Toby Johnson
    posted to alignment evolution indel model by dpollard to the group EisenLab on 2006-06-16 20:34:32 as *** along with 3 people Ayest papamicd bozdagd
  • A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e176.
    by Erika M Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D Makova
    posted to indel mammals noncoding by cisevol to the group cis-regulatory-evolution on 2007-10-28 18:28:58 as ** along with 2 people aprasad djkt
  • Genomic DNA Insertions and Deletions Occur Frequently Between Humans and Nonhuman Primates
    Genome Res., Vol. 13, No. 3. (1 March 2003), pp. 341-346.
    by Kelly A Frazer, Xiyin Chen, David A Hinds, Krishna PV Pant, Nila Patil, David R Cox
    posted to human indel by ealloza to the group BioinfoCIPF on 2006-11-16 10:09:56 as *****
  • Incorporating information from length-mutational events into phylogenetic analysis
    Molecular Phylogenetics and Evolution, Vol. 38, No. 3. (March 2006), pp. 667-676.
    by Kai Muller
    posted to phylogeny indel by druvus on 2008-09-01 15:22:40 as ** along with 2 people and 1 group aprasad cmm FAB-lab
  • Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
    Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 289-297.
    by Jaebum Kim, Saurabh Sinha
    posted to phylogeny indel alignment by druvus on 2008-09-01 15:24:36 as ** along with 2 people and 1 group aprasad indigoviolet EisenLab
  • indel-Seq-Gen: A New Protein Family Simulator Incorporating Domains, Motifs, and Indels
    Molecular Biology and Evolution, Vol. 24, No. 3. (March 2007), pp. 640-649.
    by Strope, L Cory, Scott, D Stephen, Moriyama, N Etsuko
    posted to domain indel motif proteome by druvus on 2008-08-29 12:32:05 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 phylogeny indel by druvus on 2008-09-02 11:44:19 as ** along with 1 person aprasad
  • Gaps as Characters in Sequence-Based Phylogenetic Analyses
    Systematic Biology, Vol. 49, No. 2. (2000), pp. 369-381.
    by Mark P Simmons, Helga Ochoterena
    posted to phylogeny indel alignment by druvus on 2008-09-02 12:44:49 as **
  • 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 phylogeny indel est by druvus on 2008-09-01 15:20:35 as ** along with 4 people and 1 group natstreet stajich Patola aprasad Berkeley Mycology
  • Intron Length Evolution in Drosophila.
    Mol Biol Evol (21 August 2006)
    by Daven C C Presgraves
    posted to drosophila evolution indel intron length polymorphism by dpollard on 2006-08-25 17:36:39 as *** along with 4 people and 1 group aprasad JAShapiro indigoviolet lilou EisenLab
  • When less is more: gene loss as an engine of evolutionary change.
    Am J Hum Genet, Vol. 64, No. 1. (January 1999), pp. 18-23.
    by MV Olson
    posted to evolution indel by djkt on 2006-08-04 00:54:05 as read along with 3 people and 1 group stevanspringer operon bpcusack FAB-lab
  • Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication
    Nature, Vol. 437, No. 7055., pp. 94-100.
    by Elena V Linardopoulou, Eleanor M Williams, Yuxin Fan, Cynthia Friedman, Janet M Young, Barbara J Trask
    posted to evolution indel recombination by djkt on 2006-08-04 01:15:06 as read along with 2 people and 1 group nickluscombe JeffR100 EBI-regulation
  • A distal enhancer and an ultraconserved exon are derived from a novel retroposon
    Nature (16 April 2006)
    by Gill Bejerano, Craig B Lowe, Nadav Ahituv, Bryan King, Adam Siepel, Sofie R Salama, Edward M Rubin, James W Kent, David Haussler
    posted to conservation evolution indel msa by djkt on 2006-08-04 01:30:14 as read along with 6 people and 6 groups marcius dchughes nickluscombe cisevol gjuggler carlfulp G4ID EBI-regulation BioinfoCIPF SGU-CIPF Genetics-of-Gambling cis-regulatory-evolution
  • Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.
    Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11484-11489.
    by WJ Kent, R Baertsch, A Hinrichs, W Miller, D Haussler
    posted to evolution indel by djkt on 2006-08-04 00:49:16 as read along with 5 people and 1 group bryankr pcahan1 gjuggler nuin Auger Dead 60's
  • Gene losses during human origins.
    PLoS Biol, Vol. 4, No. 3. (March 2006)
    by X Wang, WE Grus, J Zhang
    posted to evolution indel primates proteins by djkt on 2006-08-03 23:44:43 as read along with 2 people ejeffery bpcusack
  • Copy number variation: New insights in genome diversity
    Genome Res., Vol. 16, No. 8. (1 August 2006), pp. 949-961.
    by Jennifer L Freeman, George H Perry, Lars Feuk, Richard Redon, Steven A Mccarroll, David M Altshuler, Hiroyuki Aburatani, Keith W Jones, Chris Tyler-Smith, Matthew E Hurles, Nigel P Carter, Stephen W Scherer, Charles Lee
    posted to indel popgen review by djkt on 2006-08-07 18:16:31 as *** along with 7 people and 3 groups bpb balicea dchughes jri bioguru2000 debasis jasonflannick Bioinformatics G4ID Genetics-of-Gambling
  • Common deletions and SNPs are in linkage disequilibrium in the human genome
    Nature Genetics, Vol. 38, No. 1. (04 December 2005), pp. 82-85.
    by David A Hinds, Andrew P Kloek, Michael Jen, Xiyin Chen, Kelly A Frazer
    posted to indel popgen snps by djkt on 2006-08-03 23:29:27 as read along with 3 people bpb balajis balicea
  • The Diploid Genome Sequence of an Individual Human
    PLoS Biology, Vol. 5, No. 10. (1 October 2007), e254.
    by Samuel Levy, Granger Sutton, Pauline C Ng, Lars Feuk, Aaron L Halpern, Brian P Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R Macdonald, Andy W Pang, Mary Shago, Timothy B Stockwell, Alexia Tsiamouri, Vineet Bafna, Vikas Bansal, Saul A Kravitz, Dana A Busam, Karen Y Beeson, Tina C Mcintosh, Karin A Remington, Josep F Abril, John Gill, Jon Borman, Yu-Hui Rogers, Marvin E Frazier, Stephen W Scherer, Robert L Strausberg, Craig J Venter
    posted to genome indel snps by djkt on 2007-09-05 17:53:56 as ** along with 17 people and 1 group operon carlblesius bpb balicea skhadar dullhunk jackjackjjj ramensky massivemayhem jasonbobe PredictER lp2 cabbagezs xingxu hpaces maburkitt nhp Bioinformatics
  • A high-resolution survey of deletion polymorphism in the human genome
    Nature Genetics, Vol. 38, No. 1. (04 December 2005), pp. 75-81.
    by Donald F Conrad, Daniel T Andrews, Nigel P Carter, Matthew E Hurles, Jonathan K Pritchard
    posted to indel popgen by djkt on 2006-08-03 23:21:24 as read along with 4 people and 1 group bpb balajis ashandanj vplagnol Bioinformatics
  • Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.
    Genome Res, Vol. 16, No. 2. (February 2006), pp. 173-181.
    by GM Wilson, S Flibotte, PI Missirlis, MA Marra, S Jones, K Thornton, AG Clark, RA Holt
    posted to indel msa popgen primates by djkt on 2006-08-03 23:48:39 as read
  • Common deletion polymorphisms in the human genome.
    Nat Genet, Vol. 38, No. 1. (January 2006), pp. 86-92.
    by SA McCarroll, TN Hadnott, GH Perry, PC Sabeti, MC Zody, JC Barrett, S Dallaire, SB Gabriel, C Lee, MJ Daly, DM Altshuler,
    posted to indel popgen by djkt on 2006-08-03 23:22:56 as read along with 2 people balajis ashandanj
  • Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster
    PLoS Biology, Vol. 6, No. 8. (1 August 2008), e204.
    by Cathy Haag-Liautard, Nicole Coffey, David Houle, Michael Lynch, Brian Charlesworth, Peter D Keightley
    posted to evolution fly indel molclock snps by djkt on 2008-08-19 19:18:55 as *** along with 1 person aprasad
  • Sequence Context affects the rate of short insertions and deletions in flies and primates
    Genome Biology, Vol. 9 (21 February 2008), R37.
    by Amos Tanay, Eric D Siggia
    posted to evolution indel by djkt on 2008-03-12 15:32:51 as ** along with 5 people lusk biomcgary gjuggler brant aprasad
  • Recurrent Deletion and Gene Presence/Absence Polymorphism: Telomere Dynamics Dominate Evolution at the Tip of 3L in Drosophila melanogaster and D. simulans
    Genetics, Vol. 179, No. 2. (1 June 2008), pp. 1021-1027.
    by Andrew D Kern, David J Begun
    posted to fly indel recombination snps by djkt on 2008-06-18 18:53:42 as **
  • Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
    Nature (20 July 2008)
    by Dacheng Tian, Qiang Wang, Pengfei Zhang, Hitoshi Araki, Sihai Yang, Martin Kreitman, Thomas Nagylaki, Richard Hudson, Joy Bergelson, Jian-Qun Chen
    posted to snps mutation indel by djkt on 2008-09-04 17:40:37 as ** along with 4 people psique caseybrown bpcusack gjuggler
  • Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation
    PLoS Biology, Vol. 6, No. 3. (1 March 2008), e63.
    by David Brawand, Walter Wahli, Henrik Kaessmann
    posted to comparative_genomics convergent_evolution egg_yolk indel lactation mammalian_evolution marsupial pseudogene by biomcgary on 2008-03-18 16:31:42 as ** along with 1 person sunhwan
  • Resistance to therapy caused by intragenic deletion in BRCA2
    Nature (10 February 2008)
    by Stacey L Edwards, Rachel Brough, Christopher J Lord, Rachael Natrajan, Radost Vatcheva, Douglas A Levine, Jeff Boyd, Jorge S Reis-Filho, Alan Ashworth
    posted to biased_mutations breast_cancer dna_damage dna_repair frameshift homologous_recombination indel selection by biomcgary on 2008-03-03 22:11:04 as **
  • Biased distributions and decay of LINEs in the chicken genome
    Genetics (18 October 2007), genetics.106.061861.
    by Gyorgy Abrusan, Hans J Krambeck, Thomas Junier, Joti Giordano, Peter E Warburton
    posted to chicken genome_evolution indel line mutation repeats by aprasad on 2007-12-11 15:28:25 as ** along with 1 person dchughes
  • Indel-Based Evolutionary Distance and Mouse-Human Divergence
    Genome Res., Vol. 14, No. 8. (1 August 2004), pp. 1610-1616.
    by Aleksey Y Ogurtsov, Shamil Sunyaev, Alexey S Kondrashov
    posted to genetic_distance human indel mouse mutation_rate by aprasad on 2007-09-13 22:04:20 as **
  • Phylogenetic relationships of Cyprinidae (Teleostei: Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1.
    Sci China C Life Sci, Vol. 50, No. 6. (December 2007), pp. 780-788.
    by X Kong, X Wang, X Gan, J Li, S He
    posted to fish indel phylogenetics tree by aprasad on 2008-03-23 16:07:45 as **
  • The majority of recent short DNA insertions in the human genome are tandem duplications.
    Mol Biol Evol, Vol. 24, No. 5. (May 2007), pp. 1190-1197.
    by PW Messer, PF Arndt
    posted to human_genome indel mutation mutation_rate by aprasad on 2007-09-17 18:43:38 as ** along with 2 people dchughes PetrovLab
  • Pattern and Rate of Indel Evolution Inferred from Whole Chloroplast Intergenic Regions in Sugarcane, Maize and Rice.
    DNA Res (16 November 2006)
    by Kyoko Yamane, Kentaro Yano, Taihachi Kawahara
    posted to evolution indel plants by aprasad on 2006-11-21 14:00:52 as **
  • Heterotachy in mammalian promoter evolution.
    PLoS Genet, Vol. 2, No. 4. (April 2006)
    by MS Taylor, C Kai, J Kawai, P Carninci, Y Hayashizaki, CA Semple
    posted to evolution indel mammal mutation_rate promoter regulatory whole_genome by aprasad on 2006-06-27 13:35:17 as ** along with 4 people and 1 group kentsis olympos cisevol gjuggler cis-regulatory-evolution
  • Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution.
    J Mol Evol, Vol. 63, No. 5. (November 2006), pp. 682-690.
    by A Wetterbom, M Sevov, L Cavelier, TF Bergström
    posted to chimp evolution human_genome indel primate by aprasad on 2006-11-15 15:34:16 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 22 people and 3 groups bpcusack chad_davis hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen marti nuin Khavkin's lab iSEEM Green Lab
  • The Platypus Is in Its Place: Nuclear Genes and Indels Confirm the Sister Group Relation of Monotremes and Therians
    Molecular Biology and Evolution, Vol. 23, No. 3. (March 2006), pp. 587-597.
    by Teun van Rheede, Trijntje Bastiaans, David N Boone, Blair S Hedges, Wilfried W de Jong, Ole Madsen
    posted to indel monotreme phylogenetics rare_genomic_characters root theria tree by aprasad on 2006-10-26 22:04:13 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Distribution of indel lengths
    Proteins: Structure, Function, and Genetics, Vol. 45, No. 1. (2001), pp. 102-104.
    by Bin Qian, Richard A Goldstein
    posted to coding indel mutation_rate by aprasad on 2007-09-13 22:01:58 as **
  • Insertion-deletion biases and the evolution of genome size.
    Gene, Vol. 324 (7 January 2004), pp. 15-34.
    by TR Gregory
    posted to genome_size indel mutation_rate by aprasad on 2007-08-03 16:46:53 as ** along with 1 person brant
  • Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates
    Genome Res., Vol. 15, No. 9. (1 September 2005), pp. 1243-1249.
    by Louie N van de Lagemaat, Liane Gagnier, Patrik Medstrand, Dixie L Mager
    posted to deletion homoplasy indel repeat transposon by aprasad on 2007-07-12 20:57:37 as **
    • 注: このページを引用する時は次のURLでどうぞ: http://www.citeulike.org/tag/indel

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