Tag indels [58 articles] Export

Recent papers classified by the tag indels.

	MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions [My Copy] Nat Meth, Vol. 6, No. 7. (31 May 2009), pp. 473-474. by Seunghak Lee, Fereydoun Hormozdiari, Can Alkan, Michael Brudno posted to variation software sequencing indels by ongenetics on 2009-11-16 13:22:41 as along with 3 people and 1 group druvus fpattyn dakelley Neuroblastoma
	Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 21. (1 November 2009), pp. 2865-2871. by Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning posted to software short-read paired-end indels deletions by torfinnnome on 2009-11-03 14:18:02 as along with 6 people darian dakelley n00c natstreet druvus vplagnol
	A General Tendency for Conservation of Protein Length Across Eukaryotic Kingdoms [My Copy] Mol Biol Evol, Vol. 22, No. 1. (1 January 2005), pp. 142-147. by Daryi Wang, Mufen Hsieh, Wen-Hsiung Li posted to indels by gjuggler on 2009-10-08 16:27:38 as
	Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria [My Copy] Mol Biol Evol, Vol. 26, No. 7. (1 July 2009), pp. 1523-1531. by Jian-Qun Chen, Ying Wu, Haiwang Yang, Joy Bergelson, Martin Kreitman, Dacheng Tian posted to indels by gjuggler on 2009-10-08 16:26:34 as along with 3 people djkt bmajoros nuin
	Insertion–deletion biases and the evolution of genome size [My Copy] Gene, Vol. 324 (07 January 2004), pp. 15-34. by Gregory posted to indels by gjuggler on 2009-10-08 16:20:15 as
	Sensitive and accurate detection of copy number variants using read depth of coverage [My Copy] Genome Research, Vol. 19, No. 9. (5 September 2009), pp. 1586-1592. by Seungtai Yoon, Zhenyu Xuan, Vladimir Makarov, Kenny Ye, Jonathan Sebat posted to snp sequencing inversions indels coverage cnv by torfinnnome on 2009-09-16 13:29:54 as along with 7 people woodson8 scmelton dakelley n00c rdiaz jbhiatt pkonings
	BreakDancer: an algorithm for high-resolution mapping of genomic structural variation [My Copy] Nature Methods, Vol. 6, No. 9. (09 August 2009), pp. 677-681. by Ken Chen, John W. Wallis, Michael D. McLellan, et al.David E. Larson, Joelle M. Kalicki, Craig S. Pohl, Sean D. McGrath, Michael C. Wendl, Qunyuan Zhang, Devin P. Locke, Xiaoqi Shi, Robert S. Fulton, Timothy J. Ley, Richard K. Wilson, Li Ding, Elaine R. Mardis posted to short-read-mapping ngs map indels by jasontsai on 2009-08-15 18:01:45 as along with 13 people and 1 group n00c Leaflet heliopais stubrown dakelley fenghezi daed natstreet druvus sitalange qayub gdb danmaclean Journal picks
	Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes [My Copy] Genome Research, Vol. 19, No. 7. (15 July 2009), pp. 1270-1278. by Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp posted to high-throughput_sequencing indels population_genomics by dandaman on 2009-07-04 18:27:42 as along with 18 people darian hzoltan n00c rdiaz aezrin jandot GustavoLacerda guhjy jessopher megraw jonilaserson chrisamiller sameersoi djkt dakelley APRegier natstreet druvus
	Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions [My Copy] Genome Research, Vol. 19, No. 7. (July 2009), pp. 1153-1164. by Erika M. Kvikstad, Francesca Chiaromonte, Kateryna D. Makova posted to indels by gjuggler on 2009-07-03 12:17:13 as along with 3 people megraw Annab djkt
	Genome-wide identification of human functional DNA using a neutral indel model. [My Copy] PLoS computational biology, Vol. 2, No. 1. (13 January 2006) by Gerton Lunter, Chris P. Ponting, Jotun Hein posted to indels by gjuggler on 2009-05-23 20:07:48 as along with 12 people and 2 groups timflutre nklee aprasad eckart_bindewald eweaver lhonigberg acidwizard juliettecolinas bpcusack Stew cisevol mailund EisenLab cis-regulatory-evolution
	INDELible: A Flexible Simulator of Biological Sequence Evolution [My Copy] Mol Biol Evol, Vol. 26, No. 8. (1 August 2009), pp. 1879-1888. by William Fletcher, Ziheng Yang posted to indels by gjuggler on 2009-05-13 18:28:20 as along with 6 people and 2 groups friendpine zwang ppgardne djkt druvus nuin Journal picks iSEEM
	Problems and Solutions for Estimating Indel Rates and Length Distributions [My Copy] Mol Biol Evol, Vol. 26, No. 2. (1 February 2009), pp. 473-480. by Reed A. Cartwright posted to indels by gjuggler on 2009-01-14 10:54:31 as along with 2 people timflutre djkt
	How should gaps be treated in parsimony? A comparison of approaches using simulation [My Copy] Molecular Phylogenetics and Evolution, Vol. 42, No. 3. (March 2007), pp. 817-826. by Heath T. Ogden, Michael S. Rosenberg posted to 2007 accuracy alignments dna gaps indels parsimony simulation by treangen on 2008-11-25 11:52:53 as along with 1 person TaqSys
	A Catalog of Neutral and Deleterious Polymorphism in Yeast [My Copy] PLoS Genet, Vol. 4, No. 8. (2008), e1000183. by Scott W. Doniger, Hyun S. Kim, Devjanee Swain, et al.Daniella Corcuera, Morgan Williams, Shiaw-Pyng Yang, Justin C. Fay posted to indels marker polymorphism snp by druvus on 2008-10-28 08:28:46 as along with 6 people and 1 group GustavoLacerda madreach stajich emptyhb bpcusack caseybrown Mycology
	SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005) by Andy Pang, Andrew Smith, Paulo Nuin, Elisabeth Tillier posted to alngen indels by gjuggler on 2008-09-22 14:46:44 as along with 2 people pansapiens martainn
	Using evolutionary Expectation Maximization to estimate indel rates [My Copy] Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2294-2300. by Ian Holmes posted to evolution indels statistics by druvus on 2008-09-19 14:04:13 as along with 1 person aprasad
	Using evolutionary Expectation Maximization to estimate indel rates. [My Copy] Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2294-2300. by I. Holmes posted to evolution indels statistics by druvus on 2008-09-19 12:48:35 as along with 1 person nirfriedman
	Statistical alignment based on fragment insertion and deletion models [My Copy] Bioinformatics, Vol. 19, No. 4. (1 March 2003), pp. 490-499. by Dirk Metzler posted to indels statistics by druvus on 2008-09-19 12:23:14 as along with 1 person timflutre
	Phylocomposer and phylodirector: analysis and visualization of transducer indel models [My Copy] Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3263-3264. by Ian Holmes posted to indels software by druvus on 2008-09-19 12:04:59 as along with 4 people balicea djkt ryanraaum smbe2008
	Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins [My Copy] BMC Bioinformatics, Vol. 9 (25 June 2008), 293. by Michael Hsing, Artem Cherkasov posted to indels proteome by druvus on 2008-08-28 15:46:41 as along with 2 people robfsouza nuin
	Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. [My Copy] Nature, Vol. 455, No. 7209. (4 July 2008), pp. 105-108. by Dacheng Tian, Qiang Wang, Pengfei Zhang, et al.Hitoshi Araki, Sihai Yang, Martin Kreitman, Thomas Nagylaki, Richard Hudson, Joy Bergelson, Jian Q. Chen posted to indels mutation by gjuggler on 2008-07-23 10:47:15 as along with 9 people and 1 group biomcgary Annab aprasad dakelley zwang psique djkt caseybrown bpcusack parkinson's disease references
	Discovering Sequence Motifs with Arbitrary Insertions and Deletions [My Copy] PLoS Comput Biol, Vol. 4, No. 5. (9 April 2008), e1000071. by M. C. Frith, N. F. Saunders, B. Kobe, T. L. Bailey posted to indels by gjuggler on 2008-05-12 11:19:30 as along with 10 people thegoose foxpowa wowalz madreach Stew dquest cabbagesofdoom neils Ema Evangelia
	Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans [My Copy] PLoS Biology, Vol. 5, No. 11. (1 November 2007), e310. by David J. Begun, Alisha K. Holloway, Kristian Stevens, et al.Ladeana W. Hillier, Yu-Ping Poh, Matthew W. Hahn, Phillip M. Nista, Corbin D. Jones, Andrew D. Kern, Colin N. Dewey, Lior Pachter, Eugene Myers, Charles H. Langley posted to assembly indels by dmc on 2008-03-13 10:47:50 as along with 3 people bpb pradiptaray emptyhb
	Automating resequencing-based detection of insertion-deletion polymorphisms [My Copy] Nature Genetics, Vol. 38, No. 12. (19 November 2006), pp. 1457-1462. by Tushar R. Bhangale, Matthew Stephens, Deborah A. Nickerson posted to indels sequencing by dmc on 2008-03-07 13:09:21 as
	Rapid sequence turnover at an intergenic locus in Drosophila. [My Copy] Mol Biol Evol, Vol. 21, No. 4. (April 2004), pp. 670-680. by N. D. Singh, D. A. Petrov posted to drosophila genome_architecture genome_size indels noncoding by dpollard to the group EisenLab on 2007-11-14 21:13:48 as
	Pseudogene evolution in Drosophila suggests a high rate of DNA loss. [My Copy] Mol Biol Evol, Vol. 15, No. 11. (November 1998), pp. 1562-1567. by D. A. Petrov, Y. C. Chao, E. C. Stephenson, D. L. Hartl posted to drosophila genome_architecture genome_size indels pseudogene by dpollard to the group EisenLab on 2007-11-14 21:12:54 as along with 1 person skumagai
	How intron splicing affects the deletion and insertion profile in Drosophila melanogaster. [My Copy] Genetics, Vol. 162, No. 3. (November 2002), pp. 1233-1244. by S. E. Ptak, D. A. Petrov posted to drosophila genome_architecture genome_size indels splicing by dpollard to the group EisenLab on 2007-11-14 21:12:02 as
	DNA loss and evolution of genome size in Drosophila. [My Copy] Genetica, Vol. 115, No. 1. (May 2002), pp. 81-91. by D. A. Petrov posted to drosophila genome_architecture genome_size indels by dpollard to the group EisenLab on 2007-11-14 21:11:15 as along with 1 person timflutre
	Mutational equilibrium model of genome size evolution. [My Copy] Theor Popul Biol, Vol. 61, No. 4. (June 2002), pp. 531-544. by D. A. Petrov posted to genome_architecture genome_size indels model by dpollard to the group EisenLab on 2007-11-14 21:10:36 as along with 3 people operon aprasad timflutre
	Pseudogene evolution and natural selection for a compact genome. [My Copy] J Hered, Vol. 91, No. 3. (n 2000), pp. 221-227. by D. A. Petrov, D. L. Hartl posted to drosophila genome_architecture genome_size indels pseudogene selection by dpollard to the group EisenLab on 2007-11-14 21:01:00 as
	Evidence for DNA loss as a determinant of genome size. [My Copy] Science, Vol. 287, No. 5455. (11 February 2000), pp. 1060-1062. by D. A. Petrov, T. A. Sangster, J. S. Johnston, D. L. Hartl, K. L. Shaw posted to drosophila genome_architecture genome_size indels insects by dpollard to the group EisenLab on 2007-11-14 20:59:23 as along with 2 people and 1 group timflutre penka Nie
	High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. [My Copy] Mol Biol Evol, Vol. 15, No. 3. (March 1998), pp. 293-302. by D. A. Petrov, D. L. Hartl posted to drosophila genome_architecture genome_size indels by dpollard to the group EisenLab on 2007-11-14 20:58:27 as along with 2 people timflutre skumagai
	Trash DNA is what gets thrown away: high rate of DNA loss in Drosophila. [My Copy] Gene, Vol. 205, No. 1-2. (31 December 1997), pp. 279-289. by D. A. Petrov, D. L. Hartl posted to drosophila genome_architecture genome_size indels by dpollard to the group EisenLab on 2007-11-14 20:57:45 as along with 1 person klo
	High intrinsic rate of DNA loss in Drosophila. [My Copy] Nature, Vol. 384, No. 6607. (28 November 1996), pp. 346-349. by D. A. Petrov, E. R. Lozovskaya, D. L. Hartl posted to drosophila genome_architecture genome_size indels by dpollard to the group EisenLab on 2007-11-14 20:55:15 as along with 3 people timflutre urgi skumagai
	The majority of recent short DNA insertions in the human genome are tandem duplications. [My Copy] Mol Biol Evol, Vol. 24, No. 5. (May 2007), pp. 1190-1197. by P. W. Messer, P. F. Arndt posted to human-genome human-variation indels by dchughes on 2007-10-04 13:06:38 as along with 2 people aprasad PetrovLab
	Empirical models for substitution in ribosomal RNA. [My Copy] Mol Biol Evol, Vol. 21, No. 3. (March 2004), pp. 419-427. by A. D. Smith, T. W. Lui, E. R. Tillier posted to fold-evolution indels rna by martainn on 2007-05-01 12:25:54 as
	indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels. [My Copy] Mol Biol Evol, Vol. 24, No. 3. (March 2007), pp. 640-649. by C. L. Strope, S. D. Scott, E. N. Moriyama posted to beta-barrel fold-evolution indels structure by martainn on 2007-05-01 12:22:39 as
	Large-scale survey for potentially targetable indels in bacterial and protozoan proteins. [My Copy] Proteins (28 November 2005) by Artem Cherkasov, Shang-Jung J. Lee, Devki Nandan, Neil E E. Reiner posted to indels virulence by martainn on 2007-04-20 14:11:12 as along with 2 people and 2 groups ana aprasad structural_bioinformatics Bioinformatics
	Incorporating indel information into phylogeny estimation for rapidly emerging pathogens [My Copy] BMC Evolutionary Biology, Vol. 7, No. 1. (14 March 2007), 40. by Benjamin Redelings, Marc Suchard posted to alignment evolution gene indels phylogenetics by stajich on 2007-04-19 22:09:16 as along with 5 people and 1 group timflutre druvus operon aprasad dpollard EisenLab
	Distribution of Indel lengths. [My Copy] Proteins, Vol. 45, No. 1. (1 October 2001), pp. 102-104. by B. Qian, R. A. Goldstein posted to fold-evolution indels structure by martainn on 2007-04-12 18:51:36 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Empirical and structural models for insertions and deletions in the divergent evolution of proteins. [My Copy] J Mol Biol, Vol. 229, No. 4. (20 February 1993), pp. 1065-1082. by S. A. Benner, M. A. Cohen, G. H. Gonnet posted to fold-evolution indels structure by martainn on 2007-04-12 18:50:53 as along with 4 people and 4 groups gjuggler ana barry mattjb structural_bioinformatics Bioinformatics ComplexAdaptiveSystems DSTO-CAS
	Fold Change in Evolution of Protein Structures [My Copy] Journal of Structural Biology, Vol. 134, No. 2-3. (May 2001), pp. 167-185. by N. Grishin posted to fold-evolution indels structure by martainn on 2007-04-12 18:38:18 as along with 8 people and 2 groups dfdong robfsouza tomhebbron matzke ana barry pansapiens krishnaJCSG structural_bioinformatics Bioinformatics
	Logarithmic gap costs decrease alignment accuracy [My Copy] BMC Bioinformatics, Vol. 7 (05 December 2006), 527. by Reed A. Cartwright posted to indels alignment accuracy by dpollard on 2007-01-19 16:35:28 as along with 4 people and 1 group timflutre druvus treangen groepl EisenLab
	Human-specific insertions and deletions inferred from mammalian genome sequences [My Copy] 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 human-variation indels by dchughes to the group Genetics-of-Gambling on 2007-01-04 10:03:16 as along with 2 people and 1 group olympos caseybrown G4ID
	Long loops in proteins. [My Copy] Protein Eng, Vol. 8, No. 11. (November 1995), pp. 1093-1101. by A. C. Martin, K. Toda, H. J. Stirk, J. M. Thornton posted to indels loop by ana to the group Bioinformatics on 2006-08-15 20:17:35 as along with 1 person and 1 group cdallett structural_bioinformatics
	Closed loops of nearly standard size: common basic element of protein structure. [My Copy] FEBS Lett, Vol. 466, No. 2-3. (28 January 2000), pp. 283-286. by I. N. Berezovsky, A. Y. Grosberg, E. N. Trifonov posted to indels loop protein_structure by ana to the group Bioinformatics on 2006-08-15 20:13:47 as along with 1 group structural_bioinformatics
	Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function [My Copy] Nucl. Acids Res., Vol. 32, No. 9. (20 May 2004), pp. 2838-2843. by Nalin C. Goonesekere, Byungkook Lee posted to indels by ana to the group structural_bioinformatics on 2006-07-18 22:45:40 as along with 2 people and 1 group j3xucite analogAI Bioinformatics
	The protein as a variable in protein crystallization [My Copy] Journal of Structural Biology In Macromolecular crystallization in the structural genomics era, Vol. 142, No. 1. (April 2003), pp. 88-97. by Glenn E. Dale, Christian Oefner, Allan D’arcy posted to indels by ana to the group structural_bioinformatics on 2006-07-14 00:59:17 as along with 1 group Bioinformatics
	The emerging role of insertions and deletions in protein engineering [My Copy] Current Opinion in Biotechnology, Vol. 6, No. 4. (1995), pp. 387-393. by David Shortle, John Sondek posted to indels by ana to the group Bioinformatics on 2006-07-14 00:56:32 as along with 1 group structural_bioinformatics
	Loopy Proteins Appear Conserved in Evolution [My Copy] Journal of Molecular Biology, Vol. 322, No. 1. (6 September 2002), pp. 53-64. by Jinfeng Liu, Hepan Tan, Burkhard Rost posted to indels by ana to the group Bioinformatics on 2006-07-14 00:49:15 as along with 3 people and 1 group robfsouza pansapiens cdallett structural_bioinformatics

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protein_structure	21
genome_architecture	20
genome_size	20
drosophila	18
protein_sequence	15
alignment	6
fold-evolution	6
loop	6
mutation-rate	5
sequencing	5
bioinformatics	4
dna	4
evolution	4
human-variation	4
pseudogene	4
structure	4
accuracy	3
chimp	3
gene	3
genome	3
human	3
malaria	3
mechanism	3
recombination	3
repair	3
replication	3
software	3
statistics	3
structure_prediction	3
variation	3
virulence_factor	3
wavelet	3
duplication	2
hts	2
insects	2
method	2
mitochondria	2
model	2
modeling	2
mutation-accumulation	2
noncoding	2
phylogeny	2
selection	2
snp	2
splicing	2
yeast	2
2007	1
algorithm	1
alignments	1
alngen	1
assembly	1
beta-barrel	1
cnv	1
coverage	1
deletions	1
gaps	1
high-throughput_sequencing	1
human-genome	1
inversions	1
map	1
marker	1
molecular	1
mutation	1
ngs	1
paired-end	1
parsimony	1
phylogenetics	1
polymorphism	1
population_genomics	1
proteome	1
rna	1
short-read	1
short-read-mapping	1
simulation	1
substitution-rates	1
te	1
virulence	1

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