djkt's indel [43 articles] Export

Recent papers added to djkt's library classified by the tag indel. You can also see everyone's indel.

	Metabolic Adaptation after Whole Genome Duplication [My Copy] Mol Biol Evol, Vol. 26, No. 11. (1 November 2009), pp. 2441-2453. by Milan J. A. van Hoek, Paulien Hogeweg posted to yeast sysbio metabolism indel evolution duplication by djkt on 2009-10-12 17:56:15 as along with 1 person tomhebbron
	Positive Selection of Tyrosine Loss in Metazoan Evolution [My Copy] Science, Vol. 325, No. 5948. (25 September 2009), pp. 1686-1688. by Chris S. Tan, Adrian Pasculescu, Wendell A. Lim, Tony Pawson, Gary D. Bader, Rune Linding posted to signalling indel evolution by djkt on 2009-09-25 17:25:17 as along with 5 people and 2 groups nzm arjun_citeulike bpcusack jjray stajich Journal picks Mycology
	Fast mapping of short sequences with mismatches, insertions and deletions using index structures. [My Copy] PLoS computational biology, Vol. 5, No. 9. (11 September 2009), e1000502. by Steve Hoffmann, Christian Otto, Stefan Kurtz, et al.Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller posted to sequencing indel alignment by djkt on 2009-09-11 16:27:56 as along with 17 people and 4 groups darian nuin fenghezi behindtherabbit jandot walshtp torfinnnome stubrown dswan polivares orzenil natstreet jmcq n00c heliopais ppgardne druvus Bioinformatics BergmanLab iSEEM Journal picks
	Mobile elements create structural variation: Analysis of a complete human genome [My Copy] Genome Research, Vol. 19, No. 9. (13 September 2009), pp. 1516-1526. by Jinchuan Xing, Yuhua Zhang, Kyudong Han, et al.Abdel H. Salem, Shurjo K. Sen, Chad D. Huff, Qiong Zhou, Ewen F. Kirkness, Samuel Levy, Mark A. Batzer, Lynn B. Jorde posted to sv repeats indel human by djkt on 2009-09-02 23:32:04 as along with 9 people and 1 group n00c sameersoi APRegier dchughes fenghezi jandot Dulcinea natstreet JustinCrocker Journal picks
	Evolutionary flexibility of protein complexes [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (2009), 155. by Michael Seidl, Jorg Schultz posted to duplication evolution indel proteins by djkt on 2009-07-27 18:06:39 as along with 1 person and 1 group phoenixzxl iSEEM
	DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. [My Copy] BMC evolutionary biology, Vol. 7, No. 1. (12 October 2007), 191. by N. de la Chaux, P. W. Messer, P. F. Arndt posted to annotation evolution human indel selection by djkt on 2009-07-13 17:03:00 as along with 2 people gjuggler PetrovLab
	Deletional Bias across the Three Domains of Life [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (10 July 2009), pp. 145-152. by Chih-Horng Kuo, Howard Ochman posted to chromosome drift evolution indel by djkt on 2009-07-10 19:33:35 as along with 1 person and 1 group operon iSEEM
	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 evolution indel sequencing sv by djkt on 2009-07-01 22:21:57 as along with 16 people n00c rdiaz aezrin jandot GustavoLacerda guhjy jessopher megraw jonilaserson chrisamiller dandaman sameersoi 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 evolution indel by djkt on 2009-07-01 22:04:27 as along with 3 people megraw Annab gjuggler
	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 evolution indel simulation by djkt on 2009-06-09 19:34:05 as along with 6 people and 2 groups friendpine zwang ppgardne druvus nuin gjuggler Journal picks iSEEM
	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 evolution indel by djkt on 2009-06-09 19:15:48 as along with 3 people gjuggler bmajoros nuin
	Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes [My Copy] PLoS Genet, Vol. 5, No. 5. (29 May 2009), e1000496. by Cristian Cañestro, Julian M. Catchen, Adriana Rodríguez-Marí, Hayato Yokoi, John H. Postlethwait posted to duplication evolution indel by djkt on 2009-05-30 18:34:51 as along with 1 person kiekyon
	Detection of disease-associated deletions in case-control studies using SNP genotypes with application to rheumatoid arthritis. [My Copy] Human genetics, Vol. 126, No. 2. (August 2009), pp. 303-315. by Chih-Chieh C. Wu, Sanjay Shete, Wei V. Chen, et al.Bo Peng, Annette T. Lee, Jianzhong Ma, Peter K. Gregersen, Christopher I. Amos posted to association disease indel snps sv by djkt on 2009-05-22 00:27:36 as along with 1 person guhjy
	Reconstructing the History of Yeast Genomes [My Copy] PLoS Genet, Vol. 5, No. 5. (15 May 2009), e1000483. by David Sankoff posted to chromosome duplication evolution indel phylogenetics reconstruction review yeast by djkt on 2009-05-15 16:36:52 as along with 1 person emptyhb
	Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome [My Copy] PLoS Genet, Vol. 5, No. 5. (15 May 2009), e1000485. by Jonathan L. Gordon, Kevin P. Byrne, Kenneth H. Wolfe posted to chromosome duplication evolution indel reconstruction yeast by djkt on 2009-05-15 16:36:03 as along with 4 people and 1 group bpcusack cabbagesofdoom leomrtns stajich Mycology
	Deletion Rate Evolution and Its Effect on Genome Size and Coding Density [My Copy] Mol Biol Evol, Vol. 26, No. 6. (1 June 2009), pp. 1421-1430. by Mats E. Pettersson, Charles G. Kurland, Otto G. Berg posted to evolution indel by djkt on 2009-05-12 21:23:55 as along with 4 people operon bmajoros aprasad bpcusack
	PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data [My Copy] Genome Biology, Vol. 10, No. 2. (23 February 2009), R23. by Jan Korbel, Alexej Abyzov, Xinmeng Mu, et al.Nicholas Carriero, Philip Cayting, Zhengdong Zhang, Michael Snyder, Mark Gerstein posted to duplication indel sequencing sv by djkt on 2009-03-03 01:28:55 as along with 11 people orzenil adthrasher jessopher jrvalcourt dakelley Neeperando APRegier smiddha natstreet poschm druvus
	Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence [My Copy] Nature Genetics, Vol. 41, No. 3. (22 February 2009), pp. 359-364. by Sabina Benko, Judy A. Fantes, Jeanne Amiel, et al.Dirk-Jan Kleinjan, Sophie Thomas, Jacqueline Ramsay, Negar Jamshidi, Abdelkader Essafi, Simon Heaney, Christopher T. Gordon, David Mcbride, Christelle Golzio, Malcolm Fisher, Paul Perry, Véronique Abadie, Carmen Ayuso, Muriel Holder-Espinasse, Nicky Kilpatrick, Melissa M. Lees, Arnaud Picard, Karen I. Temple, Paul Thomas, Marie-Paule Vazquez, Michel Vekemans, Hugues R. Crollius, Nicholas D. Hastie, Arnold Munnich, Heather C. Etchevers, Anna Pelet, Peter G. Farlie, David R. Fitzpatrick, Stanislas Lyonnet posted to association development enhancer expression indel tf transgenic by djkt on 2009-02-25 17:54:35 as along with 1 person provero
	Inferring genomic flux in bacteria [My Copy] Genome Research, Vol. 19, 306. by Xavier Didelot, Aaron Darling, Daniel Falush posted to duplication evolution indel microbes by djkt on 2009-02-10 00:38:48 as along with 1 group iSEEM
	Mystery of intron gain: new data and new models [My Copy] Trends in Genetics, Vol. 25, No. 2. (February 2009), pp. 67-73. by Scott W. Roy, Manuel Irimia posted to duplication indel intron review by djkt on 2009-02-09 18:23:03 as
	Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites [My Copy] Genome Research (January 2009) by Girirajan, Chen, Graves, et al. Marques-Bonet, Ventura, Fronick, Fulton, Rocchi, Fulton, Wilson, Mardis, Eichler posted to chromosome duplication indel primates by djkt on 2009-01-27 23:44:29 as
	The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria [My Copy] Science, Vol. 323, No. 5912. (16 January 2009), pp. 379-382. by Nancy A. Moran, Heather J. Mclaughlin, Rotem Sorek posted to evolution indel microbes mutation by djkt on 2009-01-17 00:44:00 as along with 7 people and 2 groups kinestetika JeremyZucker emptyhb abizar behindtherabbit bpb pansapiens MetabolicModeling 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 estimation evolution indel by djkt on 2009-01-13 17:26:49 as along with 2 people gjuggler timflutre
	Dispensability of mammalian DNA [My Copy] Genome Research, Vol. 18, No. 11., 1743. by Mclean, Bejerano posted to evolution indel mammals sv by djkt on 2008-10-30 17:52:31 as
	Probabilistic Phylogenetic Inference with Insertions and Deletions [My Copy] PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000172. by Elena Rivas, Sean R. Eddy posted to evolution indel msa phylogenetics by djkt on 2008-09-26 18:53:18 as along with 11 people and 1 group BioNica mhamada treangen pradiptaray zwang nuin timflutre druvus aprasad gjuggler emptyhb iSEEM
	Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. [My Copy] Nature, Vol. 455, No. 7209. (4 September 2008), pp. 105-108. by D. Tian, Q. Wang, P. Zhang, et al.H. Araki, S. Yang, M. Kreitman, T. Nagylaki, R. Hudson, J. Bergelson, J. Q. Chen posted to indel mutation snps by djkt on 2008-09-04 17:40:37 as along with 9 people and 1 group biomcgary Annab aprasad dakelley zwang psique caseybrown bpcusack gjuggler parkinson's disease references
	Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. [My Copy] PLoS biology, Vol. 6, No. 8. (19 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 2 people operon aprasad
	Recurrent Deletion and Gene Presence/Absence Polymorphism: Telomere Dynamics Dominate Evolution at the Tip of 3L in Drosophila melanogaster and D. simulans [My Copy] 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
	Sequence Context affects the rate of short insertions and deletions in flies and primates [My Copy] 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 8 people emptyhb timflutre bpcusack lusk biomcgary gjuggler brant aprasad
	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 alignment evolution indel phylogenetics by djkt on 2007-11-27 17:01:27 as along with 4 people druvus balicea ryanraaum smbe2008
	Transducers: an emerging probabilistic framework for modeling indels on trees [My Copy] Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3258-3262. by Robert K. Bradley, Ian Holmes posted to alignment evolution indel by djkt on 2007-11-27 16:59:06 as along with 3 people timflutre druvus ryanraaum
	A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms [My Copy] PLoS Comput Biol, Vol. 3, No. 9. (14 September 2007), e176. by Erika M. Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D. Makova posted to evolution indel primates by djkt on 2007-09-15 17:00:03 as along with 4 people and 1 group timflutre Iden-J_GluR aprasad cisevol cis-regulatory-evolution
	The Diploid Genome Sequence of an Individual Human [My Copy] PLoS Biol, Vol. 5, No. 10. (4 September 2007), e254. by Samuel Levy, Granger Sutton, Pauline C. Ng, et al.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, J. Craig Venter posted to genome indel snps by djkt on 2007-09-05 17:53:56 as along with 30 people and 1 group n00c jgill pachorip Scis0000002 daforerog jessopher psique dakelley noushin jo_davies frohike adijr Neeperando operon carlblesius bpb balicea skhadar dullhunk jackjackjjj ramensky massivemayhem jasonbobe PredictER lp2 cabbagezs xingxu hpaces maburkitt nhp Bioinformatics
	Copy number variation: New insights in genome diversity [My Copy] Genome Research, Vol. 16, No. 8. (1 August 2006), pp. 949-961. by Jennifer L. Freeman, George H. Perry, Lars Feuk, et al.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 10 people and 3 groups bertelsen brianb noushin bpb balicea dchughes jri bioguru2000 debasis jasonflannick Bioinformatics G4ID Genetics-of-Gambling
	A distal enhancer and an ultraconserved exon are derived from a novel retroposon [My Copy] Nature (16 April 2006) by Gill Bejerano, Craig B. Lowe, Nadav Ahituv, et al.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 along with 5 people and 6 groups marcius dchughes nickluscombe cisevol gjuggler G4ID EBI-regulation BioinfoCIPF SGU-CIPF Genetics-of-Gambling cis-regulatory-evolution
	Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication [My Copy] 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 along with 2 people and 1 group nickluscombe JeffR100 EBI-regulation
	When less is more: gene loss as an engine of evolutionary change. [My Copy] Am J Hum Genet, Vol. 64, No. 1. (January 1999), pp. 18-23. by M. V. Olson posted to evolution indel by djkt on 2006-08-04 00:54:05 as along with 4 people and 1 group Annab stevanspringer operon bpcusack FAB-lab
	Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 20. (30 September 2003), pp. 11484-11489. by W. James Kent, Robert Baertsch, Angie Hinrichs, Webb Miller, David Haussler posted to evolution indel by djkt on 2006-08-04 00:49:16 as along with 11 people and 2 groups gdb daveGerrard ilyashl hrogers semrich polivares bryankr pcahan1 gjuggler nuin Auger BergmanLab Dead 60's
	Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. [My Copy] Genome Res, Vol. 16, No. 2. (February 2006), pp. 173-181. by G. M. Wilson, S. Flibotte, P. I. Missirlis, et al.M. A. Marra, S. Jones, K. Thornton, A. G. Clark, R. A. Holt posted to indel msa popgen primates by djkt on 2006-08-03 23:48:39 as
	Gene Losses during Human Origins [My Copy] PLoS Biol, Vol. 4, No. 3. (14 February 2006), e52. by Xiaoxia Wang, Wendy E. Grus, Jianzhi Zhang posted to evolution indel primates proteins by djkt on 2006-08-03 23:44:43 as along with 3 people and 1 group avilella ejeffery bpcusack Ensembl Compara citations
	Common deletions and SNPs are in linkage disequilibrium in the human genome [My Copy] 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 along with 4 people sameersoi bpb balajis balicea
	Common deletion polymorphisms in the human genome. [My Copy] Nat Genet, Vol. 38, No. 1. (January 2006), pp. 86-92. by S. A. McCarroll, T. N. Hadnott, G. H. Perry, et al.P. C. Sabeti, M. C. Zody, J. C. Barrett, S. Dallaire, S. B. Gabriel, C. Lee, M. J. Daly, D. M. Altshuler, posted to indel popgen by djkt on 2006-08-03 23:22:56 as along with 2 people balajis ashandanj
	A high-resolution survey of deletion polymorphism in the human genome. [My Copy] Nature genetics, Vol. 38, No. 1. (04 January 2006), pp. 75-81. by Donald F. Conrad, T. Daniel Andrews, Nigel P. Carter, Matthew E. Hurles, Jonathan K. Pritchard posted to indel popgen by djkt on 2006-08-03 23:21:24 as along with 6 people and 1 group sameersoi waszak bpb balajis ashandanj vplagnol Bioinformatics

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evolution	390
expression	248
popgen	214
selection	128
snps	126
proteins	116
human	108
metagenomics	106
microbes	101
sequencing	96
tf	95
phylogenetics	86
duplication	84
primates	83
rna	83
association	75
review	69
fly	63
conservation	59
msa	59
acceleration	57
chromatin	54
epigenetics	53
sv	51
recombination	49
yeast	47
qtl	46
arrays	43
indel	43
ecology	40
development	38
annotation	37
chromosome	36
alignment	35
diversity	34
motif	33
genome	31
mtp	31
prediction	31
rodents	31
mammals	29
repeats	27
testing	27
disease	24
divergence	23
chip-chip	21
demography	21
histone	21
mutation	21
splicing	21
variation	20
sysbio	19
molclock	18
simulation	18
virus	18
methylation	17
bgc	16
admixture	15
bayesian	15
imprinting	15
bias	14
microbiome	14
speciation	14
clustering	13
estimation	13
gccontent	13
nucleosome	13
db	12
genotyping	12
assembly	11
hmm	11
intron	11
cpg	10
domestication	10
enhancer	10
hiv	10
sex	10
stemcells	10
cancer	9
migration	9
model_selection	9
promoter	9
structure	9
design	8
environment	8
haplotype	8
dog	7
isochores	7
resampling	7
bacteria	6
community	6
geography	6
lactation	6
replication	6
schizophrenia	6
ancient_dna	5
brain	5
computing	5
immunity	4
kmer	4
model	4
pathogen	4
power	4
reconstruction	4
worm	4
bioinfo	3
drift	3
foxp2	3
gene-transfer	3
go	3
neanderthal	3
pax6	3
plants	3
synteny	3
vertebrates	3
viualization	3
acertainment	2
aging	2
cardiovascular	2
classification	2
coalescent	2
correlation	2
diet	2
epistasis	2
ethics	2
fish	2
heterochromatin	2
mixture	2
network	2
novel	2
signalling	2
species_abundance	2
theory	2
ultras	2
archaea	1
archeology	1
birds	1
centromeres	1
codon	1
ctcf	1
dimension_reduction	1
distribution	1
dna	1
enzymes	1
epidemiology	1
eukaryotes	1
forensics	1
gene_therapy	1
genome_size	1
heart	1
lactase	1
lineage_sorting	1
localization	1
lrt	1
metabolism	1
metabolomics	1
microsatellite	1
mirna	1
olfaction	1
pca	1
phosphorylation	1
placenta	1
ptmass	1
reelin	1
repeated_measures	1
svd	1
teaching	1
teeth	1
transgenic	1
utr	1
vision	1
workflow	1

djkt's indel [43 articles] Export

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