djkt's alignment [35 articles] Export

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

	Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 40. (6 October 2009), pp. 17077-17082. by Gregory E. Sims, Se-Ran R. Jun, Guohong Albert A. Wu, Sung-Hou H. Kim posted to phylogenetics mammals kmer alignment by djkt on 2009-11-04 22:44:52 as along with 7 people wendygarnica Geknitics jsatkosk mkiyer antariksh sujaikumar bpcusack
	Upcoming challenges for multiple sequence alignment methods in the high-throughput era [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2455-2465. by Carsten Kemena, Cedric Notredame posted to sequencing review alignment by djkt on 2009-09-28 19:31:26 as along with 10 people and 2 groups fstrozzi manduca rdiaz sjcockell torfinnnome walshtp nuin natstreet druvus ollieredfernwork Journal picks Orengo Group Journal Picks
	PineSAP--sequence alignment and SNP identification pipeline [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2609-2610. by Jill L. Wegrzyn, Jennifer M. Lee, John Liechty, David B. Neale posted to snps sequencing alignment by djkt on 2009-09-28 19:23:25 as along with 7 people jasontsai jsatkosk daforerog operon nuin n00c druvus
	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 16 people and 4 groups nuin fenghezi behindtherabbit jandot walshtp torfinnnome stubrown dswan polivares orzenil natstreet jmcq n00c heliopais ppgardne druvus Bioinformatics BergmanLab iSEEM Journal picks
	BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (28 August 2009), 217. by Rahul Satija, Adam Novak, Istvan Miklos, Rune Lyngso, Jotun Hein posted to conservation bayesian alignment by djkt on 2009-09-03 01:39:57 as along with 3 people and 2 groups cmzmasek cisevol phoenixzxl cis-regulatory-evolution BergmanLab
	Evolutionary Triplet Models of Structured RNA [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000483. by Robert K. Bradley, Ian Holmes posted to structure rna phylogenetics alignment by djkt on 2009-08-31 19:26:10 as along with 1 person and 2 groups ppgardne iSEEM Journal picks
	HaMStR: Profile hidden markov model based search for orthologs in ESTs [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (08 July 2009), 157. by Ingo Ebersberger, Sascha Strauss, Arndt von Haeseler posted to alignment hmm phylogenetics by djkt on 2009-07-27 18:02:32 as along with 1 group iSEEM
	SOAP2: an improved ultrafast tool for short read alignment [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1966-1967. by Ruiqiang Li, Chang Yu, Yingrui Li, et al.Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang posted to alignment sequencing by djkt on 2009-07-18 00:49:41 as along with 25 people and 6 groups agbiotec torfinnnome natstreet cthachuk jforment GustavoLacerda adijr bozdagd stubrown polivares guhjy ollieredfernwork operon cassj adamjamesreid Stew jamselem dswan idonaldson TRHvidsten humburg farhat n00c jmeppley druvus Bioinformatics Core Service BergmanLab Orengo Group Journal Picks Bioinformatics - CRUK Bioinformatics Journal picks
	Fast and accurate short read alignment with Burrows-Wheeler transform. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1754-1760. by Heng Li, Richard Durbin posted to alignment sequencing by djkt on 2009-07-02 19:23:19 as along with 31 people and 4 groups cthachuk maren bozdagd adijr heliopais jmanning2k GustavoLacerda stubrown jessopher guhjy katholt mkiyer jmcq idonaldson michaelbarton polivares darian orzenil cassj inesdesantiago TRHvidsten operon ghattem n00c danmaclean ppgardne nuin rschulz natstreet druvus humburg BergmanLab SIMR bioinformatics Bioinformatics Journal picks
	Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment [My Copy] Genome Biology and Evolution, Vol. 0 (2009), 114. by Schneider posted to alignment annotation selection sequencing by djkt on 2009-06-23 18:00:42 as
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, C. Randal Linder, Tandy Warnow posted to alignment phylogenetics by djkt on 2009-06-19 21:41:58 as along with 26 people and 4 groups gjuggler parnell kinestetika robertrentzsch xianjun gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings ppgardne dokky aprasad timflutre inquil TRHvidsten fenghezi phoenixzxl Orengo Group Journal Picks Mycology Journal picks iSEEM
	A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays [My Copy] Bioinformatics, Vol. 25, No. 13. (1 July 2009), pp. 1609-1616. by Zia Khan, Joshua S. Bloom, Leonid Kruglyak, Mona Singh posted to alignment sequencing by djkt on 2009-06-17 21:59:49 as along with 2 people n00c guhjy
	SHRiMP: Accurate Mapping of Short Color-space Reads [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (22 May 2009), e1000386. by Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno posted to alignment sequencing by djkt on 2009-06-09 00:04:12 as along with 18 people and 4 groups bozdagd ilanc burak guhjy trfield n00c natstreet adijr druvus Stew farhat humburg kshameer operon stajich GeeSharpMinor AlexBateman barry Bioinformatics - CRUK Mycology Journal picks Bioinformatics
	Fast Statistical Alignment [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (29 May 2009), e1000392. by Robert K. Bradley, Adam Roberts, Michael Smoot, et al.Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes, Lior Pachter posted to alignment hmm by djkt on 2009-05-30 18:26:16 as along with 18 people and 1 group seb1 rdowell timflutre natstreet n00c yylin aprasad Gorzomagnificent guhjy dakelley reyez rec3141 farhat operon bmduggan nuin AlexBateman druvus Journal picks
	CloudBurst: highly sensitive read mapping with MapReduce [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1363-1369. by Michael C. Schatz posted to alignment computing sequencing by djkt on 2009-05-14 18:21:22 as along with 30 people and 2 groups jfr walshtp idonaldson orzenil heliopais dakelley bozdagd agbiotec jandot guhjy n00c cymacs semrich nuin operon AlexBateman fgibson rschulz dswan mitko humburg jmeppley coela vagoskar svenrahmann natstreet brianb Neeperando druvus neils KCL & UCL Bioinformatics Bioinformatics
	Infernal 1.0: inference of RNA alignments. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 10. (15 May 2009), pp. 1335-1337. by Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy posted to alignment rna by djkt on 2009-05-07 12:59:43 as along with 6 people and 1 group reyez operon neils nuin natstreet druvus iSEEM
	Local RNA structure alignment with incomplete sequence. [My Copy] Bioinformatics (Oxford, England) (20 March 2009) by Diana L L. Kolbe, Sean R R. Eddy posted to alignment metagenomics rna structure by djkt on 2009-05-07 12:58:51 as along with 4 people and 1 group skembel reyez nuin mhamada iSEEM
	The difficulty of avoiding false positives in genome scans for natural selection [My Copy] Genome Research, Vol. 19, No. 5. (May 2009), pp. 922-933. by Swapan Mallick, Sante Gnerre, Paul Muller, David Reich posted to alignment selection testing by djkt on 2009-05-02 02:52:37 as along with 4 people operon dakelley gjuggler jbhiatt
	ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 11. (1 June 2009), pp. 1424-1425. by You Jung J. Kim, Nikhil Teletia, Victor Ruotti, et al.Christopher A. Maher, Arul M. Chinnaiyan, Ron Stewart, James A. Thomson, Jignesh M. Patel posted to alignment computing sequencing by djkt on 2009-04-08 19:41:42 as along with 11 people and 1 group mmartin n00c guhjy nuin idonaldson AlexBateman bmajoros humburg Thaverkamp druvus svenrahmann Journal picks
	Multiple whole-genome alignments without a reference organism [My Copy] Genome Research, Vol. 19, No. 4. (28 April 2009), pp. 682-689. by Inna Dubchak, Alexander Poliakov, Andrey Kislyuk, Michael Brudno posted to alignment duplication msa by djkt on 2009-04-01 20:07:53 as along with 12 people fstrozzi GustavoLacerda michaelbarton mlangill dakelley xwbcn Neeperando zwang nyyu semrich azazello mhamada
	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [My Copy] Genome Biology, Vol. 10, No. 3. (2009), R25. by Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg posted to alignment sequencing by djkt on 2009-04-01 01:53:37 as along with 34 people and 4 groups cthachuk darshan fstrozzi adijr debasis bozdagd polivares torfinnnome n00c talponer jmcq rschulz ghattem operon humburg idonaldson mmartin skembel dquest heliopais GeeSharpMinor bertelsen darian semrich dakelley idoerg vmsr hpaces admash pdexheimer mhamada fpattyn natstreet druvus BergmanLab SIMR bioinformatics iSEEM Notre Dame Bioinformatics
	Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (13 March 2009), e1000299. by Xin He, Xu Ling, Saurabh Sinha posted to alignment evolution motif tf by djkt on 2009-03-21 01:50:33 as along with 9 people roys megraw lusk TRHvidsten kieran101 nuin mhamada maximilianh druvus
	Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment [My Copy] Bioinformatics (4 December 2008), btn630. by Benedict Paten, Javier Herrero, Kathryn Beal, Ewan Birney posted to alignment msa by djkt on 2009-01-29 21:55:21 as along with 9 people BioNica guhjy dakelley semrich gjuggler rschulz birney operon druvus
	A hierarchical model for incomplete alignments in phylogenetic inference [My Copy] Bioinformatics, Vol. 25, No. 5. (1 March 2009), pp. 592-598. by Fuxia Cheng, Stefanie Hartmann, Mayetri Gupta, Joseph G. Ibrahim, Todd J. Vision posted to alignment metagenomics phylogenetics proteins by djkt on 2009-01-20 05:15:50 as along with 7 people and 1 group nuin druvus skembel mhamada jmeppley sriesenfeld jameswasmuth iSEEM
	Rose: generating sequence families. [My Copy] Bioinformatics (Oxford, England), Vol. 14, No. 2. (1 March 1998), pp. 157-163. by J. Stoye, D. Evers, F. Meyer posted to alignment proteins simulation by djkt on 2009-01-20 05:05:28 as along with 3 people and 1 group hryk gjuggler adijr iSEEM
	Specific Alignment of Structured RNA: Stochastic Grammars and Sequence Annealing. [My Copy] Bioinformatics (Oxford, England) (16 September 2008) by Robert K K. Bradley, Lior Pachter, Ian Holmes posted to alignment rna by djkt on 2008-11-22 01:18:54 as along with 3 people reyez davfre nuin
	Profile Comparer: a program for scoring and aligning profile hidden Markov models [My Copy] Bioinformatics, Vol. 24, No. 22. (15 November 2008), pp. 2630-2631. by Martin Madera posted to alignment hmm msa proteins by djkt on 2008-11-05 16:15:23 as along with 3 people and 1 group tonamswish j3xucite nuin iSEEM
	Segment-based multiple sequence alignment [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i187-192. by Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Doring, Cedric Notredame, Knut Reinert posted to alignment msa by djkt on 2008-08-09 17:19:25 as along with 9 people nuin BioNica darian Md_2007 zwang Ema APRegier aprasad groepl
	Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis [My Copy] Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635. by Ari Loytynoja, Nick Goldman posted to alignment evolution msa phylogenetics by djkt on 2008-06-20 16:18:18 as along with 28 people and 3 groups operon TRHvidsten BioNica cmzmasek timflutre pradiptaray alexeid marti bpcusack hpaces dinnes gjuggler ArtemPankin phoenixzxl jago marck imtechnology aprasad zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
	A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation [My Copy] by Sean Eddy posted to alignment by djkt on 2008-05-31 00:45:04 as
	Uncertainty in homology inferences: Assessing and improving genomic sequence alignment [My Copy] 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 by djkt on 2008-02-01 19:13:19 as along with 8 people aprasad brant treangen grahamc dandaman mailund gjuggler AaronDarling
	Alignment Uncertainty and Genomic Analysis [My Copy] Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476. by Karen M. Wong, Marc A. Suchard, John P. Huelsenbeck posted to alignment msa by djkt on 2008-01-25 15:08:08 as along with 32 people and 2 groups operon walshtp darian ptrobajo friendpine skembel druvus treangen bpb aprasad dayjm pradiptaray dpollard tny cjeans zwang lisa1 cactus biomcgary lilou dandaman gjuggler renatomilani mclarenv youdon bpcusack guhjy jdelcampo adacier gracio timflutre jfr EisenLab microbiology_nijmegen
	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
	Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. [My Copy] Genome biology, Vol. 8, No. 10. (24 October 2007), R225. by Weichun Huang, Joseph R. Nevins, Uwe Ohler posted to alignment conservation evolution simulation tf by djkt on 2007-11-13 16:31:20 as along with 5 people and 2 groups lusk dpollard stajich Garamonfok maximilianh EisenLab cis-regulatory-evolution

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evolution	390
expression	248
popgen	213
selection	125
snps	125
proteins	113
human	107
metagenomics	106
microbes	101
sequencing	95
tf	95
phylogenetics	85
duplication	83
rna	83
primates	82
association	75
review	69
fly	63
msa	59
conservation	58
acceleration	57
chromatin	54
epigenetics	53
sv	51
recombination	49
qtl	46
yeast	46
indel	43
arrays	42
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	26
testing	26
disease	24
divergence	23
chip-chip	21
histone	21
mutation	21
splicing	21
demography	20
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
hmm	11
intron	11
assembly	10
cpg	10
enhancer	10
sex	10
stemcells	10
cancer	9
domestication	9
hiv	9
migration	9
model_selection	9
promoter	9
structure	9
design	8
environment	8
haplotype	8
isochores	7
resampling	7
bacteria	6
community	6
dog	6
geography	6
lactation	6
replication	6
schizophrenia	6
ancient_dna	5
brain	5
computing	5
immunity	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
kmer	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
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 alignment [35 articles] Export

djkt's tags