djkt's phylogenetics [86 articles] Export

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

	Global Microsatellite Content Distinguishes Humans, Primates, Animals, and Plants [My Copy] Mol Biol Evol, Vol. 26, No. 12. (1 December 2009), pp. 2809-2819. by C. L. Galindo, L. J. McIver, J. F. McCormick, et al.M. A. Skinner, Y. Xie, R. A. Gelhausen, K. Ng, N. M. Kumar, H. R. Garner posted to repeats phylogenetics kmer arrays by djkt on 2009-11-11 00:45:24 as
	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
	Phylogenomics of primates and their ancestral populations [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 1929-1941. by Adam Siepel posted to review primates popgen phylogenetics evolution by djkt on 2009-11-02 19:00:34 as along with 3 people and 1 group rvosa aprasad merpublic FAB-lab
	Automatic genome-wide reconstruction of phylogenetic gene trees [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i549-558. by Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev posted to proteins phylogenetics duplication by djkt on 2009-10-09 16:29:19 as along with 7 people and 1 group biomcgary thegoose2 gjuggler stajich shigepong seitentaisei tharris Mycology
	The human protein coevolution network. [My Copy] Genome research, Vol. 19, No. 10. (20 October 2009), pp. 1861-1871. by Elisabeth R. Tillier, Robert L. Charlebois posted to sysbio proteins phylogenetics evolution by djkt on 2009-10-01 23:58:20 as along with 7 people dfdong Garamonfok venancio jperkins TRHvidsten phoenixzxl tmmurali
	Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (23 September 2009), pp. 325-339. by Olga Zhaxybayeva, W. Ford Doolittle, R. Thane Papke, J. Peter Gogarten posted to phylogenetics microbes ecology by djkt on 2009-10-01 00:13:13 as along with 1 person and 1 group skembel iSEEM
	Bayesian Phylogeography Finds Its Roots [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (25 September 2009), e1000520. by Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard posted to virus phylogenetics model geography bayesian by djkt on 2009-09-25 19:55:42 as along with 2 people and 1 group scmelton nuin iSEEM
	Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach [My Copy] Genetics, Vol. 183, No. 1. (1 September 2009), pp. 259-274. by Julien Y. Dutheil, Ganesh Ganapathy, Asger Hobolth, Thomas Mailund, Marcy K. Uyenoyama, Mikkel H. Schierup posted to recombination primates phylogenetics lineage_sorting by djkt on 2009-09-23 01:42:00 as along with 2 people operon aprasad
	The Evolutionary Origin of Man Can Be Traced in the Layers of Defunct Ancestral Alpha Satellites Flanking the Active Centromeres of Human Chromosomes [My Copy] PLoS Genet, Vol. 5, No. 9. (11 September 2009), e1000641. by Valery A. Shepelev, Alexander A. Alexandrov, Yuri B. Yurov, Ivan A. Alexandrov posted to repeats phylogenetics evolution chromosome centromeres by djkt on 2009-09-11 16:40:15 as along with 2 people and 1 group mspivako marywaye Journal picks
	Species Tree Inference by Minimizing Deep Coalescences [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (11 September 2009), e1000501. by Cuong Than, Luay Nakhleh posted to phylogenetics by djkt on 2009-09-11 16:30:16 as along with 6 people and 2 groups parnell qcjones gdb gjuggler ppgardne druvus iSEEM Journal picks
	A Phylogenetic Mixture Model for the Evolution of Gene Expression [My Copy] Mol Biol Evol, Vol. 26, No. 10. (1 October 2009), pp. 2363-2372. by Kevin H. Eng, Hector C. Bravo, Sunduz Keles posted to phylogenetics mixture expression evolution by djkt on 2009-09-05 16:07:35 as along with 2 people daveGerrard operon
	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
	Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants [My Copy] Journal of Computational Biology, Vol. 16, No. 8. (August 2009), pp. 1071-1083. by J. G. Burleigh, M. S. Bansal, A. Wehe, O. Eulenstein posted to phylogenetics evolution duplication chromosome by djkt on 2009-08-21 01:02:16 as along with 3 people biomcgary druvus natstreet
	PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2286-2288. by Nicolas Lartillot, Thomas Lepage, Samuel Blanquart posted to phylogenetics molclock bayesian by djkt on 2009-08-20 18:55:41 as along with 6 people and 1 group nesnidal leemond31 operon nuin grahamc phoenixzxl iSEEM
	A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies [My Copy] Mol Biol Evol, Vol. 26, No. 9. (1 September 2009), pp. 1931-1939. by Mayo Roettger, William Martin, Tal Dagan posted to phylogenetics by djkt on 2009-08-13 22:57:53 as along with 3 people and 2 groups gwallau stajich operon Mycology iSEEM
	Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (7 August 2009), e1000455. by Jing Tang, William P. Hanage, Christophe Fraser, Jukka Corander posted to metagenomics phylogenetics popgen by djkt on 2009-08-07 17:16:24 as along with 3 people and 1 group jjray operon skembel iSEEM
	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
	TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 18. (15 September 2009), pp. 2440-2441. by Lin Himmelmann, Dirk Metzler posted to estimation phylogenetics by djkt on 2009-07-18 00:34:20 as along with 2 people and 1 group nuin nlapalu iSEEM
	SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1722-1730. by M. Monzoorul Haque, Tarini S. Ghosh, Dinakar Komanduri, Sharmila S. Mande posted to metagenomics phylogenetics by djkt on 2009-07-02 19:02:47 as along with 5 people and 1 group dakelley sharpton sriesenfeld guhjy operon iSEEM
	Using genomic data to unravel the root of the placental mammal phylogeny. [My Copy] Genome Res, Vol. 17, No. 4. (April 2007), pp. 413-421. by W. J. Murphy, T. H. Pringle, T. A. Crider, M. S. Springer, W. Miller posted to mammals phylogenetics by djkt on 2009-06-22 19:32:59 as along with 2 people aprasad maximilianh
	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
	FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix [My Copy] Mol Biol Evol, Vol. 26, No. 7. (1 July 2009), pp. 1641-1650. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted to phylogenetics by djkt on 2009-06-09 19:06:36 as along with 8 people and 2 groups druvus houniao007 pyilmaz rneches ppgardne jwm skembel nuin iSEEM Journal picks
	PhyloExplorer: a web server to validate, explore and query phylogenetic trees [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (18 May 2009), 108. by Vincent Ranwez, Nicolas Clairon, Frederic Delsuc, et al.Saeed Pourali, Nicolas Auberval, Sorel Diser, Vincent Berry posted to phylogenetics by djkt on 2009-05-22 00:37:45 as along with 1 person and 1 group rvosa FAB-lab
	Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences [My Copy] BMC Evolutionary Biology, Vol. 9 (30 April 2009), 87. by Guy, Stijn Vansteelandt posted to bayesian clustering evolution model_selection phylogenetics by djkt on 2009-05-22 00:37:07 as
	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 2 people eannaokeefe emptyhb
	Many-core algorithms for statistical phylogenetics [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1370-1376. by Marc A. Suchard, Andrew Rambaut posted to computing phylogenetics by djkt on 2009-05-14 18:22:17 as along with 9 people and 1 group mlangill druvus nuin AlexBateman bmajoros jmeppley svenrahmann rdiaz Neeperando iSEEM
	Simultaneous Bayesian gene tree reconstruction and reconciliation analysis [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 14. (7 April 2009), pp. 5714-5719. by Ãrjan Ãkerborg, Bengt Sennblad, Lars Arvestad, Jens Lagergren posted to bayesian duplication phylogenetics by djkt on 2009-05-11 17:45:45 as along with 2 people and 1 group pinney mhamada iSEEM
	Comparative analysis of Alu repeats in primate genomes [My Copy] Genome Research, Vol. 19, No. 5. (May 2009), pp. 876-885. by George E. Liu, Can Alkan, Lu Jiang, Shaying Zhao, Evan E. Eichler posted to evolution phylogenetics primates repeats by djkt on 2009-05-02 02:51:15 as
	Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2 [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (1 May 2009), e1000377. by Joel O. Wertheim, Michael Worobey posted to hiv molclock phylogenetics by djkt on 2009-05-01 23:40:46 as
	Phylogenetic Signals in DNA Composition: Limitations and Prospects [My Copy] Mol Biol Evol, Vol. 26, No. 5. (1 May 2009), pp. 1163-1169. by Jan Mrazek posted to phylogenetics by djkt on 2009-04-14 16:25:46 as along with 5 people and 1 group dakelley jmeppley skembel druvus nuin iSEEM
	Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms [My Copy] BMC Evolutionary Biology, Vol. 9 (17 March 2009), 61. by Gordon, Douglas E. Soltis posted to phylogenetics by djkt on 2009-03-23 19:25:51 as along with 1 group iSEEM
	Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (2009) by Stephen Smith, Jeremy Beaulieu, Michael Donoghue posted to phylogenetics by djkt on 2009-02-24 23:59:01 as along with 5 people and 2 groups rs Schmidtc stajich skembel druvus iSEEM Mycology
	Addressing the Shortcomings of Three Recent Bayesian Methods for Detecting Interspecific Recombination in DNA Sequence Alignments [My Copy] Statistical Applications in Genetics and Molecular Biology, Vol. 7, No. 1., article 34. by Dirk Husmeier, Alexander V. Mantzaris posted to bayesian phylogenetics recombination by djkt on 2009-02-18 02:51:53 as along with 1 group iSEEM
	RAMI, a tool for identification and characterization of phylogenetic clusters in microbial communities [My Copy] Bioinformatics (17 February 2009), btp051. by Thomas Pommier, Bjorn Canback, Per Lundberg, Ake Hagstrom, Anders Tunlid posted to clustering metagenomics microbiome phylogenetics by djkt on 2009-02-17 18:03:50 as along with 4 people and 2 groups elbrodie hpaces skembel sriesenfeld phylocom iSEEM
	A novel method for large tree visualization. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 4. (15 February 2009), pp. 557-558. by J. Heard, W. Kaufmann, X. Guan posted to clustering phylogenetics viualization by djkt on 2009-02-13 18:26:03 as along with 9 people Torsten_Holmer jfr guhjy Yanno pkonings Cortel druvus nuin jmeppley
	STEM: species tree estimation using maximum likelihood for gene trees under coalescence [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 971-973. by Laura S. Kubatko, Bryan C. Carstens, Lacey L. Knowles posted to phylogenetics proteins by djkt on 2009-02-12 17:43:32 as along with 4 people lizbiogen aprasad nuin 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
	Phylogenetic and functional assessment of orthologs inference projects and methods. [My Copy] PLoS computational biology, Vol. 5, No. 1. (16 January 2009), e1000262. by Adrian M. Altenhoff, Christophe Dessimoz posted to annotation phylogenetics proteins by djkt on 2009-01-16 17:12:59 as along with 10 people and 1 group avilella AaronDarling skembel isimpson hpaces natstreet alpae kshameer bpcusack druvus Ensembl Compara citations
	Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics [My Copy] BMC Evolutionary Biology, Vol. 8, No. 1. (03 December 2008), 327. by J. Gregory Caporaso, Sandra Smit, Brett Easton, Lawrence Hunter, Gavin Huttley, Rob Knight posted to evolution phylogenetics proteins by djkt on 2009-01-13 23:21:53 as along with 4 people and 1 group dfdong mgomes qluo sjcockell iSEEM
	Parallel adaptations to high temperatures in the Archaean eon. [My Copy] Nature, Vol. 456, No. 7224. (18 December 2008), pp. 942-945. by B. Boussau, S. Blanquart, A. Necsulea, N. Lartillot, M. Gouy posted to evolution phylogenetics by djkt on 2008-12-17 22:38:36 as along with 3 people and 1 group chica idoerg cmzmasek iSEEM
	Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics [My Copy] Syst Biol, Vol. 57, No. 5. (1 October 2008), pp. 750-757. by Kasper Munch, Wouter Boomsma, John P. Huelsenbeck, Eske Willerslev, Rasmus Nielsen posted to metagenomics phylogenetics by djkt on 2008-12-16 05:25:16 as along with 3 people and 1 group polivares druvus sim82 iSEEM
	StepBrothers: inferring partially shared ancestries among recombinant viral sequences [My Copy] Biostat, Vol. 10, No. 1. (1 January 2009), pp. 106-120. by Erik W. Bloomquist, Karin S. Dorman, Marc A. Suchard posted to evolution phylogenetics recombination virus by djkt on 2008-12-12 23:45:43 as along with 1 person druvus
	AUGIST: inferring species trees while accommodating gene tree uncertainty [My Copy] Bioinformatics, Vol. 24, No. 24. (15 December 2008), pp. 2932-2933. by Jeffrey C. Oliver posted to phylogenetics by djkt on 2008-12-04 16:59:04 as
	Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing [My Copy] PLoS Genet, Vol. 4, No. 11. (21 November 2008), e1000255. by Susan M. Huse, Les Dethlefsen, Julie A. Huber, David M. Welch, David A. Relman, Mitchell L. Sogin posted to metagenomics phylogenetics rna sequencing by djkt on 2008-11-22 01:24:16 as along with 4 people and 2 groups Huub_odc azazello sconlan skembel microbiology_nijmegen iSEEM
	Coined quantum walks lift the cospectrality of graphs and trees [My Copy] Pattern Recognition (06 November 2008) by D. Emms, S. Severini, R. Wilson, E. Hancock posted to phylogenetics by djkt on 2008-11-14 22:03:45 as along with 1 group iSEEM
	Pattern Classification of Phylogeny Signals [My Copy] Statistical Applications in Genetics and Molecular Biology, Vol. 7, No. 1., article 30. by Xiaofei, Hong, Chris posted to clustering phylogenetics proteins by djkt on 2008-11-12 00:15:26 as along with 1 group iSEEM
	Phylogenetic distances are encoded in networks of interacting pathways [My Copy] Bioinformatics (26 September 2008), btn503. by Aurelien Mazurie, Danail Bonchev, Benno Schwikowski, Gregory A. Buck posted to evolution phylogenetics sysbio by djkt on 2008-11-05 16:07:47 as along with 4 people and 1 group behindtherabbit markchen nuin renatomilani iSEEM
	Factors affecting the concordance between orthologous gene trees and species tree in bacteria [My Copy] BMC Evolutionary Biology, Vol. 8 (30 October 2008), 300. by Santiago Castillo-Ramirez, Victor Gonzalez posted to phylogenetics proteins by djkt on 2008-11-03 19:43:57 as along with 1 person and 1 group nklee iSEEM
	Fusion and Fission of Genes Define a Metric between Fungal Genomes [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (24 October 2008), e1000200. by Pascal Durrens, Macha Nikolski, David Sherman posted to duplication phylogenetics proteins yeast by djkt on 2008-10-24 19:25:52 as along with 5 people and 2 groups jameswasmuth skembel cthachuk taguchi stajich Mycology iSEEM
	A simple, fast, and accurate method of phylogenomic inference [My Copy] Genome Biology, Vol. 9, No. 10. (13 October 2008), R151. by Martin Wu, Jonathan Eisen posted to metagenomics microbes phylogenetics proteins by djkt on 2008-10-21 21:10:44 as along with 12 people and 2 groups dakelley jeargle AaronDarling zwang cgaugain treangen Katje operon ellakat scryrps aramata druvus microbiology_nijmegen iSEEM

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evolution	390
expression	250
popgen	214
selection	128
snps	126
proteins	116
human	108
metagenomics	106
microbes	101
sequencing	97
tf	96
phylogenetics	86
duplication	84
primates	83
rna	83
association	75
review	70
fly	63
conservation	59
msa	59
acceleration	57
chromatin	54
epigenetics	53
sv	51
recombination	49
yeast	47
qtl	46
arrays	44
indel	43
ecology	41
development	39
annotation	37
chromosome	36
alignment	35
diversity	34
motif	34
prediction	32
genome	31
mtp	31
rodents	31
mammals	29
repeats	27
testing	27
disease	24
divergence	23
splicing	22
chip-chip	21
demography	21
histone	21
mutation	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
community	7
dog	7
isochores	7
resampling	7
bacteria	6
brain	6
geography	6
lactation	6
replication	6
schizophrenia	6
ancient_dna	5
computing	5
foxp2	5
immunity	4
kmer	4
model	4
pathogen	4
power	4
reconstruction	4
worm	4
bioinfo	3
drift	3
gene-transfer	3
go	3
neanderthal	3
pax6	3
plants	3
synteny	3
theory	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
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
roc	1
svd	1
teaching	1
teeth	1
transgenic	1
utr	1
vision	1
workflow	1

djkt's phylogenetics [86 articles] Export

djkt's tags