djkt's proteins [113 articles] Export

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

	An ensemble model of competitive multi-factor binding of the genome [My Copy] Genome Research, Vol. 19, No. 11. (31 November 2009), pp. 2101-2112. by Todd Wasson, Alexander J. Hartemink posted to tf proteins motif by djkt on 2009-11-02 18:15:45 as along with 6 people megraw vingron xianjun owhitney bpcusack natstreet
	Automated inference of molecular mechanisms of disease from amino acid substitutions [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2744-2750. by Biao Li, Vidhya G. Krishnan, Matthew E. Mort, et al.Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, Predrag Radivojac posted to snps proteins disease by djkt on 2009-10-23 23:57:28 as
	Temporal Constraints on the Incorporation of Regulatory Mutants in Evolutionary Pathways [My Copy] Mol Biol Evol, Vol. 26, No. 11. (1 November 2009), pp. 2455-2462. by Kyle M. Brown, Mark A. DePristo, Daniel M. Weinreich, Daniel L. Hartl posted to selection proteins evolution enzymes bacteria by djkt on 2009-10-12 17:58:59 as along with 1 person and 1 group JustinCrocker iSEEM
	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
	Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution [My Copy] Science, Vol. 325, No. 5948. (25 September 2009), pp. 1682-1686. by Liam J. Holt, Brian B. Tuch, Judit Villen, Alexander D. Johnson, Steven P. Gygi, David O. Morgan posted to yeast signalling proteins evolution by djkt on 2009-09-25 17:23:57 as along with 5 people nzm brianb walshtp jjray neils
	Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence Level [My Copy] Mol Biol Evol, Vol. 26, No. 10. (1 October 2009), pp. 2275-2284. by Yoshiyuki Suzuki, Takashi Gojobori, Sudhir Kumar posted to selection proteins cpg bias by djkt on 2009-09-05 16:12:32 as along with 1 person operon
	Interrogating 11 Fast-Evolving Genes for Signatures of Recent Positive Selection in Worldwide Human Populations [My Copy] Mol Biol Evol, Vol. 26, No. 10. (1 October 2009), pp. 2285-2297. by Andres Moreno-Estrada, Kun Tang, Martin Sikora, et al.Tomas Marques-Bonet, Ferran Casals, Arcadi Navarro, Francesc Calafell, Jaume Bertranpetit, Mark Stoneking, Elena Bosch posted to selection proteins popgen human evolution acceleration by djkt on 2009-09-05 16:10:03 as along with 3 people and 1 group operon gjuggler ppgardne Journal picks
	More than just orphans: are taxonomically-restricted genes important in evolution? [My Copy] Trends in Genetics, Vol. 25, No. 9. (27 September 2009), pp. 404-413. by Konstantin Khalturin, Georg Hemmrich, Sebastian Fraune, René Augustin, Thomas C. G. Bosch posted to proteins novel evolution by djkt on 2009-09-05 16:02:16 as along with 1 person alhufton
	Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. [My Copy] Genome research, Vol. 19, No. 9. (September 2009), pp. 1562-1569. by Sudhir Kumar, Michael P. Suleski, Glenn J. Markov, Simon Lawrence, Antonio Marco, Alan J. Filipski posted to snps proteins disease conservation by djkt on 2009-09-02 23:41:11 as along with 1 person bpcusack
	Identification of deleterious mutations within three human genomes [My Copy] Genome Research, Vol. 19, No. 9. (3 September 2009), pp. 1553-1561. by Sung Chun, Justin C. Fay posted to snps proteins disease conservation by djkt on 2009-09-02 23:37:41 as along with 9 people xingxu operon bpcusack aprasad gjuggler jessopher fenghezi jbhiatt daforerog
	Recent de novo origin of human protein-coding genes. [My Copy] Genome research, Vol. 19, No. 10. (2 October 2009), pp. 1752-1759. by David G. Knowles, Aoife McLysaght posted to proteins novel human evolution by djkt on 2009-09-02 21:58:16 as along with 8 people and 2 groups psique xianjun gjuggler biomcgary megraw fenghezi avilella bpcusack Journal picks Ensembl Compara citations
	Evolutionary History Reconstruction for Mammalian Complex Gene Clusters [My Copy] Journal of Computational Biology, Vol. 16, No. 8. (August 2009), pp. 1051-1070. by Yu Zhang, Giltae Song, Tomáš Vinař, Eric D. Green, Adam Siepel, Webb Miller posted to reconstruction proteins evolution duplication chromosome by djkt on 2009-08-21 01:03:26 as
	Architecture and secondary structure of an entire HIV-1 RNA genome. [My Copy] Nature, Vol. 460, No. 7256. (6 August 2009), pp. 711-716. by Joseph M. Watts, Kristen K. Dang, Robert J. Gorelick, et al.Christopher W. Leonard, Julian W. Bess, Ronald Swanstrom, Christina L. Burch, Kevin M. Weeks posted to genome hiv proteins rna structure virus by djkt on 2009-08-05 19:57:41 as along with 7 people and 2 groups samgj jago physics operon wsjames memerman jbhiatt Oxford Virology Journal picks
	Rapid Evolution of Sex Pheromone-Producing Enzyme Expression in Drosophila [My Copy] PLoS Biol, Vol. 7, No. 8. (4 August 2009), e1000168. by Troy R. Shirangi, Héloïse D. Dufour, Thomas M. Williams, Sean B. Carroll posted to acceleration fly proteins by djkt on 2009-08-04 16:48:55 as along with 2 people and 1 group daveGerrard biomcgary BergmanLab
	Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates [My Copy] Genome Research, Vol. 19, No. 8. (13 August 2009), pp. 1404-1418. by Karin S. Kassahn, Vinh T. Dang, Simon J. Wilkins, Andrew C. Perkins, Mark A. Ragan posted to duplication evolution expression proteins sv vertebrates by djkt on 2009-08-03 19:43:17 as along with 3 people venancio fenghezi JustinCrocker
	Domain shuffling and the evolution of vertebrates [My Copy] Genome Research, Vol. 19, No. 8. (14 August 2009), pp. 1393-1403. by Takeshi Kawashima, Shuichi Kawashima, Chisaki Tanaka, et al.Miho Murai, Masahiko Yoneda, Nicholas H. Putnam, Daniel S. Rokhsar, Minoru Kanehisa, Nori Satoh, Hiroshi Wada posted to evolution proteins sv vertebrates by djkt on 2009-08-03 19:40:59 as along with 7 people and 1 group venancio PabloMarin bpcusack ppgardne cmzmasek grahamc JustinCrocker Journal picks
	Coevolution of Interacting Fertilization Proteins [My Copy] PLoS Genet, Vol. 5, No. 7. (24 July 2009), e1000570. by Nathaniel L. Clark, Joe Gasper, Masashi Sekino, Stevan A. Springer, Charles F. Aquadro, Willie J. Swanson posted to correlation divergence evolution popgen proteins selection sex speciation by djkt on 2009-07-27 18:50:48 as along with 3 people and 2 groups dchughes stevanspringer theodorejmorgan Orengo Group Journal Picks Morgan Lab-KSU
	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
	Automated Protein Subfamily Identification and Classification [My Copy] PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e160. by Duncan P. Brown, Nandini Krishnamurthy, Kimmen Sjölander posted to classification proteins by djkt on 2009-07-18 00:30:50 as along with 5 people and 1 group druvus Einat cjeans mingzhi shung structural_bioinformatics
	Similarly Strong Purifying Selection Acts on Human Disease Genes of All Evolutionary Ages [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (22 June 2009), pp. 131-144. by James J. Cai, Elhanan Borenstein, Rong Chen, Dmitri A. Petrov posted to disease duplication proteins selection by djkt on 2009-07-10 19:32:13 as along with 2 people greg operon
	General Rules for Optimal Codon Choice [My Copy] PLoS Genet, Vol. 5, No. 7. (10 July 2009), e1000556. by Ruth Hershberg, Dmitri A. Petrov posted to bias evolution proteins by djkt on 2009-07-10 16:50:45 as along with 4 people and 1 group codonusage GustavoLacerda kiekyon stajich Mycology
	Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. [My Copy] PLoS genetics, Vol. 5, No. 7. (3 July 2009), e1000548. by Joanna L. Parmley, Martijn A. Huynen posted to bias evolution human proteins by djkt on 2009-07-03 17:22:37 as along with 4 people saunders danatcaret hrogers bpcusack
	Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. [My Copy] PLoS biology, Vol. 7, No. 6. (16 June 2009), e1000134. by Pedro Beltrao, Jonathan C. Trinidad, Dorothea Fiedler, et al.Assen Roguev, Wendell A. Lim, Kevan M. Shokat, Alma L. Burlingame, Nevan J. Krogan posted to evolution phosphorylation promoter proteins yeast by djkt on 2009-06-24 16:38:58 as along with 14 people psique dakelley robfsouza emptyhb mingzhi leemond31 chica tmmurali biomcgary kiekyon neils bpcusack renatomilani ematsen
	Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (12 June 2009), e1000413. by Yu Xia, Eric A. Franzosa, Mark B. Gerstein posted to conservation evolution proteins yeast by djkt on 2009-06-12 21:24:05 as along with 8 people and 1 group aprasad chica biomcgary gjuggler kiekyon michaelbarton RamuAnandakrishnan bpcusack Journal picks
	Translationally optimal codons associate with structurally sensitive sites in proteins. [My Copy] Molecular biology and evolution, Vol. 26, No. 7. (6 July 2009), pp. 1571-1580. by Tong Zhou, Mason Weems, Claus O. Wilke posted to bias evolution proteins structure by djkt on 2009-06-09 19:13:45 as along with 3 people and 1 group saunders paramitamandal bpcusack Journal picks
	mRNA retrotransposition coupled with 5' inversion as a possible source of new genes. [My Copy] Molecular biology and evolution (16 March 2009) by Kenji K K. Kojima, Norihiro Okada posted to duplication proteins repeats by djkt on 2009-05-12 21:27:25 as along with 3 people dchughes bpcusack clearbluespring
	Reliabilities of identifying positive selection by the branch-site and the site-prediction methods [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6700-6705. by Masafumi Nozawa, Yoshiyuki Suzuki, Masatoshi Nei posted to proteins selection simulation by djkt on 2009-05-11 17:42:18 as along with 8 people and 1 group ckenaley sameersoi rvosa ramiro2k gjuggler bpcusack atphan gulsacan FAB-lab
	Adaptive evolution of young gene duplicates in mammals. [My Copy] Genome research, Vol. 19, No. 5. (May 2009), pp. 859-867. by Mira V. Han, Jeffery P. Demuth, Casey L. McGrath, Claudio Casola, Matthew W. Hahn posted to duplication evolution mammals proteins selection by djkt on 2009-05-02 02:49:16 as along with 4 people cmzmasek clearbluespring gjuggler maximilianh
	Darwinian and demographic forces affecting human protein coding genes [My Copy] Genome Research, Vol. 19, No. 5. (1 May 2009), pp. 838-849. by Rasmus Nielsen, Melissa J. Hubisz, Ines Hellmann, et al.Dara Torgerson, Aida M. Andrés, Anders Albrechtsen, Ryan Gutenkunst, Mark D. Adams, Michele Cargill, Adam Boyko, Amit Indap, Carlos D. Bustamante, Andrew G. Clark posted to demography human popgen proteins selection by djkt on 2009-05-02 02:46:50 as along with 3 people operon daveGerrard psique
	Evolutionary rates and centrality in the yeast gene regulatory network [My Copy] Genome Biology, Vol. 10 (09 April 2009), R35. by Richard Jovelin, Patrick C. Phillips posted to evolution proteins sysbio yeast by djkt on 2009-05-01 23:46:32 as along with 2 people michaelbarton bpcusack
	Gene cluster statistics with gene families [My Copy] Mol Biol Evol (15 January 2009), msp002. by Narayanan Raghupathy, Dannie Durand posted to clustering duplication proteins by djkt on 2009-04-14 17:38:34 as along with 3 people hpaces bpcusack druvus
	The Effect of Sequence Evolution on Protein Structural Divergence [My Copy] Mol Biol Evol, Vol. 26, No. 5. (1 May 2009), pp. 1055-1065. by Simon G. Williams, Simon C. Lovell posted to evolution proteins structure by djkt on 2009-04-14 17:35:29 as along with 2 people robfsouza bpcusack
	Predicting the binding preference of transcription factors to individual DNA k-mers [My Copy] Bioinformatics, Vol. 25, No. 8. (15 April 2009), pp. 1012-1018. by Trevis M. Alleyne, Lourdes Pena-Castillo, Gwenael Badis, et al.Shaheynoor Talukder, Michael F. Berger, Andrew R. Gehrke, Anthony A. Philippakis, Martha L. Bulyk, Quaid D. Morris, Timothy R. Hughes posted to motif proteins tf by djkt on 2009-04-08 16:58:27 as along with 6 people and 1 group absterga TRHvidsten bais lptolik nuin maximilianh BenosLab
	Death and Resurrection of the Human <italic>IRGM</italic> Gene [My Copy] PLoS Genet, Vol. 5, No. 3. (6 March 2009), e1000403. by Cemalettin Bekpen, Tomas Marques-Bonet, Can Alkan, et al.Francesca Antonacci, Maria B. Leogrande, Mario Ventura, Jeffrey M. Kidd, Priscillia Siswara, Jonathan C. Howard, Evan E. Eichler posted to evolution primates proteins repeats by djkt on 2009-03-06 19:35:32 as along with 3 people aprasad fenghezi bpcusack
	Estimating the size of the bacterial pan-genome. [My Copy] Trends in genetics : TIG, Vol. 25, No. 3. (23 March 2009), pp. 107-110. by Pascal Lapierre, J. Peter Gogarten posted to evolution genome microbes proteins by djkt on 2009-03-05 16:26:53 as along with 4 people and 1 group treangen azazello skembel nyyu iSEEM
	Computational Fitness Landscape for All Gene-Order Permutations of an RNA Virus [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (6 February 2009), e1000283. by Kwang-Il Lim, John Yin posted to evolution proteins rna virus by djkt on 2009-02-28 02:51:52 as
	Universal features in the genome-level evolution of protein domains. [My Copy] Genome biology, Vol. 10, No. 1. (30 January 2009), R12. by Marco Cosentino Lagomarsino, Alessandro L. Sellerio, Philip D. Heijning, Bruno Bassetti posted to duplication evolution proteins by djkt on 2009-02-27 17:47:53 as along with 7 people docv zwang phoenixzxl idoerg VGreiff grahamc pawelszczesny
	A Signature of Evolutionary Constraint on a Subset of Ectopically Expressed Olfactory Receptor Genes [My Copy] Mol Biol Evol, Vol. 26, No. 3. (1 March 2009), pp. 491-494. by De La, Ran Blekhman, Xiaohong Zhang, Dan Nicolae, Stuart Firestein, Yoav Gilad posted to evolution expression primates proteins by djkt on 2009-02-13 17:25:09 as
	An Unbiased Estimator of Gene Diversity in Samples Containing Related Individuals [My Copy] Mol Biol Evol, Vol. 26, No. 3. (1 March 2009), pp. 501-512. by Michael Degiorgio, Noah A. Rosenberg posted to diversity popgen proteins by djkt on 2009-02-13 17:23:52 as
	Inferring Selection on Amino Acid Preference in Protein Domains [My Copy] Mol Biol Evol, Vol. 26, No. 3. (1 March 2009), pp. 527-536. by Alan M. Moses, Richard Durbin posted to bias evolution proteins by djkt on 2009-02-13 17:22:21 as along with 2 people operon gjuggler
	Origin of Primate Orphan Genes: A Comparative Genomics Approach [My Copy] Mol Biol Evol, Vol. 26, No. 3. (1 March 2009), pp. 603-612. by Macarena Toll-Riera, Nina Bosch, Nicolas Bellora, et al.Robert Castelo, Lluis Armengol, Xavier Estivill, M. Mar Alba posted to evolution primates proteins repeats by djkt on 2009-02-13 17:20:09 as along with 2 people operon nuin
	STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence [My Copy] Bioinformatics (10 February 2009), btp079. 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 3 people aprasad nuin druvus
	A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements [My Copy] Genome Research, Vol. 19, 284. by Gerhard Mittler, Falk Butter, Matthias Mann posted to proteins tf by djkt on 2009-02-10 00:41:00 as
	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
	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
	GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates [My Copy] Trends in Genetics, Vol. 25, No. 1. (January 2009), pp. 1-5. by N. Galtier, L. Duret, S. Glemin, V. Ranwez posted to bgc primates proteins by djkt on 2009-01-14 16:15:49 as
	Lactose digestion and the evolutionary genetics of lactase persistence [My Copy] Human Genetics, Vol. 124, No. 6. (1 January 2009), pp. 579-591. by Catherine Ingram, Charlotte Mulcare, Yuval Itan, Mark Thomas, Dallas Swallow posted to evolution human popgen proteins by djkt on 2009-01-13 23:31:01 as along with 2 people songpku shoshin
	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

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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 proteins [113 articles] Export

djkt's tags