djkt's annotation [37 articles] Export

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

	De novo computational prediction of non-coding RNA genes in prokaryotic genomes [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2897-2905. by Thao T. Tran, Fengfeng Zhou, Sarah Marshburn, Mark Stead, Sidney R. Kushner, Ying Xu posted to rna microbes annotation by djkt on 2009-11-04 17:41:30 as along with 4 people and 2 groups TRHvidsten jmcq ppgardne druvus iSEEM Journal picks
	Next generation tools for the annotation of human SNPs. [My Copy] Briefings in bioinformatics, Vol. 10, No. 1. (1 January 2009), pp. 35-52. by Rachel Karchin posted to snps disease association annotation by djkt on 2009-10-26 23:16:37 as along with 5 people daed tanglingfung guhjy daforerog pkonings
	ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2737-2738. by Erik Kristiansson, Philip Hugenholtz, Daniel Dalevi posted to sysbio metagenomics environment annotation by djkt on 2009-10-09 16:40:27 as along with 4 people and 1 group operon jmeppley dswan skembel iSEEM
	Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data [My Copy] Genome Biology, Vol. 10, No. 7. (22 July 2009), R79. by Piotr Balwierz, Piero Carninci, Carsten Daub, et al.Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen posted to annotation expression promoter sequencing by djkt on 2009-07-27 18:52:22 as along with 7 people vingron orzenil ptrobajo maximilianh inesdesantiago guhjy dolchan
	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
	The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species [My Copy] PLoS Comput Biol, Vol. 5, No. 7. (3 July 2009), e1000431. by The Reference Genome Group of the Gene Ontology Consortium posted to annotation by djkt on 2009-07-03 17:06:10 as along with 20 people and 2 groups Zephyrus bertelsen rdiaz ptrobajo fgibson NickFurnham guhjy VGreiff cabbagesofdoom Keywan druvus natstreet gjuggler biomcgary polivares tfuji dswan kiekyon TRHvidsten daforerog 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
	Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome [My Copy] Science, Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. J. Parker, Loren Hansen, Hatice O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted to annotation chromosome conservation dna evolution structure by djkt on 2009-04-17 16:18:24 as along with 38 people and 6 groups daveGerrard operon sujaikumar antonkratz pradiptaray roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings akundaje athma absterga rpatward timflutre stajich bpcusack jbhiatt dhlbh friendpine dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak BergmanLab Mycology structural_bioinformatics RockmanLab EisenLab cis-regulatory-evolution
	High-resolution human core-promoter prediction with CoreBoost_HM [My Copy] Genome Research, Vol. 19, 266. by Xiaowo Wang posted to annotation expression histone prediction by djkt on 2009-02-10 00:44:37 as
	A predictive model for identifying mini-regulatory modules in the mouse genome. [My Copy] Bioinformatics (Oxford, England) (3 December 2008) by Mahesh Yaragatti, Ted Sandler, Lyle Ungar posted to annotation chromatin expression by djkt on 2009-01-29 21:57:24 as along with 6 people TRHvidsten cassj idonaldson druvus operon maximilianh
	Variable Locus Length in the Human Genome Leads to Ascertainment Bias in Functional Inference For Noncoding Elements [My Copy] Bioinformatics (25 January 2009), btp043. by Leila Taher, Ivan Ovcharenko posted to annotation go testing by djkt on 2009-01-26 16:42:32 as along with 2 people and 1 group caseybrown daveGerrard BergmanLab
	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
	Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells [My Copy] Genome Biology, Vol. 9 (02 December 2008), R168. by Catia, John A. Stamatoyannopoulos posted to annotation conservation mammals tf by djkt on 2009-01-07 01:37:48 as along with 7 people and 3 groups xingxu Zephyrus oelemento xianjun samgj maximilianh cisevol Roswell Cancer Crosstalk JLab BergmanLab
	Metagenome Annotation Using a Distributed Grid of Undergraduate Students [My Copy] PLoS Biol, Vol. 6, No. 11. (25 November 2008), e296. by Pascal Hingamp, Céline Brochier, Emmanuel Talla, Daniel Gautheret, Denis Thieffry, Carl Herrmann posted to annotation metagenomics by djkt on 2008-11-26 02:43:57 as along with 17 people and 3 groups daforerog operon azazello Stew JustinCrocker nuin jmeppley xingxu guhjy nitiniitk dbikard dchughes druvus neils ptrobajo dullhunk treangen Bioinformatics - CRUK Centre de Recherches Interdisciplinaires iSEEM
	Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (7 November 2008), e1000218. by Mark Yandell, Barry Moore, Fidel Salas, et al.Chris Mungall, Andrew Macbride, Charles White, Martin G. Reese posted to annotation conservation duplication snps by djkt on 2008-11-08 19:09:37 as along with 9 people biomcgary druvus daforerog rsantana Zalanszabo rdiaz bpcusack cabbagesofdoom grahamc
	Selective Constraints in Experimentally Defined Primate Regulatory Regions [My Copy] PLoS Genet, Vol. 4, No. 8. (2008), e1000157. by Daniel J. Gaffney, Ran Blekhman, Jacek Majewski posted to annotation chip-chip conservation evolution expression primates tf by djkt on 2008-08-15 17:24:04 as along with 10 people and 2 groups daveGerrard xianjun madreach alhufton bpcusack aprasad pradiptaray caseybrown maximilianh cisevol BergmanLab cis-regulatory-evolution
	Automated mapping of large-scale chromatin structure in ENCODE. [My Copy] Bioinformatics (Oxford, England) (30 June 2008) by Heng Lian, William A A. Thompson, Robert Thurman, John A A. Stamatoyannopoulos, William Stafford S. Noble, Charles E E. Lawrence posted to annotation epigenetics by djkt on 2008-07-03 22:27:20 as along with 3 people dakelley aprasad timflutre
	Use and misuse of the gene ontology annotations [My Copy] Nature Reviews Genetics, Vol. 9, No. 7. (13 May 2008), pp. 509-515. by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici posted to annotation go by djkt on 2008-06-18 19:03:28 as along with 36 people and 3 groups druvus dullhunk suizan dolchan Borelli Zephyrus VGreiff klo thomaskelder ilyashl phoenixzxl MarcoAlvarez isakemal bertelsen daforerog jfr guhjy aheilbut mariakmejia cmzmasek A_Olympia realzhang carlk roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom tmmurali renatomilani capitall marck rvosa bpcusack 8_01 logics of knowledge FAB-lab
	Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions [My Copy] Genome Research, Vol. 18, No. 6. (25 June 2008), pp. 930-938. by Mahesh Yaragatti, Claudio Basilico, Lisa Dailey posted to annotation epigenetics expression tf by djkt on 2008-06-03 06:25:13 as along with 3 people tonamswish maximilianh inesdesantiago
	Multiple testing on the directed acyclic graph of gene ontology [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 537-544. by Jelle J. Goeman, Ulrich Mansmann posted to annotation mtp by djkt on 2008-02-13 16:51:35 as along with 9 people Zephyrus bertelsen pkonings guhjy jfr eckart_bindewald barriot seemu carlk
	High-Resolution Mapping and Characterization of Open Chromatin across the Genome. [My Copy] Cell, Vol. 132, No. 2. (25 January 2008), pp. 311-322. by A. P. Boyle, S. Davis, H. P. Shulha, et al.P. Meltzer, E. H. Margulies, Z. Weng, T. S. Furey, G. E. Crawford posted to annotation chromatin by djkt on 2008-02-06 22:01:56 as along with 7 people and 1 group athma inesdesantiago raylim Stew Eroslavochka bootsy aprasad Bioinformatics - CRUK
	Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b [My Copy] Genome Res. (10 December 2007), gr.6929408. by David M. Mcgaughey, Ryan M. Vinton, Jimmy Huynh, Amr Al-Saif, Michael A. Beer, Andrew S. Mccallion posted to annotation conservation tf by djkt on 2008-02-05 18:56:33 as along with 2 people brant maximilianh
	Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions [My Copy] Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 242-251. by Elfar Torarinsson, Zizhen Yao, Eric D. Wiklund, et al.Jesper B. Bramsen, Claus Hansen, Jorgen Kjems, Niels Tommerup, Walter L. Ruzzo, Jan Gorodkin posted to annotation rna by djkt on 2008-02-01 19:10:41 as along with 3 people galka8_diploma cabbagezs xingxu
	Qualifying the relationship between sequence conservation and molecular function [My Copy] Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 201-205. by Gregory M. Cooper, Christopher D. Brown posted to annotation msa review by djkt on 2008-02-01 19:09:40 as along with 7 people farhat emptyhb aprasad brant xingxu bpcusack nklee
	Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species [My Copy] Bioinformatics, Vol. 24, No. 2. (15 January 2008), pp. 165-171. by Xiaowo Wang, Jin Gu, Michael Q. Zhang, Yanda Li posted to annotation conservation fly rna by djkt on 2008-01-14 15:21:53 as along with 5 people and 1 group druvus heliopais Alexander_Kanitz maralena bootsy microRNA
	Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome [My Copy] Genome Biology, Vol. 9 (03 January 2008), R3. by Jia Q. Wu, Jiang Du, Joel Rozowsky, et al.Zhengdong Zhang, Alexander E. Urban, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder posted to annotation expression by djkt on 2008-01-12 17:05:20 as
	Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements [My Copy] Proceedings of the National Academy of Sciences (11 December 2007), 0705658104. by Sergey I. Nikolaev, Juan I. Montoya-Burgos, Konstantin Popadin, et al.Leila Parand, Elliott H. Margulies, National, Stylianos E. Antonarakis posted to annotation evolution mammals by djkt on 2007-12-19 18:24:18 as along with 5 people and 1 group pradiptaray cjeans zwang cisevol aprasad cis-regulatory-evolution
	Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes [My Copy] PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted to annotation evolution proteins tf by djkt on 2007-09-07 20:49:47 as along with 10 people and 3 groups druvus treangen carlk operon dpollard dquest zwang cabbagezs heliopais blobbybirdman EisenLab cis-regulatory-evolution Myxo group
	Raising the estimate of functional human sequences. [My Copy] Genome Res (9 August 2007) by Michael Pheasant, John S S. Mattick posted to acceleration annotation conservation expression rna by djkt on 2007-09-04 19:22:27 as along with 11 people and 1 group galka8_diploma hdopazo guhjy jfr andersbj grahamc lp2 cabbagezs nklee ljs mimulus_99 microRNA
	Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 760-774. by Elliott H. Margulies, Gregory M. Cooper, George Asimenos, et al.Daryl J. Thomas, Colin N. Dewey, Adam Siepel, Ewan Birney, Damian Keefe, Ariel S. Schwartz, Minmei Hou, James Taylor, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Loytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, James B. Brown, Peter Bickel, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Eric A. Stone, Kate R. Rosenbloom, James W. Kent, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V. Maduro, Baishali Maskeri, Jennifer C. Mcdowell, Morgan Park, Pamela J. Thomas, Alice C. Young, Robert W. Blakesley, Donna M. Muzny, Erica Sodergren, David A. Wheeler, Kim C. Worley, Huaiyang Jiang, George M. Weinstock, Richard A. Gibbs, Tina Graves, Robert Fulton, Elaine R. Mardis, Richard K. Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B. Jaffe, Jean L. Chang, Kerstin Lindblad-Toh, Eric S. Lander, Angie Hinrichs, Heather Trumbower, Hiram Clawson, Ann Zweig, Robert M. Kuhn, Galt Barber, Rachel Harte, Donna Karolchik, Matthew A. Field, Richard A. Moore, Carrie A. Matthewson, Jacqueline E. Schein, Marco A. Marra, Stylianos E. Antonarakis, Serafim Batzoglou, Nick Goldman, Ross Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D. Green, Arend Sidow posted to annotation conservation msa by djkt on 2007-06-14 01:05:24 as along with 11 people and 5 groups daveGerrard polivares timflutre aprasad dpollard dchughes AaronDarling ghattem Garamonfok gjuggler elfar BergmanLab Bioinformatics EisenLab G4ID Genetics-of-Gambling
	Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. [My Copy] Genome research, Vol. 17, No. 6. (1 June 2007), pp. 746-759. by F. Denoeud, P. Kapranov, C. Ucla, et al.A. Frankish, R. Castelo, J. Drenkow, J. Lagarde, T. Alioto, C. Manzano, J. Chrast, S. Dike, C. Wyss, C. N. Henrichsen, N. Holroyd, M. C. Dickson, R. Taylor, Z. Hance, S. Foissac, R. M. Myers, J. Rogers, T. Hubbard, J. Harrow, R. Guigó, T. R. Gingeras, S. E. Antonarakis, A. Reymond posted to annotation expression by djkt on 2007-06-14 01:04:19 as along with 7 people and 1 group timhubbard aprasad myrtilus olympos ghattem xingxu jasonflannick Bioinformatics
	The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 732-745. by Joel S. Rozowsky, Daniel Newburger, Fred Sayward, et al.Jiaqian Wu, Greg Jordan, Jan O. Korbel, Ugrappa Nagalakshmi, Jin Yang, Deyou Zheng, Roderic Guigo, Thomas R. Gingeras, Sherman Weissman, Perry Miller, Michael Snyder, Mark B. Gerstein posted to annotation expression by djkt on 2007-06-14 01:03:10 as along with 5 people and 1 group GeeSharpMinor olympos ghattem jasonflannick gjuggler Bioinformatics
	Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [My Copy] Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816. posted to annotation by djkt on 2007-06-13 21:14:50 as along with 30 people and 4 groups balajis bertelsen gderwin polivares Eroslavochka timflutre pengchy raistrick guhjy cmmorel dpollard ilh plofje ramensky joepickrell massivemayhem fishtank Garamonfok jmuhlich bioyang cabbagezs xingxu antonkratz mimulus_99 julianjonker gjuggler drbal maralena ep161302 jasonflannick JLab Bioinformatics EisenLab SorgerLab
	A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection [My Copy] Genome Research, Vol. 17, No. 5. (1 May 2007), pp. 632-640. by Kousuke Hanada, Xu Zhang, Justin O. Borevitz, Wen-Hsiung Li, Shin-Han Shiu posted to annotation evolution expression proteins by djkt on 2007-05-03 19:36:10 as along with 3 people and 1 group natstreet druvus cursonivel1 cursonivel1
	Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family [My Copy] posted to annotation msa by djkt on 2007-04-17 20:42:32 as
	Large-scale identification of novel transcripts in the human genome. [My Copy] Genome research, Vol. 17, No. 3. (31 March 2007), pp. 287-292. by B. A. Peters, B. St Croix, T. Sjöblom, et al.J. M. Cummins, N. Silliman, J. Ptak, S. Saha, K. W. Kinzler, C. Hatzis, V. E. Velculescu posted to annotation expression by djkt on 2007-03-01 18:22:10 as along with 6 people and 2 groups guhjy jfr dchughes olympos grahamc bpcusack G4ID Genetics-of-Gambling
	Extensions to gene set enrichment. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 3. (1 February 2007), pp. 306-313. by Zhen Jiang, Robert Gentleman posted to expression arrays annotation by djkt on 2007-02-02 17:43:15 as along with 12 people and 1 group ptrobajo guhjy tonamswish ipark-kaist jfr aviad_work ihpark ealloza waghsk heliopais giovenko magusina BioinfoCIPF

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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 annotation [37 articles] Export

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