djkt's motif [35 articles] Export

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

	Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila [My Copy] PLoS Genet, Vol. 5, No. 11. (6 November 2009), e1000709. by Margaret C. W. Ho, Holly Johnsen, Sara E. Goetz, et al.Benjamin J. Schiller, Esther Bae, Diana A. Tran, Andrey S. Shur, John M. Allen, Christoph Rau, Welcome Bender, William W. Fisher, Susan E. Celniker, Robert A. Drewell posted to tf motif fly expression evolution by djkt on 2009-11-30 17:05:54 as along with 2 people and 1 group emptyhb cisevol cis-regulatory-evolution
	MOODS: fast search for position weight matrix matches in DNA sequences [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3181-3182. by Janne Korhonen, Petri Martinmaki, Cinzia Pizzi, Pasi Rastas, Esko Ukkonen posted to tf motif by djkt on 2009-11-17 17:32:42 as along with 4 people and 2 groups Stew idonaldson ppgardne farhat Bioinformatics - CRUK Journal picks
	Combinatorial binding predicts spatio-temporal cis-regulatory activity [My Copy] Nature, Vol. 462, No. 7269. (05 November 2009), pp. 65-70. by Robert P. Zinzen, Charles Girardot, Julien Gagneur, Martina Braun, Eileen E. M. Furlong posted to tf motif expression enhancer development by djkt on 2009-11-04 21:29:14 as along with 11 people cajunsushi emptyhb toszko roys inesdesantiago fenghezi balabu iskathy megraw TRHvidsten pedrobeltrao
	Distinguishing direct versus indirect transcription factor-DNA interactions. [My Copy] Genome research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk posted to tf motif chip-chip by djkt on 2009-11-02 18:17:10 as along with 12 people sebastien_vigneau oannes nklee vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	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
	Different gene regulation strategies revealed by analysis of binding motifs [My Copy] Trends in Genetics, Vol. 25, No. 10. (06 October 2009), pp. 434-440. by Zeba Wunderlich, Leonid A. Mirny posted to tf motif expression by djkt on 2009-10-21 18:50:54 as along with 2 people and 1 group francemirko behindtherabbit iSEEM
	TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2625-2631. by Sanghamitra Bandyopadhyay, Ramkrishna Mitra posted to rna motif by djkt on 2009-10-09 16:36:18 as along with 8 people and 2 groups jforment heliopais dswan reyez morrislab TRHvidsten guhjy frohike Bioinformatics Core Service microRNA
	Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2473-2477. by Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar posted to motif fly expression development by djkt on 2009-09-28 19:28:41 as along with 8 people and 1 group Garamonfok TRHvidsten rdiaz natstreet nuin sebastien_vigneau maximilianh isimpson Jarman Lab
	Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data [My Copy] SAGMB, Vol. 8, No. 1., Article 36. by Elizabeth A. Siewert, Katerina J. Kechris posted to tf repeated_measures motif expression by djkt on 2009-09-23 16:54:33 as
	Statistical detection of cooperative transcription factors with similarity adjustment. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 16. (15 August 2009), pp. 2103-2109. by Utz J. Pape, Holger Klein, Martin Vingron posted to motif testing tf by djkt on 2009-08-07 21:41:12 as along with 2 people idonaldson TRHvidsten
	Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions [My Copy] Genome Biology, Vol. 10, No. 7. (23 July 2009), R80. by Stewart MacArthur, Xiao Y. Li, Jingyi Li, et al.James Brown, Hou C. Chu, Lucy Zeng, Brandi Grondona, Aaron Hechmer, Lisa Simirenko, Soile Keranen, David Knowles, Mark Stapleton, Peter Bickel, Mark Biggin, Michael Eisen posted to chip-chip chromatin fly motif tf by djkt on 2009-07-27 19:01:50 as along with 11 people and 2 groups venancio aalibes fenghezi idonaldson daveGerrard megraw scjparker maximilianh isimpson Stew druvus BergmanLab Bioinformatics - CRUK
	Measuring Transcription Factor-Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (22 June 2009), pp. 85-98. by Wolfgang Otto, Peter F. Stadler, Francesc Lopez-Giraldez, Jeffrey P. Townsend, Vincent J. Lynch, Gunter P. Wagner posted to yeast tf motif evolution by djkt on 2009-06-23 18:01:25 as along with 2 people druvus natstreet
	Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (19 June 2009), e1000414. by Yuanyuan Xiao, Mark R. Segal posted to chip-chip expression motif prediction sysbio yeast by djkt on 2009-06-19 16:22:10 as along with 2 people ptrobajo TRHvidsten
	Probing the Functional Impact of Sequence Variation on p53-DNA Interactions Using a Novel Microsphere Assay for Protein-DNA Binding with Human Cell Extracts [My Copy] PLoS Genet, Vol. 5, No. 5. (8 May 2009), e1000462. by Maher A. Noureddine, Daniel Menendez, Michelle R. Campbell, et al.Omari J. Bandele, Monica M. Horvath, Xuting Wang, Gary S. Pittman, Brian N. Chorley, Michael A. Resnick, Douglas A. Bell posted to expression motif tf by djkt on 2009-05-10 18:02:58 as
	KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 16. (15 August 2009), pp. 2126-2133. by Sebastian J. Schultheiss, Wolfgang Busch, Jan U. Lohmann, Oliver Kohlbacher, Gunnar Rätsch posted to motif tf by djkt on 2009-05-05 06:50:32 as along with 2 people natstreet operon
	The rise and fall of a human recombination hot spot [My Copy] Nat Genet, Vol. 41, No. 5. (May 2009), pp. 625-629. by Alec J. Jeffreys, Rita Neumann posted to human motif recombination by djkt on 2009-04-28 19:32:24 as
	DNA binding site sequence directs glucocorticoid receptor structure and activity. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5925. (17 April 2009), pp. 407-410. by Sebastiaan H. Meijsing, Miles A. Pufall, Alex Y. So, Darren L. Bates, Lin Chen, Keith R. Yamamoto posted to expression motif tf by djkt on 2009-04-17 16:23:05 as along with 7 people and 1 group Annab sebastien_vigneau JustinCrocker fenghezi absterga bpcusack jbhiatt BenosLab
	Novel Nucleotide Sequence Motifs That Produce Hotspots of Meiotic Recombination in Schizosaccharomyces pombe [My Copy] Genetics (10 April 2009), genetics.109.101253. by Walter W. Steiner, Estelle M. Steiner, Angela R. Girvin, Lauren E. Plewik posted to motif recombination yeast by djkt on 2009-04-13 17:41:55 as
	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
	High-resolution DNA-binding specificity analysis of yeast transcription factors. [My Copy] Genome research, Vol. 19, No. 4. (21 April 2009), pp. 556-566. by Cong Zhu, Kelsey J. Byers, Rachel Patton P. McCord, et al.Zhenwei Shi, Michael F. Berger, Daniel E. Newburger, Katrina Saulrieta, Zachary Smith, Mita V. Shah, Mathangi Radhakrishnan, Anthony A. Philippakis, Yanhui Hu, Federico De Masi, Marcin Pacek, Andreas Rolfs, Tal Murthy, Joshua Labaer, Martha L. Bulyk posted to motif tf yeast by djkt on 2009-04-01 19:54:10 as along with 9 people matted austin_mcdonald siebert dolchan rpatward xwbcn absterga kristallreiner aalibes
	M are better than one: an ensemble-based motif finder and its application to regulatory element prediction [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 868-874. by Chen Yanover, Mona Singh, Elena Zaslavsky posted to motif tf by djkt on 2009-03-25 17:35:09 as along with 5 people pradiptaray TRHvidsten druvus mhamada maximilianh
	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
	PASTAA: identifying transcription factors associated with sets of co-regulated genes [My Copy] Bioinformatics (9 December 2008), btn627. by Helge G. Roider, Thomas Manke, Sean O'Keeffe, Martin Vingron, Stefan A. Haas posted to expression motif testing tf by djkt on 2009-02-13 18:30:18 as along with 10 people and 1 group TRHvidsten maximilianh jimineep cassj idonaldson dswan dolchan nuin natstreet druvus Bioinformatics
	ARCS-Motif: discovering correlated motifs from unaligned biological sequences. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 2. (15 January 2009), pp. 183-189. by Shijie Zhang, Wei Su, Jiong Yang posted to motif tf by djkt on 2009-01-15 16:49:39 as along with 2 people wowalz nuin
	Evolution of Regulatory Sequences in 12 Drosophila Species [My Copy] PLoS Genet, Vol. 5, No. 1. (January 2009), e1000330. by Jaebum Kim, Xin He, Saurabh Sinha posted to evolution fly motif tf by djkt on 2009-01-09 21:39:46 as along with 12 people and 3 groups daveGerrard kevinemamy dpollard caseybrown druvus WanderingAengus JustinCrocker cisevol cajunsushi emptyhb cabbagesofdoom Stew RockmanLab BergmanLab cis-regulatory-evolution
	Analysis of combinatorial cis-regulation in synthetic and genomic promoters [My Copy] Nature, Vol. 457, No. 7226. (23 November 2008), pp. 215-218. by Jason Gertz, Eric D. Siggia, Barak A. Cohen posted to expression motif tf yeast by djkt on 2009-01-07 20:16:59 as along with 17 people and 4 groups Vincent_Rouilly pcarbo emptyhb TRHvidsten rpatward jbhiatt lusk maximilianh roys dpollard druvus sebastien_vigneau pengchy sandersl siebert isimpson xianjun TranscriptionalRegulationWithThermodynamicModels RockmanLab cis-regulatory-evolution microbiology_nijmegen
	Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_2. (1 July 2004), pp. W199-203. by Giulio Pavesi, Paolo Mereghetti, Giancarlo Mauri, Graziano Pesole posted to expression motif tf by djkt on 2009-01-07 20:05:41 as along with 8 people farhat Dulce wowalz coldmeadow dquest xiaobeizhao dandaman bryankr
	Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells [My Copy] Cell, Vol. 134, No. 3. (08 August 2008), pp. 521-533. by Alexander Marson, Stuart S. Levine, Megan F. Cole, et al.Garrett M. Frampton, Tobias Brambrink, Sarah Johnstone, Matthew G. Guenther, Wendy K. Johnston, Marius Wernig, Jamie Newman posted to motif rna stemcells tf by djkt on 2009-01-07 20:04:05 as along with 13 people and 1 group danaiancu gbloeb mtagaya valeriehilgers inesdesantiago jfr heliopais ealloza megraw bootsy pengchy maralena gdb microRNA
	Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. [My Copy] Cell, Vol. 133, No. 6. (13 June 2008), pp. 1106-1117. by X. Chen, H. Xu, P. Yuan, et al.F. Fang, M. Huss, V. B. Vega, E. Wong, Y. L. Orlov, W. Zhang, J. Jiang, Y. H. Loh, H. C. Yeo, Z. X. Yeo, V. Narang, K. R. Govindarajan, B. Leong, A. Shahab, Y. Ruan, G. Bourque, W. K. Sung, N. D. Clarke, C. L. Wei, H. H. Ng posted to motif stemcells tf by djkt on 2009-01-07 20:03:02 as along with 12 people and 2 groups isimpson shikin sebastien_vigneau cassj rschulz FJ fhalbrit jjray inesdesantiago caseybrown kengg gdb Epigenetics CTCF
	MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. [My Copy] Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006) by G. Pavesi, P. Mereghetti, F. Zambelli, M. Stefani, G. Mauri, G. Pesole posted to motif tf by djkt on 2009-01-06 23:44:47 as along with 2 people wowalz maximilianh
	WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences [My Copy] BMC Bioinformatics, Vol. 8 (07 February 2007), 46. by Giulio Pavesi, Federico Zambelli, Graziano Pesole posted to conservation motif tf by djkt on 2009-01-06 23:43:42 as along with 4 people wowalz dquest GustavoLacerda nuin
	CompMoby: comparative MobyDick for detection of cis-regulatory motifs. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by Christina Chaivorapol, Collin Melton, Grace Wei, et al.Ru-Fang F. Yeh, Miguel Ramalho-Santos, Robert Blelloch, Hao Li posted to motif tf by djkt on 2009-01-06 23:06:15 as along with 5 people guhjy heliopais xili03 maximilianh druvus
	Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs, and Boundaries. [My Copy] Genetics (28 October 2008) by Charleston W K W. Chiang, Adnan Derti, Daniel Schwartz, Michael F F. Chou, Joel N N. Hirschhorn, Chao-Ting T. Wu posted to conservation duplication motif by djkt on 2008-12-16 05:33:23 as along with 2 people treangen maximilianh
	Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif [My Copy] Genome Research, Vol. 18, No. 12., 1896. by Cheng posted to conservation evolution motif tf by djkt on 2008-12-05 03:23:21 as
	MotifMap: a human genome-wide map of candidate regulatory motif sites [My Copy] Bioinformatics, Vol. 25, No. 2. (15 January 2009), pp. 167-174. by Xiaohui Xie, Paul Rigor, Pierre Baldi posted to conservation db motif tf by djkt on 2008-11-19 18:48:16 as along with 11 people jakebiesinger kmdaily guhjy wowalz ilyashl jfr abizar heliopais nklee idonaldson nuin

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evolution	391
expression	257
popgen	215
selection	128
snps	126
proteins	116
human	108
metagenomics	106
microbes	104
sequencing	97
tf	97
phylogenetics	87
duplication	84
primates	83
rna	83
association	75
review	70
fly	64
msa	59
conservation	59
acceleration	57
epigenetics	55
chromatin	54
sv	51
recombination	50
yeast	47
qtl	46
arrays	44
indel	43
ecology	41
development	39
annotation	37
chromosome	36
alignment	35
motif	35
diversity	34
rodents	32
prediction	32
genome	31
mtp	31
mammals	29
testing	27
repeats	27
disease	24
divergence	23
histone	22
splicing	22
mutation	21
chip-chip	21
demography	21
variation	20
sysbio	20
methylation	18
simulation	18
virus	18
molclock	18
bgc	16
imprinting	16
bayesian	15
admixture	15
bias	14
speciation	14
microbiome	14
gccontent	13
estimation	13
nucleosome	13
clustering	13
genotyping	12
stemcells	12
db	12
assembly	11
hmm	11
intron	11
cpg	10
sex	10
hiv	10
enhancer	10
domestication	10
migration	9
model_selection	9
cancer	9
promoter	9
structure	9
environment	8
design	8
haplotype	8
resampling	7
community	7
isochores	7
dog	7
schizophrenia	6
brain	6
lactation	6
replication	6
geography	6
bacteria	6
foxp2	5
computing	5
ancient_dna	5
power	4
model	4
immunity	4
kmer	4
reconstruction	4
pathogen	4
worm	4
viualization	3
go	3
gene-transfer	3
neanderthal	3
bioinfo	3
drift	3
plants	3
synteny	3
pax6	3
vertebrates	3
theory	3
heterochromatin	2
acertainment	2
signalling	2
aging	2
ultras	2
coalescent	2
novel	2
mixture	2
species_abundance	2
epistasis	2
ethics	2
cardiovascular	2
classification	2
metabolomics	2
network	2
diet	2
correlation	2
fish	2
microsatellite	1
lactase	1
svd	1
dna	1
operons	1
pca	1
gene_therapy	1
centromeres	1
archaea	1
metabolism	1
enzymes	1
roc	1
birds	1
epidemiology	1
reelin	1
heart	1
forensics	1
workflow	1
eukaryotes	1
proteomics	1
vision	1
teaching	1
dimension_reduction	1
teeth	1
genome_size	1
phosphorylation	1
ptmass	1
ctcf	1
localization	1
archeology	1
codon	1
utr	1
olfaction	1
mirna	1
placenta	1
transgenic	1
repeated_measures	1
lineage_sorting	1
distribution	1
lrt	1

djkt's motif [35 articles] Export

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