maximilianh's discovery [122 articles] Export

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	info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2715-2722. by Matthieu Defrance, Jacques van Helden posted to motif discovery by maximilianh on 2009-10-13 11:41:24 as along with 3 people TRHvidsten natstreet nuin
	Discovering multiple realistic TFBS motifs based on a generalized model. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (7 October 2009), 321. by Tak-Ming M. Chan, Gang Li, Kwong-Sak S. Leung, Kin-Hong H. Lee posted to motif discovery by maximilianh on 2009-10-09 11:30:08 as along with 2 people idonaldson ashishanand
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high throughput data [My Copy] Bioinformatics (1 October 2009), btp570. by Victor X. Jin, Jeff Apostolos, Naga S. Nagisetty, Peggy J. Farnham posted to tools motif discovery by maximilianh on 2009-10-05 19:08:22 as along with 1 person nklee
	RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), gkp388. by Deepak Sharma, Debasisa Mohanty, Avadhesha Surolia posted to discovery by maximilianh on 2009-09-17 12:14:10 as along with 4 people idonaldson guhjy renatomilani cassj
	A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 6, No. 3. (p 2009), pp. 370-386. by Chengpeng Bi posted to discovery motif by maximilianh on 2009-08-05 08:21:21 as
	Motif discovery and motif finding from genome-mapped DNase footprint data. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 18. (15 September 2009), pp. 2318-2325. by Ivan V. Kulakovskiy, Alexander V. Favorov, Vsevolod J. Makeev posted to discovery motif by maximilianh on 2009-07-22 16:13:59 as along with 3 people operon nuin cisevol
	Efficient exact motif discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009) by T. Marschall, S. Rahmann posted to discovery motif by maximilianh on 2009-05-31 23:48:04 as
	DISCOVER: a feature-based discriminative method for motif search in complex genomes. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. i321-329. by Wenjie Fu, Pradipta Ray, Eric P. Xing posted to discovery motif by maximilianh on 2009-05-28 17:16:44 as along with 5 people and 1 group guhjy dquest Stew idonaldson thegoose Bioinformatics - CRUK
	Efficient exact motif discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. i356-364. by T. Marschall, S. Rahmann posted to discovery motif by maximilianh on 2009-05-28 17:15:43 as along with 4 people wowalz dquest nuin idonaldson
	Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 537 (2009), pp. 263-276. by L. Mariño-Ramírez, K. Tharakaraman, J. L. Spouge, D. Landsman posted to discovery motif by maximilianh on 2009-05-26 10:49:47 as
	COMPUTATIONAL METHODS FOR IDENTIFYING AND CHARACTERIZING THE HUMAN GENE REGULATORY REGIONS AND CIS -ELEMENTS [My Copy] by W. Huang posted to conserved discovery motif regulatory by maximilianh on 2009-05-15 16:54:53 as
	Identification of cis-Regulatory Elements in Gene Co-expression Networks Using A-GLAM. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 541 (2009), pp. 1-20. by L. Mariño-Ramírez, K. Tharakaraman, O. Bodenreider, J. Spouge, D. Landsman posted to discovery motif by maximilianh on 2009-04-23 18:07:35 as
	Detection of broadly expressed neuronal genes in C. elegans. [My Copy] Dev Biol, Vol. 302, No. 2. (15 February 2007), pp. 617-626. by I. Ruvinsky, U. Ohler, C. B. Burge, G. Ruvkun posted to discovery wholegenomescanning by maximilianh on 2009-04-20 14:14:57 as along with 3 people and 1 group thegoose2 tharris wenhan C. elegans / WormBase
	Sampling motifs on phylogenetic trees. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 27. (5 July 2005), pp. 9481-9486. by X. Li, W. H. Wong posted to conservation discovery by maximilianh on 2009-04-02 09:41:04 as
	All motifs are NOT created equal: structural properties of transcription factor-DNA interactions and the inference of sequence specificity [My Copy] Genome Biology, Vol. 6, No. 5. (2005), P7. by Michael Eisen posted to discovery by maximilianh on 2009-03-26 18:51:16 as
	Informative priors based on transcription factor structural class improve de novo motif discovery [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392. by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J. Hartemink posted to discovery by maximilianh on 2009-03-23 16:36:32 as along with 5 people megraw dquest nklee idonaldson yevishere
	A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome. [My Copy] Genes & development, Vol. 23, No. 5. (1 March 2009), pp. 602-618. by J. Jans, J. M. Gladden, E. J. Ralston, et al.C. S. Pickle, A. H. Michel, R. R. Pferdehirt, M. B. Eisen, B. J. Meyer posted to discovery motif whole by maximilianh on 2009-03-11 08:36:32 as
	Counting of oligomers in sequences generated by markov chains for DNA motif discovery. [My Copy] Journal of bioinformatics and computational biology, Vol. 7, No. 1. (February 2009), pp. 39-54. by G. Shan, W. M. Zheng posted to discovery motif by maximilianh on 2009-02-24 11:50:03 as along with 1 person wowalz
	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 discovery motif by maximilianh on 2009-02-19 23:33:41 as along with 5 people pradiptaray TRHvidsten djkt druvus mhamada
	A Bayesian Hidden Markov Model for Motif Discovery Through Joint Modeling of Genomic Sequence and ChIP-Chip Data [My Copy] Biometrics, Vol. 9999, No. 9999. (2009) by Jonathan A. L. Gelfond, Mayetri Gupta, Joseph G. Ibrahim posted to chipchip discovery motif by maximilianh on 2009-02-16 11:11:16 as along with 2 people wowalz idonaldson
	Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites [My Copy] Nucl. Acids Res. (10 February 2009), gkp077. by Keunsoo Kang, Jae H. Chung, Joomyeong Kim posted to conserved discovery motif by maximilianh on 2009-02-11 09:49:19 as along with 3 people idonaldson nklee wowalz
	MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. [My Copy] Bioinformatics (Oxford, England) (25 January 2009) by Evert-Jan J. Blom, Jos B T M B. Roerdink, Oscar P P. Kuipers, Sacha A F T A. van Hijum posted to discovery expression microarray motif by maximilianh on 2009-01-28 09:53:52 as
	Extracting transcription factor binding sites from unaligned gene sequences with statistical models. [My Copy] BMC bioinformatics, Vol. 9 Suppl 12 (2008) by C. C. Lu, W. H. Yuan, T. M. Chen posted to discovery motif by maximilianh on 2009-01-07 11:09:03 as along with 3 people and 1 group stajich kristallreiner idonaldson Mycology
	SPACER: identification of cis-regulatory elements with non-contiguous critical residues [My Copy] Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1029-1031. by Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. Deziel, Robert H. Gross posted to discovery motif by maximilianh on 2008-12-31 13:28:58 as along with 3 people nklee wenhan csdhwang
	Compo: composite motif discovery using discrete models [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Geir K. Sandve, Osman Abul, Finn Drablos posted to combination discovery motif by maximilianh on 2008-12-10 12:24:43 as along with 5 people wowalz magusina nuin lptolik druvus
	Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation. [My Copy] Nucleic acids research (5 December 2008) by Alessandro Coppe, Francesco Ferrari, Andrea Bisognin, et al.Gian Antonio A. Danieli, Sergio Ferrari, Silvio Bicciato, Stefania Bortoluzzi posted to application discovery genomeregulatoryblocks motif position by maximilianh on 2008-12-09 14:39:06 as along with 2 people wowalz nuin
	c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Katerina Kechris, Hao Li posted to discovery motif by maximilianh on 2008-12-03 00:59:09 as along with 6 people tmarscha heliopais GustavoLacerda druvus Md_2007 neils
	BayesMD: Flexible Biological Modeling for Motif Discovery. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 10. (December 2008), pp. 1347-1363. by M. H. Tang, A. Krogh, O. Winther posted to discovery motif by maximilianh on 2008-12-02 16:12:07 as along with 3 people bertelsen druvus nuin
	Ab initio identification of functionally interacting pairs of cis-regulatory elements. [My Copy] Genome research, Vol. 18, No. 10. (October 2008), pp. 1643-1651. by B. A. Friedman, M. B. Stadler, N. Shomron, Y. Ding, C. B. Burge posted to combination discovery motif by maximilianh on 2008-11-29 20:54:23 as along with 2 people dandaman jfr
	A transdimensional Bayesian model for pattern recognition in DNA sequences [My Copy] Biostat, Vol. 9, No. 4. (1 October 2008), pp. 668-685. by Sierra M. Li, Jon Wakefield, Steve Self posted to discovery motif by maximilianh on 2008-11-29 17:45:35 as along with 1 person orzenil
	Combining phylogenetic data with co-regulated genes to identify regulatory motifs. [My Copy] Bioinformatics, Vol. 19, No. 18. (12 December 2003), pp. 2369-2380. by T. Wang, G. D. Stormo posted to conserved discovery motif pwmcomparison by maximilianh on 2008-10-28 17:27:48 as along with 5 people coldmeadow balajis eckart_bindewald dquest natstreet
	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 comparative conservation discovery motif by maximilianh on 2008-10-28 12:55:52 as along with 5 people guhjy heliopais djkt xili03 druvus
	Evolutionary computation for discovery of composite transcription factor binding sites. [My Copy] Nucleic acids research (15 October 2008) by Gary B B. Fogel, V William W. Porto, Gabor Varga, et al.Ernst R R. Dow, Andrew M M. Craven, David M M. Powers, Harry B B. Harlow, Eric W W. Su, Jude E E. Onyia, Chen Su posted to discovery motif by maximilianh on 2008-10-26 23:01:43 as
	Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells [My Copy] Genome Res. (15 May 2008), gr.072769.107. by Dan Xie, Jun Cai, Na-Yu Chia, Huck Ng, Sheng Zhong posted to discovery enhancerprediction by maximilianh on 2008-10-03 17:09:44 as along with 7 people lusk dandaman idonaldson isimpson GustavoLacerda phoenixzxl yoonk
	MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders. [My Copy] Bioinformatics (Oxford, England) (12 August 2008) by Edward Wijaya, Siu-Ming M. Yiu, Ngo Thanh T. Son, Rajaraman Kanagasabai, Wing-Kin K. Sung posted to competition discovery motif by maximilianh on 2008-09-03 09:05:51 as along with 5 people wowalz druvus nuin chad_davis idonaldson
	Seeder: Discriminative Seeding DNA Motif Discovery. [My Copy] Bioinformatics (Oxford, England) (21 August 2008) by François Fauteux, Mathieu Blanchette, Martina V V. Strömvik posted to competition discovery motif rennes by maximilianh on 2008-08-25 15:00:09 as along with 7 people wowalz druvus natstreet nuin brant isimpson idonaldson
	Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data [My Copy] Nature Methods, Vol. 5, No. 9. (17 August 2008), pp. 829-834. by Anton Valouev, David S. Johnson, Andreas Sundquist, et al.Catherine Medina, Elizabeth Anton, Serafim Batzoglou, Richard M. Myers, Arend Sidow posted to chipseq discovery motif by maximilianh on 2008-08-21 18:31:46 as along with 19 people and 1 group jwfoley ewilban1 nklee bertelsen stajich smiddha clearbluespring WanderingAengus polivares ptrobajo mdperry idonaldson gdb megraw kengg alhufton guhjy kjglennie bryankr Mycology
	The cis-regulatory map of Shewanella genomes. [My Copy] Nucleic acids research (13 August 2008) by Jiajian Liu, Xing Xu, Gary D D. Stormo posted to comparative discovery motif scanning by maximilianh on 2008-08-18 09:23:53 as
	A deterministic motif finding algorithm with application to the human genome [My Copy] Bioinformatics, Vol. 22, No. 9. (1 May 2006), pp. 1047-1054. by Lawrence S. Hon, Ajay N. Jain posted to discovery motif by maximilianh on 2008-07-26 10:48:29 as along with 5 people and 1 group wowalz shwu idonaldson dquest nklee Motif Discovery
	Integrating regulatory motif discovery and genome-wide expression analysis [My Copy] Proceedings of the National Academy of Sciences, Vol. 100, No. 6. (18 March 2003), pp. 3339-3344. by Erin M. Conlon, Shirley X. Liu, Jason D. Lieb, Jun S. Liu posted to discovery microarray motif by maximilianh on 2008-07-26 10:46:48 as along with 3 people wowalz danish_punter nuin
	Associating transcription factor-binding site motifs with target GO terms and target genes [My Copy] Nucl. Acids Res. (10 June 2008), gkn374. by Mikael Boden, Timothy L. Bailey posted to discovery go motif by maximilianh on 2008-06-11 15:28:01 as along with 5 people suizifish aramesh2 mikaelboden guhjy dgroth
	Systematic identification of cell cycle regulated transcription factors from microarray time series data [My Copy] BMC Genomics, Vol. 9 (03 March 2008), 116. by Chao Cheng, Lei M. Li posted to application discovery motif rennes by maximilianh on 2008-06-06 23:38:57 as
	Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites [My Copy] BMC Bioinformatics, Vol. 9 (04 June 2008), 262. by Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Marino-Ramirez, John L. Spouge posted to discovery motif by maximilianh on 2008-06-06 23:38:01 as along with 2 people wowalz xili03
	RSAT: regulatory sequence analysis tools [My Copy] Nucl. Acids Res. (21 May 2008), gkn304. by Morgane Thomas-Chollier, Olivier Sand, Jean-Valery Turatsinze, et al.Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohee, Jacques van Helden posted to application comparison discovery motif review by maximilianh on 2008-05-23 14:55:45 as along with 6 people cassj idonaldson natstreet druvus guhjy dullhunk
	Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. [My Copy] Genome research (14 April 2008) by Chaim Linhart, Yonit Halperin, Ron Shamir posted to discovery motif by maximilianh on 2008-05-09 16:05:47 as along with 12 people and 1 group dolchan akshayk wowalz natstreet valeriehilgers jfr ealloza idonaldson maralena fpattyn isimpson tmmurali BergmanLab
	An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 5, No. 1. (r 2008), pp. 1-14. by C. B. Congdon, J. C. Aman, G. M. Nava, H. R. Gaskins, C. J. Mattingly posted to discovery motif by maximilianh on 2008-05-07 18:36:26 as along with 1 person svenrahmann
	Using weeder for the discovery of conserved transcription factor binding sites. [My Copy] Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], Vol. Chapter 2 (October 2006) by G. Pavesi, G. Pesole posted to discovery motif by maximilianh on 2008-04-24 08:43:07 as
	Using PhyloCon to identify conserved regulatory motifs. [My Copy] Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], Vol. Chapter 2 (September 2007) by T. Wang posted to conserved discovery motif by maximilianh on 2008-04-24 08:42:26 as
	An efficient motif discovery algorithm with unknown motif length and number of binding sites. [My Copy] International journal of data mining and bioinformatics, Vol. 1, No. 2. (2006), pp. 201-215. by H. C. Leung, F. Y. Chin posted to discovery motif by maximilianh on 2008-04-12 23:49:39 as along with 1 person wowalz
	ModuleMiner: improved computational detection of cis-regulatory modules. Different modes of gene regulation in embryonic development and adult tissues? [My Copy] Genome Biology, Vol. 9, No. 4. (2008) by Peter Van Loo, Stein Aerts, Bernard Thienpont, Bart De Moor, Yves Moreau, Peter Marynen posted to combination discovery motif promoters by maximilianh on 2008-04-09 07:41:36 as along with 5 people heliopais brant djkt natstreet phoenixzxl

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fromconnotea	411
motif	169
discovery	122
duplicates	59
scanning	57
enhancer	55
synteny	54
tandem	53
syntenypaper	52
enhancerprediction	43
molecularbiologytechniques	41
combination	36
cns-differences	34
factors	32
cns	31
geneorder	29
cross-species-enhancer	27
noalignment	27
wnt	26
review	23
ncrna	22
conserved	21
phylogenomics	21
alignment	19
phylogeny	18
transcription	18
chipchip	17
promoter	17
ultraconserved	17
notconserved	16
rennes	16
repeated	16
otx	15
cis-trans	14
genome	14
pcr	14
whole	14
cluster	12
enhancerpromotercompatibility	12
insulator	12
disease	11
pwm	11
chromatin	10
ciona	10
cns-enhancer-screen	10
cns-ranking	10
mirna	10
pwmimprovement	10
randombreakage	10
websites	10
cns-collaboration	9
dna	9
tools	9
3dstructure	8
cns-similarity	8
genome-papers	8
pitx	8
promoters	8
application	7
conservation	7
genes	7
genomeregulatoryblocks	7
genomicregulatoryblocks	7
pwmcomparison	7
bidirectionalpromoters	6
enhanceosome	6
enhancer-screen	6
enhancer-vertebrate-invertebrate	6
long-range	6
orthology	6
phenotype	6
position	6
promoterprediction	6
redundancy	6
snp	6
syntenytools	6
comparative	5
enhancer-and-repeats	5
enhancerdistances	5
genecoregulation	5
methylation	5
microrna	5
similarity	5
structure	5
textmining	5
validated	5
antisensetranscription	4
chipseq	4
comparison	4
competition	4
enhancersharing	4
expression	4
footprinting	4
interchromosomal	4
introns	4
otxpaper	4
recognition	4
region	4
silencer	4
wholegenomescanning	4
cionapopulationgenetics	3
coding	3
composition	3
copy-number-variation	3
encode	3
enhancerincodingregion	3
evoluation	3
factorclass	3
genometrees	3
go	3
interaction	3
inter-cns-distances	3
matrix	3
mirnaenhancer	3
model-species	3
mutations	3
myarticles	3
ncrnas	3
phylotypicstage	3
promoter-minimal	3
regions	3
regulatory	3
rna-binding	3
syntenyorientation	3
term_recognition	3
tf	3
thermodynamicalmodels	3
trainingset	3
3putr	2
ascidians	2
assayscisregwetlab	2
binding	2
bullshitarticles	2
cellsortingbasedanalysis	2
ciona-gene-annotation	2
cns-database	2
core	2
drosophila	2
enhancer-prediction	2
enhancer-stage-specificity	2
factorinteractions	2
genomiccontext	2
grn	2
histones	2
jshypotheses	2
mammals	2
microarray	2
molecularbiologytools	2
ncrna-long	2
networks	2
of	2
pituitary	2
pluripotency	2
polymorphism	2
prediction	2
protocols	2
pvalue-multiplicity	2
rearrangement	2
regulatory-flexibility	2
replicationorigins	2
site-prediction	2
spacing	2
strengthofmatch	2
tfsynergy	2
ultraconserveddefinition	2
whyconserved	2
applicationbioinf	1
arx	1
autoregulation	1
bioinformatics	1
books	1
cell-cultures	1
ciona-gene-annotations	1
cisregdatabase	1
cns-difference	1
cns-enhance	1
cns-enhancer	1
codingconservation	1
decoy	1
degeneratesites	1
dlx	1
doublets	1
drosophia	1
drosphila	1
duplicatese	1
element	1
enhancer-contextanalysis	1
factorsclass	1
fastindexing	1
fugu	1
genefamilyfootprinting	1
genemodels	1
generalregulation	1
generegulatorynetworks	1
gibbs	1
grns	1
hmm	1
igh	1
impossible	1
insertionsdeletions	1
intra-primate	1
kernel	1
noaccess	1
nomotif	1
notconservedfunction	1
nucleosome	1
olfactoryreceptors	1
pax6	1
phylogenytools	1
positiveselection	1
primers	1
purificationfromdna	1
sites	1
smarts	1
statistics	1
suppressor	1
syntenypapers	1
transgenesis	1
tr-reviews	1
turnover	1
word	1
writing	1

maximilianh's discovery [122 articles] Export

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