maximilianh's scanning [57 articles] Export

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	A probabilistic method to detect regulatory modules. [My Copy] Bioinformatics, Vol. 19 Suppl 1 (2003) by S. Sinha, E. van Nimwegen, E. D. Siggia posted to combination motif scanning by maximilianh on 2009-04-28 13:27:41 as along with 4 people and 2 groups indigoviolet dquest lusk cisevol EisenLab cis-regulatory-evolution
	CoMoDis: composite motif discovery in mammalian genomes [My Copy] Nucleic Acids Research, Vol. 35, No. 1. (January 2007), pp. e1-e1. by Donaldson, J. Ian, Gottgens, Berthold posted to scanning wholegenomescanning by maximilianh on 2009-04-15 17:32:50 as along with 2 people wowalz dquest
	TFBScluster web server for the identification of mammalian composite regulatory elements. [My Copy] Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006) by I. J. Donaldson, B. Göttgens posted to cluster scanning by maximilianh on 2009-04-02 16:47:32 as along with 1 person idonaldson
	New scoring schema for finding motifs in DNA Sequences [My Copy] BMC Bioinformatics, Vol. 10 (20 March 2009), 93. by Fatemeh, Bahram Goliaei posted to pwmimprovement scanning by maximilianh on 2009-03-26 00:19:57 as along with 5 people and 1 group svenrahmann cassj idonaldson ElenaGrassi nuin cube_and_beyond
	Indexing strategies for rapid searches of short words in genome sequences. [My Copy] PLoS ONE, Vol. 2, No. 6. (2007) by C. Iseli, G. Ambrosini, P. Bucher, C. V. Jongeneel posted to fastindexing scanning by maximilianh on 2009-03-25 20:50:11 as along with 2 people druvus natstreet
	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 enhancerpromotercompatibility promoter promoter-minimal scanning by maximilianh on 2009-03-25 19:34:47 as along with 10 people and 1 group TRHvidsten jimineep cassj idonaldson dswan djkt dolchan nuin natstreet druvus Bioinformatics
	Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3 [My Copy] Proceedings of the National Academy of Sciences (12 March 2009) by Francesco Vallania, Davide Schiavone, Sarah Dewilde, et al.Emanuela Pupo, Serge Garbay, Raffaele Calogero, Marco Pontoglio, Paolo Provero, Valeria Poli posted to conservation enhancerprediction scanning by maximilianh on 2009-03-17 17:55:40 as along with 2 people idonaldson merpublic
	PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups [My Copy] BMC Genomics, Vol. 9 (26 November 2008), 561. by Wen-Chi, Rong-Long Pan posted to combination motif scanning websites by maximilianh on 2008-11-29 13:28:39 as along with 3 people tg150 lptolik agustinarce
	CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008), 495. by Matthew S. Hestand, Michiel van Galen, Michel P. Villerius, Gert-Jan J. van Ommen, Johan T. den Dunnen, Peter A. 't Hoen posted to conserved motif scanning tools websites by maximilianh on 2008-11-27 09:21:41 as along with 9 people and 1 group farhat avilella heliopais lptolik nklee nuin GustavoLacerda natstreet druvus Ensembl Compara citations
	High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. [My Copy] Nucleic acids research, Vol. 37, No. 1. (1 January 2009), pp. 14-25. by Tom Whitington, Andrew C. Perkins, Timothy L. Bailey posted to chromatin promoterprediction scanning site-prediction by maximilianh on 2008-11-12 10:43:25 as along with 7 people vingron akundaje inesdesantiago polivares lptolik WanderingAengus xili03
	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
	MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs [My Copy] Nucl. Acids Res. (7 July 2008), gkn407. by Jianfei Hu, Haiyan Hu, Xiaoman Li posted to cns-similarity combination motif noalignment scanning by maximilianh on 2008-07-07 17:15:10 as along with 2 people fenghezi wowalz
	Detecting cis-regulatory binding sites for cooperatively binding proteins [My Copy] Nucl. Acids Res., Vol. 36, No. 8. (1 May 2008), e46. by Liesbeth van Oeffelen, Pierre Cornelis, Wouter Van Delm, Fedor De Ridder, Bart De Moor, Yves Moreau posted to combination motif scanning by maximilianh on 2008-05-06 15:27:19 as along with 3 people tmmurali idonaldson isimpson
	Using TESS to predict transcription factor binding sites in DNA sequence. [My Copy] Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], Vol. Chapter 2 (March 2008) by J. Schug posted to motif scanning by maximilianh on 2008-04-24 08:43:41 as along with 2 people xingxu guhjy
	Statistical modeling of transcription factor binding affinities predicts regulatory interactions. [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (March 2008) by T. Manke, H. G. Roider, M. Vingron posted to combination scanning tfsynergy by maximilianh on 2008-03-30 18:52:53 as along with 2 people jjray eskay
	An efficient method for statistical significance calculation of transcription factor binding sites. [My Copy] Bioinformation, Vol. 2, No. 5. (2007), pp. 169-174. by Z. Qian, L. Lu, L. Qi, Y. Li posted to matrix pwm pwmimprovement scanning by maximilianh on 2008-03-01 21:46:59 as along with 3 people and 1 group nklee idonaldson isimpson Motif Discovery
	Computational prediction of novel components of lung transcriptional networks [My Copy] Bioinformatics, Vol. 23, No. 1. (1 January 2007), pp. 21-29. by Juanita M. Martinez, Andrew D. Smith, Bilan Li, Michael Q. Zhang, Kevin S. Harrod posted to enhancerprediction motif scanning by maximilianh on 2008-02-29 17:19:30 as along with 1 person olympos
	Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. [My Copy] Genome Res, Vol. 12, No. 7. (July 2002), pp. 1019-1028. by M. S. Halfon, Y. Grad, G. M. Church, A. M. Michelson posted to combination conserved enhancerprediction motif scanning by maximilianh on 2008-02-29 13:02:28 as along with 2 people maximilianh_otx isimpson
	Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control [My Copy] Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 26-33. by A. D. J. van Dijk, Ter, R. G. Immink, G. C. Angenent, R. C. H. J. van Ham posted to combination factors scanning by maximilianh on 2008-01-18 14:20:23 as along with 3 people heliopais idonaldson isimpson
	A global genomic transcriptional code associated with CNS-expressed genes [My Copy] Experimental Cell Research, Vol. 312, No. 16. (1 October 2006), pp. 3108-3119. by Peter J. Bailey, Joanna M. Klos, Elisabet Andersson, et al.Mattias Karlen, Magdalena Kallstrom, Jasmina Ponjavic, Jonas Muhr, Boris Lenhard, Albin Sandelin, Johan Ericson posted to enhancerprediction motif scanning by maximilianh on 2008-01-15 18:01:27 as
	Locating potential enhancer elements by comparative genomics using the EEL software. [My Copy] Nat Protoc, Vol. 1, No. 1. (2006), pp. 368-374. by K. Palin, J. Taipale, E. Ukkonen posted to enhancerprediction scanning by maximilianh on 2008-01-14 16:04:07 as along with 1 person Terkko
	A Hybrid Model for Robust Detection of Transcription Factor Binding Sites. [My Copy] Bioinformatics (9 January 2008) by Sumedha Gunewardena, Zhaolei Zhang posted to discovery motif pwm scanning by maximilianh on 2008-01-12 11:11:46 as along with 3 people isimpson guhjy idonaldson
	Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Victor Levitsky, Elena Ignatieva, Elena Ananko, et al.Igor Turnaev, Tatyana Merkulova, Nikolay Kolchanov, T. Hodgman posted to scanning by maximilianh on 2007-12-22 20:14:15 as along with 5 people druvus nklee yevishere csdhwang xili03
	Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes. [My Copy] PLoS ONE, Vol. 2, No. 11. (2007) by S. Aerts, J. van Helden, O. Sand, B. A. Hassan posted to cns conserved drosophila enhancerprediction scanning by maximilianh on 2007-12-08 15:34:13 as along with 5 people and 1 group operon brant idonaldson barwil isimpson cis-regulatory-evolution
	Exploring Conservation of Transcription Factor Binding Sites with CONREAL. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 437-448. by E. Berezikov, V. Guryev, E. Cuppen posted to alignment cns scanning by maximilianh on 2007-11-29 14:59:05 as along with 1 person nklee
	Reliable prediction of regulator targets using 12 Drosophila genomes [My Copy] Genome Research, Vol. 17, No. 12. (7 December 2007), pp. 1919-1931. by Pouya Kheradpour, Alexander Stark, Sushmita Roy, Manolis Kellis posted to scanning by maximilianh on 2007-11-28 10:22:08 as along with 9 people and 2 groups heliopais valeriehilgers dpollard lp2 nklee roys caseybrown emptyhb barwil EisenLab cis-regulatory-evolution
	Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 319-328. by E. Barta posted to alignment conserved footprinting scanning by maximilianh on 2007-11-27 13:04:18 as
	Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 425-436. by P. V. Benos, D. L. Corcoran, E. Feingold posted to alignment cns footprinting scanning by maximilianh on 2007-11-27 13:02:58 as
	OSCAR: One-class SVM for Accurate Recognition of Cis-elements [My Copy] Bioinformatics (5 October 2007), btm473. by Bo Jiang, Michael Q. Zhang, Xuegong Zhang posted to motif scanning by maximilianh on 2007-11-17 13:05:06 as along with 7 people suizifish cassj tmmurali chad_davis cabbagezs idonaldson isimpson
	MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules [My Copy] PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216. by Saurabh Sinha, Xin He posted to alignment discovery motif scanning by maximilianh on 2007-11-15 16:50:37 as along with 7 people and 2 groups ana dpollard cjeans zwang hpaces Ema uwe EisenLab cis-regulatory-evolution
	A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast [My Copy] PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e215. by Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink posted to dna scanning by maximilianh on 2007-11-15 16:46:32 as along with 5 people TRHvidsten aalibes zwang nklee megraw
	TREMOR a tool for retrieving transcriptional modules by incorporating motif covariance [My Copy] Nucl. Acids Res. (25 October 2007), gkm885. by Larry N. Singh, Li-San Wang, Sridhar Hannenhalli posted to cluster motif pwmcomparison scanning by maximilianh on 2007-10-27 23:30:07 as along with 1 person tmmurali
	MATCH: A tool for searching transcription factor binding sites in DNA sequences. [My Copy] Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3576-3579. by A. E. Kel, E. Gössling, I. Reuter, E. Cheremushkin, O. V. Kel-Margoulis, E. Wingender posted to scanning by maximilianh on 2007-10-10 09:36:16 as along with 7 people farhat setar aprasad reidy nklee danish_punter emptyhb
	Identification of novel Regulatory Factor X (RFX) target genes by comparative genomics in Drosophila species [My Copy] Genome Biology, Vol. 8 (17 September 2007), R195. by Anne C. Laurencon, Raphaelle Dubruille, Evgeni Efimenko, et al.Guillaume Grenier, Ryan E. Bissett, Elisabeth Cortier, Vivien Rolland, Peter Swoboda, Benedicte Durand posted to cns conserved genome scanning by maximilianh on 2007-09-26 18:30:23 as along with 3 people and 1 group isimpson thegoose2 tharris C. elegans / WormBase
	Transcriptional Control in the Segmentation Gene Network of Drosophila [My Copy] PLoS Biology, Vol. 2 (Sep 2004), pp. 271-271. by Mark Schroeder, Michael Pearce, John Fak, et al.Hongqing Fan, Ulrich Unnerstall, Eldon Emberly, Nikolaus Rajewsky, Eric Siggia, Ulrike Gaul posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome [My Copy] Proceedings of the National Academy of Sciences, Vol. 99 (Jan 2002), pp. 757-762. by Benjamin Berman, Yutaka Nibu, Barret Pfeiffer, et al.Pavel Tomancak, Susan Celniker, Michael Levine, Gerald Rubin, Michael Eisen posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. [My Copy] BMC bioinformatics, Vol. 3 (Oct 2002), pp. 30-30. by Nikolaus Rajewsky, Massimo Vergassola, Ulrike Gaul, Eric Siggia posted to cluster scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Identification of regulatory regions which confer muscle-specific gene expression. [My Copy] Journal of molecular biology, Vol. 278 (Apr 1998), pp. 167-181. by W. W. Wasserman, J. W. Fickett posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. [My Copy] Genome biology, Vol. 5 (xx 2004), pp. 61-61. by Benjamin Berman, Barret Pfeiffer, Todd Laverty, et al.Steven Salzberg, Gerald Rubin, Michael Eisen, Susan Celniker posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Simultaneous alignment and annotation of cis-regulatory regions -- Bais et al. 23 (2): e44 -- Bioinformatics [My Copy] posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Predicting transcription factor affinities to DNA from a biophysical model -- Roider et al. 23 (2): 134 -- Bioinformatics [My Copy] posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Predicting tissue-specific enhancers in the human genome. [My Copy] Genome Res (Jan 2007) by Len Pennacchio, Gabriela Loots, Marcelo Nobrega, Ivan Ovcharenko posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:12 as
	A specialized learner for inferring structured cis-regulatory modules. [My Copy] BMC bioinformatics, Vol. 7 (xx 2006), pp. 528-528. by Keith Noto, Mark Craven posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:12 as
	Predicting transcription factor affinities to DNA from a biophysical model. [My Copy] Bioinformatics (Oxford, England), Vol. 23 (Jan 2007), pp. 134-141. by Helge Roider, Aditi Kanhere, Thomas Manke, Martin Vingron posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:11 as
	Computing exact P-values for DNA motifs -- Zhang et al. 23 (5): 531 -- Bioinformatics [My Copy] posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:11 as
	Context Specific Transcription Factor Prediction. [My Copy] Ann Biomed Eng (Mar 2007) by Eric Yang, David Simcha, Richard Almon, Debra Dubois, William Jusko, Ioannis Androulakis posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:11 as
	CEAS: Cis-regulatory Element Annotation System [My Copy] posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:10 as
	Multiple Non-Collinear TF-map Alignments of Promoter Regions. [My Copy] BMC Bioinformatics, Vol. 8 (Apr 2007), pp. 138-138. by Enrique Blanco, Roderic Guigo, Xavier Messeguer posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:10 as
	A new statistical model to select target sequences bound by transcription factors. [My Copy] Genome informatics. International Conference on Genome Informatics, Vol. 17 (xx 2006), pp. 134-140. by Utz Pape, Steffen Grossmann, Stefanie Hammer, Silke Sperling, Martin Vingron posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:09 as
	Identification of polymorphic antioxidant response elements in the human genome -- Wang et al. 16 (10): 1188 -- Human Molecular Genetics [My Copy] posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:09 as

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fromconnotea	411
motif	171
discovery	124
duplicates	59
scanning	57
synteny	56
enhancer	55
tandem	53
syntenypaper	52
enhancerprediction	43
molecularbiologytechniques	41
combination	36
cns-differences	34
factors	32
cns	31
geneorder	29
cross-species-enhancer	28
noalignment	28
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
cis-trans	15
otx	15
genome	14
pcr	14
whole	14
cluster	12
enhancerpromotercompatibility	12
insulator	12
disease	11
pwm	11
tools	11
websites	11
chromatin	10
ciona	10
cns-enhancer-screen	10
cns-ranking	10
mirna	10
pwmimprovement	10
randombreakage	10
cns-collaboration	9
dna	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
syntenytools	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
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
enhancer-prediction	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
codingconservation	2
core	2
drosophila	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
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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
decoy	1
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doublets	1
drosophia	1
drosphila	1
duplicatese	1
element	1
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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 scanning [57 articles] Export

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