maximilianh's motif [171 articles] Export

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	Discovery of Regulatory Elements is Improved by a Discriminatory Approach [My Copy] PLoS Comput Biol, Vol. 5, No. 11. (13 November 2009), e1000562. by Eivind Valen, Albin Sandelin, Ole Winther, Anders Krogh posted to motif enhancer-prediction discovery by maximilianh on 2009-11-17 15:00:29 as along with 3 people ptrobajo TRHvidsten bertelsen
	Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes. [My Copy] Nucleic acids research (11 November 2009) by Guojun Li, Bingqiang Liu, Ying Xu posted to motif discovery by maximilianh on 2009-11-13 14:42:29 as
	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
	D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs. [My Copy] Bioinformation, Vol. 3, No. 10. (2009), pp. 415-418. by Naresh Sen, Manoj Mishra, Feroz Khan, Abha Meena, Ashok Sharma posted to websites tools motif by maximilianh on 2009-10-05 19:09:34 as
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3191-3193. 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 3 people idonaldson farhat nklee
	MEME SUITE: tools for motif discovery and searching [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W202-208. by Timothy L. Bailey, Mikael Boden, Fabian A. Buske, et al.Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble posted to websites tools motif by maximilianh on 2009-09-17 12:13:05 as along with 6 people suizifish jlike natstreet idonaldson nuin 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
	Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. [My Copy] Nucleic acids research (29 May 2009) by Ken Daigoro D. Yokoyama, Uwe Ohler, Gregory A A. Wray posted to motif position by maximilianh on 2009-06-02 21:54:11 as along with 1 person idonaldson
	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
	Detection of cis -element clusters in higher eukaryotic DNA [My Copy] Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 878-889. by Martin C. Frith, Ulla Hansen, Zhiping Weng posted to combination motif by maximilianh on 2009-04-28 13:29:14 as along with 2 people and 2 groups daveGerrard indigoviolet BergmanLab EisenLab
	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
	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
	Homotypic regulatory clusters in Drosophila. [My Copy] Genome Res, Vol. 13, No. 4. (April 2003), pp. 579-588. by A. P. Lifanov, V. J. Makeev, A. G. Nazina, D. A. Papatsenko posted to cluster combination motif by maximilianh on 2009-04-02 16:27:21 as along with 3 people and 1 group isimpson indigoviolet tresch EisenLab
	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 Kjetil K. Sandve, Osman Abul, Finn Drabløs 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
	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
	Motif Tool Manager: a web-based framework for motif discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 24. (15 December 2008), pp. 2930-2931. by Vinhthuy Phan, Nicholas A. Furlotte posted to motif tools websites by maximilianh on 2008-11-23 22:13:13 as along with 5 people wowalz nklee nuin natstreet druvus
	Combining phylogenetic data with co-regulated genes to identify regulatory motifs. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 18. (12 December 2003), pp. 2369-2380. by Ting Wang, Gary D. Stormo posted to conserved discovery motif pwmcomparison by maximilianh on 2008-10-28 17:27:48 as along with 6 people roys 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
	Evolutionary computation for discovery of composite transcription factor binding sites [My Copy] Nucl. Acids Res., Vol. 36, No. 21. (1 December 2008), e142. by Gary B. Fogel, V. William Porto, Gabor Varga, et al.Ernst R. Dow, Andrew M. Craven, David M. Powers, Harry B. Harlow, Eric W. Su, Jude E. Onyia, Chen Su posted to combination motif by maximilianh on 2008-10-16 13:43:54 as along with 5 people nklee wowalz lptolik idonaldson davfre
	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
	Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and myogenin [My Copy] Nucl. Acids Res. (29 May 2008), gkn340. by Anat Yafe, Jeny Shklover, Pnina Weisman-Shomer, Eyal Bengal, Michael Fry posted to combination motif trainingset by maximilianh on 2008-08-14 08:47:27 as along with 2 people and 1 group nklee jmrivort G-quadruplex
	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
	Modeling Promoter Grammars with Evolving Hidden Markov Models. [My Copy] Bioinformatics (Oxford, England) (5 June 2008) by Kyoung-Jae J. Won, Albin Sandelin, Troels Torben T. Marstrand, Anders Krogh posted to combination motif by maximilianh on 2008-07-22 00:06:04 as along with 2 people lusk niallhaslam
	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
	Discovering sequence motifs. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 231-251. by T. L. Bailey posted to motif review by maximilianh on 2008-06-22 21:36:09 as along with 2 people wowalz zdai

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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
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
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 motif [171 articles] Export

maximilianh's tags