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Tag motifs [198 articles]

Recent papers classified by the tag motifs.
  • Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site.
    PLoS ONE, Vol. 2, No. 8. (2007)
    by Y Tabach, R Brosh, Y Buganim, A Reiner, O Zuk, A Yitzhaky, M Koudritsky, V Rotter, E Domany
    posted to location motifs my promoter by YuvalTabach on 2008-08-03 09:09:50 as read
  • The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation
    Molecular Systems Biology, Vol. 1, No. 1. (18 October 2005), pp. msb4100030-E1-msb4100030-E15.
    by Yuval Tabach, Michael Milyavsky, Igor Shats, Ran Brosh, Or Zuk, Assif Yitzhaky, Roberto Mantovani, Eytan Domany, Varda Rotter, Yitzhak Pilpel
    posted to promoter p53 my motifs location by YuvalTabach on 2008-09-04 16:07:57 as **** along with 3 people rklancer jfr tuck
  • PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
    PLoS Comput Biol, Vol. 1, No. 7. (December 2005)
    by R Siddharthan, ED Siggia, E van Nimwegen
    posted to mining motifs by yevishere on 2008-01-04 00:07:13 as ** along with 11 people and 3 groups ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou idonaldson isimpson structural_bioinformatics Bioinformatics EBI-regulation
  • ZIFIBI: Prediction of DNA binding sites for zinc finger proteins.
    Biochem Biophys Res Commun (3 March 2008)
    by Soo Young Y Cho, Myungguen Chung, Minyoung Park, Sungjin Park, Young Seek S Lee
    posted to mining motifs by yevishere on 2008-03-24 20:57:08 as ** along with 1 person maximilianh
  • Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Victor Levitsky, Elena Ignatieva, Elena Ananko, Igor Turnaev, Tatyana Merkulova, Nikolay Kolchanov, T Hodgman
    posted to mining motifs tools by yevishere on 2008-01-08 00:22:02 as **** along with 4 people nklee maximilianh csdhwang xili03
  • notes Model-based deconvolution of genome-wide DNA binding.
    Bioinformatics (1 December 2007)
    by David J J Reiss, Marc T T Facciotti, Nitin S S Baliga
    posted to hnf4 motifs by yevishere on 2008-01-03 23:58:02 as **** along with 5 people djkt idonaldson jyuh vega isimpson
  • Discovering Motifs in Ranked Lists of DNA Sequences
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39.
    by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini
    posted to motifs tools by yevishere on 2008-01-04 00:22:30 as ** along with 3 people and 1 group dpollard dquest chad_davis EisenLab
  • A survey of motif discovery methods in an integrated framework
    Biology Direct, Vol. 1, No. 1. (06 April 2006), 11.
    by Geir K Sandve, Finn Drabløs
    posted to mining motifs tools by yevishere on 2008-01-04 00:23:12 as ** along with 6 people and 1 group aprasad dpollard samal csdhwang idonaldson yoonk EisenLab
  • A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.
    Nucleic Acids Res, Vol. 34, No. 20. (2006), pp. 5730-5739.
    by BT Naughton, E Fratkin, S Batzoglou, DL Brutlag
    posted to motifs tools by yevishere on 2008-01-04 00:20:45 as **** along with 4 people and 1 group indigoviolet nklee xili03 GustavoLacerda EisenLab
  • Position dependencies in transcription factor binding sites.
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 933-941.
    by A Tomovic, EJ Oakeley
    posted to mining motifs by yevishere on 2008-01-08 00:29:53 as ** along with 2 people aalibes nklee
  • Evolution of transcription factor DNA binding sites.
    Gene, Vol. 347, No. 2. (14 March 2005), pp. 255-263.
    by EA Kotelnikova, VJ Makeev, MS Gelfand
    posted to mining motifs tool by yevishere on 2008-01-08 00:28:18 as ** along with 4 people and 1 group balajis gpalidwor nklee cisevol cis-regulatory-evolution
  • A survey of DNA motif finding algorithms
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Modan Das, Ho K Dai
    posted to mining motifs review tools by yevishere on 2008-01-08 00:27:21 as ** along with 7 people dquest nklee maximilianh csdhwang brant xili03 pradiptaray
  • An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.
    Nat Biotechnol, Vol. 20, No. 8. (August 2002), pp. 835-839.
    by XS Liu, DL Brutlag, JS Liu
    posted to motifs by yevishere on 2008-01-04 00:06:49 as ** along with 4 people troels_marstrand opheliav dquest xili03
  • Toucan: deciphering the cis-regulatory logic of coregulated genes.
    Nucleic Acids Res, Vol. 31, No. 6. (15 March 2003), pp. 1753-1764.
    by S Aerts, G Thijs, B Coessens, M Staes, Y Moreau, B De Moor
    posted to mining motifs tools by yevishere on 2008-01-08 00:20:26 as ** along with 5 people and 1 group troels_marstrand kaspermunch nur77 nklee xili03 Bioinformatics
  • TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
    BMC Genomics, Vol. 8 (29 November 2007), 441.
    by Alison P Lee, Yuchen Yang, Sydney Brenner, Byrappa Venkatesh
    posted to mining motifs tools by yevishere on 2008-01-08 00:26:52 as ** along with 3 people nklee maximilianh jyuh
  • Network motifs: simple building blocks of complex networks.
    Science, Vol. 298, No. 5594. (25 October 2002), pp. 824-827.
    by R Milo, S Shen-Orr, S Itzkovitz, N Kashtan, D Chklovskii, U Alon
    posted to sysbio networks network motifs by wnpx on 2006-02-24 15:26:29 as ** along with 39 people and 8 groups camster korakot aalibes ChaTo imouthesmp Borelli lfriedl alexg balicea tny ssb ddahlem cmm donade neveaire griota gurkanbebek jtaylor josepe iris_2001 michaelmampaey rebeccamancy karfunkel lenov Evangelia roys tfogal zibuyu maralena stefanoallesina pbull cmor renatomilani shikin carlk applesnow subhacom i-stevenson ethkim Philosophy_of_Information dbk-lab Blog_and_Wiki_Research kdl FAB-lab ColDyn ADMiRes GeneGo
  • Formation of Regulatory Patterns During Signal Propagation in a Mammalian Cellular Network
    Science, Vol. 309, No. 5737. (12 August 2005), pp. 1078-1083.
    by Avi Ma'ayan, Sherry L Jenkins, Susana Neves, Anthony Hasseldine, Elizabeth Grace, Benjamin Dubin-Thaler, Narat J Eungdamrong, Gehzi Weng, Prahlad T Ram, Jeremy J Rice, Aaron Kershenbaum, Gustavo A Stolovitzky, Robert D Blitzer, Ravi Iyengar
    posted to motifs netoworks patterns by wnpx on 2005-12-30 15:23:50 as ** along with 2 people xlli oelemento
  • Interlinked Fast and Slow Positive Feedback Loops Drive Reliable Cell Decisions
    Science, Vol. 310, No. 5747. (21 October 2005), pp. 496-498.
    by Onn Brandman, James E Ferrell, Rong Li, Tobias Meyer
    posted to motifs networks by wnpx on 2005-12-30 15:17:35 as ** along with 8 people rklancer jyuh kentsis monod tuck jmeppley balajis margaritis
  • Dynamical Motifs: Building Blocks of Complex Dynamics in Sparsely Connected Random Networks
    Physical Review Letters, Vol. 92, No. 23. (2004)
    by Valentin P Zhigulin
    posted to dynamical-systems dynamics modular motifs networks neural by watson on 2008-03-20 09:42:47 as *** along with 2 people and 5 groups jjray jwdietrich MathBio Cybernetics NeuralNetworks Biomedical_Cybernetics AQUA-FONTIS-Study
  • Comment on "Network motifs: simple building blocks of complex networks" and "Superfamilies of evolved and designed networks".
    Science, Vol. 305, No. 5687. (20 August 2004)
    by Y Artzy-Randrup, SJ Fleishman, N Ben-Tal, L Stone
    posted to analysis complex dynamics evolution function methods modular motifs networks neural structure by watson on 2008-03-20 06:40:22 as ***** along with 3 people and 1 group camster tmmurali ddahlem dbk-lab
  • Practical Strategies for Discovering Regulatory DNA Sequence Motifs
    PLoS Computational Biology, Vol. 2, No. 4. (1 April 2006), e36.
    by Kenzie D Macisaac, Ernest Fraenkel
    posted to discovery domains motifs patterns by svdate on 2007-12-14 15:26:57 as ***** along with 7 people and 2 groups bryankr ana chad_davis balicea hggr GustavoLacerda kristallreiner structural_bioinformatics Bioinformatics
  • Rational design of DNA nanoarchitectures.
    Angew Chem Int Ed Engl, Vol. 45, No. 12. (13 March 2006), pp. 1856-1876.
    by U Feldkamp, CM Niemeyer
    posted to design motifs review self-assembly tile by stsaft on 2008-02-08 00:50:21 as ** along with 1 person eckart_bindewald
  • Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.
    Proc Natl Acad Sci U S A, Vol. 102, No. 14. (5 April 2005), pp. 4966-4971.
    by D Papatsenko, M Levine
    posted to drosophila motifs by Stew on 2007-09-18 01:00:35 as ** along with 1 person and 1 group adepace EisenLab
  • Network motifs in the transcriptional regulation network of Escherichia coli
    Nat Genet, Vol. 31, No. 1. (May 2002), pp. 64-68.
    by Shai S Shen-Orr, Ron Milo, Shmoolik Mangan, Uri Alon
    posted to motifs networks by ssb on 2005-12-09 09:01:05 as ** along with 13 people and 1 group jstajic jjray nickluscombe gurkanbebek jtaylor jayster4 karfunkel blobbybirdman zibuyu maralena hannahrajasingh Borelli ethkim EBI-regulation
  • Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.
    J Biol, Vol. 4, No. 2. (2005)
    by LV Zhang, OD King, SL Wong, DS Goldberg, AH Tong, G Lesage, B Andrews, H Bussey, C Boone, FP Roth
    posted to motifs networks by ssb on 2005-12-09 09:11:12 as ** along with 10 people and 1 group lfriedl marcora jjray benny nirfriedman koller iris_2001 gwcarter carlk ksiek kdl
  • Superfamilies of evolved and designed networks.
    Science, Vol. 303, No. 5663. (5 March 2004), pp. 1538-1542.
    by R Milo, S Itzkovitz, N Kashtan, R Levitt, S Shen-Orr, I Ayzenshtat, M Sheffer, U Alon
    posted to motifs networks by ssb on 2005-12-09 09:09:22 as read along with 17 people and 7 groups ChaTo lfriedl alexg yish balicea ddahlem cmm j3xucite donade bigbossman gurkanbebek shenorr ltabourier michaelmampaey zibuyu tnhh karfunkel kdl mathgamespatterns dtl vds-arg eni FAB-lab ADMiRes
  • Local graph alignment and motif search in biological networks.
    Proc Natl Acad Sci U S A, Vol. 101, No. 41. (12 October 2004), pp. 14689-14694.
    by J Berg, M Lässig
    posted to motifs networks by ssb on 2005-12-08 22:06:51 as read along with 3 people and 1 group Ema camster alexisgallagher dbk-lab
  • Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.
    Proc Natl Acad Sci U S A, Vol. 101, No. 16. (20 April 2004), pp. 5934-5939.
    by E Yeger-Lotem, S Sattath, N Kashtan, S Itzkovitz, R Milo, RY Pinter, U Alon, H Margalit
    posted to motifs networks by snuppepuppan on 2005-03-22 14:05:32 as ** along with 9 people and 4 groups camster dbk korakot LeightonP hununu jtextori koller maralena carlk streptomyces Philosophy_of_Information dbk-lab Blog_and_Wiki_Research
  • Dynamical motifs: building blocks of complex dynamics in sparsely connected random networks.
    Phys Rev Lett, Vol. 92, No. 23. (11 June 2004)
    by VP Zhigulin
    posted to motifs networks by snuppepuppan on 2005-03-22 14:06:09 as ** along with 3 people and 2 groups korakot jtextori ddahlem Philosophy_of_Information Blog_and_Wiki_Research
  • Structure and function of the feed-forward loop network motif.
    Proc Natl Acad Sci U S A, Vol. 100, No. 21. (14 October 2003), pp. 11980-11985.
    by S Mangan, U Alon
    posted to genecircuits motifs by rklancer on 2005-05-01 21:13:23 as read along with 12 people and 3 groups camster korakot zqshen jstajic jjray alexg balicea ddahlem jtaylor gcalda marck hannahrajasingh Philosophy_of_Information dbk-lab Blog_and_Wiki_Research
  • The B. subtilis SIN Operon: An Evolvable Network Motif.
    Genetics (30 September 2004)
    by Christopher A Voigt, Denise Wolf, Adam P Arkin
    posted to arkin_lab dynamics evolvability motifs by rklancer on 2005-03-18 18:35:34 as *** along with 4 people and 1 group camster lingchong dbikard heliopais dbk-lab
  • Spontaneous evolution of modularity and network motifs.
    Proc Natl Acad Sci U S A (20 September 2005)
    by Nadav Kashtan, Uri Alon
    posted to motifs by rebeccamancy on 2007-06-20 00:22:50 as ** along with 15 people and 6 groups mcphee marimo monod Borelli alexg i41m cmm Peterfine javierFellow rgb mattjb cwr phreeza stefanoallesina carlk MathBio FAB-lab ComplexAdaptiveSystems pileWorks DSTO-CAS ColDyn
  • Biological networks: the tinkerer as an engineer.
    Science, Vol. 301, No. 5641. (26 September 2003), pp. 1866-1867.
    by U Alon
    posted to motifs by rebeccamancy on 2007-06-20 00:08:28 as ** along with 8 people and 2 groups monod Borelli alexg ddahlem shivakumar3_14 cmm lshaw Ema FAB-lab ColDyn
  • Topological generalizations of network motifs
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 70, No. 3. (2004)
    by N Kashtan, S Itzkovitz, R Milo, U Alon
    posted to motifs by rebeccamancy on 2007-06-20 00:19:31 as ** along with 1 group ColDyn
  • Rediscovering secondary structures as network motifsan unsupervised learning approach
    Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. e163-e169.
    by Raveh, Barak, Rahat, Ofer, Schreiber, Gideon
    posted to motifs by rebeccamancy on 2007-06-20 00:15:50 as ** along with 1 person and 1 group GustavoLacerda ColDyn
  • Genomic analysis of regulatory network dynamics reveals large topological changes.
    Nature, Vol. 431, No. 7006. (16 September 2004), pp. 308-312.
    by NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein
    posted to evolution motifs by rebeccamancy on 2007-06-20 00:29:31 as ** along with 20 people and 6 groups camster snuppepuppan hununu icases lna lfriedl alexg nirfriedman dgront nickluscombe kairita comb kengg gespim koller timflutre fishtank cjeans faion carlk dbk-lab kdl EBI-regulation TNT ColDyn Plantandetc
  • False occurrences of functional motifs in protein sequences highlight evolutionary constraints
    BMC Bioinformatics, Vol. 8 (01 March 2007), 68.
    by Allegra Via, Pier F Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo S Tomba, Manuela H Citterich
    posted to motifs sequence_analysis by rabio on 2007-03-06 09:26:14 as ** along with 1 person zwang
  • Sequence motifs and antimotifs in beta-barrel membrane proteins from a genome-wide analysis: the Ala-Tyr dichotomy and chaperone binding motifs.
    J Mol Biol, Vol. 363, No. 2. (20 October 2006), pp. 611-623.
    by R Jackups, S Cheng, J Liang
    posted to beta_barrel membrane motifs protein by pansapiens on 2006-11-20 20:44:54 as ***
  • Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites
    Proceedings of the National Academy of Sciences (31 October 2007), 0700997104.
    by Alan M Moses, Muluye E Liku, Joachim J Li, Richard Durbin
    posted to elements motifs protein regulatory by oelemento on 2007-11-01 05:31:04 as ****
  • Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
    Proceedings of the National Academy of Sciences (27 May 2008), 0802406105.
    by David A Hendrix, Joung-Woo Hong, Julia Zeitlinger, Daniel S Rokhsar, Michael S Levine
    posted to drosophila motifs by oelemento on 2008-05-28 09:50:44 as ** along with 1 person and 1 group cisevol BergmanLab
  • Efficient representation and P-value computation for high-order Markov motifs.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by PG da Fonseca, KS Guimarães, MF Sagot
    posted to markov motifs by nuin on 2008-08-12 18:10:09 as **
  • STOP: searching for Transcription Factor motifs using gene expression.
    Bioinformatics (8 May 2007)
    by Libi Hertzberg, Shai Izraeli, Eytan Domany
    posted to motifs software by nuin on 2008-06-26 18:20:54 as ** along with 1 person and 1 group dpollard EisenLab
  • Method for identifying transcription factor binding sites in yeast
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. 1675-1681.
    by Huai-Kuang Tsai, Grace T Huang, Meng-Yuan Chou, Henry H Lu, Wen-Hsiung Li
    posted to identification methods motifs by nuin on 2008-06-26 18:14:44 as ** along with 1 person dquest
  • Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions
    BMC Bioinformatics, Vol. 8 (24 May 2007), 174.
    by Davide Cora', Ferdinando Di Cunto, Michele Caselle, Paolo Provero
    posted to identification motifs by nuin on 2008-06-26 15:34:09 as ** along with 4 people and 2 groups andersbj mtagaya GustavoLacerda bertelsen Bioinformatics microRNA
  • Assessing Clusters and Motifs from Gene Expression Data
    Genome Res., Vol. 11, No. 1. (1 January 2001), pp. 112-123.
    by Lars M Jakt, Liang Cao, Kathryn S Cheah, David K Smith
    posted to clusters enhancing motifs by nuin on 2008-06-26 15:32:48 as **
  • Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
    PLoS Computational Biology, Vol. 2, No. 10. (1 October 2006), e130.
    by Alan M Moses, Daniel A Pollard, David A Nix, Venky N Iyer, Xiao-Yong Li, Mark D Biggin, Michael B Eisen
    posted to identification motifs by nuin on 2008-06-26 18:10:10 as ** along with 1 person and 1 group nickluscombe EBI-regulation
  • A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1789-1796.
    by M Stepanova, T Tiazhelova, M Skoblov, A Baranova
    posted to comparison motifs by nuin on 2008-06-26 15:25:15 as ** along with 1 person troels_marstrand
  • dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2619-2621.
    by Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, Sun Kim
    posted to identification motifs by nuin on 2008-06-26 18:19:25 as ** along with 3 people maximilianh idonaldson isimpson
  • Finding motifs from all sequences with and without binding sites*
    Bioinformatics (26 July 2006)
    by Henry C M C Leung, Francis Y L Y Chin
    posted to identification motifs by nuin on 2008-06-26 18:13:32 as ** along with 2 people eckart_bindewald dquest
  • Long-range upstream and downstream enhancers control distinct subsets of the complex spatiotemporal Sox9 expression pattern
    Developmental Biology, Vol. 291, No. 2. (15 March 2006), pp. 382-397.
    by Stefan Bagheri-Fam, Francisco Barrionuevo, Ulrike Dohrmann, Thomas Günther, Roland Schüle, Rolf Kemler, Moisés Mallo, Benoit Kanzler, Gerd Scherer
    posted to motifs by nuin on 2008-06-26 18:17:57 as **
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