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Tag motif [394 articles]

Recent papers classified by the tag motif.
  • DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e61.
    by Shaun Mahony, Philip E Auron, Panayiotis V Benos
    posted to clustering dna motif by zwang on 2007-04-19 15:10:17 as * along with 3 people aalibes nklee heliopais
  • Network motifs: theory and experimental approaches
    Nature Reviews Genetics, Vol. 8, No. 6., pp. 450-461.
    by Uri Alon
    posted to motif network review by zwang on 2007-05-28 02:00:47 as **** along with 14 people and 3 groups Borelli icases aalibes cmmorel jtaylor dbikard margaritis shigepong grinfish Pascalichouchou xingxu karfunkel vietanh0 haarcuba TNT Centre de Recherches Interdisciplinaires SynBioSys
  • Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e178.
    by Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A Marti-Renom, Baldo Oliva
    posted to interaction interface motif prediction protein by zwang on 2007-10-22 05:23:09 as **** along with 2 people Ema winterschlaefer
  • Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
    PLoS Comput Biol, Vol. 3, No. 10. (26 October 2007), pp. 1993-2002.
    by JJ Ward, JM Thornton
    posted to evolution modeling motif network transcription yeast by zwang on 2007-11-20 08:52:20 as ** along with 2 people cabbagezs grottenolm
  • Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
    PLoS Computational Biology, Vol. preprint, No. 2007. (1 July 2007), e178.eor.
    by Ramon Aragues, Andrej Sali, Jaume Bonet, Marc Marti-Renom, Baldomero Oliva
    posted to hub interaction motif protein by zwang on 2007-08-09 02:37:44 as ***
  • Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family
    Genes Dev., Vol. 21, No. 15. (1 August 2007), pp. 1882-1894.
    by Peter C Hollenhorst, Atul A Shah, Christopher Hopkins, Barbara J Graves
    posted to genefamily genome-wide motif promoter regulation by zwang on 2007-08-09 02:28:24 as * along with 2 people sbranco ale
  • 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 dna motif by zwang on 2007-03-30 08:47:32 as *** along with 6 people isimpson eckart_bindewald GeeSharpMinor ppark idonaldson hpaces
  • Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
    Nature Methods, Vol. 4, No. 7. (24 June 2007), pp. 563-565.
    by Laurence Ettwiller, Benedict Paten, Mirana Ramialison, Ewan Birney, Joachim Wittbrodt
    posted to chromatin motif prediction regulatory by zwang on 2007-08-28 03:56:29 as * along with 3 people and 1 group brant maximilianh fpattyn EisenLab
  • Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e178.
    by Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A Marti-Renom, Baldo Oliva
    posted to hub interaction motif protein by zwang on 2007-11-02 08:03:44 as **** along with 1 person bicko
  • Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
    PLoS Genetics, Vol. 3, No. 8. (1 August 2007), e145.
    by Marica Grskovic, Christina Chaivorapol, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos
    posted to human motif prediction regulatory sequence systematic by zwang on 2007-09-03 04:40:58 as **
  • Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
    PNAS, Vol. 104, No. 3. (16 January 2007), pp. 808-813.
    by Tom Young, Robert Abel, Byungchan Kim, Bruce J Berne, Richard A Friesner
    posted to molecularrecognition motif protein by zwang on 2007-04-16 13:42:41 as ** along with 2 people daevans jwagoner
  • Structural motifs of biomolecules
    Proceedings of the National Academy of Sciences, Vol. 104, No. 44. (30 October 2007), pp. 17283-17286.
    by Jayanth R Banavar, Trinh X Hoang, John H Maddocks, Amos Maritan, Chiara Poletto, Andrzej Stasiak, Antonio Trovato
    posted to motif structure by zwang on 2007-11-01 02:15:29 as ** along with 3 people and 1 group sobolevnrm afenley hpaces baker-group
  • A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.
    Mol Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350.
    by O Elemento, N Slonim, S Tavazoie
    posted to clustering genome motif prediction yeast by zwang on 2007-11-01 02:15:02 as *** along with 12 people and 2 groups ana brant cwbrown aswin cjeans cabbagezs nklee maximilianh idonaldson sb_journal_club kristen barwil EisenLab Motif Discovery
  • 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 Helmer-Citterich
    posted to evolution motif protein by zwang on 2007-03-19 12:56:19 as ** along with 1 person rabio
  • Systematic identification of mammalian regulatory motifs' target genes and functions
    Nature Methods, Vol. 5, No. 4. (02 March 2008), pp. 347-353.
    by Jason B Warner, Anthony A Philippakis, Savina A Jaeger, Fangxue S He, Jolinta Lin, Martha L Bulyk
    posted to motif regulatory by zwang on 2008-04-02 07:26:28 as ** along with 4 people isimpson jyuh tmmurali ptrobajo
  • High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons.
    Nat Biotechnol (1 April 2007)
    by Patrick T T McGrath, Honglak Lee, Li Zhang, Antonio A A Iniesta, Alison K K Hottes, Meng How H Tan, Nathan J J Hillson, Ping Hu, Lucy Shapiro, Harley H H McAdams
    posted to motif promoter transcription by zwang on 2007-05-10 17:03:41 as ** along with 1 person aswin
  • 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 biological complex motif network by zibuyu on 2008-02-01 13:43:56 as ** along with 12 people and 1 group hannahrajasingh Borelli jstajic jjray ssb nickluscombe gurkanbebek jtaylor jayster4 karfunkel blobbybirdman maralena EBI-regulation
  • Empirical study on clique-degree distribution of networks
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 3. (2007)
    by Wei K Xiao, Jie Ren, Feng Qi, Zhi W Song, Meng X Zhu, Hong F Yang, Hui Y Jin, Bing H Wang, Tao Zhou
    posted to complex motif network by zibuyu on 2008-01-30 15:50:35 as **
  • Subgraph centrality in complex networks.
    Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 71, No. 5 Pt 2. (May 2005)
    by E Estrada, JA Rodríguez-Velázquez
    posted to motif by zibuyu on 2008-01-30 15:31:59 as ** along with 7 people and 3 groups korakot ansobol jrw aalibes tmmurali okarsligil BarrosH Philosophy_of_Information Blog_and_Wiki_Research Bioinformatics
  • Network motifs in computational graphs: A case study in software architecture
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 72, No. 2. (2005)
    by Sergi Valverde, Ricard V Solé
    posted to motif by zibuyu on 2008-01-30 15:28:11 as **
  • 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 motif by zibuyu on 2008-01-30 15:20:19 as ***** along with 16 people and 7 groups tnhh ChaTo lfriedl alexg yish balicea ssb ddahlem cmm j3xucite donade bigbossman gurkanbebek shenorr ltabourier michaelmampaey kdl mathgamespatterns dtl vds-arg eni FAB-lab ADMiRes
  • 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 motif by zibuyu on 2008-01-30 15:19:26 as ***** along with 38 people and 8 groups renatomilani subhacom cmor carlk pbull i-stevenson applesnow shikin camster korakot aalibes ChaTo imouthesmp Borelli lfriedl alexg balicea tny ssb wnpx ddahlem cmm donade neveaire griota gurkanbebek jtaylor josepe iris_2001 michaelmampaey rebeccamancy karfunkel lenov Evangelia roys tfogal maralena stefanoallesina GeneGo Philosophy_of_Information dbk-lab Blog_and_Wiki_Research kdl FAB-lab ColDyn ADMiRes
  • Computing exact P-values for DNA motifs
    Bioinformatics, Vol. 23, No. 5. (March 2007), pp. 531-537.
    by Zhang, Jing, Jiang, Bo, Li, Ming, Tromp, John, Zhang, Xuegong, Zhang, Q Michael
    posted to motif by zhouyu on 2008-04-02 09:11:32 as ** along with 2 people GustavoLacerda Ema
  • Computational prediction of transcription-factor binding site locations.
    Genome Biol, Vol. 5, No. 1. (2003)
    by ML Bulyk
    posted to mining motif pbm by yevishere on 2008-01-02 23:51:30 as ** along with 6 people and 1 group aalibes kaarsinogen lusk Stew nklee xili03 EisenLab
  • Positional bias of general and tissue-specific regulatory motifs in mouse promoters
    BMC Genomics, Vol. 8, No. 1. (2007)
    by Nicolas Bellora, Domenec Farre, Mar
    posted to hnf4 motif prediction by yevishere on 2008-01-02 23:15:28 as ** along with 3 people maximilianh barriot gjuggler
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
    Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816.
    by
    posted to encode hnf4 motif myc taf1 tss by yevishere on 2008-01-11 00:36:27 as ***** along with 9 people and 2 groups jyuh jfr chad_davis kengg olympos blobbybirdman shikin fpattyn elfar Bioinformatics UH - Computational Biology
  • Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by BC Foat, AV Morozov, HJ Bussemaker
    posted to mining motif by yevishere on 2008-01-03 23:53:02 as **** along with 3 people xili03 dquest lusk
  • Informative priors based on transcription factor structural class improve de novo motif discovery
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392.
    by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J Hartemink
    posted to mining motif by yevishere on 2008-01-03 23:51:50 as **** along with 3 people dquest nklee idonaldson
  • An equilibrium partitioning model connecting gene expression and cis-motif content
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e368-374.
    by Joe Mellor, Charles Delisi
    posted to mining motif by yevishere on 2008-01-03 23:50:55 as ** along with 1 person and 1 group dpollard EisenLab
  • Identification of transcriptional regulators using binding site enrichment analysis.
    In Silico Biol, Vol. 6, No. 6. (2006), pp. 531-544.
    by TM Kim, MH Jung
    posted to enrichment hnf4 mining motif by yevishere on 2008-01-03 23:14:06 as **** along with 1 person heliopais
  • Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.
    J Mol Biol, Vol. 345, No. 5. (4 February 2005), pp. 1281-1294.
    by O Keskin, B Ma, R Nussinov
    posted to interaction motif structure by xz on 2006-05-23 14:53:26 as ** along with 8 people and 2 groups mdimmic ana barry baaden okarsligil bicko j3xucite bilab structural_bioinformatics Bioinformatics
  • CARRIE web service: automated transcriptional regulatory network inference and interactive analysis.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by PM Haverty, MC Frith, Z Weng
    posted to database microarray motif by xwbcn on 2006-04-23 18:55:37 as ** along with 2 people dquest heliopais
  • Reliable prediction of transcription factor binding sites by phylogenetic verification.
    Proc Natl Acad Sci U S A, Vol. 102, No. 47. (22 November 2005), pp. 16945-16950.
    by X Li, S Zhong, WH Wong
    posted to genome genome_alignment motif by xwbcn on 2006-02-25 11:11:02 as ***** along with 2 people postrational nklee
  • Genome-wide analysis of mammalian promoter architecture and evolution
    Nature Genetics, Vol. 38, No. 6. (28 April 2006), pp. 626-635.
    by Piero Carninci, Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin AM Semple, Martin S Taylor, Pär G Engström, Martin C Frith, Alistair RR Forrest, Wynand B Alkema, Sin L Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M Grimmond, Christine A Wells, Valerio Orlando, Claes Wahlestedt, Edison T Liu, Matthias Harbers, Jun Kawai, Vladimir B Bajic, David A Hume, Yoshihide Hayashizaki
    posted to genome human motif promoter by xwbcn on 2006-07-16 13:02:13 as ** along with 10 people and 4 groups jasonflannick jfr dchughes tabu samal nickluscombe xiaobeizhao cisevol eviledv gjuggler G4ID EBI-regulation Genetics-of-Gambling cis-regulatory-evolution
  • Predicting gene expression from sequence.
    Cell, Vol. 117, No. 2. (16 April 2004), pp. 185-198.
    by MA Beer, S Tavazoie
    posted to microarray motif tf by xwbcn on 2006-04-05 03:17:26 as ** along with 8 people and 4 groups klo ana adepace nickluscombe noano koller jrest phoenixzxl structural_bioinformatics Bioinformatics EisenLab EBI-regulation
  • Identifying regulatory networks by combinatorial analysis of promoter elements.
    Nat Genet, Vol. 29, No. 2. (October 2001), pp. 153-159.
    by Y Pilpel, P Sudarsanam, GM Church
    posted to microarray motif tf by xwbcn on 2006-04-05 03:16:44 as ** along with 7 people and 1 group windman83 ihpark imouthesmp troels_marstrand wnpx noano koller Bioinformatics
  • Computational evidence for hundreds of non-conserved plant microRNAs.
    BMC Genomics, Vol. 6 (13 September 2005)
    by M Lindow, A Krogh
    posted to evolution genome mirna motif by xwbcn on 2006-03-09 12:14:52 as ** along with 4 people and 3 groups jwortman kaspermunch mortenlindow cdawson Bioinformatics microRNA GIG
  • Identification of plant promoter constituents by analysis of local distribution of short sequences
    BMC Genomics, Vol. 8 (08 March 2007), 67.
    by Yoshiharu Y Yamamoto, Hiroyuki Ichida, Minami Matsui, Junichi Obokata, Teshuya Sakurai, Masakazu Satou, Motoaki Seki, Kazuo Shinozaki, Tomoko Abe
    posted to arabidopsis comparative_study g genome motif promoter rice by xwbcn on 2007-05-02 08:08:59 as ** along with 5 people and 1 group kengg saru byy Jporci natstreet Plantandetc
  • Large-scale Cis-element Detection by Analysis of Correlated Expression and Sequence Conservation between Arabidopsis and Brassica oleracea.
    Plant Physiol (6 October 2006)
    by Georg Haberer, Michael T T Mader, Peter Kosarev, Manuel Spannagl, Li Yang, Klaus Fx F Mayer
    posted to arabidopsis chip comparative_study genome microarray motif promoter by xwbcn on 2006-10-13 02:53:11 as ** along with 4 people and 1 group dpollard kengg nklee xili03 EisenLab
  • Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.
    Proc Natl Acad Sci U S A (31 March 2006)
    by Ji-Young Y Lee, Juliette Colinas, Jean Y Y Wang, Daniel Mace, Uwe Ohler, Philip N N Benfey
    posted to arabidopsis microarray mirna motif tf by xwbcn on 2006-04-05 02:16:36 as *** along with 2 people and 1 group cdawson dlmace GIG
  • Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
    Physiol Genomics, Vol. 17, No. 2. (13 April 2004), pp. 87-100.
    by J Yazaki, Z Shimatani, A Hashimoto, Y Nagata, F Fujii, K Kojima, K Suzuki, T Taya, M Tonouchi, C Nelson, A Nakagawa, Y Otomo, K Murakami, K Matsubara, J Kawai, P Carninci, Y Hayashizaki, S Kikuchi
    posted to arabidopsis chip genome microarray motif rice by xwbcn on 2006-03-07 09:50:02 as *****
  • Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis.
    Plant Physiol, Vol. 141, No. 4. (August 2006), pp. 1219-1232.
    by C Benedict, M Geisler, J Trygg, N Huner, V Hurry
    posted to arabidopsis chip cold comparative_study data_mining expression genome microarray motif networks transcriptome by xwbcn on 2007-06-11 15:16:05 as ** along with 1 person natstreet
  • Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine.
    Genome Res (19 January 2006)
    by Yunhai Li, Kee Khoon K Lee, Sean Walsh, Caroline Smith, Sophie Hadingham, Karim Sorefan, Gavin Cawley, Michael W W Bevan
    posted to arabidopsis chip motif by xwbcn on 2006-04-04 14:20:09 as **
  • Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana.
    Bioinformatics, Vol. 21, No. 14. (15 July 2005), pp. 3074-3081.
    by W Zhang, J Ruan, TH Ho, Y You, T Yu, RS Quatrano
    posted to arabidopsis microarray motif by xwbcn on 2006-05-02 18:55:11 as ***** along with 2 people imouthesmp natstreet
  • Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks.
    PLoS Biol, Vol. 3, No. 12. (15 November 2005)
    by Victor Neduva, Rune Linding, Isabelle Su-Angrand, Alexander Stark, Federico de D Masi, Toby J J Gibson, Joe Lewis, Luis Serrano, Robert B B Russell
    posted to gene_family genome motif by xwbcn on 2006-02-18 11:03:59 as ***** along with 10 people and 2 groups chad_davis rklancer okarsligil bicko Ayest drastic ezotenko grahamc Evangelia oelemento Bioinformatics ParkinsonLab_at_MaRS
  • Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity
    Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59.
    by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen, Jussi Taipale
    posted to genome human_genome motif by xwbcn on 2006-02-20 02:14:04 as ** along with 12 people and 5 groups Terkko kaarsinogen tuck brant dchughes nickluscombe olympos cabbagezs karfunkel maximilianh heliopais oelemento Bioinformatics EisenLab G4ID EBI-regulation Genetics-of-Gambling
  • Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.
    Proc Natl Acad Sci U S A, Vol. 104, No. 17. (24 April 2007), pp. 7145-7150.
    by X Xie, TS Mikkelsen, A Gnirke, K Lindblad-Toh, M Kellis, ES Lander
    posted to genome_alignment human human_genome mammal motif networks tf by xwbcn on 2007-05-11 09:54:09 as ** along with 4 people bpcusack aprasad olympos rschulz
  • DNA motif representation with nucleotide dependency.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 5, No. 1. (r 2008), pp. 110-119.
    by F Chin, HC Leung
    posted to dependency motif by xili03 on 2008-04-06 03:38:03 as read along with 3 people Stew AbnerCYH maximilianh
  • notes Discovering gapped binding sites of yeast transcription factors
    Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2527-2532.
    by Chien-Yu Chen, Huai-Kuang Tsai, Chen-Ming Hsu, May, Hao-Geng Hung, Grace T Huang, Wen-Hsiung Li
    posted to gapped motif by xili03 on 2008-04-05 05:11:24 as ***
  • A new subfamily of high molecular mass CDC2-related kinases with PITAI/VRE motifs.
    Biochem Biophys Res Commun, Vol. 279, No. 3. (29 December 2000), pp. 832-837.
    by F Marquès, Et Al
    posted to 5 cdc2-like cdc2-related cdc2l5 cdk cdk13 cell ctd cycl cycle cyclinl development early kinase motif mrna novel pitaivre rnapolii sea splicing sr subfamily synthesis urchin by xico on 2007-05-18 01:46:26 as read along with 1 group WetBiology
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