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GustavoLacerda's regulation [29 articles]

Recent papers added to GustavoLacerda's library classified by the tag regulation. You can also see everyone's regulation.
  • 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 regulation by GustavoLacerda on 2008-08-08 05:02:42 as ** along with 4 people and 1 group indigoviolet nklee yevishere xili03 EisenLab
  • SCORE: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data
    Proceedings of the National Academy of Sciences, Vol. 99, No. 15. (23 July 2002), pp. 9888-9893.
    by Mark Rebeiz, Nick L Reeves, James W Posakony
    posted to regulation by GustavoLacerda on 2008-08-08 05:02:28 as ** along with 2 people and 1 group indigoviolet isimpson EisenLab
  • Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells
    Genome Res. (15 May 2008), gr.072769.107.
    by Dan Xie, Jun Cai, Na-Yu Chia, Huck Ng, Sheng Zhong
    posted to regulation by GustavoLacerda on 2008-06-30 22:16:07 as ** along with 5 people maximilianh idonaldson isimpson phoenixzxl yoonk
  • Everything you wanted to know about small RNA but were afraid to ask
    Laboratory Investigation, Vol. aop, No. current.
    by Scott D Boyd
    posted to microrna regulation by GustavoLacerda on 2008-06-13 21:20:34 as ** along with 3 people and 1 group balicea heliopais bootsy microRNA
  • Mireval: a web tool for simple microRNA prediction in genome sequences
    Bioinformatics, Vol. 24, No. 11. (1 June 2008), pp. 1394-1396.
    by William Ritchie, Francois-Xavier Theodule, Daniel Gautheret
    posted to microrna regulation by GustavoLacerda on 2008-05-20 19:03:26 as ** along with 2 people tharris jfr
  • CompariMotif: quick and easy comparisons of sequence motifs
    Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1307-1309.
    by Richard J Edwards, Norman E Davey, Denis C Shields
    posted to motif regulation by GustavoLacerda on 2008-05-09 13:42:20 as ** along with 2 people maximilianh jyuh
  • 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 regulation by GustavoLacerda on 2008-01-21 19:35:00 as ** along with 8 people and 2 groups nuin bryankr ana chad_davis balicea hggr svdate kristallreiner structural_bioinformatics Bioinformatics
  • Divergence of Transcription Factor Binding Sites Across Related Yeast Species
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 815-819.
    by Anthony R Borneman, Tara A Gianoulis, Zhengdong D Zhang, Haiyuan Yu, Joel Rozowsky, Michael R Seringhaus, Lu Y Wang, Mark Gerstein, Michael Snyder
    posted to regulation by GustavoLacerda on 2008-01-09 15:24:55 as ** along with 18 people and 2 groups caseybrown bryankr aalibes chad_davis dpollard djkt mikaelhuss lusk cjeans sujaikumar zwang Jporci maximilianh cisevol njcitulike emptyhb nklee anka EisenLab cis-regulatory-evolution
  • BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences.
    Bioinformatics (27 July 2007)
    by Hailong Meng, Arunava Banerjee, Lei Zhou
    posted to regulation by GustavoLacerda on 2007-12-10 19:47:14 as ** along with 2 people and 1 group grahamc maximilianh ParkinsonLab_at_MaRS
  • Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e90.
    by Timothy E Reddy, Charles Delisi, Boris E Shakhnovich
    posted to regulation by GustavoLacerda on 2007-11-24 03:16:41 as **** along with 5 people and 1 group aalibes dpollard medic0747 mircea marti EisenLab
  • Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes.
    Brief Bioinform (12 July 2007)
    by Nikolay A A Kolchanov, Tatyana I I Merkulova, Elena V V Ignatieva, Elena A A Ananko, Dmitry Yu Y Oshchepkov, Viktor G G Levitsky, Gennady V V Vasiliev, Nataly V V Klimova, Vasily M M Merkulov, T Charles C Hodgman
    posted to regulation by GustavoLacerda on 2007-10-25 14:46:58 as ** along with 3 people and 2 groups ana cabbagezs xili03 structural_bioinformatics Bioinformatics
  • Tree Gibbs Sampler: Identifying Conserved Motifs without Aligning Orthologous Sequences.
    Bioinformatics (31 May 2007)
    by Xiaohui Cai, Haiyan Hu, Xiaoman Shawn S Li
    posted to regulation by GustavoLacerda on 2007-08-17 17:43:45 as ** along with 2 people and 1 group grahamc cjeans ParkinsonLab_at_MaRS
  • Promoters and their regulation in Ustilago maydis and other phytopathogenic fungi
    FEMS Microbiology Letters, Vol. 254, No. 2. (2006), pp. 208-216.
    by Christoph W Basse, Jan W Farfsing
    posted to regulation fungi by GustavoLacerda on 2007-08-07 03:14:28 as **
  • Functional analysis of the cellobiohydrolase I promoter of the filamentous fungus Trichoderma reesei
    Molecular and General Genetics MGG, Vol. 253, No. 3. (22 December 1996), pp. 303-314.
    by M Ilmén, ML Onnela, S Klemsdal, S Keränen, M Penttilä
    posted to fungi regulation by GustavoLacerda on 2007-07-30 19:03:36 as **
  • A novel ensemble learning method for de novo computational identification of DNA binding sites
    BMC Bioinformatics, Vol. 8 (12 July 2007), 249.
    by Arijit Chakravarty, Jonathan M Carlson, Radhika S Khetani, Robert H Gross
    posted to regulation by GustavoLacerda on 2007-07-27 22:35:01 as ** along with 2 people and 1 group chad_davis nklee Bioinformatics
  • Prediction of DNA-binding residues from sequence
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i347-353.
    by Yanay Ofran, Venkatesh Mysore, Burkhard Rost
    posted to regulation by GustavoLacerda on 2007-07-25 22:06:50 as ** along with 3 people aalibes kaarsinogen chrn
  • Transcription Factor Map Alignment of Promoter Regions
    PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e49.
    by Enrique Blanco, Xavier Messeguer, Temple F Smith, Roderic Guigó
    posted to regulation by GustavoLacerda on 2007-06-28 17:24:32 as ** along with 2 people reidy Garamonfok
  • Mining, compressing and classifying with extensible motifs
    Algorithms for Molecular Biology, Vol. 1 (23 March 2006), 4.
    by Alberto Apostolico, Matteo Comin, Laxmi Parida
    posted to regulation by GustavoLacerda on 2007-06-12 06:15:09 as **
  • 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 regulation by GustavoLacerda on 2007-06-11 21:16:40 as ** along with 4 people and 2 groups andersbj mtagaya bertelsen nuin Bioinformatics microRNA
  • Multiple Non-Collinear TF-map Alignments of Promoter Regions
    BMC Bioinformatics, Vol. 8 (24 April 2007), 138.
    by Enrique Blanco, Roderic Guigo, Xavier Messeguer
    posted to regulation by GustavoLacerda on 2007-06-11 21:06:13 as ** along with 1 person oscarluoinau
  • Statistical significance of cis-regulatory modules
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Dustin Schones, Andrew Smith, Michael Zhang
    posted to regulation by GustavoLacerda on 2007-06-01 16:42:45 as ** along with 9 people and 1 group indigoviolet dpollard dquest sebastien_vigneau shigepong SeungjoonOh nklee xili03 sconlan EisenLab
  • WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences
    BMC Bioinformatics, Vol. 8 (07 February 2007), 46.
    by Giulio Pavesi, Federico Zambelli, Graziano Pesole
    posted to regulation by GustavoLacerda on 2007-06-01 16:39:03 as ** along with 2 people dquest nuin
  • Genomic regulatory regions: insights from comparative sequence analysis.
    Curr Opin Genet Dev, Vol. 13, No. 6. (December 2003), pp. 604-610.
    by GM Cooper, A Sidow
    posted to regulation by GustavoLacerda on 2007-05-02 20:00:01 as **
  • A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by D Vlieghe, A Sandelin, PJ De Bleser, K Vleminckx, WW Wasserman, F van Roy, B Lenhard
    posted to regulation by GustavoLacerda on 2007-05-02 19:51:38 as ** along with 2 people postrational dandaman
  • TRANSFAC: transcriptional regulation, from patterns to profiles.
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 374-378.
    by V Matys, E Fricke, R Geffers, E Gössling, M Haubrock, R Hehl, K Hornischer, D Karas, AE Kel, OV Kel-Margoulis, DU Kloos, S Land, B Lewicki-Potapov, H Michael, R Münch, I Reuter, S Rotert, H Saxel, M Scheer, S Thiele, E Wingender
    posted to regulation by GustavoLacerda on 2007-05-02 19:48:53 as ** along with 6 people and 1 group aalibes setar chad_davis marti Auger kmdaily Dead 60's
  • 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 regulation by GustavoLacerda on 2007-04-20 05:18:43 as ** along with 1 person and 1 group rebeccamancy ColDyn
  • Mclip: motif detection based on cliques of gapped local profile-to-profile alignments
    Bioinformatics, Vol. 23, No. 4. (15 February 2007), pp. 502-503.
    by Frickey, Tancred, Weiller, Georg
    posted to regulation by GustavoLacerda on 2007-04-20 04:06:58 as ** along with 1 person csdhwang
  • 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 regulation by GustavoLacerda on 2007-04-20 04:00:54 as ** along with 2 people Ema zhouyu
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James W Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to regulation by GustavoLacerda on 2007-04-20 03:22:03 as ** along with 26 people and 6 groups emptyhb bryankr icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos nklee mdimon dandaman vietanh0 ep161302 nuin Stew structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
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