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blobbybirdman binding-site-prediction [51 articles]

最近 blobbybirdman さんのライブラリに追加された論文の中から タグ binding-site-prediction. You can also see everyone's binding-site-prediction.
  • Non-additivity in protein-DNA binding.
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2254-2263.
    by RA O'Flanagan, G Paillard, R Lavery, AM Sengupta
    posted to binding-site-prediction bioinformatics svm by blobbybirdman on 2008-01-24 20:09:14 as *** along with 2 people and 1 group reidy nklee UH - Computational Biology
  • Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure
    Cell, Vol. 131, No. 3. (2 November 2007), pp. 530-543.
    by Rohit Joshi, Jonathan M Passner, Remo Rohs, Rinku Jain, Alona Sosinsky, Michael A Crickmore, Vinitha Jacob, Aneel K Aggarwal, Barry Honig, Richard S Mann
    posted to binding-site-prediction dna-binding hox transcription-factors by blobbybirdman on 2008-01-24 20:01:55 as **** along with 2 people and 1 group cwbrown oelemento EisenLab
  • Hox transcription factors and their elusive mammalian gene targets
    Heredity, Vol. aop, No. current.
    by T Svingen, KF Tonissen,
    posted to binding-site-prediction dna-binding hox transcription-factors by blobbybirdman on 2008-01-24 19:45:50 as read along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Mining ChIP-chip data for transcription factor and cofactor binding sites.
    Bioinformatics, Vol. 21 Suppl 1 (June 2005)
    by AD Smith, P Sumazin, D Das, MQ Zhang
    posted to algorithms binding-site-prediction chip-chip gene-expression h_sapiens by blobbybirdman on 2007-10-16 12:33:28 as read along with 2 people dquest Ao_Li2007
  • A regulatory code for neurogenic gene expression in the Drosophila embryo.
    Development, Vol. 131, No. 10. (May 2004), pp. 2387-2394.
    by M Markstein, R Zinzen, P Markstein, KP Yee, A Erives, A Stathopoulos, M Levine
    posted to binding-site-prediction cis-regulatory-elements drosophila by blobbybirdman on 2007-10-15 12:57:18 as ** along with 2 people dquest maximilianh
  • Discovering DNA regulatory elements with bacteria
    Nature Biotechnology, Vol. 23, No. 8., pp. 942-944.
    by Martha L Bulyk
    posted to bacterial binding-site-prediction by blobbybirdman on 2007-10-11 15:25:41 as ***** along with 1 person yevishere
  • DNA microarray technologies for measuring protein-DNA interactions
    Current Opinion in Biotechnology, Vol. 17, No. 4. (August 2006), pp. 422-430.
    by Martha L Bulyk
    posted to binding-site-prediction chip-chip microarray by blobbybirdman on 2007-10-11 15:23:49 as ***** along with 2 people and 2 groups dchughes kristallreiner G4ID Genetics-of-Gambling
  • A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and ChIP-chip experiments: systematically incorporating validated biological knowledge.
    Bioinformatics (12 October 2006)
    by Jiang Du, Joel S S Rozowsky, Jan O O Korbel, Zhengdong D D Zhang, Thomas E E Royce, Martin H H Schultz, Michael Snyder, Mark Gerstein
    posted to binding-site-prediction chip-chip hmm integration by blobbybirdman on 2007-10-11 14:49:26 as **** along with 8 people and 2 groups bais miguel tuck eckart_bindewald djkt SeungjoonOh inesdesantiago xingxu Bioinformatics UH - Computational Biology
  • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.
    Proc Natl Acad Sci U S A, Vol. 98, No. 13. (19 June 2001), pp. 7158-7163.
    by ML Bulyk, X Huang, Y Choo, GM Church
    posted to binding-site-prediction cis-regulatory-elements microarray by blobbybirdman on 2007-10-11 14:00:13 as *** along with 2 people medic0747 yevishere
  • Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm
    J Mol Biol, Vol. 318, No. 1. (2002), pp. 71-81.
    by Z Zhu, Y Pilpel, GM Church
    posted to algorithms binding-site-prediction gene-expression microarray s-cerevisiae by blobbybirdman on 2007-10-09 17:56:41 as read
  • Bayesian adaptive sequence alignment algorithms
    Bioinformatics, Vol. 14, No. 1. (1998), pp. 25-39.
    by J Zhu, JS Liu, CE Lawrence
    posted to algorithms bayesian-statistics binding-site-prediction sequence-alignment by blobbybirdman on 2007-10-09 17:56:41 as read
  • PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (2004), pp. W318-20.
    by S Yellaboina, J Seshadri, MS Kumar, A Ranjan
    posted to binding-site-prediction cis-regulatory-elements database operons prokaryotes by blobbybirdman on 2007-10-09 17:56:41 as ***
  • High affinity YY1 binding motifs: identification of two core types (ACAT and CCAT) and distribution of potential binding sites within the human beta globin cluster
    Nucleic Acids Res, Vol. 23, No. 21. (1995), pp. 4353-62.
    by SR Yant, W Zhu, D Millinoff, JL Slightom, M Goodman, DL Gumucio
    posted to binding-site-prediction cis-regulatory-elements h_sapiens by blobbybirdman on 2007-10-09 17:56:40 as **
  • PatMatch: a program for finding patterns in peptide and nucleotide sequences
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (2005), pp. W262-6.
    by T Yan, D Yoo, TZ Berardini, LA Mueller, DC Weems, S Weng, JM Cherry, SY Rhee
    posted to algorithms arabidopsis binding-site-prediction cis-regulatory-elements sequence-analysis by blobbybirdman on 2007-10-09 17:56:40 as **
  • Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences
    Bioinformatics, Vol. 14, No. 4. (1998), pp. 317-25.
    by T Yada, Y Totoki, M Ishikawa, K Asai, K Nakai
    posted to algorithms binding-site-prediction cis-regulatory-elements hmm by blobbybirdman on 2007-10-09 17:56:40 as ***
  • Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
    Nature, Vol. 434, No. 7031. (2005), pp. 338-45.
    by X Xie, J Lu, EJ Kulbokas, TR Golub, V Mootha, Lindblad K Toh, ES Lander, M Kellis
    posted to binding-site-prediction evolutionary-comparision mammals mirna by blobbybirdman on 2007-10-09 17:56:40 as ****
  • ANN-Spec: a method for discovering transcription factor binding sites with improved specificity
    Pac Symp Biocomput (2000), pp. 467-78.
    by CT Workman, GD Stormo
    posted to algorithms binding-site-prediction gibbs-sampling neural-networks by blobbybirdman on 2007-10-09 17:56:40 as ***
  • Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis
    Genes Dev, Vol. 16, No. 2. (2002), pp. 235-44.
    by AS Weinmann, PS Yan, MJ Oberley, TH Huang, PJ Farnham
    posted to binding-site-prediction chip-chip h_sapiens microarray by blobbybirdman on 2007-10-09 17:56:40 as **
  • Applied bioinformatics for the identification of regulatory elements
    Nat Rev Genet, Vol. 5, No. 4. (2004), pp. 276-87.
    by WW Wasserman, A Sandelin
    posted to binding-site-prediction bioinformatics cis-regulatory-elements review by blobbybirdman on 2007-10-09 17:56:40 as read along with 1 group UH - Computational Biology
  • Human-mouse genome comparisons to locate regulatory sites
    Nat Genet, Vol. 26, No. 2. (2000), pp. 225-8.
    by WW Wasserman, M Palumbo, W Thompson, JW Fickett, CE Lawrence
    posted to binding-site-prediction evolutionary-comparisons h_sapiens mouse by blobbybirdman on 2007-10-09 17:56:40 as read along with 1 group UH - Computational Biology
  • In silico identification of metazoan transcriptional regulatory regions
    Naturwissenschaften, Vol. 90, No. 4. (2003), pp. 156-66.
    by WW Wasserman, W Krivan
    posted to binding-site-prediction bioinformatics review by blobbybirdman on 2007-10-09 17:56:40 as ***
  • Identification of regulatory regions which confer muscle-specific gene expression
    J Mol Biol, Vol. 278, No. 1. (1998), pp. 167-81.
    by WW Wasserman, JW Fickett
    posted to binding-site-prediction evolutionary-comparisons expression-clustering gene-regulation by blobbybirdman on 2007-10-09 17:56:40 as read
  • Combining phylogenetic data with co-regulated genes to identify regulatory motifs
    Bioinformatics, Vol. 19, No. 18. (2003), pp. 2369-80.
    by T Wang, GD Stormo
    posted to algorithms binding-site-prediction evolutionary-comparisions expression-clustering by blobbybirdman on 2007-10-09 17:56:40 as ***
  • Chromatin immunoprecipitation (ChIP) scanning identifies primary glucocorticoid receptor target genes
    Proc Natl Acad Sci U S A, Vol. 101, No. 44. (2004), pp. 15603-8.
    by JC Wang, MK Derynck, DF Nonaka, DB Khodabakhsh, C Haqq, KR Yamamoto
    posted to binding-site-prediction chip molecular-biology-techniques by blobbybirdman on 2007-10-09 17:56:39 as ***
  • Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals
    J Mol Biol, Vol. 297, No. 2. (2000), pp. 335-53.
    by A Vanet, L Marsan, A Labigne, MF Sagot
    posted to bacterial binding-site-prediction statistical by blobbybirdman on 2007-10-09 17:56:39 as ***
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nat Biotechnol, Vol. 23, No. 1. (2005), pp. 137-44.
    by M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, MC Frith, Y Fu, WJ Kent, VJ Makeev, AA Mironov, WS Noble, G Pavesi, G Pesole, M Regnier, N Simonis, S Sinha, G Thijs, J van Helden, M Vandenbogaert, Z Weng, C Workman, C Ye, Z Zhu
    posted to algorithms binding-site-prediction evaluation by blobbybirdman on 2007-10-09 17:56:38 as read along with 1 group UH - Computational Biology
  • Lecture Notes on Biological Sequence Analysis
    No. 2000-06-01. (2000)
    by M Tompa
    posted to binding-site-prediction bioinformatics review sequence-analysis by blobbybirdman on 2007-10-09 17:56:38 as read
  • Decoding human regulatory circuits
    Genome Res, Vol. 14, No. 10A. (2004), pp. 1967-74.
    by W Thompson, MJ Palumbo, WW Wasserman, JS Liu, CE Lawrence
    posted to algorithms binding-site-prediction gibbs-sampling h_sapiens modular by blobbybirdman on 2007-10-09 17:56:38 as ***
  • A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
    J Comput Biol, Vol. 9, No. 2. (2002), pp. 447-64.
    by G Thijs, K Marchal, M Lescot, S Rombauts, B De Moor, P Rouze, Y Moreau
    posted to algorithms binding-site-prediction expression-clustering gibbs-sampling by blobbybirdman on 2007-10-09 17:56:38 as read
  • A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
    Bioinformatics, Vol. 17, No. 12. (2001), pp. 1113-22.
    by G Thijs, M Lescot, K Marchal, S Rombauts, B De Moor, P Rouze, Y Moreau
    posted to algorithms binding-site-prediction gibbs-sampling mm by blobbybirdman on 2007-10-09 17:56:38 as read
  • A comparative genomics approach to prediction of new members of regulons
    Genome Res, Vol. 11, No. 4. (2001), pp. 566-84.
    by K Tan, Moreno G Hagelsieb, Collado J Vides, GD Stormo
    posted to bacterial binding-site-prediction evolutionary-comparisons gene-regulation by blobbybirdman on 2007-10-09 17:56:36 as ****
  • Making connections between novel transcription factors and their DNA motifs
    Genome Res, Vol. 15, No. 2. (2005), pp. 312-20.
    by K Tan, LA Mccue, GD Stormo
    posted to algorithms bacterial binding-site-prediction integration by blobbybirdman on 2007-10-09 17:56:36 as **
  • Integrating binding site predictions using non-linear classification methods
    Vol. 3635 (2005)
    by Y Sun, M Robinson, R Adams, P Kaye, AG Rust, N Davey
    edited by J Winkler, M Niranjan
    posted to binding-site-prediction integration machine-learning by blobbybirdman on 2007-10-09 17:56:36 as read
  • Specificity, free energy and information content in protein-DNA interactions
    Trends Biochem Sci, Vol. 23, No. 3. (1998), pp. 109-13.
    by GD Stormo, DS Fields
    posted to binding-site-prediction dna-binding by blobbybirdman on 2007-10-09 17:56:36 as read
  • DNA binding sites: representation and discovery
    Bioinformatics, Vol. 16, No. 1. (2000), pp. 16-23.
    by GD Stormo
    posted to algorithms binding-site-prediction by blobbybirdman on 2007-10-09 17:56:36 as read along with 1 group Myxo group
  • Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions
    Nucleic Acids Res, Vol. 27, No. 19. (1999), pp. 3899-910.
    by N Stojanovic, L Florea, C Riemer, D Gumucio, J Slightom, M Goodman, W Miller, R Hardison
    posted to algorithms binding-site-prediction evolutionary-comparisons by blobbybirdman on 2007-10-09 17:56:36 as ***
  • Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding
    Proc Natl Acad Sci U S A, Vol. 100, No. 5. (2003), pp. 2580-5.
    by B van Steensel, J Delrow, HJ Bussemaker
    posted to binding-site-prediction dna-binding drosophila genomics by blobbybirdman on 2007-10-09 17:56:36 as ***
  • CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments
    Bioinformatics, Vol. 19 Suppl 1 (2003), pp. i283-91.
    by R Sharan, I Ovcharenko, Ben A Hur, RM Karp
    posted to algorithms binding-site-prediction bioinformatics clustering h_sapiens modularity mouse by blobbybirdman on 2007-10-09 17:56:35 as ***
  • CREME: Cis-Regulatory Module Explorer for the human genome
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (2004), pp. W253-6.
    by R Sharan, Ben A Hur, GG Loots, I Ovcharenko
    posted to algorithms binding-site-prediction bioinformatics clustering h_sapiens modularity mouse by blobbybirdman on 2007-10-09 17:56:35 as **
  • Sequence logos: a new way to display consensus sequences
    Nucleic Acids Res, Vol. 18, No. 20. (1990), pp. 6097-100.
    by TD Schneider, RM Stephens
    posted to binding-site-prediction bioinformatics computational-tools dna-binding information-theory by blobbybirdman on 2007-10-09 17:56:35 as read
  • Reading of DNA sequence logos: prediction of major groove binding by information theory
    Methods Enzymol, Vol. 274 (1996), pp. 445-55.
    by TD Schneider
    posted to binding-site-prediction computational-biology dna-binding genomics information-theory by blobbybirdman on 2007-10-09 17:56:35 as read
  • Information content of individual genetic sequences
    J Theor Biol, Vol. 189, No. 4. (1997), pp. 427-41.
    by TD Schneider
    posted to binding-site-prediction computational-biology dna-binding genomics information-theory by blobbybirdman on 2007-10-09 17:56:35 as ****
  • Consensus Sequence Zen
    Applied Bioinformatics, Vol. 1, No. 3. (2002), pp. 111-119.
    by TD Schneider
    posted to binding-site-prediction dna-binding information-theory by blobbybirdman on 2007-10-09 17:56:34 as read
  • Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons
    Science, Vol. 288, No. 5463. (2000), pp. 136-40.
    by GG Loots, RM Locksley, CM Blankespoor, ZE Wang, W Miller, EM Rubin, KA Frazer
    posted to binding-site-prediction evolutionary-comparison gene-regulation by blobbybirdman on 2007-10-09 17:56:28 as read
  • Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
    Genome Res, Vol. 9, No. 9. (1999), pp. 815-24.
    by N Jareborg, E Birney, R Durbin
    posted to binding-site-prediction evolutionary-comparisons by blobbybirdman on 2007-10-09 17:56:22 as **
  • PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches
    Nucleic Acids Res, Vol. 29, No. 19. (2001), pp. 3988-96.
    by W Fujibuchi, JS Anderson, D Landsman
    posted to algorihtms binding-site-prediction expression-clustering microarray software-tools by blobbybirdman on 2007-10-09 17:56:20 as **
  • Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster
    Hum Mol Genet, Vol. 10, No. 4. (2001), pp. 371-82.
    by J Flint, C Tufarelli, J Peden, K Clark, RJ Daniels, R Hardison, W Miller, S Philipsen, Tan KC Un, T Mcmorrow, J Frampton, BP Alter, AM Frischauf, DR Higgs
    posted to binding-site-prediction evolutionary-comparisions synteny by blobbybirdman on 2007-10-09 17:56:19 as ***
  • Discovering novel cis-regulatory motifs using functional networks
    Genome Res, Vol. 13, No. 5. (2003), pp. 883-95.
    by LM Ettwiller, J Rung, E Birney
    posted to algorithms binding-site-prediction bioinformatics networks by blobbybirdman on 2007-10-09 17:56:18 as ***
  • Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
    BMC Bioinformatics, Vol. 3, No. 1. (2002)
    by M Caselle, F Di Cunto, P Provero
    posted to binding-site-prediction eukaryotes expression-clustering gene-regulation microarray by blobbybirdman on 2007-10-09 17:56:15 as **
  • Verbumculus and the Discovery of Unusual Words
    Journal of Computer Science and Technology, Vol. 19, No. 1. (2004), pp. 22-41.
    by A Apostolico, F Gong, S Lonardi
    posted to algorithms binding-site-prediction statistical by blobbybirdman on 2007-10-09 17:56:10 as read
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