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chad_davis' gene_regulation [40 articles]

Artikler nylig sendt til chad_davis' bibliotek klassifisert med nøkkelordet gene_regulation. You can also see everyone's gene_regulation.
  • MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders.
    Bioinformatics (Oxford, England) (12 August 2008)
    by Edward Wijaya, Siu, Ngo, Rajaraman Kanagasabai, Wing
    posted to algorithm classification ensemble gene_regulation proj_credo by chad_davis on 2008-08-26 18:08:44 as **** along with 2 people maximilianh idonaldson
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia G Canut, Luis Serrano
    posted to embl evolution gene_regulation networks proj_mol_evo by chad_davis on 2008-07-07 12:11:29 as read along with 18 people and 4 groups aalibes tmmurali dullhunk neils cmzmasek AbnerCYH josedavid biehl caseybrown Garamonfok austin hryk dbikard cactus margaritis michaelbarton aheilbut zwang GEB Centre de Recherches Interdisciplinaires SynBioSys BergmanLab
  • notes Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    Bioinformatics, Vol. 15, No. 7. (1 July 1999), pp. 563-577.
    by Gz Hertz, Gd Stormo
    posted to algorithm alignment download gene_regulation proj_credo statistics by chad_davis on 2008-07-06 17:25:57 as read along with 4 people and 1 group tuck indigoviolet dquest lusk EisenLab
  • Intrinsically Disordered Proteins in Human Diseases: Introducing the D(2) Concept.
    Annual review of biophysics, Vol. 37 (9 June 2008), pp. 215-246.
    by Vladimir NN Uversky, Christopher JJ Oldfield, Keith
    posted to disease disorder gene_regulation proj_disocons review structure binding by chad_davis on 2008-06-29 10:56:16 as *** along with 1 person allmensch
  • 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 algorithm gene_regulation proj_credo statistics yeast by chad_davis on 2008-06-26 08:21:09 as **** along with 3 people and 1 group dpollard dquest yevishere EisenLab
  • Alternative splicing and protein structure evolution.
    Nucleic Acids Res, Vol. 36, No. 2. (February 2008), pp. 550-558.
    by F Birzele, G Csaba, R Zimmer
    posted to annotation evolution gene_regulation proj_mol_evo structure by chad_davis on 2008-06-18 12:00:48 as read along with 3 people bootsy msierk balicea
  • Eukaryotic transcription factor binding sites - modeling and integrative search methods
    Bioinformatics (21 April 2008), btn198.
    by Sridhar Hannenhalli
    posted to gene_regulation proj_credo review binding by chad_davis on 2008-06-15 13:35:43 as **** along with 7 people hplatero maximilianh heliopais bootsy Ema sameetmehta jyuh
  • Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e7.
    by Daniela Raijman, Ron Shamir, Amos Tanay
    posted to evolution gene_regulation proj_credo yeast by chad_davis on 2008-03-17 22:09:23 as **** along with 7 people and 1 group aalibes sebastien_vigneau lusk Garamonfok nklee maximilianh emptyhb BioinfoCIPF
  • Decoding human regulatory circuits.
    Genome Res, Vol. 14, No. 10A. (October 2004), pp. 1967-1974.
    by W Thompson, MJ Palumbo, WW Wasserman, JS Liu, CE Lawrence
    posted to algorithm gene_regulation proj_credo statistics by chad_davis on 2008-03-13 13:07:37 as *** along with 1 person and 1 group indigoviolet EisenLab
  • The Eukaryotic Promoter Database (EPD)
    Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 302-303.
    by Rouaida C Perier, Viviane Praz, Thomas Junier, Claude Bonnard, Philipp Bucher
    posted to database gene_regulation proj_credo web_service by chad_davis on 2008-03-10 10:18:59 as read
  • Assessment of composite motif discovery methods
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Kjetil Klepper, Geir Sandve, Osman Abul, Jostein Johansen, Finn Drablos
    posted to gene_regulation proj_credo review by chad_davis on 2008-02-26 21:25:14 as ***** along with 7 people and 1 group nklee maximilianh idonaldson xili03 csdhwang isimpson yoonk Motif Discovery
  • An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance
    BMC Bioinformatics, Vol. 9 (07 February 2008), 89.
    by Ana C Casimiro, Susana Vinga, Ana T Freitas, Arlindo L Oliveira
    posted to gene_regulation statistics validation yeast algorithm proj_credo by chad_davis on 2008-02-11 15:05:30 as *** along with 3 people idonaldson xili03 isimpson
  • SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics
    BMC Bioinformatics, Vol. 9 (31 January 2008), 73.
    by Fabrice Touzain, Sophie Schbath, Isabelle D Rennesson, Bertrand Aigle, Gregory Kucherov, Pierre Leblond
    posted to algorithm gene_regulation statistics proj_credo by chad_davis on 2008-02-04 14:02:53 as *** along with 2 people dquest xili03
  • Natural Similarity Measures between Position Frequency Matrices with an Application to Clustering.
    Bioinformatics (2 January 2008)
    by Utz JJ Pape, Sven Rahmann, Martin Vingron
    posted to algorithm clustering gene_regulation statistics proj_credo by chad_davis on 2008-01-31 16:22:47 as **** along with 5 people nklee maximilianh mclarenv csdhwang kmdaily
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean B Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
    posted to experimental gene_regulation networks yeast proj_credo by chad_davis on 2008-01-28 10:24:50 as **** along with 24 people and 8 groups alokm tuck lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee cisevol njcitulike xili03 brant mariakmejia kristallreiner snow_dragon aalibes Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • 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 classification gene_regulation review proj_credo by chad_davis on 2008-01-28 10:22:04 as *** along with 7 people and 2 groups bryankr ana balicea hggr GustavoLacerda svdate kristallreiner structural_bioinformatics Bioinformatics
  • EnsemPro: An ensemble approach to predicting transcription start sites in human genomic DNA sequences.
    Genomics (26 December 2007)
    by Hong, Min, Seonwoo Kim, Jong
    posted to ensemble proj_credo feature_selection gene_regulation by chad_davis on 2008-01-06 10:21:47 as ***** along with 1 person maximilianh
  • Applied bioinformatics for the identification of regulatory elements.
    Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287.
    by WW Wasserman, A Sandelin
    posted to proj_credo gene_regulation review by chad_davis on 2007-12-11 14:02:48 as read along with 16 people and 8 groups icases ana moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen Stew nklee jdiezperezj ArtemPankin mariakmejia isimpson structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
  • Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
    BMC Bioinformatics, Vol. 8 (09 November 2007), 437.
    by Xueping Yu, Jimmy Lin, Donald J Zack, Jiang Qian
    posted to algorithm proj_credo gene_regulation by chad_davis on 2007-11-21 11:03:32 as *** along with 8 people jyuh mikaelhuss nklee maximilianh idonaldson njcitulike bootsy snow_dragon
  • OSCAR: One-class SVM for Accurate Recognition of Cis-elements
    Bioinformatics (5 October 2007), btm473.
    by Bo Jiang, Michael Q Zhang, Xuegong Zhang
    posted to algorithm proj_credo classification feature_selection gene_regulation by chad_davis on 2007-11-19 10:24:43 as read along with 6 people and 1 group cassj tmmurali cabbagezs maximilianh idonaldson isimpson csb_journal_club_public
  • Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by T Okumura, H Makiguchi, Y Makita, R Yamashita, K Nakai
    posted to ensemble gene_regulation web_service proj_credo by chad_davis on 2007-11-16 13:36:52 as ***** along with 1 person jyuh
  • SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
    Bioinformatics, Vol. 15, No. 7-8. (g 1999), pp. 607-611.
    by J Zhu, MQ Zhang
    posted to database proj_credo gene_regulation yeast by chad_davis on 2007-11-09 09:10:32 as read along with 4 people xiaobeizhao lusk nklee njcitulike
  • 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 proj_credo evolution gene_regulation networks yeast by chad_davis on 2007-10-27 13:32:42 as read along with 17 people and 2 groups bryankr aalibes dpollard djkt mikaelhuss lusk cjeans sujaikumar zwang GustavoLacerda Jporci maximilianh cisevol njcitulike emptyhb nklee anka EisenLab cis-regulatory-evolution
  • 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 algorithm download ensemble feature_selection gene_regulation web_service proj_credo by chad_davis on 2007-08-08 12:26:30 as read along with 2 people and 1 group GustavoLacerda nklee Bioinformatics
  • Intrinsic disorder in yeast transcriptional regulatory network.
    Proteins, Vol. 68, No. 3. (15 August 2007), pp. 602-605.
    by GP Singh, D Dash
    posted to disorder gene_regulation networks yeast proj_disocons binding by chad_davis on 2007-08-08 10:30:42 as *** along with 1 person kfm9876
  • 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 Encode Consortium
    posted to annotation classic evolution gene_regulation proj_credo by chad_davis on 2007-07-26 16:13:18 as ** along with 10 people and 2 groups jyuh jfr kengg olympos blobbybirdman shikin fpattyn yevishere elfar eskay Bioinformatics UH - Computational Biology
  • Error bars in experimental biology
    J. Cell Biol., Vol. 177, No. 1. (9 April 2007), pp. 7-11.
    by Geoff Cumming, Fiona Fidler, David L Vaux
    posted to classic classification gene_regulation microarray statistics validation by chad_davis on 2007-06-06 08:37:34 as *** along with 32 people and 5 groups brian ana batallah manduca kuhn Borelli dayjm kristina tny dullhunk rabu lechristophe nelmor jdelcampo fishtank emmahe lisa1 Daria_G devender bmaust cabbagezs natstreet winterschlaefer krokicki loopback007 wilbur tdmckee renatomilani delenca arindrartow jyuh mjoach structural_bioinformatics Bioinformatics VisionLab FlowCytometry Microbial-Ecology
  • Signaling by fibroblast growth factors: the inside story.
    Sci STKE, Vol. 2001, No. 106. (30 October 2001)
    by M Goldfarb
    posted to evolution gene_regulation networks review binding by chad_davis on 2007-03-26 16:35:39 as read
  • Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling.
    J Mol Recognit, Vol. 18, No. 5. (t 2005), pp. 343-384.
    by VN Uversky, CJ Oldfield, AK Dunker
    posted to disorder gene_regulation proj_disocons review by chad_davis on 2006-07-22 17:38:44 as ***** along with 1 person Evangelia
  • Intrinsic disorder in transcription factors.
    Biochemistry, Vol. 45, No. 22. (6 June 2006), pp. 6873-6888.
    by J Liu, NB Perumal, CJ Oldfield, EW Su, VN Uversky, AK Dunker
    posted to disorder gene_regulation proj_disocons by chad_davis on 2006-07-21 13:22:46 as *****
  • EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences
    BMC Bioinformatics, Vol. 7 (13 July 2006), 342.
    by Jianjun Hu, Yifeng D Yang, Daisuke Kihara
    posted to algorithm proj_credo gene_regulation by chad_davis on 2006-07-21 08:15:01 as read along with 1 person dquest
  • 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 Goessling, M Haubrock, R Hehl, K Hornischer, D Karas, AE Kel, Kel OV Margoulis, DU Kloos, S Land, Lewicki B Potapov, H Michael, R Muench, I Reuter, S Rotert, H Saxel, M Scheer, S Thiele, E Wingender
    posted to database proj_credo gene_regulation by chad_davis on 2006-06-19 18:06:41 as read along with 6 people and 1 group aalibes setar GustavoLacerda marti Auger kmdaily Dead 60's
  • TFBS: Computational framework for transcription factor binding site analysis.
    Bioinformatics, Vol. 18, No. 8. (August 2002), pp. 1135-1136.
    by B Lenhard, WW Wasserman
    posted to gene_regulation toolkit proj_credo by chad_davis on 2006-05-11 18:19:21 as read along with 1 person oannes
  • Searching for regulatory elements in human noncoding sequences.
    Curr Opin Struct Biol, Vol. 7, No. 3. (June 1997), pp. 399-406.
    by L Duret, P Bucher
    posted to gene_regulation proj_credo by chad_davis on 2006-05-10 12:02:26 as read along with 1 person lusk
  • Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.
    J Biol, Vol. 2, No. 2. (2003)
    by Z Zhang, M Gerstein
    posted to gene_regulation proj_credo by chad_davis on 2006-05-10 12:01:15 as read
  • CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences.
    Bioinformatics, Vol. 21, No. 23. (1 December 2005), pp. 4304-4306.
    by T Hindemitt, KF Mayer
    posted to gene_regulation proj_credo by chad_davis on 2006-05-09 17:14:08 as read
  • Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
    Science, Vol. 301, No. 5629. (4 July 2003), pp. 71-76.
    by P Cliften, P Sudarsanam, A Desikan, L Fulton, B Fulton, J Majors, R Waterston, BA Cohen, M Johnston
    posted to gene_regulation proj_credo by chad_davis on 2006-05-09 15:56:43 as read along with 4 people and 1 group evaf dquest Eonwe cisevol cis-regulatory-evolution
  • Identification and analysis of eukaryotic promoters: recent computational approaches.
    Trends Genet, Vol. 17, No. 2. (February 2001), pp. 56-60.
    by U Ohler, H Niemann
    posted to proj_credo gene_regulation review by chad_davis on 2006-05-09 15:48:26 as read along with 3 people and 2 groups rklancer ana barry structural_bioinformatics Bioinformatics
  • 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 Regnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to proj_credo gene_regulation review by chad_davis on 2006-05-09 15:47:40 as read along with 25 people and 6 groups bryankr icases ana barry aalibes aprasad jfr tuck lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 ep161302 nuin Stew structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Identifying active transcription factors and kinases from expression data using pathway queries.
    Bioinformatics, Vol. 21, No. Supplement 2. (1 September 2005)
    by Florian Sohler, Ralf Zimmer
    posted to gene_regulation networks by chad_davis on 2005-10-14 15:20:58 as read
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