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blobbybirdman non-us [87 articles]

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  • Operons in Escherichia coli: genomic analyses and predictions
    Proc Natl Acad Sci U S A, Vol. 97, No. 12. (2000), pp. 6652-7.
    by H Salgado, Moreno G Hagelsieb, TF Smith, Collado J Vides
    posted to bacterial coligenetics escherichia genetic genome govt non-phs non-us operon research support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:34 as **
  • Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA
    In Silico Biol, Vol. 1, No. 1. (1998), pp. 21-8.
    by E Roulet, I Fisch, T Junier, P Bucher, N Mermod
    posted to algorithms base binding biological computer dnageneticsmetabolism factorsmetabolism govt humans in models non-us research sequence simulation sitesgenetics software support transcription vitro bibtex-import by blobbybirdman on 2007-10-09 17:56:34 as **
  • High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites
    Nat Biotechnol, Vol. 20, No. 8. (2002), pp. 831-5.
    by E Roulet, S Busso, AA Camargo, AJ Simpson, N Mermod, P Bucher
    posted to base binding biological biologymethods ccaat-enhancer-binding computational computer consensus dna-binding dnageneticsmetabolism elementsgenetics expression factorsmetabolism gene genome genomicsmethods govt ligands models non-us protein proteinsmetabolism regulation research response sequence sequencegenetics simulation sites specificity substrate support transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:34 as **
  • A role for activator-mediated TFIIB recruitment in diverse aspects of transcriptional regulation
    Curr Biol, Vol. 5, No. 5. (1995), pp. 508-16.
    by SG Roberts, B Choy, SS Walker, YS Lin, MR Green
    posted to expression factor factorsphysiology gene genetic govt mutation non-us phs regulation research support tfiib trans-activatorsclassificationphysiology transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • Reverse engineering of regulatory networks: simulation studies on a genetic algorithm approach for ranking hypotheses
    Biosystems, Vol. 66, No. 1-2. (2002), pp. 31-41.
    by D Repsilber, H Liljenstrom, SG Andersson
    posted to algorithms engineering expression gene genetic govt models non-us regulation research support bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • Genome-wide location and function of DNA binding proteins
    Science, Vol. 290, No. 5500. (2000), pp. 2306-9.
    by B Ren, F Robert, JJ Wyrick, O Aparicio, EG Jennings, I Simon, J Zeitlinger, J Schreiber, N Hannett, E Kanin, TL Volkert, CJ Wilson, SP Bell, RA Young
    posted to analysis array binding cell cerevisiae cerevisiaegeneticsmetabolismphysiology cycle dna dna-binding expression factorsmetabolism fungal fungalgeneticsmetabolism galactosemetabolism gene genes genetics genome govt non-us oligonucleotide peptidespharmacology phs profiling promoter proteins proteinsmetabolism regions regulation research saccharomyces sequence sites support trans-activation transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors
    Methods Enzymol, Vol. 376 (2004), pp. 304-15.
    by B Ren, BD Dynlacht
    posted to analysis animals array chain chromatingeneticsmetabolism cross-linking dna-binding expression factorsgeneticsmetabolism gene genetics genome govt humans mammalsgenetics non-us oligonucleotide polymerase precipitin profiling promoter proteinsmetabolism reaction reagentsmetabolism regions research sequence support testsmethods transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data
    Nucleic Acids Res, Vol. 23, No. 23. (1995), pp. 4878-84.
    by K Quandt, K Frech, H Karas, E Wingender, T Werner
    posted to analysismethods base consensus conserved data govt molecular non-us sequence software support bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • Motif discovery in heterogeneous sequence data
    Pac Symp Biocomput (2004), pp. 348-59.
    by A Prakash, M Blanchette, S Sinha, M Tompa
    posted to algorithms analysis animals binding biology caenorhabditis computational data dnastatistics elegansgenetics genes genetic genomicsstatistics govt helminth models non-phs non-us numerical phs regulator research sequence sitesgenetics support us bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins
    Bioinformatics, Vol. 15, No. 7-8. (1999), pp. 687-703.
    by MP Ponomarenko, JV Ponomarenko, AS Frolov, NL Podkolodny, LK Savinkova, NA Kolchanov, GC Overton
    posted to acid algorithms animals base binding box chemistry computer conformation data databases dnachemistrygeneticsmetabolism factorsgeneticsmetabolism factual govt human molecular mutation myogenic non-us nucleic phs physical proteinsmetabolism regulatory sequence sitesgenetics support systems tata us bibtex-import by blobbybirdman on 2007-10-09 17:56:31 as **
  • Bilaterian origins: significance of new experimental observations
    Dev Biol, Vol. 219, No. 1. (2000), pp. 1-17.
    by KJ Peterson, RA Cameron, EH Davidson
    posted to animals annelida biological chordata development developmental echinodermata evolution expression family gene genes govt homeobox invertebratesgeneticsgrowth models mollusca multigene non-phs non-us nonvertebrate phs phylogeny regulation research support us bibtex-import by blobbybirdman on 2007-10-09 17:56:31 as **
  • Design superiority of palindromic DNA sites for site-specific recognition of proteins: tests using protein stitchery
    Proc Natl Acad Sci U S A, Vol. 90, No. 11. (1993), pp. 4892-6.
    by C Park, JL Campbell, 3rd
    posted to acid amino base binding comparative conformation data dna-binding dnageneticsmetabolism gene genes govt homology jun leucine macromolecular models molecular non-phs non-us nucleic oligodeoxyribonucleotideschemical oncogene p65gag-jungeneticsmetabolism peptideschemical protein proteinsgeneticsmetabolism rearrangement research secondary sequence sites structural structure study substances support synthesismetabolism us zippersgeneticsphysiology bibtex-import by blobbybirdman on 2007-10-09 17:56:31 as **
  • Dosage sensitivity and the evolution of gene families in yeast
    Nature, Vol. 424, No. 6945. (2003), pp. 194-7.
    by B Papp, C Pal, LD Hurst
    posted to binding cerevisiae cerevisiaegeneticsphysiology dosage evolution family fungal gene genes genetic govt heterozygote macromolecular models molecular multigene mutagenesis non-us protein proteinsgenetics research saccharomyces substances support bibtex-import by blobbybirdman on 2007-10-09 17:56:31 as **
  • Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers
    Genome Res, Vol. 12, No. 3. (2002), pp. 470-81.
    by DA Papatsenko, VJ Makeev, AP Lifanov, M Regnier, AG Nazina, C Desplan
    posted to acidgenetics algorithms animals bacterial base binding chromosome coli comparative data developmentalgenetics dna-binding drosophila elements enhancer escherichia expression factors familygenetics gene genes geneticsgenetics govt homeodomain insectgenetics mappingmethodsstatistics melanogastergenetics molecular multigene non-phs non-us nucleic numerical phs proteins proteinsgenetics protozoan regulation regulatory repeat research sequence sequences sequencesgenetics sitesgenetics structural study support tandem transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:30 as **
  • Simulating evolution by gene duplication
    Genetics, Vol. 115, No. 1. (1987), pp. 207-13.
    by T Ohta
    posted to alleles crossing evolution family frequency gene genetic genetics govt models multigene non-us over research selection support bibtex-import by blobbybirdman on 2007-10-09 17:56:30 as **
  • Location analysis of DNA-bound proteins at the whole-genome level: untangling transcriptional regulatory networks
    Bioessays, Vol. 23, No. 6. (2001), pp. 473-6.
    by B Nal, E Mohr, P Ferrier
    posted to cerevisiaegenetics dna-binding dnachemistrygeneticsmetabolism factorsmetabolism fungal genome govt non-us proteinsmetabolism research saccharomyces support transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:30 as **
  • A powerful non-homology method for the prediction of operons in prokaryotes
    Bioinformatics, Vol. 18 Suppl 1 (2002), pp. S329-36.
    by Moreno G Hagelsieb, Collado J Vides
    posted to acid algorithms amino analysis bacteriagenetics bacterial bacterialgenetics base cells chromosome comparative data dnamethods expression factorsgenetics gene genome govt homology mappingmethods molecular non-us operongenetics profilingmethods prokaryotic regulation research sequence study support transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:30 as **
  • Phosphorylation-independent bacterial chemoresponses correlate with changes in the cytoplasmic level of fumarate
    J Bacteriol, Vol. 178, No. 23. (1996), pp. 6882-7.
    by M Montrone, D Oesterhelt, W Marwan
    posted to acid bacterial benzoatespharmacology benzoic chemotaxisdrug coligeneticsmetabolismphysiology cytoplasmmetabolism deletion effects enzyme escherichia fumarate fumaratesmetabolism gene govt hydrataseantagonists indolespharmacology inhibitorsgeneticsmetabolism inhibitorspharmacology membrane non-us oxidation-reduction phosphorylation proteins proteinsmetabolism research signal support transduction bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • Regulation of switching frequency and bias of the bacterial flagellar motor by CheY and fumarate
    J Bacteriol, Vol. 180, No. 13. (1998), pp. 3375-80.
    by M Montrone, M Eisenbach, D Oesterhelt, W Marwan
    posted to arabinosepharmacology bacterial chemotaxis colidrug deletion effectsgeneticsphysiology escherichia factors flagellaphysiology fumaratespharmacology gene genotype govt kinetics membrane non-us proteins proteinsbiosynthesisgeneticsmetabolism research support time bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
    Bioinformatics, Vol. 22, No. 5. (2006), pp. 637-40.
    by SB Montgomery, OL Griffith, MC Sleumer, CM Bergman, M Bilenky, ED Pleasance, Y Prychyna, X Zhang, SJ Jones
    posted to binding database databases documentationmethods expression factorsgenetics gene genetic geneticsgenetics govt internet language management natural non-us periodicals processing promoter protein regions regulationgenetics research sites support systems transcription variation bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • Deciphering genetic regulatory codes: a challenge for functional genomics
    Proc Natl Acad Sci U S A, Vol. 99, No. 2. (2002), pp. 546-8.
    by AM Michelson
    posted to algorithms animals binding developmental drosophila elements enhancer expression factorsmetabolism gene genes genetic genetics genomics govt insect melanogasterembryologygenetics models non-us regulation regulator research sitesgenetics support transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
    Genome Res, Vol. 10, No. 6. (2000), pp. 744-57.
    by AM Mcguire, JD Hughes, GM Church
    posted to acid alignment bacterial bacterialanalysis biology comparative computational conserved dna expression gene genes genome govt homology non-phs non-us nucleic regulation regulatory sequence sequencegenetics sequences structural study support us bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • TRANSFAC: transcriptional regulation, from patterns to profiles
    Nucleic Acids Res, Vol. 31, No. 1. (2003), pp. 374-8.
    by V Matys, E Fricke, R Geffers, E Gossling, M Haubrock, R Hehl, K Hornischer, D Karas, AE Kel, Kel OV Margoulis, DU Kloos, S Land, Lewicki B Potapov, H Michael, R Munch, I Reuter, S Rotert, H Saxel, M Scheer, S Thiele, E Wingender
    posted to animals binding cellsmetabolism databases developmental distribution eukaryotic expression factorsgeneticsmetabolism gene genetic genetics govt human mice non-us profiling promoter regions regulation saccharomycesgeneticsmetabolism sites support tissue transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • Theory of time-resolved somatic complementation and its use to explore the sporulation control network in Physarum polycephalum
    Genetics, Vol. 164, No. 1. (2003), pp. 105-15.
    by W Marwan
    posted to animals data dominant factors genes govt interpretation kinetics light mutation non-us physarum polycephalumgeneticsphysiology protozoan recessive spores statistical support time bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • Detecting functional interactions in a gene and signaling network by time-resolved somatic complementation analysis
    Bioessays, Vol. 25, No. 10. (2003), pp. 950-60.
    by W Marwan
    posted to animals biological cell complementation factors fusion genes genetic genetically govt models modified mutation non-us physarum polycephalumgenetics regulator signal support test time transduction bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    Pac Symp Biocomput (2001), pp. 127-38.
    by X Liu, DL Brutlag, JS Liu
    posted to alignmentstatistics amp analysisstatistics array bacillus base binding box cerevisiaegeneticsmetabolism chains coligeneticsmetabolism conserved cyclic data dnageneticsmetabolism escherichia expression gene genes genetic govt gtp-binding markov models non-phs non-us numerical oligonucleotide phs profilingstatistics proteinmetabolism proteinsmetabolism rap1 receptor regulator saccharomyces sequence sites software subtilisgeneticsmetabolism support tata us bibtex-import by blobbybirdman on 2007-10-09 17:56:27 as **
  • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    Nat Genet, Vol. 28, No. 4. (2001), pp. 327-34.
    by JD Lieb, X Liu, D Botstein, PO Brown
    posted to binding bindingphysiology cerevisiae cerevisiaegeneticsmetabolism chromosome deacetylasesmetabolism dna dna-binding dnametabolism expression framesphysiology fungal fungalphysiology gene genes geneticsphysiology genome glycolysisgenetics govt histone iimetabolism information intergenicmetabolism mappingmethods non-phs non-us open physical polymerase promoter protein proteins proteinsgenetics proteinsmetabolism reading regions regulationphysiology regulator research ribosomal rna saccharomyces silent sirtuins sitesgenetics support telomeremetabolism trans-activatorsmetabolism us bibtex-import by blobbybirdman on 2007-10-09 17:56:26 as **
  • Identification of the binding sites of regulatory proteins in bacterial genomes
    Proc Natl Acad Sci U S A, Vol. 99, No. 18. (2002), pp. 11772-7.
    by H Li, V Rhodius, C Gross, ED Siggia
    posted to algorithms bacterial base binding dna factorsmetabolism genome govt non-phs non-us phs proteinsmetabolism research sequence sites support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:26 as **
  • Apollo: a sequence annotation editor
    Genome Biol, Vol. 3, No. 12. (2002)
    by SE Lewis, SM Searle, N Harris, M Gibson, V Lyer, J Richter, C Wiel, L Bayraktaroglir, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smithy, JL Tupy, GM Rubin, S Misra, CJ Mungall, ME Clamp
    posted to acid animals database databases design govt human interface management non-us nucleic phs software support systems us user-computer bibtex-import by blobbybirdman on 2007-10-09 17:56:26 as **
  • Enrichment of regulatory signals in conserved non-coding genomic sequence
    Bioinformatics, Vol. 17, No. 10. (2001), pp. 871-7.
    by S Levy, S Hannenhalli, C Workman
    posted to algorithms alignmentstatistics analysis animals binding biology computational conserved data dnageneticsmetabolism dnastatistics factorsmetabolism genes genetic genome govt human mice models non-us numerical regulator sequence sitesgenetics support transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:26 as **
  • Transcription regulatory regions database (TRRD): its status in 2000
    Nucleic Acids Res, Vol. 28, No. 1. (2000), pp. 298-301.
    by NA Kolchanov, OA Podkolodnaya, EA Ananko, EV Ignatieva, IL Stepanenko, Kel OV Margoulis, AE Kel, TI Merkulova, TN Goryachkovskaya, TV Busygina, FA Kolpakov, NL Podkolodny, AN Naumochkin, IM Korostishevskaya, AG Romashchenko, GC Overton
    posted to acid databases elements enhancer factual genetic genetics govt internet non-us nucleic phs promoter regions regulatory sequences support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:25 as **
  • Transcription Regulatory Regions Database (TRRD):its status in 1999
    Nucleic Acids Res, Vol. 27, No. 1. (1999), pp. 303-6.
    by NA Kolchanov, EA Ananko, OA Podkolodnaya, EV Ignatieva, IL Stepanenko, Kel OV Margoulis, AE Kel, TI Merkulova, TN Goryachkovskaya, TV Busygina, FA Kolpakov, NL Podkolodny, AN Naumochkin, AG Romashchenko
    posted to acidgenetics and animals base binding cell cells databases elements elementsgenetics enhancer eukaryotic expression factorsgenetics factualtrends gene geneticgenetics geneticsgenetics glutathione govt information interface internet line mice non-us nucleic organ peroxidasegenetics promoter regions regulationgenetics regulatory response retrieval russia sequence sequences sites specificity storage support transcription user-computer bibtex-import by blobbybirdman on 2007-10-09 17:56:25 as **
  • COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation
    Nucleic Acids Res, Vol. 28, No. 1. (2000), pp. 311-5.
    by Kel OV Margoulis, AG Romashchenko, NA Kolchanov, E Wingender, AE Kel
    posted to acid database databases expression factual gene genetic govt interface internet management non-us nucleic regulation regulatory sequences support systems transcription user-computer bibtex-import by blobbybirdman on 2007-10-09 17:56:24 as **
  • TRANSCompel: a database on composite regulatory elements in eukaryotic genes
    Nucleic Acids Res, Vol. 30, No. 1. (2002), pp. 332-4.
    by Kel OV Margoulis, AE Kel, I Reuter, IV Deineko, E Wingender
    posted to acid and animals binding cellsmetabolism databases eukaryotic factorsmetabolism genetic genetics govt human information integration internet macromolecular non-us nucleic promoter regions regulatory retrieval sequences sites storage support systems trans-activation transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:24 as **
  • A compilation of composite regulatory elements affecting gene transcription in vertebrates
    Nucleic Acids Res, Vol. 23, No. 20. (1995), pp. 4097-103.
    by OV Kel, AG Romaschenko, AE Kel, E Wingender, NA Kolchanov
    posted to acidgenetics animals base binding data databases dna-binding dnagenetics factors factual geneticgenetics govt molecular non-phs non-us nucleic proteins regulatory sequence sequences sites support transcription us vertebratesgenetics bibtex-import by blobbybirdman on 2007-10-09 17:56:24 as **
  • MATCH: A tool for searching transcription factor binding sites in DNA sequences
    Nucleic Acids Res, Vol. 31, No. 13. (2003), pp. 3576-9.
    by AE Kel, E Gossling, I Reuter, E Cheremushkin, Kel OV Margoulis, E Wingender
    posted to acid algorithms analysis binding dnamethods factorsmetabolism govt interface internet non-us nucleic regulatory sequence sequences sites software support transcription user-computer bibtex-import by blobbybirdman on 2007-10-09 17:56:24 as **
  • Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells
    J Mol Biol, Vol. 288, No. 3. (1999), pp. 353-76.
    by A Kel, Kel O Margoulis, V Babenko, E Wingender
    posted to acid activationgenetics animals ap-1chemistrymetabolism base binding data dna dna-binding expression factor factorschemistrymetabolism gene genetics govt homology human lymphocyte lymphokinesgenetics mice molecular non-us nucleic promoter proteinschemistrymetabolism regions sequence sites support t-lymphocytesimmunology transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:23 as **