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blobbybirdman us [92 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 **
  • REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
    Nucleic Acids Res, Vol. 31, No. 13. (2003), pp. 3487-90.
    by C Roven, HJ Bussemaker
    posted to acid algorithms analysis analysismethods animals array binding cerevisiaegeneticsmetabolism database design dna drosophila expression factorsmetabolism gene genetic govt internet management melanogastergeneticsmetabolism messengermetabolism nucleic oligonucleotide phs profilingmethods regression regulatory rna saccharomyces sequence sequences sites software support systems transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:34 as **
  • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    Nat Biotechnol, Vol. 16, No. 10. (1998), pp. 939-45.
    by FP Roth, JD Hughes, PW Estep, GM Church
    posted to acid cerevisiaegeneticsgrowth cloning development dnagenetics expression fungal galactosemetabolism gene glucosemetabolism govt messengergenetics molecular non-phs nucleic peptidesgenetics regulation regulatory rna saccharomyces sequences support us bibtex-import by blobbybirdman on 2007-10-09 17:56:34 as **
  • The relative importance of transcriptional and post transcriptional regulation of Drosophila chorion gene expression during oogenesis
    Dev Genet, Vol. 12, No. 3. (1991), pp. 196-205.
    by CP Romano, Martinez JC Cruzado, FC Kafatos
    posted to animals blotting chorionmetabolism densitometry development dnaanalysis drosophila expression gene genetic govt iimetabolism mapping melanogastergeneticsgrowth oogenesisgenetics phs polymerase regulation research restriction rna rnaanalysis southern support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:33 as **
  • Transcriptional enhancer activity of hr5 requires dual-palindrome half sites that mediate binding of a dimeric form of the baculovirus transregulator IE1
    J Virol, Vol. 69, No. 9. (1995), pp. 5368-75.
    by SM Rodems, PD Friesen
    posted to animals base binding cell chain competitive data dna dna-binding elements enhancer expression gene genetics govt immediate-early line molecular nucleopolyhedrovirusgeneticsmetabolism nucleusmetabolism phs plasmids polymerase primers probes promoter proteins proteinschemistrymetabolism reaction regions regulation research sequence sites spodoptera support trans-activation trans-activatorschemistrymetabolism us viral viralmetabolism bibtex-import by blobbybirdman on 2007-10-09 17:56:33 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 **
  • 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 **
  • A complete second gut induced by transplanted micromeres in the sea urchin embryo
    Science, Vol. 259, No. 5098. (1993), pp. 1134-8.
    by A Ransick, EH Davidson
    posted to animals blastomeresphysiologytransplantation cell differentiation digestive division ectodermcytologyphysiology embryo gastrulacytologyphysiology govt nonmammaliancytologyphysiology phs research sea support systemcytologyembryology urchinsembryology us bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • Micromeres are required for normal vegetal plate specification in sea urchin embryos
    Development, Vol. 121, No. 10. (1995), pp. 3215-22.
    by A Ransick, EH Davidson
    posted to animals biological blastomerescytologyphysiology embryo embryonic gastrulacytologyphysiology govt induction models morphogenesis nonmammalianphysiology phs research sea support urchinsembryology us bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
    BMC Bioinformatics, Vol. 3, No. 1. (2002)
    by N Rajewsky, M Vergassola, U Gaul, ED Siggia
    posted to acid algorithms amino animals binding biologymethods body chromosome comparative computational consensus developmentalgenetics drosophila expression gene geneticgenetics genomicsmethods govt mappingmethods melanogasterembryologygenetics motifs non-phs patterninggenetics phs proteinsgenetics regulation research sequence sitesgenetics software study support trans-activatorsgeneticsmetabolism transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:32 as **
  • Classification and knowledge discovery in protein databases
    J Biomed Inform, Vol. 37, No. 4. (2004), pp. 224-39.
    by P Radivojac, NV Chawla, AK Dunker, Z Obradovic
    posted to algorithms alignmentmethods analysis and artificial automatedmethods cluster comparative database databases govt information intelligence management non-phs of pattern phs protein proteinmethods proteinsanalysischemistryclassification recognition reproducibility research results retrievalmethods sensitivity sequence specificity storage study support systems us 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 **
  • 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 **
  • Coregulator-dependent facilitation of chromatin occupancy by GATA-1
    Proc Natl Acad Sci U S A, Vol. 101, No. 4. (2004), pp. 980-5.
    by S Pal, AB Cantor, KD Johnson, TB Moran, ME Boyer, SH Orkin, EH Bresnick
    posted to carrier cell chain chromatinmetabolism dna-binding factorsgeneticsphysiology genetic govt line nuclear phs polymerase proteinsgeneticsphysiology proteinsphysiology reaction research reverse support transcriptase transcription transformed us bibtex-import by blobbybirdman on 2007-10-09 17:56:30 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 **
  • Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
    Nucleic Acids Res, Vol. 29, No. 3. (2001), pp. 774-82.
    by L Mccue, W Thompson, C Carmack, MP Ryan, JS Liu, V Derbyshire, CE Lawrence
    posted to acid alignment bacterial bacterialgenetics bacterialgeneticsmetabolism base binding coligenetics databases dna escherichia factorsmetabolism factual gammaproteobacteriagenetics genes genome govt homology nucleic phs phylogeny protein sequence sitesgenetics support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:29 as **
  • A regulatory code for neurogenic gene expression in the Drosophila embryo
    Development, Vol. 131, No. 10. (2004), pp. 2387-94.
    by M Markstein, R Zinzen, P Markstein, KP Yee, A Erives, A Stathopoulos, M Levine
    posted to animals anophelesgenetics base chain cloning data developmentalgenetics drosophila ectodermphysiology elements embryo enhancer expression factorsgenetics gene geneticsgenetics govt male melanogasterembryologygenetics mesodermphysiology molecular mutagenesis nervous nonmammalianphysiology phs polymerase proteinsgenetics reaction regulation regulationgenetics repressor research sequence support systemembryology transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:28 as **
  • Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo
    Proc Natl Acad Sci U S A, Vol. 99, No. 2. (2002), pp. 763-8.
    by M Markstein, P Markstein, V Markstein, MS Levine
    posted to animals base binding dnageneticsmetabolism drosophila drosophilaembryologygeneticsmetabolism factors family female genes genetically genome govt homeodomain hybridization in insect lac male modified multigene nuclear operon phosphoproteinsmetabolism phs proteins proteinsgenetics proteinsmetabolism repressor research sequence sitesgenetics situ support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:28 as **
  • Decoding cis-regulatory DNAs in the Drosophila genome
    Curr Opin Genet Dev, Vol. 12, No. 5. (2002), pp. 601-6.
    by M Markstein, M Levine
    posted to acid animals binding biology body computational drosophila factorsmetabolism family genes genetic genetics genome govt insect melanogasterembryologygeneticsmetabolism multigene nucleic patterninggenetics phs promoter regions regulator regulatory research sequences sitesgenetics support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:28 as **
  • rVista for comparative sequence-based discovery of functional transcription factor binding sites
    Genome Res, Vol. 12, No. 5. (2002), pp. 832-9.
    by GG Loots, I Ovcharenko, L Pachter, I Dubchak, EM Rubin
    posted to animals base binding biologymethods comparative computational cytokineschemistrygenetics factorschemistrygenetics familygenetics geneticsgenetics govt human mice multigene non-phs phs promoter regions sequencegenetics sitesgenetics software study support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:28 as **
  • Definition and prediction of the full range of transcription factor binding sites--the hepatocyte nuclear factor 1 dimeric site
    Nucleic Acids Res, Vol. 30, No. 17. (2002), pp. 3809-17.
    by J Locker, D Ghosh, PV Luc, J Zheng
    posted to algorithms assay base binding competitive dna-binding electrophoretic factorsgeneticsmetabolism govt mobility nuclear oligonucleotidesgeneticsmetabolism phs protein proteins research sequence shift sitesgenetics support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:27 as **
  • An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
    Nat Biotechnol, Vol. 20, No. 8. (2002), pp. 835-9.
    by XS Liu, DL Brutlag, JS Liu
    posted to algorithms analysismethods and array base binding biologymethods cerevisiae cerevisiaegenetics chromatingeneticsmetabolism computational dna-binding dnageneticsmetabolism elementsgenetics expression factors factorsmetabolism fungalgenetics gene genes govt internet non-phs oligonucleotide phs precipitin protein proteinsmetabolism regulation response saccharomyces sensitivity sequence sites software specificity support telomere-binding telomeregeneticsmetabolism testsmethods time transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:27 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 **
  • Transcription regulation and animal diversity
    Nature, Vol. 424, No. 6945. (2003), pp. 147-51.
    by M Levine, R Tjian
    posted to acid animals chromatinphysiology dna ecosystem expression factorsphysiology gene genetic govt human nucleic phs regulation regulatory sequences support transcription us bibtex-import by blobbybirdman on 2007-10-09 17:56:26 as **
  • Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment
    Science, Vol. 262, No. 5131. (1993), pp. 208-14.
    by CE Lawrence, SF Altschul, MS Boguski, JS Liu, AF Neuwald, JC Wootton
    posted to acid algorithms alignmentmethods amino carrier data govt helix-loop-helix isoprenylation models molecular motifs phs protein proteinschemistry secondary sequence software statistical structure support transferaseschemistry us bibtex-import by blobbybirdman on 2007-10-09 17:56:26 as **
  • In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment
    Methods, Vol. 19, No. 3. (1999), pp. 425-33.
    by MH Kuo, CD Allis
    posted to cell chromatinchemistry cross-linking dna-binding govt nucleuschemistry phs precipitin proteinsanalysisisolation purification reagents research support testsmethods us yeastsgenetics bibtex-import by blobbybirdman on 2007-10-09 17:56:25 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 **
  • Direct study of DNA-protein interactions in repressed and active chromatin in living cells
    Embo J, Vol. 15, No. 22. (1996), pp. 6290-300.
    by MP Kladde, M Xu, RT Simpson
    posted to cerevisiaemetabolism chain chromatinchemistry cytosinemetabolism cytosine-specificmetabolism dna dna-binding dnametabolism estrogenmetabolism estrogenspharmacology expression footprinting gene geneticsgenetics govt methylation methyltransferase nucleosomesmetabolism phs polymerase promoter proteinsgenetics proteinsmetabolism reaction receptors regions regulationgenetics repressor research saccharomyces site-specific support us bibtex-import by blobbybirdman on 2007-10-09 17:56:25 as **
  • Identification of regulatory elements using a feature selection method
    Bioinformatics, Vol. 18, No. 9. (2002), pp. 1167-75.
    by S Keles, M van der Laan, MB Eisen
    posted to acid amino analysis analysismethods and array base carlo cerevisiaegenetics data dnamethods expression gene genetic govt method mitosisgenetics models molecular monte motifsgenetics of oligonucleotide pattern phs recognition regulationgenetics reproducibility results saccharomyces sensitivity sequence specificity statistical support us 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