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blobbybirdman algorithms [79 articles]

Recent papers added to blobbybirdman library classified by the tag algorithms. You can also see everyone's algorithms.
  • A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e126.
    by Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald Breaker, Martin Tompa, Walter L Ruzzo
    posted to algorithms bioinformatics genomics mirna prokaryotes by blobbybirdman on 2007-10-16 19:42:47 as **** along with 4 people sebastien_vigneau zwang lp2 cabbagezs
  • 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
  • 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
  • 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 ***
  • DIGIT: a novel gene finding program by combining gene-finders
    Pac Symp Biocomput (2003), pp. 375-87.
    by T Yada, T Takagi, Y Totoki, Y Sakaki, Y Takaeda
    posted to algorithms gene-prediction integration 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 ***
  • 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 ***
  • 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
  • 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
  • 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 **
  • 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 ***
  • Identification of common molecular subsequences
    J Mol Biol, Vol. 147, No. 1. (1981), pp. 195-7.
    by TF Smith, MS Waterman
    posted to algorithms bioinformatics sequence-alignment by blobbybirdman on 2007-10-09 17:56:35 as ***
  • Discovery of novel transcription factor binding sites by statistical overrepresentation
    Nucleic Acids Res, Vol. 30, No. 24. (2002), pp. 5549-60.
    by S Sinha, M Tompa
    posted to algorithms binding-site-predictions bioinformatics expression-clustering s_cerevisiae by blobbybirdman on 2007-10-09 17:56:35 as ****
  • YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation
    Nucleic Acids Res, Vol. 31, No. 13. (2003), pp. 3586-8.
    by S Sinha, M Tompa
    posted to algorithms binding-site-predictions bioinformatics expression-clustering by blobbybirdman on 2007-10-09 17:56:35 as **
  • PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences
    BMC Bioinformatics, Vol. 5 (2004)
    by S Sinha, M Blanchette, M Tompa
    posted to algorithms binding-site-predictions bioinformatics drosophila evolutionary-comparisons expression-clustering h_sapiens s_cerevisiae statistical by blobbybirdman on 2007-10-09 17:56:35 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 **
  • MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences
    Nucleic Acids Res, Vol. 31, No. 13. (2003), pp. 3518-24.
    by S Schwartz, L Elnitski, M Li, M Weirauch, C Riemer, A Smit, ED Green, RC Hardison, W Miller
    posted to algorithms binding-site-predictions bioinformatics evolutionary-comparisons multiple-alignment by blobbybirdman on 2007-10-09 17:56:35 as ***
  • Transcriptional control in the segmentation gene network of Drosophila
    PLoS Biol, Vol. 2, No. 9. (2004)
    by MD Schroeder, M Pearce, J Fak, H Fan, U Unnerstall, E Emberly, N Rajewsky, ED Siggia, U Gaul
    posted to algorithms binding-site-predictions clustering development drosophila modularity by blobbybirdman on 2007-10-09 17:56:35 as ****
  • Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
    J Mol Biol, Vol. 338, No. 2. (2004), pp. 207-15.
    by A Sandelin, WW Wasserman
    posted to algorithms alignment animals base binding biology computational conformation data factorschemistryclassificationgeneticsmetabolism humans internet mice molecular protein sequence sites transcription 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 **
  • 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 **
  • 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 **
  • 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 **
  • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    Proc Natl Acad Sci U S A, Vol. 102, No. 8. (2005), pp. 2685-9.
    by KR Patil, J Nielsen
    posted to algorithms cerevisiaegeneticsmetabolism genetic nadpmetabolism saccharomyces transcription 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 **
  • Gibbs motif sampling: detection of bacterial outer membrane protein repeats
    Protein Sci, Vol. 4, No. 8. (1995), pp. 1618-32.
    by AF Neuwald, JS Liu, CE Lawrence
    posted to acid algorithms amino animals bacterial chemical colichemistry data escherichia homology human membrane models molecular outer proteinschemistry sequence 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 **
  • 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 **
  • rVISTA 2.0: evolutionary analysis of transcription factor binding sites
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (2004), pp. W217-21.
    by GG Loots, I Ovcharenko
    posted to acid algorithms alignment analysis binding dna dnachemistrymetabolism evolution factorsmetabolism interface internet molecular nucleic regulatory sequence sequences sites software transcription user-computer 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 **
  • A suite of web-based programs to search for transcriptional regulatory motifs
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (2004), pp. W204-7.
    by Y Liu, L Wei, S Batzoglou, DL Brutlag, JS Liu, XS Liu
    posted to acid algorithms binding dnachemistrymetabolism expression factorsmetabolism gene genetic interface internet nucleic regulation regulatory sequences sites software transcription user-computer 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 **
  • 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 **
  • 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 **
  • An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    Proteins, Vol. 7, No. 1. (1990), pp. 41-51.
    by CE Lawrence, AA Reilly
    posted to acid algorithms ampgeneticsmetabolism base binding coligenetics conformation cyclic data dna-binding escherichia information molecular nucleic proteinsgenetics receptors sequence sites statistics systems 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 **
  • Combining frequency and positional information to predict transcription factor binding sites
    Bioinformatics, Vol. 17, No. 11. (2001), pp. 1019-26.
    by SM Kielbasa, JO Korbel, D Beule, J Schuchhardt, H Herzel
    posted to algorithms base binding biology cerevisiaegeneticsmetabolism computational databases dna dnageneticsmetabolism factorsmetabolism fungalgeneticsmetabolism genetic genetics human promoter regions saccharomyces sequence sitesgenetics software transcription bibtex-import by blobbybirdman on 2007-10-09 17:56:25 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 **
  • Subtle motifs: defining the limits of motif finding algorithms
    Bioinformatics, Vol. 18, No. 10. (2002), pp. 1382-90.
    by U Keich, PA Pevzner
    posted to acid acidgenetics algorithms alignmentmethods amino analysis analysismethods and base benchmarking comparative consensus control data dna dnagenetics dnamethods genetic models molecular motifsgenetics mutational nucleic of processes quality regulatory reproducibility results sensitivity sequence sequencegenetics sequences software specificity statistical stochastic study bibtex-import by blobbybirdman on 2007-10-09 17:56:23 as **
  • Finding motifs in the twilight zone
    Bioinformatics, Vol. 18, No. 10. (2002), pp. 1374-81.
    by U Keich, PA Pevzner
    posted to acid acidgenetics algorithms alignmentmethods amino analysis and base benchmarking cerevisiaegeneticsmetabolism coligeneticsmetabolism comparative consensus control data dna-binding dnagenetics dnamethods escherichia geneticsgenetics molecular motifsgenetics nucleic promoter proteinsgenetics quality regions regulatory saccharomyces sensitivity sequence sequencegenetics sequences specificity study bibtex-import by blobbybirdman on 2007-10-09 17:56:23 as **
  • BioOptimizer: a Bayesian scoring function approach to motif discovery
    Bioinformatics, Vol. 20, No. 10. (2004), pp. 1557-64.
    by ST Jensen, JS Liu
    posted to acid