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Tag inside [55 articles]

Recent papers classified by the tag inside.
  • The positive inside rule is not determined by the polarity of the delta psi (transmembrane electrical potential)
    Mol Microbiol, Vol. 29, No. 4. (August 1998), pp. 1125-1127.
    by JL van de Vossenberg, SV Albers, C van der Does, AJ Driessen, W van Klompenburg
    posted to inside positive rule by sulfolob on 2008-03-16 21:52:34 as **
  • Position specific variation in the rate of evolution in transcription factor binding sites.
    BMC Evol Biol, Vol. 3, No. 1. (28 August 2003)
    by AM Moses, DY Chiang, M Kellis, ES Lander, MB Eisen
    posted to inside by lusk on 2007-05-03 17:46:18 as ** along with 6 people and 2 groups emptyhb briann dpollard adepace nklee cisevol EisenLab cis-regulatory-evolution
  • cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster.
    Mol Cell Biol, Vol. 25, No. 9. (May 2005), pp. 3411-3420.
    by MM Kulkarni, DN Arnosti
    posted to inside by lusk on 2007-04-21 18:30:27 as **** along with 2 people and 1 group adepace olympos EisenLab
  • A systems view of Drosophila segmentation
    Genome Biology, Vol. 9 (11 February 2008), 207.
    by Mike Levine
    posted to segmentation inside by lusk on 2008-04-30 04:49:19 as ** along with 1 person grahamc
  • Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.
    Pac Symp Biocomput (2004), pp. 324-335.
    by AM Moses, DY Chiang, MB Eisen
    posted to inside by lusk on 2007-05-03 17:45:55 as ** along with 3 people wenhan eckart_bindewald dquest
  • De novo cis-regulatory module elicitation for eukaryotic genomes
    PNAS, Vol. 102, No. 20. (17 May 2005), pp. 7079-7084.
    by Mayetri Gupta, Jun S Liu
    posted to inside module_inference by lusk on 2007-04-13 20:13:18 as ** along with 3 people and 1 group ihpark tuck indigoviolet EisenLab
  • Gene expression from random libraries of yeast promoters.
    Genetics, Vol. 172, No. 4. (April 2006), pp. 2113-2122.
    by M Ligr, R Siddharthan, FR Cross, ED Siggia
    posted to inside random_library by lusk on 2007-04-21 18:28:38 as ***** along with 1 person tresch
  • Analysis of computational approaches for motif discovery
    Algorithms for Molecular Biology, Vol. 1, No. 1. (19 May 2006), 8.
    by Nan Li, Martin Tompa
    posted to inside review by lusk on 2007-05-03 17:45:28 as ** along with 9 people and 2 groups ana barry tuck chad_davis dquest nklee maximilianh xi03 csdhwang structural_bioinformatics Bioinformatics
  • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.
    J Mol Evol, Vol. 22, No. 2. (1985), pp. 160-174.
    by M Hasegawa, H Kishino, T Yano
    posted to hky inside by lusk on 2007-05-03 17:45:03 as ** along with 2 people AaronDarling Natasha
  • Sequence Context affects the rate of short insertions and deletions in flies and primates
    Genome Biology, Vol. 9 (21 February 2008), R37.
    by Amos Tanay, Eric D Siggia
    posted to deletion insertion inside by lusk on 2008-04-15 02:02:12 as ** along with 5 people aprasad brant djkt biomcgary gjuggler
  • 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-Bosco 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 inside by lusk on 2007-05-03 17:43:35 as ** along with 22 people and 8 groups kristallreiner mariakmejia brant alokm tuck chad_davis lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller nklee cisevol njcitulike xili03 Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • 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 inside by lusk on 2007-05-04 04:00:44 as ** along with 4 people chad_davis xiaobeizhao nklee njcitulike
  • Functional variation and evolution of non-coding DNA
    Current Opinion in Genetics & Development, Vol. 16, No. 6. (December 2006), pp. 559-564.
    by Christine P Bird, Barbara E Stranger, Emmanouil T Dermitzakis
    posted to inside review by lusk on 2007-02-13 23:45:16 as *** along with 7 people and 4 groups dpollard dchughes adepace sujaikumar candypmcg Stew cisevol EisenLab G4ID Genetics-of-Gambling cis-regulatory-evolution
  • The molecular population genetics of regulatory genes
    Molecular Ecology, Vol. 9, No. 10. (2000), pp. 1451-1461.
    by Michael D Purugganan
    posted to inside popgen review by lusk on 2007-02-13 23:43:42 as ***
  • Coherence and Timing of Cell Cycle Start Examined at Single-Cell Resolution
    Molecular Cell, Vol. 21, No. 1. (6 January 2006), pp. 3-14.
    by James M Bean, Eric D Siggia, Frederick R Cross
    posted to flow_cytometry inside by lusk on 2007-05-08 01:30:44 as ***** along with 1 person balabu
  • Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.
    Mol Biol Evol, Vol. 15, No. 7. (July 1998), pp. 910-917.
    by AL Halpern, WJ Bruno
    posted to inside by lusk on 2007-05-03 17:42:54 as ** along with 1 person and 1 group dpollard EisenLab
  • The transcriptional regulatory code of eukaryotic cells - insights from genome-wide analysis of chromatin organization and transcription factor binding
    Current Opinion in Cell Biology, Vol. 18, No. 3. (June 2006), pp. 291-298.
    by Leah O Barrera, Bing Ren
    posted to inside review by lusk on 2007-02-13 23:42:55 as *** along with 4 people and 4 groups dchughes cmm oannes vietanh0 FAB-lab G4ID Regulomics_UCHSC Genetics-of-Gambling
  • Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi.
    PLoS Biol, Vol. 2, No. 12. (9 November 2004)
    by Audrey P P Gasch, Alan M M Moses, Derek Y Y Chiang, Hunter B B Fraser, Mark Berardini, Michael B B Eisen
    posted to inside by lusk on 2007-05-03 17:42:35 as ** along with 4 people and 3 groups mbeisen tsackton nickluscombe cisevol EisenLab EBI-regulation cis-regulatory-evolution
  • Transcriptional regulation of a pair-rule stripe in Drosophila.
    Genes Dev, Vol. 5, No. 5. (May 1991), pp. 827-839.
    by S Small, R Kraut, T Hoey, R Warrior, M Levine
    posted to eve flies inside by lusk on 2008-04-13 01:46:37 as ** along with 1 person and 1 group dpollard EisenLab
  • Conserved sequences and the evolution of gene regulatory signals.
    Curr Opin Genet Dev, Vol. 15, No. 6. (December 2005), pp. 628-633.
    by MD Adams
    posted to inside review by lusk on 2007-04-21 18:12:02 as ** along with 2 people and 1 group dpollard cconboy EisenLab
  • 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 inside review by lusk on 2007-05-03 17:42:03 as ** along with 1 person chad_davis
  • Evolution of cis-regulatory regions versus codifying regions.
    Int J Dev Biol, Vol. 47, No. 7-8. (2003), pp. 665-673.
    by F Rodríguez-Trelles, R Tarrío, FJ Ayala
    posted to inside review by lusk on 2007-02-13 23:36:06 as ***
  • A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
    BMC Evolutionary Biology, Vol. 6 (22 November 2006), 99.
    by David A Fitzpatrick, Mary E Logue, Jason E Stajich, Geraldine Butler
    posted to fungal_phylogeny inside by lusk on 2007-04-13 19:45:55 as ** along with 3 people and 1 group dpollard stajich cmzmasek EisenLab
  • On the power of profiles for transcription factor binding site detection.
    Stat Appl Genet Mol Biol, Vol. 2 (2003)
    by S Rahmann, T Müller, M Vingron
    posted to inside by lusk on 2007-04-25 21:34:47 as ** along with 1 person bluto
  • MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
    Genome Biol, Vol. 5, No. 12. (2004)
    by AM Moses, DY Chiang, DA Pollard, VN Iyer, MB Eisen
    posted to inside by lusk on 2007-05-03 17:46:39 as ** along with 5 people and 2 groups ihpark tuck indigoviolet Garamonfok cisevol EisenLab cis-regulatory-evolution
  • PhyloScan: Identification of transcription factor binding sites using cross-species evidence
    Algorithms for Molecular Biology, Vol. 2 (23 January 2007), 1.
    by Steven C Carmack, Lee A Mccue, Lee A Newberg, Charles E Lawrence
    posted to identification inside by lusk on 2007-05-03 17:41:41 as ** along with 3 people and 1 group dpollard dquest nklee EisenLab
  • Computational prediction of transcription-factor binding site locations.
    Genome Biol, Vol. 5, No. 1. (2003)
    by ML Bulyk
    posted to inside review by lusk on 2007-05-03 17:41:14 as ** along with 6 people and 1 group aalibes kaarsinogen Stew nklee yevishere xili03 EisenLab
  • Orchestrated response: a symphony of transcription factors for gene control.
    Genes Dev, Vol. 14, No. 20. (15 October 2000), pp. 2551-2569.
    by B Lemon, R Tjian
    posted to inside review by lusk on 2007-02-13 23:32:20 as *** along with 2 people and 3 groups ana nickluscombe structural_bioinformatics Bioinformatics EBI-regulation
  • LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731.
    by M Brudno, CB Do, GM Cooper, MF Kim, E Davydov, ED Green, A Sidow, S Batzoglou,
    posted to alignment inside by lusk on 2007-05-03 17:40:50 as ** along with 12 people and 1 group Neeperando operon balajis dpollard xwbcn dquest adepace hdopazo Garamonfok adijr natstreet nklee EisenLab
  • Extensive low-affinity transcriptional interactions in the yeast genome.
    Genome Res (29 June 2006)
    by Amos Tanay
    posted to inside by lusk on 2007-09-25 03:01:44 as ** along with 6 people and 1 group devin indigoviolet dpollard balicea koller emptyhb EisenLab
  • Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by BC Foat, AV Morozov, HJ Bussemaker
    posted to affinity inside by lusk on 2007-05-02 03:37:15 as ** along with 3 people xili03 dquest yevishere
  • Transcriptional coactivator complexes.
    Annu Rev Biochem, Vol. 70 (2001), pp. 475-501.
    by AM Näär, BD Lemon, R Tjian
    posted to review inside by lusk on 2007-02-13 23:30:32 as *** along with 1 person and 1 group nickluscombe EBI-regulation
  • Constructing transcriptional regulatory networks
    Genes Dev., Vol. 19, No. 13. (1 July 2005), pp. 1499-1511.
    by Alexandre Blais, Brian D Dynlacht
    posted to inside review by lusk on 2007-04-25 21:11:37 as ***** along with 6 people and 2 groups brant balicea xico tabu braingrind jtomasch EisenLab WetBiology
  • Determining the requirements for cooperative DNA binding by Swi5p and Pho2p (Grf10p/Bas2p) at the HO promoter.
    J Biol Chem, Vol. 270, No. 49. (8 December 1995), pp. 29151-29161.
    by RM Brazas, LT Bhoite, MD Murphy, Y Yu, Y Chen, DW Neklason, DJ Stillman
    posted to bibus inside by lusk on 2007-05-03 17:40:23 as **
  • Transcriptional regulation in Drosophila: the post-genome challenge.
    Funct Integr Genomics, Vol. 1, No. 4. (March 2001), pp. 223-234.
    by MD Biggin, R Tjian
    posted to inside review by lusk on 2007-02-13 23:29:27 as ***
  • Computational methods for transcriptional regulation
    Current Opinion in Genetics & Development, Vol. 15, No. 2. (April 2005), pp. 214-221.
    by Eric D Siggia
    posted to inside review by lusk on 2007-04-25 21:08:54 as *****
  • 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 inside by lusk on 2007-04-25 21:47:19 as ** along with 4 people and 1 group chad_davis tuck indigoviolet dquest EisenLab
  • Transcription regulation and animal diversity.
    Nature, Vol. 424, No. 6945. (10 July 2003), pp. 147-151.
    by M Levine, R Tjian
    posted to inside review by lusk on 2007-02-13 23:28:22 as *** along with 6 people and 2 groups brant xico nickluscombe djkt Jporci heliopais WetBiology EBI-regulation
  • Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both.
    Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402.
    by T Vavouri, G Elgar
    posted to inside by lusk on 2007-05-03 17:49:54 as ** along with 6 people and 2 groups brant troels_marstrand kaspermunch dpollard adepace Stew Bioinformatics EisenLab
  • Regulatory diversity among metazoan co-activator complexes.
    Nat Rev Mol Cell Biol, Vol. 5, No. 5. (May 2004), pp. 403-410.
    by DJ Taatjes, MT Marr, R Tjian
    posted to inside review by lusk on 2007-02-13 23:27:57 as ***
  • Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA.
    EMBO J, Vol. 17, No. 21. (2 November 1998), pp. 6327-6336.
    by PL Blaiseau, D Thomas
    posted to bibus inside by lusk on 2007-05-03 17:39:57 as **
  • Improved tools for biological sequence comparison.
    Proc Natl Acad Sci U S A, Vol. 85, No. 8. (April 1988), pp. 2444-2448.
    by WR Pearson, DJ Lipman
    posted to inside by lusk on 2007-04-25 21:45:51 as ** along with 8 people and 2 groups Ema arcticrasta ffranca gurkanbebek bsmagic CitoJam cjeans sujaikumar Bioinformatics bioinplant
  • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
    J Mol Biol, Vol. 193, No. 4. (20 February 1987), pp. 723-750.
    by OG Berg, PH von Hippel
    posted to bibus inside by lusk on 2007-05-03 17:39:37 as ** along with 7 people and 2 groups zambujo brant jjray indigoviolet discreteonyxorb cisevol Ema EisenLab cis-regulatory-evolution
  • DNA binding sites: representation and discovery.
    Bioinformatics, Vol. 16, No. 1. (January 2000), pp. 16-23.
    by GD Stormo
    posted to inside review by lusk on 2007-05-03 17:49:30 as ** along with 5 people kaarsinogen mbj dquest ezralanglois xili03
  • Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
    Proc Int Conf Intell Syst Mol Biol, Vol. 2 (1994), pp. 28-36.
    by TL Bailey, C Elkan
    posted to bibus inside by lusk on 2007-05-03 17:39:10 as ** along with 1 person dquest
  • Doxycycline, the drug used to control the tet-regulatable promoter system, has no effect on global gene expression in Saccharomyces cerevisiae.
    Yeast, Vol. 22, No. 7. (May 2005), pp. 565-569.
    by JA Wishart, A Hayes, L Wardleworth, N Zhang, SG Oliver
    posted to inside methods by lusk on 2007-04-17 21:23:32 as **
  • Basic local alignment search tool.
    J Mol Biol, Vol. 215, No. 3. (5 October 1990), pp. 403-410.
    by SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman
    posted to bibus inside by lusk on 2007-05-03 17:38:42 as ** along with 41 people and 5 groups granujilla benwei ashaytan camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti hervelequere dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
  • A probabilistic method to detect regulatory modules.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by S Sinha, E van Nimwegen, ED Siggia
    posted to inside by lusk on 2007-05-03 17:49:04 as ** along with 3 people and 2 groups indigoviolet dquest cisevol EisenLab cis-regulatory-evolution
  • PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.
    BMC Bioinformatics, Vol. 5 (28 October 2004)
    by S Sinha, M Blanchette, M Tompa
    posted to inside by lusk on 2007-05-03 17:48:44 as ** along with 4 people eckart_bindewald dquest adsmitty xili03
  • PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
    PLoS Comput Biol, Vol. 1, No. 7. (December 2005)
    by R Siddharthan, ED Siggia, E van Nimwegen
    posted to inside by lusk on 2007-05-03 17:48:21 as ** along with 11 people and 3 groups isimpson ana postrational dquest AaronDarling nickluscombe noano adsmitty lilou idonaldson yevishere structural_bioinformatics Bioinformatics EBI-regulation
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