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yevisheres library [248 articles]

Neue Artikel in yevisheres library ordered by importance.
  • 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
    posted to encode hnf4 motif myc taf1 tss by yevishere on 2008-01-11 00:36:27 as ***** along with 9 people and 2 groups jyuh jfr chad_davis kengg olympos blobbybirdman shikin fpattyn elfar Bioinformatics UH - Computational Biology
  • Quantitative profiling of protein-DNA binding on microarrays.
    Methods Mol Biol, Vol. 338 (2006), pp. 261-280.
    by J Ragoussis, S Field, IA Udalova
    posted to pbm by yevishere on 2008-01-04 00:06:29 as *****
  • Accuracy and reproducibility of protein-DNA microarray technology.
    Adv Biochem Eng Biotechnol, Vol. 104 (2007), pp. 87-110.
    by S Field, I Udalova, J Ragoussis
    posted to pbm by yevishere on 2008-01-04 00:03:46 as *****
  • Hepatocyte nuclear factor 4 alpha ligand binding and F domains mediate interaction and transcriptional synergy with the pancreatic islet LIM HD transcription factor Isl1.
    J Mol Biol, Vol. 364, No. 4. (8 December 2006), pp. 567-581.
    by J Eeckhoute, I Briche, M Kurowska, P Formstecher, B Laine
    posted to hnf4 ligands pancreas by yevishere on 2008-01-03 23:29:59 as *****
  • Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Victor Levitsky, Elena Ignatieva, Elena Ananko, Igor Turnaev, Tatyana Merkulova, Nikolay Kolchanov, T Hodgman
    posted to mining motifs tools by yevishere on 2008-01-08 00:22:02 as **** along with 4 people xili03 nklee maximilianh csdhwang
  • Effects of filtering by Present call on analysis of microarray experiments.
    BMC Bioinformatics, Vol. 7 (2006)
    by JN McClintick, HJ Edenberg
    posted to affymetrix analysis filtering by yevishere on 2008-01-04 00:35:46 as **** along with 2 people ghattem waszak
  • A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.
    Nucleic Acids Res, Vol. 34, No. 20. (2006), pp. 5730-5739.
    by BT Naughton, E Fratkin, S Batzoglou, DL Brutlag
    posted to motifs tools by yevishere on 2008-01-04 00:20:45 as **** along with 3 people and 1 group xili03 indigoviolet nklee EisenLab
  • notes Model-based deconvolution of genome-wide DNA binding.
    Bioinformatics (1 December 2007)
    by David J J Reiss, Marc T T Facciotti, Nitin S S Baliga
    posted to hnf4 motifs by yevishere on 2008-01-03 23:58:02 as **** along with 5 people isimpson vega jyuh djkt idonaldson
  • 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 mining motif by yevishere on 2008-01-03 23:53:02 as **** along with 3 people xili03 dquest lusk
  • Informative priors based on transcription factor structural class improve de novo motif discovery
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392.
    by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J Hartemink
    posted to mining motif by yevishere on 2008-01-03 23:51:50 as **** along with 3 people dquest nklee idonaldson
  • Getting started in tiling microarray analysis.
    PLoS Comput Biol, Vol. 3, No. 10. (26 October 2007), pp. 1842-1844.
    by XS Liu
    posted to chipchip review by yevishere on 2008-01-03 23:44:16 as **** along with 4 people cassj jfr cabbagezs waszak
  • Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes
    BMC Genomics, Vol. 8 (11 April 2007), 99.
    by Diederik van Deursen, Gert-Jan Botma, Hans Jansen, Adrie JM Verhoeven
    posted to genomics hnf4 mining targets by yevishere on 2008-01-03 23:20:00 as **** along with 1 group VUMCGenomics
  • Identification of transcriptional regulators using binding site enrichment analysis.
    In Silico Biol, Vol. 6, No. 6. (2006), pp. 531-544.
    by TM Kim, MH Jung
    posted to enrichment hnf4 mining motif by yevishere on 2008-01-03 23:14:06 as **** along with 1 person heliopais
  • Statistical Significance of quantitative PCR
    BMC Bioinformatics, Vol. 8 (20 April 2007), 131.
    by Yann Karlen, Alan Mcnair, Sebastien Perseguers, Christian Mazza, Nicolas Mermod
    posted to qpcr by yevishere on 2008-06-11 03:44:17 as ** along with 2 people jyuh jfr
  • ZIFIBI: Prediction of DNA binding sites for zinc finger proteins.
    Biochem Biophys Res Commun (3 March 2008)
    by Soo Young Y Cho, Myungguen Chung, Minyoung Park, Sungjin Park, Young Seek S Lee
    posted to mining motifs by yevishere on 2008-03-24 20:57:08 as ** along with 1 person maximilianh
  • Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions
    Genome Biology, Vol. 2, No. 2. (2001), pp. research0004.1-research0004.13.
    by Brian Haab, Maitreya Dunham, Patrick Brown
    posted to microarray pbm by yevishere on 2008-03-14 20:48:53 as **
  • A unified nomenclature system for the nuclear receptor superfamily.
    Cell, Vol. 97, No. 2. (16 April 1999), pp. 161-163.
    by
    posted to nuclear receptor review by yevishere on 2008-01-18 22:18:12 as **
  • Overview of nomenclature of nuclear receptors.
    Pharmacol Rev, Vol. 58, No. 4. (December 2006), pp. 685-704.
    by P Germain, B Staels, C Dacquet, M Spedding, V Laudet
    posted to nuclear receptor review by yevishere on 2008-01-18 22:10:55 as **
  • Genome-Wide Identification of Estrogen Receptor alpha-Binding Sites in Mouse Liver
    Mol Endocrinol, Vol. 22, No. 1. (1 January 2008), pp. 10-22.
    by Hui Gao, Susann Falt, Albin Sandelin, Jan-Ake Gustafsson, Karin Dahlman-Wright
    posted to chipchip er nuclear receptor by yevishere on 2008-01-17 22:19:08 as ** along with 1 person jyuh
  • Functional conservation of Rel binding sites in drosophilid genomes
    Genome Res., Vol. 17, No. 9. (1 September 2007), pp. 1327-1335.
    by Richard R Copley, Maxim Totrov, Jane Linnell, Simon Field, Jiannis Ragoussis, Irina A Udalova
    posted to pbm by yevishere on 2008-01-08 21:48:23 as ** along with 3 people and 2 groups dpollard Stew cisevol EisenLab cis-regulatory-evolution
  • Position dependencies in transcription factor binding sites.
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 933-941.
    by A Tomovic, EJ Oakeley
    posted to mining motifs by yevishere on 2008-01-08 00:29:53 as ** along with 2 people aalibes nklee
  • Evolution of transcription factor DNA binding sites.
    Gene, Vol. 347, No. 2. (14 March 2005), pp. 255-263.
    by EA Kotelnikova, VJ Makeev, MS Gelfand
    posted to mining motifs tool by yevishere on 2008-01-08 00:28:18 as ** along with 4 people and 1 group balajis gpalidwor nklee cisevol cis-regulatory-evolution
  • A survey of DNA motif finding algorithms
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Modan Das, Ho K Dai
    posted to mining motifs review tools by yevishere on 2008-01-08 00:27:21 as ** along with 6 people xili03 brant dquest nklee maximilianh csdhwang
  • TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
    BMC Genomics, Vol. 8 (29 November 2007), 441.
    by Alison P Lee, Yuchen Yang, Sydney Brenner, Byrappa Venkatesh
    posted to mining motifs tools by yevishere on 2008-01-08 00:26:52 as ** along with 3 people jyuh nklee maximilianh
  • Toucan: deciphering the cis-regulatory logic of coregulated genes.
    Nucleic Acids Res, Vol. 31, No. 6. (15 March 2003), pp. 1753-1764.
    by S Aerts, G Thijs, B Coessens, M Staes, Y Moreau, B De Moor
    posted to mining motifs tools by yevishere on 2008-01-08 00:20:26 as ** along with 5 people and 1 group troels_marstrand kaspermunch nur77 nklee xili03 Bioinformatics
  • Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters.
    Bioconjug Chem, Vol. 4, No. 2. (r 1993), pp. 105-111.
    by RB Mujumdar, LA Ernst, SR Mujumdar, CJ Lewis, AS Waggoner
    posted to dutp labeling by yevishere on 2008-01-04 22:04:59 as **
  • Cyanine dye dUTP analogs for enzymatic labeling of DNA probes.
    Nucleic Acids Res, Vol. 22, No. 15. (11 August 1994), pp. 3226-3232.
    by H Yu, J Chao, D Patek, R Mujumdar, S Mujumdar, AS Waggoner
    posted to dutp labeling microarray by yevishere on 2008-01-04 22:04:27 as **
  • Fluorescent high-density labeling of DNA: error-free substitution for a normal nucleotide
    Journal of Biotechnology, Vol. 86, No. 3. (13 April 2001), pp. 237-253.
    by Zeno Foldes-Papp, Bernhard Angerer, Waltraud Ankenbauer, Rudolf Rigler
    posted to dutp labeling microarray by yevishere on 2008-01-04 21:28:10 as **
  • Development of a DNA-Labeling System for Array-Based Comparative Genomic Hybridization
    J Biomol Tech, Vol. 16, No. 2. (1 June 2005), pp. 104-111.
    by Pauline T Lieu, Peter Jozsi, Patrick Gilles, Todd Peterson
    posted to dna labeling microarray by yevishere on 2008-01-04 21:11:29 as **
  • Pre-filtering improves reliability of Affymetrix GeneChips results when used to analyze gene expression in complex tissues.
    Mol Cell Probes (28 November 2007)
    by Dario Greco, Damiana Leo, Umberto di Porzio, Carla Perrone Capano, Petri Auvinen
    posted to affymetrix analysis microarray by yevishere on 2008-01-04 00:34:49 as ** along with 1 person Terkko
  • An overview of image-processing methods for Affymetrix GeneChips.
    Brief Bioinform (5 December 2007)
    by Jose M M Arteaga-Salas, Harry Zuzan, William B B Langdon, Graham J G J Upton, Andrew P P Harrison
    posted to affymetrix analysis by yevishere on 2008-01-04 00:33:28 as ** along with 2 people jfr aswin
  • Quality assessment of Affymetrix GeneChip data.
    OMICS, Vol. 10, No. 3. (2006), pp. 358-368.
    by S Heber, B Sick
    posted to analysis microarray by yevishere on 2008-01-04 00:23:59 as ** along with 3 people bertelsen jfr maldi
  • A survey of motif discovery methods in an integrated framework
    Biology Direct, Vol. 1, No. 1. (06 April 2006), 11.
    by Geir K Sandve, Finn Drabløs
    posted to mining motifs tools by yevishere on 2008-01-04 00:23:12 as ** along with 5 people and 1 group idonaldson aprasad dpollard samal csdhwang EisenLab
  • 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 motifs tools by yevishere on 2008-01-04 00:22:30 as ** along with 3 people and 1 group chad_davis dpollard dquest EisenLab
  • GOstat: find statistically overrepresented Gene Ontologies within a group of genes.
    Bioinformatics, Vol. 20, No. 9. (12 June 2004), pp. 1464-1465.
    by T Beissbarth, TP Speed
    posted to tools by yevishere on 2008-01-04 00:19:57 as ** along with 6 people and 1 group ellakat Yanno miguel RMGraze indigoviolet jdiggans EisenLab
  • Sequence logos: a new way to display consensus sequences.
    Nucleic Acids Res, Vol. 18, No. 20. (25 October 1990), pp. 6097-6100.
    by TD Schneider, RM Stephens
    posted to tools by yevishere on 2008-01-04 00:19:33 as ** along with 3 people and 1 group austin analogAI indigoviolet EisenLab
  • WebLogo: A Sequence Logo Generator
    Genome Res., Vol. 14, No. 6. (1 June 2004), pp. 1188-1190.
    by Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner
    posted to tools by yevishere on 2008-01-04 00:16:26 as ** along with 4 people and 2 groups analogAI indigoviolet xiaobeizhao sobolevnrm EisenLab baker-group
  • Quantitative prediction of NF-kappa B DNA-protein interactions.
    Proc Natl Acad Sci U S A, Vol. 99, No. 12. (11 June 2002), pp. 8167-8172.
    by IA Udalova, R Mott, D Field, D Kwiatkowski
    posted to pbm by yevishere on 2008-01-04 00:11:43 as ** along with 1 person and 2 groups dpollard EisenLab cis-regulatory-evolution
  • Genome-Wide Location and Function of DNA Binding Proteins
    Science, Vol. 290, No. 5500. (22 December 2000), pp. 2306-2309.
    by Bing Ren, Francois Robert, John J Wyrick, Oscar Aparicio, Ezra G Jennings, Itamar Simon, Julia Zeitlinger, Jorg Schreiber, Nancy Hannett, Elenita Kanin, Thomas L Volkert, Christopher J Wilson, Stephen P Bell, Richard A Young
    posted to chipchip by yevishere on 2008-01-04 00:09:31 as ** along with 6 people kristallreiner miguel kaarsinogen johncumbers tvdbulck epigenetics
  • 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 mining motifs by yevishere on 2008-01-04 00:07:13 as ** along with 11 people and 3 groups isimpson ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou idonaldson structural_bioinformatics Bioinformatics EBI-regulation
  • An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.
    Nat Biotechnol, Vol. 20, No. 8. (August 2002), pp. 835-839.
    by XS Liu, DL Brutlag, JS Liu
    posted to motifs by yevishere on 2008-01-04 00:06:49 as ** along with 4 people troels_marstrand opheliav dquest xili03
  • Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
    Nature Genetics, Vol. 36, No. 12. (14 November 2004), 1331.
    by Sonali Mukherjee, Michael F Berger, Ghil Jona, Xun S Wang, Dale Muzzey, Michael Snyder, Richard A Young, Martha L Bulyk
    posted to pbm by yevishere on 2008-01-04 00:05:04 as ** along with 5 people kristallreiner johncumbers olympos nklee emptyhb
  • Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins.
    Methods Mol Biol, Vol. 338 (2006), pp. 245-260.
    by MF Berger, ML Bulyk
    posted to pbm by yevishere on 2008-01-04 00:04:46 as **
  • Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays.
    Methods Enzymol, Vol. 410 (2006), pp. 279-299.
    by ML Bulyk
    posted to pbm by yevishere on 2008-01-04 00:04:26 as **
  • Protein binding microarrays for the characterization of DNA-protein interactions.
    Adv Biochem Eng Biotechnol, Vol. 104 (2007), pp. 65-85.
    by ML Bulyk
    posted to pbm by yevishere on 2008-01-04 00:04:05 as **
  • Immobilization of DNA onto poly(dimethylsiloxane) surfaces and application to a microelectrochemical enzyme-amplified DNA hybridization assay.
    Langmuir, Vol. 20, No. 14. (6 July 2004), pp. 5905-5910.
    by D Liu, RK Perdue, L Sun, RM Crooks
    posted to pbm by yevishere on 2008-01-04 00:00:56 as **
  • Expression of constitutive androstane receptor, hepatic nuclear factor 4 alpha, and P450 oxidoreductase genes determines interindividual variability in basal expression and activity of a broad scope of xenobiotic metabolism genes in the human liver.
    Drug Metab Dispos, Vol. 35, No. 9. (September 2007), pp. 1700-1710.
    by M Wortham, M Czerwinski, L He, A Parkinson, YJ Wan
    posted to drugs hnf4 by yevishere on 2008-01-03 23:59:33 as ** along with 1 person ggeneraux
  • Normalization and experimental design for ChIP-chip data
    BMC Bioinformatics, Vol. 8 (25 June 2007), 219.
    by Shouyong Peng, Artyom A Alekseyenko, Erica Larschan, Mitzi I Kuroda, Peter J Park
    posted to analysis chipchip by yevishere on 2008-01-03 23:58:25 as ** along with 4 people and 2 groups caseybrown jyuh kengg Stew EisenLab Plantandetc
  • Effects of hepatocyte nuclear factor-4alpha on the regulation of the hepatic acute phase response.
    J Mol Biol, Vol. 371, No. 2. (10 August 2007), pp. 323-335.
    by Z Wang, PA Burke
    posted to expresion hnf4 by yevishere on 2008-01-03 23:54:04 as **
  • An equilibrium partitioning model connecting gene expression and cis-motif content
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e368-374.
    by Joe Mellor, Charles Delisi
    posted to mining motif by yevishere on 2008-01-03 23:50:55 as ** along with 1 person and 1 group dpollard EisenLab
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