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isimpsons library [192 articles]

Neue Artikel in isimpsons Bibliothek.
  • Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features
    BMC Bioinformatics, Vol. 7 (2006)
    by JR Semeiks, A Rizki, MJ Bissell, IS Mian
    posted to must-read ensemble-clustering by isimpson on 2008-10-10 12:16:55 as *****
  • An ensemble framework for clustering protein-protein interaction networks
    Bioinformatics, Vol. 23 (Jul 2007), pp. 29-40.
    by S Asur, D Ucar, S Parthasarathy
    posted to must-read ensemble-clustering by isimpson on 2008-10-10 12:16:55 as *****
  • Ensemble clustering method based on the resampling similarity measure for gene expression data
    Stat Methods Med Res, Vol. 16 (Dec 2007), pp. 539-564.
    by SY Kim, JW Lee
    posted to must-read ensemble-clustering by isimpson on 2008-10-10 12:16:55 as *****
  • Ensemble non-negative matrix factorization methods for clustering protein-protein interactions
    Bioinformatics, Vol. 24 (Aug 2008), pp. 1722-1728.
    by D Greene, G Cagney, N Krogan, P Cunningham
    posted to must-read ensemble-clustering by isimpson on 2008-10-10 12:16:55 as *****
  • Fuzzy ensemble clustering based on random projections for DNA microarray data analysis
    Artif Intell Med (Sep 2008)
    by R Avogadri, G Valentini
    posted to must-read ensemble-clustering by isimpson on 2008-10-10 12:16:55 as *****
  • CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.
    Proc Natl Acad Sci U S A, Vol. 101, No. 33. (17 August 2004), pp. 12114-12119.
    by Q Zhou, WH Wong
    posted to transcription-regulation must-read motifs motif-discovery database by isimpson on 2008-10-09 10:52:02 as ***** along with 3 people and 1 group indigoviolet dpollard ep161302 EisenLab
  • Homotypic regulatory clusters in Drosophila.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 579-588.
    by AP Lifanov, VJ Makeev, AG Nazina, DA Papatsenko
    posted to transcription-regulation must-read motifs motif-discovery database by isimpson on 2008-10-09 10:51:42 as ***** along with 2 people and 1 group indigoviolet tresch EisenLab
  • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
    BMC Bioinformatics, Vol. 3 (24 October 2002)
    by N Rajewsky, M Vergassola, U Gaul, ED Siggia
    posted to transcription-regulation must-read motifs motif-discovery database by isimpson on 2008-10-09 10:51:16 as ***** along with 6 people and 1 group ansobol indigoviolet adepace koller Stew csdhwang EisenLab
  • Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model.
    Genome Res, Vol. 12, No. 7. (July 2002), pp. 1019-1028.
    by MS Halfon, Y Grad, GM Church, AM Michelson
    posted to transcription-regulation must-read motifs motif-discovery database by isimpson on 2008-10-09 10:50:50 as ***** along with 1 person maximilianh
  • Hierarchical Dirichlet Processes
    Journal of the American Statistical Association, Vol. 101 (2006), pp. 1566-1581.
    by Teh Y Whye, Jordan, Beal, Blei
    posted to eccb08 by isimpson on 2008-10-08 11:53:20 as *****
  • Probabilistic Latent Semantic Analysis
    (1999), pp. 289-297.
    by Thomas Hofmann
    posted to eccb08 by isimpson on 2008-10-07 12:40:57 as *****
  • Modeling cellular machinery through biological network comparison
    Nature Biotechnology, Vol. 24, No. 4. (06 April 2006), pp. 427-433.
    by Roded Sharan, Trey Ideker
    posted to eccb08 by isimpson on 2008-10-07 12:33:24 as ***** along with 17 people and 2 groups tmmurali kuhn tuck yas balajis wnpx ma_ko gurkanbebek koller gcalda grahamc massivemayhem karfunkel mingzhi vietanh0 cdeane carlk T_lab ParkinsonLab_at_MaRS
  • Network-based classification of breast cancer metastasis
    Mol Syst Biol, Vol. 3 (16 October 2007)
    by Han-Yu Chuang, Eunjung Lee, Yu-Tsueng Liu, Doheon Lee, Trey Ideker
    posted to eccb08 by isimpson on 2008-10-07 12:26:30 as ***** along with 18 people and 2 groups winterschlaefer ihpark bertelsen jfr kengg frohike mikaelhuss cjeans zwang cerami abhattac shikin oelemento roys ptrobajo dap5087 saman_vp verdicchio Bioinformatics GeneGo
  • Validation and refinement of gene-regulatory pathways on a network of physical interactions.
    Genome Biol, Vol. 6, No. 7. (2005)
    by CH Yeang, HC Mak, S McCuine, C Workman, T Jaakkola, T Ideker
    posted to eccb08 by isimpson on 2008-10-07 12:24:44 as ***** along with 13 people and 1 group hplatero snuppepuppan abhik tmmurali textoris wnpx noano koller ccr cdppublications AlexanderPico carlk jago CDP
  • MaxAlign: maximizing usable data in an alignment
    BMC Bioinformatics, Vol. 8 (28 August 2007), 312.
    by Rodrigo Gouveia-Oliveira, Peter W Sackett, Anders G Pedersen
    posted to eccb08 by isimpson on 2008-10-07 12:22:20 as ***** along with 1 person and 1 group grahamc ParkinsonLab_at_MaRS
  • Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i41-49.
    by Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial
    posted to eccb08 by isimpson on 2008-10-07 12:20:04 as ***** along with 5 people chad_davis druvus nklee sconlan nuin
  • Integration of biological networks and gene expression data using Cytoscape.
    Nat Protoc, Vol. 2, No. 10. (2007), pp. 2366-2382.
    by MS Cline, M Smoot, E Cerami, A Kuchinsky, N Landys, C Workman, R Christmas, I Avila-Campilo, M Creech, B Gross, K Hanspers, R Isserlin, R Kelley, S Killcoyne, S Lotia, S Maere, J Morris, K Ono, V Pavlovic, AR Pico, A Vailaya, PL Wang, A Adler, BR Conklin, L Hood, M Kuiper, C Sander, I Schmulevich, B Schwikowski, GJ Warner, T Ideker, GD Bader
    posted to eccb08 by isimpson on 2008-10-07 12:03:52 as ***** along with 9 people and 1 group emmackinnon yaredo Stew jyuh jfr shikin shung thomaskelder AlexanderPico GeneGo
  • A Systems Approach to Mapping DNA Damage Response Pathways
    Science, Vol. 312, No. 5776. (19 May 2006), pp. 1054-1059.
    by Christopher T Workman, Craig H Mak, Scott Mccuine, Jean-Bosco Tagne, Maya Agarwal, Owen Ozier, Thomas J Begley, Leona D Samson, Trey Ideker
    posted to eccb08 by isimpson on 2008-10-07 11:24:38 as ***** along with 6 people biozhang2001 jfr nirfriedman cconboy koller tmmurali
  • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
    Science, Vol. 292, No. 5518. (4 May 2001), pp. 929-934.
    by T Ideker, V Thorsson, JA Ranish, R Christmas, J Buhler, JK Eng, R Bumgarner, DR Goodlett, R Aebersold, L Hood
    posted to eccb08 by isimpson on 2008-09-23 18:01:20 as ***** along with 11 people and 3 groups snuppepuppan BioGeek dragonrez bpb okarsligil opheliav wnpx gurkanbebek raiyar thomaskelder shikin Bioinformatics steinmetzlab GeneGo
  • Discovering regulatory and signalling circuits in molecular interaction networks.
    Bioinformatics, Vol. 18 Suppl 1 (2002)
    by T Ideker, O Ozier, B Schwikowski, AF Siegel
    posted to eccb08 by isimpson on 2008-09-23 18:00:18 as ***** along with 9 people and 2 groups cswinburne yaredo dragonrez okarsligil lfriedl noano koller frohike carlk kdl Bioinformatics
  • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    Nature (02 January 2008)
    by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul
    posted to transcription-regulation tfbs prediction must-read by isimpson on 2008-09-16 15:24:31 as read along with 14 people and 1 group dakelley tmmurali eckart_bindewald djkt bootsy biomcgary idonaldson roys emptyhb pkharchenko meiklej jrest tresch siebert Jarman Lab
  • Factor analysis for gene regulatory networks and transcription factor activity profiles
    BMC Bioinformatics, Vol. 8 (23 February 2007), 61.
    by Iosifina Pournara, Lorenz Wernisch
    posted to eccb08 by isimpson on 2008-09-12 14:48:16 as ***** along with 7 people akastrin jyuh shigepong lp2 hms kyriakos heliopais
  • An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression.
    Genome Res, Vol. 14, No. 10B. (October 2004), pp. 2041-2047.
    by DN Messina, J Glasscock, W Gish, M Lovett
    posted to transcription-regulation transcription helix-loop-helix genetics genes by isimpson on 2008-09-12 13:00:30 as read along with 5 people and 1 group m9array tabu nickluscombe ale mariakmejia EBI-regulation
  • Drosophila C-terminal binding protein, dCtBP is required for sensory organ prepattern and sharpens proneural transcriptional activity of the GATA factor Pnr.
    Developmental biology (22 August 2008)
    by Biryukova Inna, Heitzler Pascal
    posted to no-tag by isimpson on 2008-09-10 14:01:31 as *** along with 1 group Jarman Lab
  • Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler
    Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 2071-2078.
    by Marco Grzegorczyk, Dirk Husmeier, Kieron D Edwards, Peter Ghazal, Andrew J Millar
    posted to transcription-regulation transcription network models modelling bayesian by isimpson on 2008-09-08 15:44:28 as ***** along with 1 person and 1 group verdicchio Jarman Lab
  • GENETICS: Enhancing Gene Regulation
    Science, Vol. 321, No. 5894. (5 September 2008), pp. 1300-1301.
    by Gregory A Wray, Courtney C Babbitt
    posted to transcription-regulation must-read by isimpson on 2008-09-05 13:24:41 as ***** along with 4 people and 1 group sebastien_vigneau bpcusack Ema gracio BenosLab
  • Human-Specific Gain of Function in a Developmental Enhancer
    Science, Vol. 321, No. 5894. (5 September 2008), pp. 1346-1350.
    by Shyam Prabhakar, Axel Visel, Jennifer A Akiyama, Malak Shoukry, Keith D Lewis, Amy Holt, Ingrid Plajzer-Frick, Harris Morrison, David R Fitzpatrick, Veena Afzal, Len A Pennacchio, Edward M Rubin, James P Noonan
    posted to transcription-regulation regulatory must-read by isimpson on 2008-09-05 13:24:03 as ***** along with 11 people and 1 group Stew shoshin bpcusack emptyhb Zephyrus sebastien_vigneau djkt natstreet maximilianh caseybrown eskay Roswell Cancer Crosstalk
  • Shadow Enhancers as a Source of Evolutionary Novelty
    Science, Vol. 321, No. 5894. (5 September 2008), 1314.
    by Joung-Woo Hong, David A Hendrix, Michael S Levine
    posted to transcription-regulation regulatory regulator must-read by isimpson on 2008-09-05 13:22:43 as ***** along with 12 people and 3 groups emptyhb dlobo sebastien_vigneau Stew bpcusack Ema carlfulp Zephyrus djkt natstreet maximilianh caseybrown GEB Roswell Cancer Crosstalk Jarman Lab
  • On the origin of new genes in Drosophila.
    Genome research (30 July 2008)
    by Qi Zhou, Guojie Zhang, Yue Zhang, Shiyu Xu, Ruoping Zhao, Zubing Zhan, Xin Li, Yun Ding, Shuang Yang, Wen Wang
    posted to genetics evolution drosophila by isimpson on 2008-09-01 17:08:19 as **** along with 1 person and 1 group msierk Jarman Lab
  • DNA binding sites: representation and discovery.
    Bioinformatics, Vol. 16, No. 1. (January 2000), pp. 16-23.
    by GD Stormo
    posted to transcription-regulation review must-read motifs motif-discovery by isimpson on 2008-09-01 16:41:35 as ***** along with 7 people emptyhb kaarsinogen mbj dquest lusk ezralanglois xili03
  • Computational identification of transcriptional regulatory elements in DNA sequence
    Nucl. Acids Res., Vol. 34, No. 12. (19 July 2006), pp. 3585-3598.
    by Debraj Guhathakurta
    posted to transcription-regulation review must-read motifs motif-discovery gene by isimpson on 2008-09-01 16:35:53 as ***** along with 9 people and 1 group tmmurali jfr johncumbers reidy giovanni cabbagezs ankur_iitg vietanh0 xili03 GeschwindLab
  • Seeder: Discriminative Seeding DNA Motif Discovery.
    Bioinformatics (Oxford, England) (21 August 2008)
    by François Fauteux, Mathieu Blanchette, Martina V V Strömvik
    posted to must-read by isimpson on 2008-08-28 16:25:34 as ***** along with 4 people nuin brant maximilianh idonaldson
  • Ultraconservation identifies a small subset of extremely constrained developmental enhancers.
    Nat Genet (6 January 2008)
    by Axel Visel, Shyam Prabhakar, Jennifer A A Akiyama, Malak Shoukry, Keith D D Lewis, Amy Holt, Ingrid Plajzer-Frick, Veena Afzal, Edward M M Rubin, Len A A Pennacchio
    posted to must-read by isimpson on 2008-08-28 16:21:56 as ** along with 5 people Stew maximilianh gjuggler emptyhb bpcusack
  • Altered Molecular Regionalization and Normal Thalamocortical Connections in Cortex-Specific Pax6 Knock-Out Mice
    J. Neurosci., Vol. 28, No. 35. (27 August 2008), pp. 8724-8734.
    by Maria C Pinon, Tran C Tuoc, Ruth Ashery-Padan, Zoltan Molnar, Anastassia Stoykova
    posted to simpson2008 by isimpson on 2008-08-28 10:12:46 as ***
  • Drosophila DLMO is a positive regulator of transcription during thoracic bristle development.
    Genetics (9 August 2008)
    by Shamir Zenvirt, Yael Nevo-Caspi, Sigal Rencus-Lazar, Daniel Segal
    posted to no-tag by isimpson on 2008-08-19 16:57:54 as ** along with 1 group Jarman Lab
  • FlyPNS, a database of the Drosophila embryonic and larval peripheral nervous system.
    BMC developmental biology, Vol. 5 (2005)
    by V Orgogozo, WB Grueber
    posted to drosophila by isimpson on 2008-08-15 11:37:33 as read
  • GIMSAN: A Gibbs motif finder with significance analysis
    Bioinformatics (14 August 2008), btn408.
    by Patrick Ng, Uri Keich
    posted to algorithm must-read prediction tfbs by isimpson on 2008-08-15 11:02:24 as *****
  • Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by O Johansson, W Alkema, WW Wasserman, J Lagergren
    posted to prediction tfbs by isimpson on 2008-08-14 10:19:35 as ***** along with 2 people and 1 group indigoviolet xili03 EisenLab
  • Applied bioinformatics for the identification of regulatory elements.
    Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287.
    by WW Wasserman, A Sandelin
    posted to prediction tfbs by isimpson on 2008-08-14 10:18:46 as ***** along with 16 people and 8 groups icases ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen Stew nklee jdiezperezj ArtemPankin mariakmejia structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
  • GAPWM: A Genetic Algorithm Method for Optimizing a Position Weight Matrix.
    Bioinformatics (6 March 2007)
    by Leping Li, Yu Liang, Robert L L Bass
    posted to algorithm software by isimpson on 2008-08-14 10:14:33 as ***** along with 4 people and 2 groups dpollard grahamc cjeans ghattem EisenLab ParkinsonLab_at_MaRS
  • Negative-feedback regulation of proneural proteins controls the timing of neural precursor division
    Development (13 August 2008), dev.021923.
    by Pao-Ju Chang, Yun-Ling Hsiao, An-Chi Tien, Yi-Chen Li, Haiwei Pi
    posted to drosophila by isimpson on 2008-08-14 09:51:02 as ***** along with 1 group Jarman Lab
  • Conservation of sequence and function of the pag-3 genes from C. elegans and C. briggsae.
    Gene, Vol. 243, No. 1-2. (8 February 2000), pp. 67-74.
    by E Aamodt, L Shen, M Marra, J Schein, B Rose, JB McDermott
    posted to senseless site-source tfbs by isimpson on 2008-08-13 14:30:02 as read along with 1 person and 2 groups tharris C. elegans / WormBase Jarman Lab
  • Senseless physically interacts with proneural proteins and functions as a transcriptional co-activator.
    Development (Cambridge, England), Vol. 133, No. 10. (May 2006), pp. 1979-1989.
    by M Acar, H Jafar-Nejad, N Giagtzoglou, S Yallampalli, G David, Y He, C Delidakis, HJ Bellen
    posted to senseless site-source tfbs by isimpson on 2008-08-13 14:28:49 as read along with 1 group Jarman Lab
  • Gfi-1 encodes a nuclear zinc finger protein that binds DNA and functions as a transcriptional repressor.
    Molecular and cellular biology, Vol. 16, No. 8. (August 1996), pp. 4024-4034.
    by PA Zweidler-Mckay, HL Grimes, MM Flubacher, PN Tsichlis
    posted to site-source tfbs by isimpson on 2008-08-13 14:09:22 as *** along with 1 group Jarman Lab
  • Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors.
    Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3589-3592.
    by A Sosinsky, CP Bonin, RS Mann, B Honig
    posted to prediction software tfbs transcription-regulation by isimpson on 2008-08-13 13:12:54 as **** along with 2 people wenhan oelemento
  • Hox and Senseless Antagonism Functions as a Molecular Switch to Regulate EGF Secretion in the Drosophila PNS
    Developmental Cell, Vol. 15, No. 2. (12 August 2008), pp. 298-308.
    by David Li-Kroeger, Lorraine M Witt, Leighton H Grimes, Tiffany A Cook, Brian Gebelein
    posted to no-tag by isimpson on 2008-08-13 10:44:07 as ***
  • Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks.
    Mol Biol Evol, Vol. 21, No. 1. (January 2004), pp. 36-44.
    by K Tamura, S Subramanian, S Kumar
    posted to no-tag by isimpson on 2008-08-11 10:51:41 as read along with 1 person and 1 group indigoviolet EisenLab
  • Specificity of Atonal and Scute bHLH factors: analysis of cognate E box binding sites and the influence of Senseless.
    Genes to cells : devoted to molecular & cellular mechanisms (4 August 2008)
    by Lynn M M Powell, Aimée M M Deaton, Martin A A Wear, Andrew P P Jarman
    posted to no-tag by isimpson on 2008-08-08 10:03:37 as ***** along with 1 group Jarman Lab
  • The genetics of early telencephalon patterning: some assembly required.
    Nature reviews. Neuroscience (6 August 2008)
    by Jean M M Hébert, Gord Fishell
    posted to no-tag by isimpson on 2008-08-08 09:46:34 as **
  • Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study
    Genome Biology, Vol. 8 (08 November 2007), R236.
    by Arjun Bhutkar, William M Gelbart, Temple F Smith
    posted to no-tag by isimpson on 2008-07-21 14:01:19 as ** along with 5 people and 1 group indigoviolet dpollard balicea maximilianh hpaces EisenLab
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