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oannes's library [44 articles]

Recent papers added to oannes's library.
  • A Gentle Tutorial on the EM Algorithm and its Application to Parameter Estimation for Gaussian Mixture and Hidden Markov Models
    (1997)
    by J Bilmes
    posted to no-tag by oannes on 2007-09-19 21:54:10 as ** along with 9 people and 4 groups bigga danpopovici pool007 nojhan sugarexpletive vitalaswp3 360varial asterix77 eddymier EvolutionaryComputation Regulomics_UCHSC Metaheuristics Optimization
  • Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
    by Yoav Benjamini, Yosef Hochberg
    posted to test multiple by oannes on 2007-01-15 14:10:29 as ** along with 12 people and 2 groups dragonrez jyuh RMGraze vplagnol frohike grahamc shigepong ccr axelon ugengma amsantos rschulz Bioinformatics Regulomics_UCHSC
  • Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span.
    BMC Bioinformatics, Vol. 7, No. 1. (8 May 2006)
    by D M Blei, K Franks, M I Jordan, I S Mian
    posted to latent_semantic_analysis by oannes on 2006-06-20 22:23:35 as ** along with 3 people and 4 groups irenas yas caporaso dbk-lab T_lab biomedical-nlp Regulomics_UCHSC
  • Identifying biological concepts from a protein-related corpus with a probabilistic topic model.
    BMC Bioinformatics, Vol. 7 (2006)
    by B Zheng, DC McLean, X Lu
    posted to latent_semantic_analysis by oannes on 2006-06-20 22:22:48 as ** along with 1 person and 2 groups yas T_lab Regulomics_UCHSC
  • Finding genomic ontology terms in text using evidence content.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by FM Couto, MJ Silva, PM Coutinho
    posted to feature nlp-reading semantic by oannes on 2006-06-16 23:22:56 as ***** along with 3 people and 3 groups irenas helliontroy josepe dbk-lab biomedical-nlp Regulomics_UCHSC
  • Automatically annotating documents with normalized gene lists.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by J Crim, R McDonald, F Pereira
    posted to feature nlp-reading semantic by oannes on 2006-06-16 23:17:33 as ***** along with 2 people and 1 group zlu vlachmore Regulomics_UCHSC
  • Finding scientific topics.
    Proc Natl Acad Sci U S A, Vol. 101 Suppl 1 (6 April 2004), pp. 5228-5235.
    by TL Griffiths, M Steyvers
    posted to latent_semantic_analysis by oannes on 2006-06-16 20:50:12 as ***** along with 6 people and 1 group egh bundschu julianpan bhaddow dejori roys Regulomics_UCHSC
  • Mixed-membership models of scientific publications.
    Proc Natl Acad Sci U S A, Vol. 101 Suppl 1 (6 April 2004), pp. 5220-5227.
    by E Erosheva, S Fienberg, J Lafferty
    posted to latent_semantic_analysis by oannes on 2006-06-16 20:49:40 as ***** along with 1 person and 1 group mshafiei Regulomics_UCHSC
  • ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by A Elfilali, S Lair, C Verbeke, P La Rosa, F Radvanyi, E Barillot
    posted to cancer disease nar regulomics by oannes on 2006-06-06 21:05:18 as ** along with 1 group Regulomics_UCHSC
  • Interplay between VHL/HIF1α and Wnt/β-catenin pathways during colorectal tumorigenesis
    Oncogene, Vol. aop, No. current.
    by RH Giles, MP Lolkema, CM Snijckers, M Belderbos, P van der Groep, DA Mans, M van Beest, M van Noort, R Goldschmeding, PJ van Diest, H Clevers, EE Voest
    posted to disease vhl by oannes on 2006-06-06 20:21:30 as ** along with 1 group Regulomics_UCHSC
  • Inactivation of von Hippel-Lindau Gene Induces Constitutive Phosphorylation of MET Protein in Clear Cell Renal Carcinoma
    Cancer Res, Vol. 66, No. 7. (1 April 2006), pp. 3699-3705.
    by Noboru Nakaigawa, Masahiro Yao, Masaya Baba, Shingo Kato, Takeshi Kishida, Keiko Hattori, Yoji Nagashima, Yoshinobu Kubota
    posted to disease vhl by oannes on 2006-06-06 20:20:21 as ** along with 1 group Regulomics_UCHSC
  • 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 chromatin tfbs by oannes on 2006-06-01 03:23:43 as ***** along with 4 people and 4 groups dchughes cmm lusk vietanh0 FAB-lab G4ID Regulomics_UCHSC Genetics-of-Gambling
  • Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations.
    Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1190-1197.
    by A Kel, T Konovalova, T Waleev, E Cheremushkin, O Kel-Margoulis, E Wingender
    posted to crm tfbs by oannes on 2006-06-01 03:18:40 as ***** along with 1 group Regulomics_UCHSC
  • Human Transcription Factors Contain a High Fraction of Intrinsically Disordered Regions Essential for Transcriptional Regulation.
    J Mol Biol (25 April 2006)
    by Yoshiaki Minezaki, Keiichi Homma, Akira R R Kinjo, Ken Nishikawa
    posted to structure tfbs by oannes on 2006-06-01 03:12:36 as **** along with 1 person and 1 group biomcgary Regulomics_UCHSC
  • BioMed Central | Abstract | 1471-2105-7-229 | Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data
    posted to crm tfbs by oannes on 2006-05-26 21:47:51 as ** along with 1 group Regulomics_UCHSC
  • Transcription in four dimensions: nuclear receptor-directed initiation of gene expression.
    EMBO Rep, Vol. 7, No. 2. (February 2006), pp. 161-167.
    by R Métivier, G Reid, F Gannon
    posted to dynamic tfbs by oannes on 2006-05-25 17:26:35 as ** along with 1 group Regulomics_UCHSC
  • SUMO and ubiquitin in the nucleus: different functions, similar mechanisms?
    Genes Dev., Vol. 18, No. 17. (1 September 2004), pp. 2046-2059.
    by Grace Gill
    posted to sumo tfbs by oannes on 2006-05-25 17:12:41 as ** along with 2 people and 1 group imouthesmp cjeans Regulomics_UCHSC
  • Contrasting effects on HIF-1alpha regulation by disease-causing pVHL mutations correlate with patterns of tumourigenesis in von Hippel-Lindau disease.
    Hum Mol Genet, Vol. 10, No. 10. (1 May 2001), pp. 1029-1038.
    by SC Clifford, ME Cockman, AC Smallwood, DR Mole, ER Woodward, PH Maxwell, PJ Ratcliffe, ER Maher
    posted to disease vhl by oannes on 2006-05-23 20:34:53 as ** along with 1 group Regulomics_UCHSC
  • p53 Stabilization and Transactivation by a von Hippel-Lindau Protein.
    Mol Cell, Vol. 22, No. 3. (5 May 2006), pp. 395-405.
    by JS Roe, H Kim, SM Lee, ST Kim, EJ Cho, HD Youn
    posted to disease vhl by oannes on 2006-05-23 20:31:21 as ** along with 1 group Regulomics_UCHSC
  • Hypoxia-inducible factors: where, when and why?
    Vol. 69, No. 1. (0000), pp. 15-17.
    by JM Gleadle, DR Mole, CW Pugh
    posted to disease vhl by oannes on 2006-05-23 20:14:41 as ** along with 1 group Regulomics_UCHSC
  • Activation of TRAP/Mediator Subunit TRAP220/Med1 Is Regulated by Mitogen-Activated Protein Kinase-Dependent Phosphorylation
    Mol. Cell. Biol., Vol. 25, No. 24. (15 December 2005), pp. 10695-10710.
    by Pradeep K Pandey, TS Udayakumar, Xinjie Lin, Dipali Sharma, Paul S Shapiro, Joseph D Fondell
    posted to mediator pair tfbs by oannes on 2006-05-18 23:15:58 as ** along with 1 group Regulomics_UCHSC
  • Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.
    Nucleic Acids Res, Vol. 33, No. 2. (2005), pp. 546-558.
    by Z Liu, F Mao, JT Guo, B Yan, P Wang, Y Qu, Y Xu
    posted to structure tfbs by oannes on 2006-05-18 05:57:41 as ** along with 1 person and 1 group kaarsinogen Regulomics_UCHSC
  • Modeling gene expression control using Omes Law
    Mol Syst Biol, Vol. 2, No. 1. (11 April 2006), pp. msb4100055-E1-msb4100055-E3.
    by Harmen J Bussemaker
    posted to pair tfbs by oannes on 2006-05-09 21:11:26 as ** along with 2 people and 2 groups okarsligil nsamways Bioinformatics Regulomics_UCHSC
  • Local Regulatory Variation in Saccharomyces cerevisiae.
    PLoS Genet, Vol. 1, No. 2. (19 August 2005)
    by James Ronald, Rachel B B Brem, Jacqueline Whittle, Leonid Kruglyak
    posted to qtl regulomics by oannes on 2006-05-09 20:50:49 as ***** along with 1 person and 1 group rklancer Regulomics_UCHSC
  • Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors
    Nat Genet, Vol. 35, No. 1. (2003), pp. 57-64.
    by Gael Yvert, Rachel B Brem, Jacqueline Whittle, Joshua M Akey, Eric Foss, Erin N Smith, Rachel Mackelprang, Leonid Kruglyak
    posted to qtl regulomics by oannes on 2006-05-09 20:48:43 as ** along with 3 people and 1 group RMGraze xwbcn lp2 Regulomics_UCHSC
  • Genetic Dissection of Transcriptional Regulation in Budding Yeast
    Science, Vol. 296, No. 5568. (26 April 2002), pp. 752-755.
    by Rachel B Brem, Gael Yvert, Rebecca Clinton, Leonid Kruglyak
    posted to qtl regulomics by oannes on 2006-05-09 20:41:23 as ***** along with 9 people and 3 groups RMGraze JAShapiro brant dpollard adepace raiyar lp2 jo_davies mimulus_99 EisenLab Regulomics_UCHSC steinmetzlab
  • Learning the parts of objects by non-negative matrix factorization.
    Nature, Vol. 401, No. 6755. (21 October 1999), pp. 788-791.
    by DD Lee, HS Seung
    posted to feature nlp-reading semantic by oannes on 2006-05-05 05:40:02 as read along with 13 people and 4 groups JacquesC davidr dragonrez anar jfr yas yama_tah pliz scis0000001 cerkut atbrew zeppe kintoki NU-PRL T_lab Regulomics_UCHSC contact-id
  • Discovering semantic features in the literature: a foundation for building functional associations.
    BMC Bioinformatics, Vol. 7, No. 1. (26 January 2006)
    by Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, Jose M Carazo, Alberto Pascual-Montano
    posted to feature nlp-reading semantic by oannes on 2006-05-05 05:31:20 as read along with 3 people and 3 groups yas caporaso helliontroy T_lab biomedical-nlp Regulomics_UCHSC
  • Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.
    Genome Res (10 April 2006)
    by Mathieu Blanchette, Alain R R Bataille, Xiaoyu Chen, Christian Poitras, Josée Laganière, Céline Lefèbvre, Geneviève Deblois, Vincent Giguère, Vincent Ferretti, Dominique Bergeron, Benoit Coulombe, François Robert
    posted to tfbs by oannes on 2006-04-27 20:24:12 as ***** along with 1 group Regulomics_UCHSC
  • Protein-DNA binding specificity predictions with structural models.
    Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 5781-5798.
    by AV Morozov, JJ Havranek, D Baker, ED Siggia
    posted to tfbs by oannes on 2006-04-27 20:20:00 as ** along with 1 person and 1 group aalibes Regulomics_UCHSC
  • Annotating significant pairs of transcription factor binding sites in regulatory DNA.
    In Silico Biol, Vol. 4, No. 4. (2004), pp. 479-487.
    by K Rateitschak, T Müller, M Vingron
    posted to pair tfbs by oannes on 2006-04-27 20:17:24 as ** along with 1 group Regulomics_UCHSC
  • Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.
    Nucleic Acids Res, Vol. 31, No. 20. (15 October 2003), pp. 6016-6026.
    by VJ Makeev, AP Lifanov, AG Nazina, DA Papatsenko
    posted to distance pair tfbs by oannes on 2006-04-27 20:16:27 as read along with 2 people and 2 groups dpollard lusk EisenLab Regulomics_UCHSC
  • Predicting transcription factor synergism.
    Nucleic Acids Res, Vol. 30, No. 19. (1 October 2002), pp. 4278-4284.
    by S Hannenhalli, S Levy
    posted to pair tfbs by oannes on 2006-04-27 20:13:23 as read along with 1 group Regulomics_UCHSC
  • Annotating significant pairs of transcription factor binding sites in regulatory DNA
    posted to pair tfbs by oannes on 2006-04-27 20:10:10 as read along with 1 group Regulomics_UCHSC
  • Genome-wide prediction and analysis of function-specific transcription factor binding sites
    posted to pair tfbs by oannes on 2006-04-27 20:08:38 as read along with 1 group Regulomics_UCHSC
  • STEM: Short Time-series Expression Miner
    posted to series time by oannes on 2006-04-27 09:04:25 as ** along with 1 group Regulomics_UCHSC
  • Statistic of Financial Markets
    posted to no-tag by oannes on 2006-04-27 09:00:23 as ** along with 1 group Regulomics_UCHSC
  • Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering.
    Bioinformatics, Vol. 22, No. 7. (1 April 2006), pp. 843-848.
    by K Hakamada, M Okamoto, T Hanai
    posted to clustering course microarray time by oannes on 2006-04-27 08:11:47 as ** along with 1 group Regulomics_UCHSC
  • R: Analysis of Multiple Time Course Data
    posted to no-tag by oannes on 2006-04-27 07:58:53 as ***** along with 1 group Regulomics_UCHSC
  • Differential and trajectory methods for time course gene expression data
    Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 3009-3016.
    by Yulan Liang, Bamidele Tayo, Xueya Cai, Arpad Kelemen
    posted to clustering course microarray time by oannes on 2006-04-27 05:53:06 as ** along with 1 person and 1 group dquest Regulomics_UCHSC
  • Integrated analysis of gene expression by Association Rules Discovery.
    BMC Bioinformatics, Vol. 7 (2006)
    by P Carmona-Saez, M Chagoyen, A Rodriguez, O Trelles, JM Carazo, A Pascual-Montano
    posted to arm by oannes on 2006-04-27 05:36:13 as ** along with 2 people and 1 group macavity1g dps Regulomics_UCHSC
  • A multi-step approach to time series analysis and gene expression clustering.
    Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 589-596.
    by R Amato, A Ciaramella, N Deniskina, C Del Mondo, D di Bernardo, C Donalek, G Longo, G Mangano, G Miele, G Raiconi, A Staiano, R Tagliaferri
    posted to clustering microarray by oannes on 2006-04-27 05:19:03 as *** along with 1 person and 1 group jyuh Regulomics_UCHSC
  • Schema for TFBS Conserved - HMR Conserved Transcription Factor Binding Sites
    posted to tfbs by oannes on 2006-04-24 18:44:07 as read along with 1 group Regulomics_UCHSC
  • Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae.
    Nucleic Acids Res, Vol. 34, No. 3. (2006), pp. 917-927.
    by X Yu, J Lin, T Masuda, N Esumi, DJ Zack, J Qian
    posted to distance pair tfbs by oannes on 2006-04-21 21:53:08 as ***** along with 3 people and 1 group balajis malcook lusk Regulomics_UCHSC
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