Searching journal content for articles similar to Halfon et al. 12 (7): 1019.

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  1. Methods: Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
    • Mathieu Blanchette,
    • Alain R. Bataille,
    • Xiaoyu Chen,
    • Christian Poitras,
    • Josée Laganière,
    • Céline Lefèbvre,
    • Geneviève Deblois,
    • Vincent Giguère,
    • Vincent Ferretti,
    • Dominique Bergeron,
    • Benoit Coulombe,
    • and François Robert
    Genome Res. May 2006 16: 656-668; Published in Advance April 10, 2006, doi:10.1101/gr.4866006
    ...the alignment blocks. To measure more accurately the extent to which sequence conservation alone can be used to predict known regulatory modules, sensitivity curves were computed based on the noncoding interspecies conserved regions identified by the PhastCons program ( Siepel et al. 2005 ) (See Supplemental...
  2. Methods: Genome-wide discovery of human heart enhancers
    • Leelavati Narlikar,
    • Noboru J. Sakabe,
    • Alexander A. Blanski,
    • Fabio E. Arimura,
    • John M. Westlund,
    • Marcelo A. Nobrega,
    • and Ivan Ovcharenko
    Genome Res. March 2010 20: 381-392; Published in Advance January 14, 2010, doi:10.1101/gr.098657.109
    ...pathways involved in development. We describe a strategy to systematically identify tissue-specific cis -regulatory elements that share combinations of sequence motifs. Using heart development as an experimental framework, we employed a combination of Gibbs sampling and linear regression to build...
    OPEN ACCESS ARTICLE
  3. LETTER: Genome-wide Co-occurrence of Promoter Elements Reveals a cis-Regulatory Cassette of rRNA Transcription Motifs in Saccharomyces cerevisiae
    • Priya Sudarsanam,
    • Yitzhak Pilpel,
    • and George M. Church
    Genome Res. November 1, 2002 12: 1723-1731; doi:10.1101/gr.301202
    ....M. , Michelson A.M. ( 2002 ) Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12 : 1019 – 1028 . ↵ Hughes J.D. , Estep P.W. , Tavazoie S. , Church G.M. ( 2000 ) Computational identification of cis -regulatory...
  4. LETTER: Homotypic Regulatory Clusters in Drosophila
    • Alexander P. Lifanov,
    • Vsevolod J. Makeev,
    • Anna G. Nazina,
    • and Dmitri A. Papatsenko
    Genome Res. April 1, 2003 13: 579-588; doi:10.1101/gr.668403
    ...accuracy in large DNA sequences. Genome Res. 10 : 1631 – 1642 . ↵ Halfon M.S. , Grad Y. , Church G.M. , Michelson A.M. ( 2002 ) Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12 : 1019 – 1028 . ↵ Hertel...
  5. LETTER: Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures
    • Markus J. Herrgård,
    • Markus W. Covert,
    • and Bernhard ø. Palsson
    Genome Res. November 2003 13: 2423-2434; Published in Advance January 1, 2003, doi:10.1101/gr.1330003
    ...413 target genes through 925 RIs. Because of the existence of a comprehensive database on transcriptional regulation for E. coli , RegulonDB ( Salgado et al. 2001 ), the E. coli regulatory network is more complete and better validated than the yeast network used in this study. We used gene expression...
  6. LETTER: Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles
    • Rosa María Gutiérrez-Ríos,
    • David A. Rosenblueth,
    • José Antonio Loza,
    • Araceli M. Huerta,
    • Jeremy D. Glasner,
    • Fred R. Blattner,
    • and Julio Collado-Vides
    Genome Res. November 2003 13: 2435-2443; doi:10.1101/gr.1387003
    .... The regulation of transcription initiation by integration host factor. Mol. Microbiol. 16 : 1 -7. ↵ Halfon, M.S., Grad, Y., Church, G.M., and Michelson, A.M. 2002 . Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome...
  7. ARTICLE: Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells
    • Ran Elkon,
    • Chaim Linhart,
    • Roded Sharan,
    • Ron Shamir,
    • and Yosef Shiloh
    Genome Res. May 1, 2003 13: 773-780; doi:10.1101/gr.947203
    ...promoters. In Silico Biol. 1 : 29 – 38 . ↵ Halfon M.S. , Grad Y. , Church G.M. , Michelson A.M. ( 2002 ) Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12 : 1019 – 1028 . ↵ Herzig R.P. , Scacco S...
  8. Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
    • Chencheng Xu,
    • Suying Bao,
    • Ye Wang,
    • Wenxing Li,
    • Hao Chen,
    • Yufeng Shen,
    • Tao Jiang,
    • and Chaolin Zhang
    Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
    ...sequences are shuffled randomly and divided into batches of b = 48 sequences for each training step. In each training step, the feature representations for all sequences in the training batch are extracted with the feature-extraction module, and the predictions in the single-sequence mode are computed based...
    OPEN ACCESS ARTICLE
  9. Research: Tracing human stem cell lineage during development using DNA methylation
    • Lucas A. Salas,
    • John K. Wiencke,
    • Devin C. Koestler,
    • Ze Zhang,
    • Brock C. Christensen,
    • and Karl T. Kelsey
    Genome Res. September 2018 28: 1285-1295; Published in Advance August 2, 2018, doi:10.1101/gr.233213.117
    ...cells for CpG boundary probes that colocate with active histone marks, DNase I hypersensitivity, and transcription factor binding sites (Fig. 4). In addition, a middle region, which is devoid of regulatory motifs, displayed contrasting methylation features in each type of cell. The entire 15.5-kb region...
    OPEN ACCESS ARTICLE
  10. Methods: Refinement and expansion of signaling pathways: The osmotic response network in yeast
    • Irit Gat-Viks and
    • Ron Shamir
    Genome Res. March 2007 17: 358-367; Published in Advance January 31, 2007, doi:10.1101/gr.5750507
    ...investigating signaling pathways. We formalize existing qualitative knowledge as a probabilistic model that depicts known interactions between molecules (genes, proteins, etc.) as a network and known regulatory relations as logics. We present algorithms that analyze experimental results (e.g., transcription...
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