XcisClique: analysis of regulatory bicliques

Autor: Grene Ruth, Heath Lenwood S, Vasquez-Robinet Cecilia, Pati Amrita, Murali TM

Publikováno v: BMC Bioinformatics, Vol 7, Iss 1, p 218 (2006)

Abstract Background Modeling of cis-elements or regulatory motifs in promoter (upstream) regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a set of genes is mode

Externí odkaz: https://doaj.org/article/1cf87b63982a44f2affacd32c107ea70

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Current and future directions in network biology.

Autor: Zitnik M; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States., Li MM; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States., Wells A; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States.; Lucy Family Institute for Data and Society, University of Notre Dame, Notre Dame, IN 46556, United States.; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, United States., Glass K; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States., Morselli Gysi D; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States.; Department of Statistics, Federal University of Paraná, Curitiba, Paraná 81530-015, Brazil.; Department of Physics, Northeastern University, Boston, MA 02115, United States., Krishnan A; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States., Murali TM; Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States., Radivojac P; Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, United States., Roy S; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53715, United States.; Wisconsin Institute for Discovery, Madison, WI 53715, United States., Baudot A; Aix Marseille Université, INSERM, MMG, Marseille, France., Bozdag S; Department of Computer Science and Engineering, University of North Texas, Denton, TX 76203, United States.; Department of Mathematics, University of North Texas, Denton, TX 76203, United States., Chen DZ; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States., Cowen L; Department of Computer Science, Tufts University, Medford, MA 02155, United States., Devkota K; Department of Computer Science, Tufts University, Medford, MA 02155, United States., Gitter A; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53715, United States.; Morgridge Institute for Research, Madison, WI 53715, United States., Gosline SJC; Biological Sciences Division, Pacific Northwest National Laboratory, Seattle, WA 98109, United States., Gu P; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States., Guzzi PH; Department of Medical and Surgical Sciences, University Magna Graecia of Catanzaro, Catanzaro, 88100, Italy., Huang H; Department of Computer Science, University of Maryland College Park, College Park, MD 20742, United States., Jiang M; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States., Kesimoglu ZN; Department of Computer Science and Engineering, University of North Texas, Denton, TX 76203, United States.; National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, United States., Koyuturk M; Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH 44106, United States., Ma J; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, United States., Pico AR; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, United States., Pržulj N; Department of Computer Science, University College London, London, WC1E 6BT, England.; ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, 08010, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain., Przytycka TM; National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, United States., Raphael BJ; Department of Computer Science, Princeton University, Princeton, NJ 08544, United States., Ritz A; Department of Biology, Reed College, Portland, OR 97202, United States., Sharan R; School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel., Shen Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, United States., Singh M; Department of Computer Science, Princeton University, Princeton, NJ 08544, United States.; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States., Slonim DK; Department of Computer Science, Tufts University, Medford, MA 02155, United States., Tong H; Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States., Yang XH; Department of Pediatrics, University of Chicago, Chicago, IL 60637, United States., Yoon BJ; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, United States.; Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, United States., Yu H; Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, United States., Milenković T; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States.; Lucy Family Institute for Data and Society, University of Notre Dame, Notre Dame, IN 46556, United States.; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, United States.

Publikováno v: Bioinformatics advances [Bioinform Adv] 2024 Aug 14; Vol. 4 (1), pp. vbae099. Date of Electronic Publication: 2024 Aug 14 (Print Publication: 2024).