Identification of potent inhibitors of SARS-CoV-2 infection by combined pharmacological evaluation and cellular network prioritization

Autor: Patten, J.J. ¹, Keiser, Patrick T. ¹, Morselli-Gysi, Deisy ^{2, 3}, Menichetti, Giulia ^{2, 3}, Mori, Hiroyuki ¹, Donahue, Callie J. ¹, Gan, Xiao ^{2, 3}, Valle, Italo do ², Geoghegan-Barek, Kathleen ¹, Anantpadma, Manu ^{1, 10}, Boytz, RuthMabel ¹, Berrigan, Jacob L. ^{1, 11}, Stubbs, Sarah H. ¹, Ayazika, Tess ¹, O’Leary, Colin ⁴, Jalloh, Sallieu ¹, Wagner, Florence ⁵, Ayehunie, Seyoum ⁶, Elledge, Stephen J. ⁴, Anderson, Deborah ¹, Loscalzo, Joseph ³, Zitnik, Marinka ⁷, Gummuluru, Suryaram ¹, Namchuk, Mark N. ⁸, Barabási, Albert-László ^{2, 3, 9}, Davey, Robert A. ^{1, 12, ∗}

Publikováno v: In iScience 16 September 2022 25(9)

Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA).

Autor: Morselli Gysi, Deisy¹ (AUTHOR) katja.nowick@fu-berlin.de, de Miranda Fragoso, Tiago² (AUTHOR), Zebardast, Fatemeh³ (AUTHOR), Bertoli, Wesley⁴ (AUTHOR), Busskamp, Volker^5,6 (AUTHOR), Almaas, Eivind^7,8 (AUTHOR), Nowick, Katja³ (AUTHOR) katja.nowick@fu-berlin.de

Publikováno v: PLoS ONE. 10/15/2020, Vol. 15 Issue 10, p1-28. 28p.

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).

Network medicine framework for identifying drug-repurposing opportunities for COVID-19.

Autor: Morselli Gysi D; Network Science Institute, Northeastern University, Boston, MA 02115.; Department of Physics, Northeastern University, Boston, MA 02115.; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115., do Valle Í; Network Science Institute, Northeastern University, Boston, MA 02115.; Department of Physics, Northeastern University, Boston, MA 02115., Zitnik M; Department of Biomedical Informatics, Harvard University, Boston, MA 02115.; Harvard Data Science Initiative, Harvard University, Cambridge, MA 02138., Ameli A; Department of Physics, Northeastern University, Boston, MA 02115.; Data Science Department, Scipher Medicine, Waltham, MA 02453., Gan X; Network Science Institute, Northeastern University, Boston, MA 02115.; Department of Physics, Northeastern University, Boston, MA 02115.; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115., Varol O; Network Science Institute, Northeastern University, Boston, MA 02115.; Department of Physics, Northeastern University, Boston, MA 02115.; Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey., Ghiassian SD; Data Science Department, Scipher Medicine, Waltham, MA 02453., Patten JJ; Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118., Davey RA; Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118., Loscalzo J; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115., Barabási AL; Network Science Institute, Northeastern University, Boston, MA 02115; a.barabasi@northeastern.edu.; Department of Physics, Northeastern University, Boston, MA 02115.; Department of Network and Data Science, Central European University, Budapest 1051, Hungary.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2021 May 11; Vol. 118 (19).

Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19.

Autor: Morselli Gysi D; Network Science Institute and Department of Physics, Northeastern University, Boston, MA 02115, USA.; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Do Valle Í; Network Science Institute and Department of Physics, Northeastern University, Boston, MA 02115, USA., Zitnik M; Department of Biomedical Informatics, Harvard University, Boston, MA 02115, USA.; Harvard Data Science Initiative, Harvard University, Cambridge, MA 02138, USA., Ameli A; Scipher Medicine, 221 Crescent St, Suite 103A, Waltham, MA 02453.; Department of Physics, Northeastern University, Boston, MA 02115, USA., Gan X; Network Science Institute and Department of Physics, Northeastern University, Boston, MA 02115, USA.; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Varol O; Network Science Institute and Department of Physics, Northeastern University, Boston, MA 02115, USA.; Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey., Ghiassian SD; Scipher Medicine, 221 Crescent St, Suite 103A, Waltham, MA 02453., Patten JJ; Department of microbiology, NEIDL, Boston University, Boston, MA, USA., Davey R; Department of microbiology, NEIDL, Boston University, Boston, MA, USA., Loscalzo J; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Barabási AL; Network Science Institute and Department of Physics, Northeastern University, Boston, MA 02115, USA.; Department of Network and Data Science, Central European University, Budapest 1051, Hungary.

Publikováno v: ArXiv [ArXiv] 2020 Apr 15. Date of Electronic Publication: 2020 Apr 15.