Cell reprogramming design by transfer learning of functional transcriptional networks.

Autor: Wytock TP; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208.; Center for Network Dynamics, Northwestern University, Evanston, IL 60208., Motter AE; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208.; Center for Network Dynamics, Northwestern University, Evanston, IL 60208.; Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208.; Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208.; National Institute for Theory and Mathematics in Biology, Evanston, IL 60208.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2024 Mar 12; Vol. 121 (11), pp. e2312942121. Date of Electronic Publication: 2024 Mar 04.

Assessment of community efforts to advance network-based prediction of protein-protein interactions.

Autor: Wang XW; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA., Madeddu L; Translational and Precision Medicine Department Sapienza University of Rome, Rome, Italy., Spirohn K; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA., Martini L; Department of Computer, Control, and Management Engineering 'Antonio Rubert', Sapienza University of Rome, Rome, Italy., Fazzone A; CENTAI Institute, Turin, Italy., Becchetti L; Department of Computer, Control, and Management Engineering 'Antonio Rubert', Sapienza University of Rome, Rome, Italy., Wytock TP; Department of Physics and Astronomy, Northwestern University, Evanston, IL, 60208, USA., Kovács IA; Department of Physics and Astronomy, Northwestern University, Evanston, IL, 60208, USA.; Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, 60208, USA., Balogh OM; Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary., Benczik B; Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.; Pharmahungary Group, 6722, Szeged, Hungary., Pétervári M; Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary., Ágg B; Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.; Pharmahungary Group, 6722, Szeged, Hungary., Ferdinandy P; Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.; Pharmahungary Group, 6722, Szeged, Hungary., Vulliard L; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.; Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria., Menche J; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.; Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria.; Faculty of Mathematics, University of Vienna, Vienna, Austria., Colonnese S; Department of Information Engineering, Electronics, and Telecommunications (DIET), University of Rome 'Sapienza', Rome, Italy., Petti M; Department of Computer, Control, and Management Engineering 'Antonio Rubert', Sapienza University of Rome, Rome, Italy., Scarano G; Department of Information Engineering, Electronics, and Telecommunications (DIET), University of Rome 'Sapienza', Rome, Italy., Cuomo F; Department of Information Engineering, Electronics, and Telecommunications (DIET), University of Rome 'Sapienza', Rome, Italy., Hao T; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA., Laval F; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Laboratory of Molecular and Cellular Epigenetic, GIGA Institute, University of Liège, Liège, Belgium.; Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium.; TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium., Willems L; Laboratory of Molecular and Cellular Epigenetic, GIGA Institute, University of Liège, Liège, Belgium.; TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium., Twizere JC; Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium.; TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium., Vidal M; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA., Calderwood MA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA., Petrillo E; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.; Department of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, 02115, USA., Barabási AL; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.; Network Science Institute and Department of Physics, Northeastern University, Boston, MA, 02115, USA.; Department of Network and Data Science, Central European University, Budapest, H-1051, Hungary., Silverman EK; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA., Loscalzo J; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA., Velardi P; Translational and Precision Medicine Department Sapienza University of Rome, Rome, Italy. velardi@di.uniroma1.it., Liu YY; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA. yyl@channing.harvard.edu.; Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA. yyl@channing.harvard.edu.

Publikováno v: Nature communications [Nat Commun] 2023 Mar 22; Vol. 14 (1), pp. 1582. Date of Electronic Publication: 2023 Mar 22.

Extreme Antagonism Arising from Gene-Environment Interactions.

Autor: Wytock TP; Department of Physics and Astronomy, Northwestern University, Evanston, Illinois., Zhang M; The Committee on Microbiology, University of Chicago, Chicago, Illinois., Jinich A; Division of Infectious Diseases, Weill Department of Medicine, Weill-Cornell Medical College, New York, New York., Fiebig A; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan., Crosson S; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan., Motter AE; Department of Physics and Astronomy, Northwestern University, Evanston, Illinois; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois; Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois. Electronic address: motter@northwestern.edu.

Publikováno v: Biophysical journal [Biophys J] 2020 Nov 17; Vol. 119 (10), pp. 2074-2086. Date of Electronic Publication: 2020 Oct 15.

Predicting growth rate from gene expression.

Autor: Wytock TP; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208., Motter AE; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208; motter@northwestern.edu.; Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208.; Chicago Region Physical Sciences-Oncology Center, Northwestern University, Evanston, IL 60208.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2019 Jan 08; Vol. 116 (2), pp. 367-372. Date of Electronic Publication: 2018 Dec 21.

Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate.

Autor: Wytock TP; Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America., Fiebig A; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America., Willett JW; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America., Herrou J; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America., Fergin A; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America., Motter AE; Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America.; Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America., Crosson S; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America.; Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America.

Publikováno v: PLoS genetics [PLoS Genet] 2018 Mar 27; Vol. 14 (3), pp. e1007284. Date of Electronic Publication: 2018 Mar 27 (Print Publication: 2018).