Structure-informed mutagenesis identifies a conserved region critical for mouse insulin receptor 5'UTR IRES function.

Autor: Dahl WB, Lan TCT, Rouskin S, Marr MT

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Nov 05. Date of Electronic Publication: 2024 Nov 05.

Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses.

Autor: Normandin E; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA., Triana S; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA. Electronic address: strianas@broadinstitute.org., Raju SS; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA., Lan TCT; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA., Lagerborg K; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA., Rudy M; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Adams GC; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA., DeRuff KC; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Logue J; Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA., Liu D; Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA., Strebinger D; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Rao A; Columbia University, New York, NY, USA; Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA., Messer KS; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Sacks M; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Adams RD; Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA., Janosko K; Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA., Kotliar D; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA., Shah R; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Crozier I; Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA., Rinn JL; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA., Melé M; Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Catalonia, Spain., Honko AN; Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA., Zhang F; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Babadi M; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Luban J; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA., Bennett RS; Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA., Shalek AK; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA., Barkas N; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Lin AE; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA., Hensley LE; Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA. Electronic address: lisa.hensley@usda.gov., Sabeti PC; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address: pardis@broadinstitute.org., Siddle KJ; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA. Electronic address: katherine_siddle@brown.edu.

Publikováno v: Cell genomics [Cell Genom] 2023 Nov 21; Vol. 3 (12), pp. 100440. Date of Electronic Publication: 2023 Nov 21 (Print Publication: 2023).

Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells.

Autor: Lan TCT; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA., Allan MF; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Department of Microbiology, Harvard Medical School, Boston, MA, USA.; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA., Malsick LE; National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA, USA., Woo JZ; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Department of Microbiology, Harvard Medical School, Boston, MA, USA., Zhu C; Department of Nutritional Sciences & Toxicology, University of California, Berkley, CA, 94720, USA.; Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA., Zhang F; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Khandwala S; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.; Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA., Nyeo SSY; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.; Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA., Sun Y; Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA., Guo JU; Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA., Bathe M; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA., Näär A; Department of Nutritional Sciences & Toxicology, University of California, Berkley, CA, 94720, USA.; Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA., Griffiths A; National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA, USA., Rouskin S; Whitehead Institute for Biomedical Research, Cambridge, MA, USA. silvi_rouskin@hms.harvard.edu.; Department of Microbiology, Harvard Medical School, Boston, MA, USA. silvi_rouskin@hms.harvard.edu.

Publikováno v: Nature communications [Nat Commun] 2022 Mar 02; Vol. 13 (1), pp. 1128. Date of Electronic Publication: 2022 Mar 02.

Author Correction: Determination of RNA structural diversity and its role in HIV-1 RNA splicing.

Autor: Tomezsko PJ; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Program in Virology, Harvard Medical School, Boston, MA, USA.; Brigham and Women's Hospital, Boston, MA, USA., Corbin VDA; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia., Gupta P; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Swaminathan H; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Glasgow M; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Massachusetts Institute of Technology, Cambridge, MA, USA., Persad S; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Massachusetts Institute of Technology, Cambridge, MA, USA., Edwards MD; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA., Mcintosh L; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.; Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia., Papenfuss AT; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.; Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia., Emery A; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Swanstrom R; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Zang T; Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA., Lan TCT; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Bieniasz P; Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA., Kuritzkes DR; Brigham and Women's Hospital, Boston, MA, USA.; Department of Medicine, Harvard Medical School, Boston, MA, USA., Tsibris A; Brigham and Women's Hospital, Boston, MA, USA.; Department of Medicine, Harvard Medical School, Boston, MA, USA., Rouskin S; Whitehead Institute for Biomedical Research, Cambridge, MA, USA. srouskin@wi.mit.edu.

Publikováno v: Nature [Nature] 2020 Dec; Vol. 588 (7837), pp. E16.

Determination of RNA structural diversity and its role in HIV-1 RNA splicing.

Autor: Tomezsko PJ; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Program in Virology, Harvard Medical School, Boston, MA, USA.; Brigham and Women's Hospital, Boston, MA, USA., Corbin VDA; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia., Gupta P; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Swaminathan H; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Glasgow M; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Massachusetts Institute of Technology, Cambridge, MA, USA., Persad S; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Massachusetts Institute of Technology, Cambridge, MA, USA., Edwards MD; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA., Mcintosh L; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.; Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia., Papenfuss AT; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.; Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia., Emery A; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Swanstrom R; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Zang T; Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA., Lan TCT; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Bieniasz P; Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA., Kuritzkes DR; Brigham and Women's Hospital, Boston, MA, USA.; Department of Medicine, Harvard Medical School, Boston, MA, USA., Tsibris A; Brigham and Women's Hospital, Boston, MA, USA.; Department of Medicine, Harvard Medical School, Boston, MA, USA., Rouskin S; Whitehead Institute for Biomedical Research, Cambridge, MA, USA. srouskin@wi.mit.edu.

Publikováno v: Nature [Nature] 2020 Jun; Vol. 582 (7812), pp. 438-442. Date of Electronic Publication: 2020 May 06.