Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.

Autor: Hadi K; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA., Yao X; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Behr JM; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Deshpande A; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Xanthopoulakis C; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Tian H; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA., Kudman S; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Rosiene J; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA., Darmofal M; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA., DeRose J; New York Genome Center, New York, NY 10013, USA., Mortensen R; New York Genome Center, New York, NY 10013, USA., Adney EM; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA., Shaiber A; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Gajic Z; New York Genome Center, New York, NY 10013, USA., Sigouros M; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Eng K; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA., Wala JA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Wrzeszczyński KO; New York Genome Center, New York, NY 10013, USA., Arora K; New York Genome Center, New York, NY 10013, USA., Shah M; New York Genome Center, New York, NY 10013, USA., Emde AK; New York Genome Center, New York, NY 10013, USA., Felice V; New York Genome Center, New York, NY 10013, USA., Frank MO; New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA., Darnell RB; New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA., Ghandi M; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Huang F; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Dewhurst S; Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA., Maciejowski J; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA., de Lange T; Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA., Setton J; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA., Riaz N; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA., Reis-Filho JS; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA., Powell S; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA., Knowles DA; New York Genome Center, New York, NY 10013, USA; Department of Computer Science, Columbia University, New York, NY 10027, USA., Reznik E; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA., Mishra B; Departments of Computer Science, Mathematics and Cell Biology, Courant Institute and NYU School of Medicine, New York University, New York, NY 10012, USA., Beroukhim R; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Zody MC; New York Genome Center, New York, NY 10013, USA., Robine N; New York Genome Center, New York, NY 10013, USA., Oman KM; Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA., Sanchez CA; Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA., Kuhner MK; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Smith LP; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA., Galipeau PC; Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA., Paulson TG; Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA., Reid BJ; Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Li X; Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA., Wilkes D; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Sboner A; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA., Mosquera JM; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Elemento O; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA., Imielinski M; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA. Electronic address: mski@mskilab.org.

Publikováno v: Cell [Cell] 2020 Oct 01; Vol. 183 (1), pp. 197-210.e32.

Author Correction: L1 drives IFN in senescent cells and promotes age-associated inflammation.

Autor: De Cecco M; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA., Ito T; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA., Petrashen AP; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA., Elias AE; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA., Skvir NJ; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA., Criscione SW; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA., Caligiana A; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.; Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Brocculi G; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.; Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Adney EM; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Boeke JD; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Le O; Centre de Recherche CHU Ste-Justine, and Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada., Beauséjour C; Centre de Recherche CHU Ste-Justine, and Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada., Ambati J; Center for Advanced Vision Science and Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA., Ambati K; Center for Advanced Vision Science and Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA., Simon M; Department of Biology, University of Rochester, Rochester, NY, USA., Seluanov A; Department of Biology, University of Rochester, Rochester, NY, USA., Gorbunova V; Department of Biology, University of Rochester, Rochester, NY, USA., Slagboom PE; Department of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands., Helfand SL; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA., Neretti N; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.; Center for Computational Molecular Biology, Brown University, Providence, RI, USA., Sedivy JM; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA. john_sedivy@brown.edu.

Publikováno v: Nature [Nature] 2019 Aug; Vol. 572 (7767), pp. E5.

Dissection of affinity captured LINE-1 macromolecular complexes.

Autor: Taylor MS; Department of Pathology, Massachusetts General Hospital, Boston, United States., Altukhov I; Moscow Institute of Physics and Technology, Dolgoprudny, Russia., Molloy KR; Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States., Mita P; Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States., Jiang H; Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States., Adney EM; Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States.; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States., Wudzinska A; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States., Badri S; Department of Pathology, NYU Langone Health, New York, United States., Ischenko D; Moscow Institute of Physics and Technology, Dolgoprudny, Russia., Eng G; Department of Pathology, Massachusetts General Hospital, Boston, United States., Burns KH; Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States.; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States., Fenyö D; Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States., Chait BT; Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States., Alexeev D; Novosibirsk State University, Novosibirsk, Russia., Rout MP; Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States., Boeke JD; Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States., LaCava J; Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States.; Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States.

Publikováno v: ELife [Elife] 2018 Jan 08; Vol. 7. Date of Electronic Publication: 2018 Jan 08.

Chemical reactivity of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 hemoglobins: covalent heme attachment and bishistidine coordination.

Autor: Nothnagel HJ; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA., Preimesberger MR, Pond MP, Winer BY, Adney EM, Lecomte JT

Publikováno v: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry [J Biol Inorg Chem] 2011 Apr; Vol. 16 (4), pp. 539-52. Date of Electronic Publication: 2011 Jan 15.