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Most large structural variants in cancer genomes can be detected without long reads.

Autor: Choo ZN; New York Genome Center, New York, NY, USA.; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.; Tri-institutional MD PhD Program, Weill Cornell Medicine, New York, NY, USA.; Physiology and Biophysics PhD Program, Weill Cornell Medicine, New York, NY, USA., Behr JM; New York Genome Center, New York, NY, USA.; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.; Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA., Deshpande A; New York Genome Center, New York, NY, USA.; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.; Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA., Hadi K; New York Genome Center, New York, NY, USA.; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.; Physiology and Biophysics PhD Program, Weill Cornell Medicine, New York, NY, USA., Yao X; New York Genome Center, New York, NY, USA.; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.; Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA., Tian H; New York Genome Center, New York, NY, USA.; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.; Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA., Takai K; Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA., Zakusilo G; Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA., Rosiene J; New York Genome Center, New York, NY, USA.; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA., Da Cruz Paula A; Memorial Sloan Kettering Cancer Center, New York, NY, USA., Weigelt B; Memorial Sloan Kettering Cancer Center, New York, NY, USA., Setton J; Memorial Sloan Kettering Cancer Center, New York, NY, USA., Riaz N; Memorial Sloan Kettering Cancer Center, New York, NY, USA., Powell SN; Memorial Sloan Kettering Cancer Center, New York, NY, USA., Busam K; Memorial Sloan Kettering Cancer Center, New York, NY, USA., Shoushtari AN; Memorial Sloan Kettering Cancer Center, New York, NY, USA., Ariyan C; Memorial Sloan Kettering Cancer Center, New York, NY, USA., Reis-Filho J; Memorial Sloan Kettering Cancer Center, New York, NY, USA., de Lange T; Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA., Imieliński M; New York Genome Center, New York, NY, USA. mski@mskilab.org.; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA. mski@mskilab.org.; Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA. mski@mskilab.org.; Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA. mski@mskilab.org.

Publikováno v: Nature genetics [Nat Genet] 2023 Dec; Vol. 55 (12), pp. 2139-2148. Date of Electronic Publication: 2023 Nov 09.

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.

Translational Brain Mapping at the University of Rochester Medical Center: Preserving the Mind Through Personalized Brain Mapping.

Autor: Mahon BZ; Department of Neurosurgery, University of Rochester Medical Center; Department of Psychology, Carnegie Mellon University; bmahon@andrew.cmu.edu., Mead JA; Public Relations and Communications, University of Rochester Medical Center., Chernoff BL; Department of Psychology, Carnegie Mellon University., Sims MH; University of Rochester Medical Center., Garcea FE; MOSS Rehabilitation Research Institute, Cognitive Neuroscience., Prentiss E; University of Rochester Medical Center., Belkhir R; Department of Psychology, Carnegie Mellon University., Haber SJ; Department of Neurosurgery, University of Rochester Medical Center., Gannon SB; University of Rochester Medical Center., Erickson S; University of Rochester Medical Center., Wright KA; University of Rochester Medical Center., Schmidt MZ; University of Rochester Medical Center., Paulzak A; Department of Neurosurgery, University of Rochester Medical Center., Milano VC; Department of Neurosurgery, University of Rochester Medical Center., Paul DA; Department of Neurosurgery, University of Rochester Medical Center., Foxx K; Department of Neurosurgery, University of Rochester Medical Center., Tivarus M; Department of Imaging Sciences, University of Rochester Medical Center; Department of Neuroscience, University of Rochester Medical Center., Nadler JW; Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center., Behr JM; Department of Neurosurgery, University of Rochester Medical Center., Smith SO; Department of Neurosurgery, University of Rochester Medical Center., Li YM; Department of Neurosurgery, University of Rochester Medical Center., Walter K; Department of Neurosurgery, University of Rochester Medical Center., Pilcher WH; Department of Neurosurgery, University of Rochester Medical Center.

Publikováno v: Journal of visualized experiments : JoVE [J Vis Exp] 2019 Aug 12 (150). Date of Electronic Publication: 2019 Aug 12.

Bioprinted gelatin hydrogel platform promotes smooth muscle cell contractile phenotype maintenance.

Autor: Tijore A; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore., Behr JM; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore., Irvine SA; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore. sairvine@ntu.edu.sg., Baisane V; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore., Venkatraman S; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.

Publikováno v: Biomedical microdevices [Biomed Microdevices] 2018 Mar 28; Vol. 20 (2), pp. 32. Date of Electronic Publication: 2018 Mar 28.