Experimental and In Silico Analysis of TEM β-Lactamase Adaptive Evolution

Autor: Standley, Melissa, Blay, Vincent, Beleva Guthrie, Violeta, Kim, Jay, Lyman, Audrey, Moya, Andrés, Karchin, Rachel, Camps, Manel

Publikováno v: ACS infectious diseases, vol 8, iss 12

Multiple mutations often have non-additive (epistatic) phenotypic effects. Epistasis is of fundamental biological relevance but is not well understood mechanistically. Adaptive evolution, i.e., the evolution of new biochemical activities, is rich in

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https://escholarship.org/uc/item/0rv5j6w7

Multiregion whole-exome sequencing of intraductal papillary mucinous neoplasms reveals frequent somatic KLF4mutations predominantly in low-grade regions

Autor: Fujikura, Kohei, Hosoda, Waki, Felsenstein, Mattha¨us, Song, Qianqian, Reiter, Johannes G, Zheng, Lily, Beleva Guthrie, Violeta, Rincon, Natalia, Dal Molin, Marco, Dudley, Jonathan, Cohen, Joshua D, Wang, Pei, Fischer, Catherine G, Braxton, Alicia M, Noe¨, Michae¨l, Jongepier, Martine, Fernández-del Castillo, Carlos, Mino-Kenudson, Mari, Schmidt, C Max, Yip-Schneider, Michele T, Lawlor, Rita T, Salvia, Roberto, Roberts, Nicholas J, Thompson, Elizabeth D, Karchin, Rachel, Lennon, Anne Marie, Jiao, Yuchen, Wood, Laura D

Publikováno v: Gut; 2021, Vol. 70 Issue: 5 p928-939, 12p

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Experimental and In Silico Analysis of TEM β-Lactamase Adaptive Evolution.

Autor: Standley M; Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California95064, United States., Blay V; Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California95064, United States.; Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), 46980Valencia, Spain., Beleva Guthrie V; Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland21218, United States., Kim J; Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California95064, United States., Lyman A; Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California95064, United States., Moya A; Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), 46980Valencia, Spain.; Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO), 46021Valencia, Spain.; CIBER in Epidemiology and Public Health (CIBEResp), 28029Madrid, Spain., Karchin R; Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland21218, United States., Camps M; Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California95064, United States.

Publikováno v: ACS infectious diseases [ACS Infect Dis] 2022 Dec 09; Vol. 8 (12), pp. 2451-2463. Date of Electronic Publication: 2022 Nov 14.

Genomic characterization of malignant progression in neoplastic pancreatic cysts.

Autor: Noë M; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Niknafs N; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Fischer CG; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Hackeng WM; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Department of Pathology, The University Medical Center Utrecht, Utrecht, The Netherlands., Beleva Guthrie V; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Hosoda W; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan., Debeljak M; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Papp E; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Adleff V; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., White JR; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Luchini C; Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy., Pea A; Department of Surgery - The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy., Scarpa A; Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy.; ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy., Butturini G; Department of Surgery, Pederzoli Hospital, Peschiera del Garda, Italy., Zamboni G; Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy.; Pathology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy., Castelli P; Pathology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy., Hong SM; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea., Yachida S; Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan., Hiraoka N; Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan., Gill AJ; University of Sydney, Sydney, NSW, Australia.; NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, NSW, Australia.; Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, NSW, Australia., Samra JS; University of Sydney, Sydney, NSW, Australia.; Upper Gastrointestinal Surgical Unit, Royal North Shore Hospital, Sydney, NSW, Australia.; Faculty of Medical and Health Sciences, Macquarie University, Sydney, Australia., Offerhaus GJA; Department of Pathology, The University Medical Center Utrecht, Utrecht, The Netherlands., Hoorens A; Department of Pathology, Ghent University Hospital, Ghent, Belgium., Verheij J; Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands., Jansen C; LABPON, Laboratory for Pathology Eastern Netherlands, Hengelo, The Netherlands., Adsay NV; Koc University School of Medicine, Istanbul, Turkey., Jiang W; Department of Pathology, Thomas Jefferson University, Philadelphia, PA, USA., Winter J; University Hospitals Cleveland Medical Center and Seidman Cancer Center, Cleveland, OH, USA.; Case Comprehensive Cancer Center, Cleveland, OH, USA., Albores-Saavedra J; Department of Pathology, Medica Sur Clinic and Foundation, Mexico City, Mexico., Terris B; Service de Pathologie, AP-HP, Hôpital Cochin, Université Paris Descartes, Paris, France., Thompson ED; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Roberts NJ; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Hruban RH; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Karchin R; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Scharpf RB; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Brosens LAA; Department of Pathology, The University Medical Center Utrecht, Utrecht, The Netherlands.; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands., Velculescu VE; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA., Wood LD; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. ldwood@jhmi.edu.; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. ldwood@jhmi.edu.

Publikováno v: Nature communications [Nat Commun] 2020 Aug 14; Vol. 11 (1), pp. 4085. Date of Electronic Publication: 2020 Aug 14.