C
Christopher Tomkins-Tinch
Researcher at Broad Institute
Publications - 33
Citations - 3880
Christopher Tomkins-Tinch is an academic researcher from Broad Institute. The author has contributed to research in topics: Medicine & Zika virus. The author has an hindex of 13, co-authored 27 publications receiving 2171 citations. Previous affiliations of Christopher Tomkins-Tinch include Harvard University & Rochester Institute of Technology.
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Journal ArticleDOI
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.
Leonid Yurkovetskiy,Xue Wang,Kristen E. Pascal,Christopher Tomkins-Tinch,Thomas Nyalile,Yetao Wang,Alina Baum,William E. Diehl,Ann Dauphin,Claudia Carbone,Kristen Veinotte,Shawn B. Egri,Stephen F. Schaffner,Stephen F. Schaffner,Jacob E. Lemieux,James B. Munro,Ashique Rafique,Abhi Barve,Pardis C. Sabeti,Christos A. Kyratsous,Natalya Dudkina,Kuang Shen,Jeremy Luban +22 more
TL;DR: It is shown that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin.
Journal ArticleDOI
Bioconda: sustainable and comprehensive software distribution for the life sciences.
Björn Grüning,Ryan K. Dale,Andreas Sjödin,Andreas Sjödin,Brad Chapman,Jillian Rowe,Christopher Tomkins-Tinch,Christopher Tomkins-Tinch,Renan Valieris,Johannes Köster,Johannes Köster +10 more
TL;DR: The present Bioconda, a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda, improves analysis reproducibility by allowing users to define isolated environments with defined software versions.
Journal ArticleDOI
Sustainable data analysis with Snakemake.
Felix Mölder,Kim Philipp Jablonski,Kim Philipp Jablonski,Brice Letcher,Michael B Hall,Christopher Tomkins-Tinch,Christopher Tomkins-Tinch,Vanessa Sochat,Jan Forster,Jan Forster,Soohyun Lee,Sven Twardziok,Alexander Kanitz,Alexander Kanitz,Andreas Wilm,Manuel Holtgrewe,Sven Rahmann,Sven Nahnsen,Johannes Köster,Johannes Köster +19 more
TL;DR: It is shown how the popular workflow management system Snakemake can be used to guarantee reproducibility, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.
Journal ArticleDOI
Zika virus evolution and spread in the Americas
Hayden C. Metsky,Hayden C. Metsky,Christian B. Matranga,Shirlee Wohl,Shirlee Wohl,Stephen F. Schaffner,Stephen F. Schaffner,Catherine A. Freije,Catherine A. Freije,Sarah M. Winnicki,Kendra West,James Qu,Mary Lynn Baniecki,Adrianne Gladden-Young,Aaron E. Lin,Aaron E. Lin,Christopher Tomkins-Tinch,Simon Ye,Simon Ye,Daniel J. Park,Cynthia Y. Luo,Cynthia Y. Luo,Kayla G. Barnes,Kayla G. Barnes,Rickey R. Shah,Rickey R. Shah,Bridget Chak,Bridget Chak,Giselle Barbosa-Lima,Edson Delatorre,Yasmine Rangel Vieira,Lauren M. Paul,Amanda L Tan,Carolyn M. Barcellona,Mario C. Porcelli,Chalmers Vasquez,Andrew C. Cannons,Marshall R. Cone,Kelly N. Hogan,Edgar W. Kopp,Joshua J. Anzinger,Kimberly García,Leda Parham,Rosa Margarita Gelvez Ramirez,Maria Conseulo Miranda Montoya,Diana Patricia Rojas,Catherine M. Brown,Scott Hennigan,Brandon Sabina,Sarah Scotland,Karthik Gangavarapu,Nathan D. Grubaugh,Glenn Oliveira,Refugio Robles-Sikisaka,Andrew Rambaut,Andrew Rambaut,Lee Gehrke,Lee Gehrke,Sandra Smole,M. Elizabeth Halloran,M. Elizabeth Halloran,Luis Angel Villar,Salim Mattar,Ivette Lorenzana,José Cerbino-Neto,Clarissa Valim,Clarissa Valim,Wim Degrave,Patrícia T. Bozza,Andreas Gnirke,Kristian G. Andersen,Kristian G. Andersen,Sharon Isern,Scott F. Michael,Fernando A. Bozza,Thiago Moreno L. Souza,Irene Bosch,Nathan L. Yozwiak,Nathan L. Yozwiak,Bronwyn MacInnis,Bronwyn MacInnis,Pardis C. Sabeti +81 more
TL;DR: It is found that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections.
Journal ArticleDOI
Genomic epidemiology reveals multiple introductions of Zika virus into the United States.
Nathan D. Grubaugh,Jason T. Ladner,Moritz U. G. Kraemer,Moritz U. G. Kraemer,Gytis Dudas,Amanda L Tan,Karthik Gangavarapu,Michael R. Wiley,Stephen White,Julien Thézé,Diogo M. Magnani,Karla Prieto,Karla Prieto,Daniel Reyes,Daniel Reyes,Andrea M. Bingham,Lauren M. Paul,Refugio Robles-Sikisaka,Glenn Oliveira,Darryl Pronty,Carolyn M. Barcellona,Hayden C. Metsky,Mary Lynn Baniecki,Kayla G. Barnes,Bridget Chak,Catherine A. Freije,Adrianne Gladden-Young,Andreas Gnirke,Cynthia Y. Luo,Bronwyn MacInnis,Christian B. Matranga,Daniel J. Park,James Qu,Stephen F. Schaffner,Christopher Tomkins-Tinch,Kendra West,Sarah M. Winnicki,Shirlee Wohl,Nathan L. Yozwiak,Joshua Quick,Joseph R. Fauver,Kamran Khan,Shannon E Brent,Robert C. Reiner,Paola Lichtenberger,Michael J. Ricciardi,Varian K. Bailey,David I. Watkins,Marshall R. Cone,Edgar W. Kopp,Kelly N. Hogan,Andrew C. Cannons,Reynald Jean,Andrew J. Monaghan,Robert F. Garry,Nicholas J. Loman,Nuno R. Faria,Mario C. Porcelli,Chalmers Vasquez,Elyse R. Nagle,Elyse R. Nagle,Derek A. T. Cummings,Danielle Stanek,Andrew Rambaut,Andrew Rambaut,Mariano Sanchez-Lockhart,Pardis C. Sabeti,Pardis C. Sabeti,Pardis C. Sabeti,Leah D Gillis,Scott F. Michael,Trevor Bedford,Oliver G. Pybus,Sharon Isern,Gustavo Palacios,Kristian G. Andersen,Kristian G. Andersen +76 more
TL;DR: It is shown that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016—several months before its initial detection.