T
Timothy D. Arthur
Researcher at University of California, Berkeley
Publications - 10
Citations - 714
Timothy D. Arthur is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Genome-wide association study & Microbiome. The author has an hindex of 3, co-authored 10 publications receiving 349 citations. Previous affiliations of Timothy D. Arthur include University of California, San Diego & Harvard University.
Papers
More filters
Journal ArticleDOI
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
Andrew Brantley Hall,Andrew Brantley Hall,Moran Yassour,Moran Yassour,Jenny Sauk,Jenny Sauk,Ashley L. Garner,Ashley L. Garner,Xiaofang Jiang,Xiaofang Jiang,Timothy D. Arthur,Timothy D. Arthur,Georgia K. Lagoudas,Georgia K. Lagoudas,Tommi Vatanen,Tommi Vatanen,Nadine Fornelos,Nadine Fornelos,Robin G. Wilson,Madeline Bertha,Melissa Cohen,John J. Garber,Hamed Khalili,Dirk Gevers,Dirk Gevers,Dirk Gevers,Ashwin N. Ananthakrishnan,Subramaniam Kugathasan,Eric S. Lander,Eric S. Lander,Eric S. Lander,Paul C. Blainey,Paul C. Blainey,Hera Vlamakis,Hera Vlamakis,Ramnik J. Xavier,Curtis Huttenhower,Curtis Huttenhower +37 more
TL;DR: In this article, the authors performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples) and identified strain-specific functional correlates with IBD outcomes.
Journal ArticleDOI
Global chemical effects of the microbiome include new bile-acid conjugations
Robert A. Quinn,Robert A. Quinn,Alexey V. Melnik,Alison Vrbanac,Ting Fu,Kathryn A. Patras,Mitchell P. Christy,Zsolt Bodai,Pedro Belda-Ferre,Anupriya Tripathi,Anupriya Tripathi,Lawton K. Chung,Michael Downes,Ryan D. Welch,Melissa Ann Quinn,Greg Humphrey,Morgan Panitchpakdi,Kelly C. Weldon,Kelly C. Weldon,Alexander A. Aksenov,Ricardo Silva,Julian Avila-Pacheco,Clary B. Clish,Sena Bae,Himel Mallick,Himel Mallick,Eric A. Franzosa,Eric A. Franzosa,Jason Lloyd-Price,Jason Lloyd-Price,Robert Bussell,Taren Thron,Andrew T. Nelson,Mingxun Wang,Eric C. Leszczynski,Fernando Vargas,Julia M. Gauglitz,Michael J. Meehan,Emily C. Gentry,Timothy D. Arthur,Timothy D. Arthur,Alexis C. Komor,Orit Poulsen,Brigid S. Boland,John T. Chang,William J. Sandborn,Meerana Lim,Neha Garg,Neha Garg,Julie C. Lumeng,Ramnik J. Xavier,Barbara I. Kazmierczak,Ruchi Jain,Marie E. Egan,Kyung E. Rhee,David P. Ferguson,Manuela Raffatellu,Hera Vlamakis,Gabriel G. Haddad,Dionicio Siegel,Curtis Huttenhower,Curtis Huttenhower,Sarkis K. Mazmanian,Ronald M. Evans,Victor Nizet,Victor Nizet,Rob Knight,Pieter C. Dorrestein,Pieter C. Dorrestein +68 more
TL;DR: It is found that the microbiota affects the chemistry of all organs, including amino acid conjugations of host bile acids that were used to produce phenylalanocholic acid, tyrosocholic acid and leucocholic Acid, which have not previously been characterized despite extensive research on bile-acid chemistry.
Journal ArticleDOI
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.
Jon G. Sanders,Sergey Nurk,Rodolfo A. Salido,Jeremiah J. Minich,Zhenjiang Zech Xu,Qiyun Zhu,Cameron Martino,Marcus W. Fedarko,Timothy D. Arthur,Feng Chen,Brigid S. Boland,Greg Humphrey,Caitriona Brennan,Karenina Sanders,James Gaffney,Kristen Jepsen,Mahdieh Khosroheidari,Cliff Green,Marlon Liyanage,Jason Dang,Vanessa V. Phelan,Robert A. Quinn,Robert A. Quinn,Anton Bankevich,John T. Chang,Tariq M. Rana,Douglas Conrad,William J. Sandborn,Larry Smarr,Pieter C. Dorrestein,Pieter C. Dorrestein,Pavel A. Pevzner,Rob Knight +32 more
TL;DR: A benchmark of library prep and sequencing using internal references generated by synthetic long-read technology is introduced, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves.
Journal ArticleDOI
SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues.
Matteo D’Antonio,Jennifer Nguyen,Timothy D. Arthur,Hiroko Matsui,Agnieszka D'Antonio-Chronowska,Kelly A. Frazer +5 more
TL;DR: In this article, the authors identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity, and perform genetic fine mapping to compute 99% credible SNP sets.
Posted ContentDOI
Insights into genetic factors contributing to variability in SARS-CoV-2 susceptibility and COVID-19 disease severity
Matteo D’Antonio,Timothy D. Arthur,Jennifer P. Nguyen,Hiroko Matsui,Agnieszka D'Antonio-Chronowska,Kelly A. Frazer +5 more
TL;DR: In this paper, the authors applied colocalization to compare summary statistics for 16 GWASs from the COVID-19 Host Genetics Initiative to investigate similarities and differences in their genetic signals.