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Kalen Cantrell
Researcher at University of California, San Diego
Publications - 9
Citations - 210
Kalen Cantrell is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Biology & Microbiome. The author has an hindex of 2, co-authored 3 publications receiving 92 citations. Previous affiliations of Kalen Cantrell include University of California, Berkeley & University of Minnesota.
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Journal ArticleDOI
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.
Qiyun Zhu,Uyen Mai,Wayne Pfeiffer,Stefan Janssen,Stefan Janssen,Francesco Asnicar,Jon G. Sanders,Pedro Belda-Ferre,Gabriel A. Al-Ghalith,Evguenia Kopylova,Daniel McDonald,Tomasz Kosciolek,Tomasz Kosciolek,John Yin,Shi Huang,Nimaichand Salam,Jian-Yu Jiao,Zijun Wu,Zhenjiang Zech Xu,Kalen Cantrell,Yimeng Yang,Erfan Sayyari,Maryam Rabiee,James T. Morton,Sheila Podell,Dan Knights,Wen-Jun Li,Curtis Huttenhower,Curtis Huttenhower,Nicola Segata,Larry Smarr,Siavash Mirarab,Rob Knight +32 more
TL;DR: A reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, is built, providing an updated view of domain-level relationships between Archaea and Bacteria.
Journal ArticleDOI
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes.
George Armstrong,Kalen Cantrell,Shi Huang,Daniel McDonald,Niina Haiminen,Anna Paola Carrieri,Qiyun Zhu,Antonio Gonzalez,Imran McGrath,Kristen L. Beck,Daniel Hakim,Aki S. Havulinna,Guillaume Méric,Teemu J. Niiranen,Leo Lahti,Veikko Salomaa,Mohit Jain,Michael Inouye,Austin D. Swafford,Ho-Cheol Kim,Laxmi Parida,Yoshiki Vázquez-Baeza,Rob Knight +22 more
TL;DR: Stacked Faith's phylogenetic diversity (SFPhD) as mentioned in this paper enables the calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm.
Posted ContentDOI
EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets
Kalen Cantrell,Marcus W. Fedarko,Gibraan Rahman,Daniel McDonald,Yimeng Yang,Thant Zaw,Antonio Gonzalez,Stefan Janssen,Mehrbod Estaki,Niina Haiminen,Kristen L. Beck,Qiyun Zhu,Qiyun Zhu,Erfan Sayyari,Jamie Morton,Anupriya Tripathi,Julia M. Gauglitz,Clarisse Marotz,Clarisse Marotz,Nathaniel L. Matteson,Cameron Martino,Jon G. Sanders,Anna Paola Carrieri,Se Jin Song,Austin D. Swafford,Pieter C. Dorrestein,Pieter C. Dorrestein,Kristian G. Andersen,Laxmi Parida,Ho-Cheol Kim,Yoshiki Vázquez-Baeza,Rob Knight +31 more
TL;DR: EMPress provides novel functionality—including ordination integration and animations—alongside many standard tree visualization features, and thus simplifies exploratory analyses of many forms of ‘omic data.
Posted ContentDOI
Greengenes2 enables a shared data universe for microbiome studies
Daniel McDonald,Yueyu Jiang,M. Erdal Balaban,Kalen Cantrell,Qiyun Zhu,Antonio Gonzalez,James T. Morton,Giorgia Nicolaou,Donovan H. Parks,Søren Michael Karst,Mads Albertsen,Philip Hugenholtz,Todd Z. DeSantis,Se Jin Song,Andrew Bartko,Aki S. Havulinna,Pekka Jousilahti,Susan Cheng,Teemu J. Niiranen,Mohit P. Jain,Veikko Salomaa,Leo Lahti,Siavash Mirarab,Rob Knight +23 more
TL;DR: Greengenes2 as mentioned in this paper showed that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy, and in phenotype effect size when analyzed with the same tree.
Journal ArticleDOI
Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles
James T. Morton,Dongxue Jin,Robert H. Mills,Yan Shao,Gibraan Rahman,Daniel McDonald,Qiyun Zhu,M. Erdal Balaban,Yueyu Jiang,Kalen Cantrell,Antonio Gonzalez,Linoy Mia Frankiensztajn,Sandra Martin-Brevet,Kirsten Berding,Brittany D. Needham,María Fernanda Zurita,Maude M. David,Olga V. Averina,Alexey S. Kovtun,Antonio Noto,Michele Mussap,Mingbang Wang,Daniel N. Frank,Ellen Li,Wenhao Zhou,Vassilios Fanos,Valery N. Danilenko,Dennis P. Wall,Paul Cardenas,Manuel E. Baldeón,Sébastien Jacquemont,Omry Koren,Evan Elliott,Ramnik J. Xavier,Sarkis K. Mazmanian,Rob Knight,Jack A. Gilbert,Sharon M. Donovan,Trevor D. Lawley,Bob Carpenter,Richard Bonneau,Gaspar Taroncher-Oldenburg +41 more
TL;DR: In this paper , a Bayesian differential ranking algorithm was used to identify ASD-associated molecular and taxa profiles across 10 cross-sectional microbiome datasets and 15 other datasets, including dietary patterns, metabolomics, cytokine profiles and human brain gene expression profiles.