Publications by authors named "Robert A Edwards"

161Publications

A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation.

Authors:
Daniel Cazares Adrian Cazares Wendy Figueroa Gabriel Guarneros Robert A Edwards Pablo Vinuesa

mSystems 2021 Feb 2;6(1). Epub 2021 Feb 2.

Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico

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February 2021

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes.

Authors:
Katelyn McNair Carol L Ecale Zhou Brian Souza Stephanie Malfatti Robert A Edwards

Microorganisms 2021 Jan 8;9(1). Epub 2021 Jan 8.

Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.

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January 2021

NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index.

Authors:
Joan Martí-Carreras Alejandro Rafael Gener Sierra D Miller Anderson F Brito Christiam E Camacho Ryan Connor Ward Deboutte Cody Glickman David M Kristensen Wynn K Meyer Sejal Modha Alexis L Norris Surya Saha Anna K Belford Evan Biederstedt James Rodney Brister Jan P Buchmann Nicholas P Cooley Robert A Edwards Kiran Javkar Michael Muchow Harihara Subrahmaniam Muralidharan Charles Pepe-Ranney Nidhi Shah Migun Shakya Michael J Tisza Benjamin J Tully Bert Vanmechelen Valerie C Virta Jake L Weissman Vadim Zalunin Alexandre Efremov Ben Busby

Viruses 2020 12 10;12(12). Epub 2020 Dec 10.

National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA.

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December 2020

PhANNs, a fast and accurate tool and web server to classify phage structural proteins.

Authors:
Vito Adrian Cantu Peter Salamon Victor Seguritan Jackson Redfield David Salamon Robert A Edwards Anca M Segall

PLoS Comput Biol 2020 11 2;16(11):e1007845. Epub 2020 Nov 2.

Computational Science Research Center, San Diego State University, San Diego, United States of America.

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November 2020

Antibody Response to a Nucleocapsid Epitope as a Marker for COVID-19 Disease Severity.

Authors:
Sanjana Sen Emily C Sanders Kristin N Gabriel Brian M Miller Hariny M Isoda Gabriela S Salcedo Jason E Garrido Rebekah P Dyer Rie Nakajima Aarti Jain Alicia M Santos Keertna Bhuvan Delia F Tifrea Joni L Ricks-Oddie Philip L Felgner Robert A Edwards Sudipta Majumdar Gregory A Weiss

bioRxiv 2020 Oct 16. Epub 2020 Oct 16.

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October 2020

Genome-Wide Asymptomatic B-Cell, CD4 and CD8 T-Cell Epitopes, that are Highly Conserved Between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Immune Targets for Pre-Emptive Pan-Coronavirus Vaccines.

Authors:
Swayam Prakash Ruchi Srivastava Pierre-Gregoire Coulon Nisha R Dhanushkodi Aziz A Chentoufi Delia F Tifrea Robert A Edwards Cesar J Figueroa Sebastian D Schubl Lanny Hsieh Michael J Buchmeier Mohammed Bouziane Anthony B Nesburn Baruch D Kuppermann Lbachir BenMohamed

bioRxiv 2020 Sep 28. Epub 2020 Sep 28.

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September 2020

Publisher Correction: Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt.

Authors:
Amber N Habowski Jessica L Flesher Jennifer M Bates Chia-Feng Tsai Kendall Martin Rui Zhao Anand K Ganesan Robert A Edwards Tujin Shi H Steven Wiley Yongsheng Shi Klemens J Hertel Marian L Waterman

Commun Biol 2020 Sep 3;3(1):495. Epub 2020 Sep 3.

Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA.

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September 2020

α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer.

Authors:
Thai Q Tran Eric A Hanse Amber N Habowski Haiqing Li Mari B Ishak Gabra Ying Yang Xazmin H Lowman Amelia M Ooi Shu Y Liao Robert A Edwards Marian L Waterman Mei Kong

Nat Cancer 2020 Mar 20;1(3):345-358. Epub 2020 Mar 20.

Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA.

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March 2020

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt.

Authors:
Amber N Habowski Jessica L Flesher Jennifer M Bates Chia-Feng Tsai Kendall Martin Rui Zhao Anand K Ganesan Robert A Edwards Tujin Shi H Steven Wiley Yongsheng Shi Klemens J Hertel Marian L Waterman

Commun Biol 2020 Aug 19;3(1):453. Epub 2020 Aug 19.

Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA.

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August 2020

A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes.

Authors:
Maria I Rojas Giselle S Cavalcanti Katelyn McNair Sean Benler Amanda T Alker Ana G Cobián-Güemes Melissa Giluso Kyle Levi Forest Rohwer Barbara A Bailey Sinem Beyhan Robert A Edwards Nicholas J Shikuma

mSystems 2020 Jul 28;5(4). Epub 2020 Jul 28.

Viral Information Institute, San Diego State University, San Diego, California, USA

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July 2020

Standardized bacteriophage purification for personalized phage therapy.

Authors:
Tiffany Luong Ann-Charlott Salabarria Robert A Edwards Dwayne R Roach

Nat Protoc 2020 09 24;15(9):2867-2890. Epub 2020 Jul 24.

Department of Biology, San Diego State University, San Diego, CA, USA.

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September 2020

The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge.

Authors:
Michael P Doane Megan M Morris Bhavya Papudeshi Lauren Allen Dnyanada Pande John M Haggerty Shaili Johri Abigail C Turnlund Meredith Peterson Dovi Kacev Andy Nosal Deni Ramirez Kevin Hovel Julia Ledbetter Amanda Alker Jackeline Avalos Kristi Baker Shruti Bhide Emma Billings Steven Byrum Molly Clemens Amelia Juliette Demery Lais Farias Oliveira Lima Oscar Gomez Omar Gutierrez Selena Hinton Donald Kieu Angie Kim Rebeca Loaiza Alexander Martinez Jordan McGhee Kristine Nguyen Sabrina Parlan Amanda Pham Rosalyn Price-Waldman Robert A Edwards Elizabeth A Dinsdale

Microbiome 2020 06 13;8(1):93. Epub 2020 Jun 13.

Biology Department, San Diego State University, San Diego, CA, USA.

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June 2020

Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics.

Authors:
Ellen Kuang Matthew Marney Daniel Cuevas Robert A Edwards Erica M Forsberg

Metabolites 2020 Apr 17;10(4). Epub 2020 Apr 17.

Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA.

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April 2020

Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents.

Authors:
Beverly J French Yan Wei Lim Brian J Zgliczynski Robert A Edwards Forest Rohwer Stuart A Sandin

Ecol Evol 2020 Apr 10;10(7):3413-3423. Epub 2020 Mar 10.

Center for Marine Biodiversity and Conservation Scripps Institution of Oceanography University of California San Diego CA USA.

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April 2020

Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network.

Authors:
Laís F O Lima Maya Weissman Micheal Reed Bhavya Papudeshi Amanda T Alker Megan M Morris Robert A Edwards Samantha J de Putron Naveen K Vaidya Elizabeth A Dinsdale

mBio 2020 03 3;11(2). Epub 2020 Mar 3.

Department of Biology, San Diego State University, San Diego, California, USA

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March 2020

Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes.

Authors:
Cynthia B Silveira Felipe H Coutinho Giselle S Cavalcanti Sean Benler Michael P Doane Elizabeth A Dinsdale Robert A Edwards Ronaldo B Francini-Filho Cristiane C Thompson Antoni Luque Forest L Rohwer Fabiano Thompson

BMC Genomics 2020 Feb 5;21(1):126. Epub 2020 Feb 5.

SAGE/COPPE, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941- 599, Brazil.

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February 2020

PHANOTATE: a novel approach to gene identification in phage genomes.

Authors:
Katelyn McNair Carol Zhou Elizabeth A Dinsdale Brian Souza Robert A Edwards

Bioinformatics 2019 11;35(22):4537-4542

Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA.

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November 2019

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Authors:
Robert A Edwards Alejandro A Vega Holly M Norman Maria Ohaeri Kyle Levi Elizabeth A Dinsdale Ondrej Cinek Ramy K Aziz Katelyn McNair Jeremy J Barr Kyle Bibby Stan J J Brouns Adrian Cazares Patrick A de Jonge Christelle Desnues Samuel L Díaz Muñoz Peter C Fineran Alexander Kurilshikov Rob Lavigne Karla Mazankova David T McCarthy Franklin L Nobrega Alejandro Reyes Muñoz German Tapia Nicole Trefault Alexander V Tyakht Pablo Vinuesa Jeroen Wagemans Alexandra Zhernakova Frank M Aarestrup Gunduz Ahmadov Abeer Alassaf Josefa Anton Abigail Asangba Emma K Billings Vito Adrian Cantu Jane M Carlton Daniel Cazares Gyu-Sung Cho Tess Condeff Pilar Cortés Mike Cranfield Daniel A Cuevas Rodrigo De la Iglesia Przemyslaw Decewicz Michael P Doane Nathaniel J Dominy Lukasz Dziewit Bashir Mukhtar Elwasila A Murat Eren Charles Franz Jingyuan Fu Cristina Garcia-Aljaro Elodie Ghedin Kristen M Gulino John M Haggerty Steven R Head Rene S Hendriksen Colin Hill Heikki Hyöty Elena N Ilina Mitchell T Irwin Thomas C Jeffries Juan Jofre Randall E Junge Scott T Kelley Mohammadali Khan Mirzaei Martin Kowalewski Deepak Kumaresan Steven R Leigh David Lipson Eugenia S Lisitsyna Montserrat Llagostera Julia M Maritz Linsey C Marr Angela McCann Shahar Molshanski-Mor Silvia Monteiro Benjamin Moreira-Grez Megan Morris Lawrence Mugisha Maite Muniesa Horst Neve Nam-Phuong Nguyen Olivia D Nigro Anders S Nilsson Taylor O'Connell Rasha Odeh Andrew Oliver Mariana Piuri Aaron J Prussin Ii Udi Qimron Zhe-Xue Quan Petra Rainetova Adán Ramírez-Rojas Raul Raya Kim Reasor Gillian A O Rice Alessandro Rossi Ricardo Santos John Shimashita Elyse N Stachler Lars C Stene Ronan Strain Rebecca Stumpf Pedro J Torres Alan Twaddle MaryAnn Ugochi Ibekwe Nicolás Villagra Stephen Wandro Bryan White Andy Whiteley Katrine L Whiteson Cisca Wijmenga Maria M Zambrano Henrike Zschach Bas E Dutilh

Nat Microbiol 2019 10 8;4(10):1727-1736. Epub 2019 Jul 8.

Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.

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October 2019

CRTAM Shapes the Gut Microbiota and Enhances the Severity of Infection.

Authors:
Araceli Perez-Lopez Sean-Paul Nuccio Irina Ushach Robert A Edwards Rachna Pahu Steven Silva Albert Zlotnik Manuela Raffatellu

J Immunol 2019 07 29;203(2):532-543. Epub 2019 May 29.

Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093;

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July 2019

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages.

Authors:
Jakub Barylski François Enault Bas E Dutilh Margo Bp Schuller Robert A Edwards Annika Gillis Jochen Klumpp Petar Knezevic Mart Krupovic Jens H Kuhn Rob Lavigne Hanna M Oksanen Matthew B Sullivan Ho Bin Jang Peter Simmonds Pakorn Aiewsakun Johannes Wittmann Igor Tolstoy J Rodney Brister Andrew M Kropinski Evelien M Adriaenssens

Syst Biol 2020 01;69(1):110-123

Department of Functional & Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK.

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January 2020