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Daniel A. Cuevas
Researcher at San Diego State University
Publications - 18
Citations - 1344
Daniel A. Cuevas is an academic researcher from San Diego State University. The author has contributed to research in topics: Genome & Metagenomics. The author has an hindex of 12, co-authored 18 publications receiving 995 citations. Previous affiliations of Daniel A. Cuevas include Life Technologies.
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Journal ArticleDOI
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software
Alexander Sczyrba,Peter Hofmann,Peter Hofmann,Peter Belmann,David Koslicki,Stefan Janssen,Johannes Dröge,Johannes Dröge,Ivan Gregor,Ivan Gregor,Stephan Majda,Jessika Fiedler,Eik Dahms,Eik Dahms,Andreas Bremges,Adrian Fritz,Ruben Garrido-Oter,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Nicole Shapiro,Philip D. Blood,Alexey Gurevich,Yang Bai,Dmitrij Turaev,Matthew Z. DeMaere,Rayan Chikhi,Niranjan Nagarajan,Christopher Quince,Fernando Meyer,Monika Balvočiūtė,Lars Hestbjerg Hansen,Søren J. Sørensen,Burton Kuan Hui Chia,Bertrand Denis,Jeff Froula,Zhong Wang,Robert Egan,Dongwan Don Kang,Jeffrey J. Cook,Charles Deltel,Michael Beckstette,Claire Lemaitre,Pierre Peterlongo,Guillaume Rizk,Dominique Lavenier,Yu Wei Wu,Yu Wei Wu,Steven W. Singer,Steven W. Singer,Chirag Jain,Marc Strous,Heiner Klingenberg,Peter Meinicke,Michael D. Barton,Thomas Lingner,Hsin-Hung Lin,Yu-Chieh Liao,Genivaldo G. Z. Silva,Daniel A. Cuevas,Robert Edwards,Surya Saha,Vitor C. Piro,Vitor C. Piro,Bernhard Y. Renard,Mihai Pop,Hans-Peter Klenk,Markus Göker,Nikos C. Kyrpides,Tanja Woyke,Julia A. Vorholt,Paul Schulze-Lefert,Edward M. Rubin,Aaron E. Darling,Thomas Rattei,Alice C. McHardy +75 more
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
Journal ArticleDOI
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Robert 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,Patrick A. de Jonge,Christelle Desnues,Samuel L. Díaz Muñoz,Samuel L. Díaz Muñoz,Peter C. Fineran,Alexander Kurilshikov,Rob Lavigne,Karla Mazankova,David Thomas McCarthy,Franklin L. Nobrega,Alejandro Reyes Muñoz,German Tapia,Nicole Trefault,Alexander V. Tyakht,Pablo Vinuesa,Jeroen Wagemans,Alexandra Zhernakova,Frank Møller Aarestrup,Gunduz Ahmadov,Abeer Alassaf,Josefa Antón,Abigail E. Asangba,Emma 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 M. A. P. Franz,Jingyuan Fu,Cristina García-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 M. Kowalewski,Deepak Kumaresan,Steven R. Leigh,David A. Lipson,Eugenia S. Lisitsyna,Montserrat Llagostera,Julia M. Maritz,Linsey C. Marr,Angela McCann,Shahar Molshanski-Mor,Silvia Monteiro,Benjamin Moreira-Grez,Megan M. Morris,Lawrence Mugisha,Maite Muniesa,Horst Neve,Nam Nguyen,Olivia D. Nigro,Anders S. Nilsson,Taylor O'Connell,Rasha Odeh,Andrew Oliver,Mariana Piuri,Aaron J. Prussin,Udi Qimron,Zhe Xue Quan,Petra Rainetova,Adán Ramírez-Rojas,Raúl R. Raya,Kim Reasor,Gillian A.O. Rice,Alessandro Rossi,Alessandro Rossi,Ricardo Santos,John Shimashita,Elyse Stachler,Lars C. Stene,Ronan Strain,Rebecca M. Stumpf,Pedro J. Torres,Alan Twaddle,Mary Ann Ugochi Ibekwe,Nicolás A. Villagra,Stephen Wandro,Bryan A. White,Andrew S. Whiteley,Katrine Whiteson,Cisca Wijmenga,María Mercedes Zambrano,Henrike Zschach,Bas E. Dutilh,Bas E. Dutilh +120 more
TL;DR: It is concluded that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
Journal ArticleDOI
Accessing the SEED Genome Databases via Web Services API: Tools for Programmers
Terry Disz,Terry Disz,Sajia Akhter,Daniel A. Cuevas,Robert Olson,Ross Overbeek,Veronika Vonstein,Rick Stevens,Robert Edwards,Robert Edwards +9 more
TL;DR: A novel approach to access the SEED database using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once.
Journal ArticleDOI
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
TL;DR: FOCUS is introduced, an agile composition based approach using non-negative least squares (NNLS) to report the organisms present in metagenomic samples and profile their abundances and the results show that the approach accurately predicts the organism present in microbial communities.
Posted ContentDOI
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Robert 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,Patrick A. de Jonge,Christelle Desnues,Samuel L. Díaz Muñoz,Samuel L. Díaz Muñoz,Peter C. Fineran,Alexander Kurilshikov,Rob Lavigne,Karla Mazankova,David Thomas McCarthy,Franklin L. Nobrega,Alejandro Reyes Muñoz,German Tapia,Nicole Trefault,Alexander V. Tyakht,Pablo Vinuesa,Jeroen Wagemans,Alexandra Zhernakova,Frank Møller Aarestrup,Gunduz Ahmadov,Abeer Alassaf,Josefa Antón,Abigail E. Asangba,Emma 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 M. A. P. Franz,Jingyuan Fu,Cristina García-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,Martin M. Kowalewski,Deepak Kumaresan,Steven R. Leigh,Eugenia S. Lisitsyna,Montserrat Llagostera,Julia M. Maritz,Linsey C. Marr,Angela McCann,Mohammadali Khan Mirzaei,Shahar Molshanski-Mor,Silvia Monteiro,Ben Moreira-Grez,Megan M. Morris,Lawrence Mugisha,Maite Muniesa,Horst Neve,Nam Nguyen,Olivia D. Nigro,Anders S. Nilsson,Taylor O'Connell,Rasha Odeh,Andrew Oliver,Mariana Piuri,Aaron J. Prussin,Udi Qimron,Zhe Xue Quan,Petra Rainetova,Adán Ramírez-Rojas,Raúl R. Raya,Gillian A.O. Rice,Alessandro Rossi,Alessandro Rossi,Ricardo Santos,John Shimashita,Elyse Stachler,Lars C. Stene,Ronan Strain,Rebecca M. Stumpf,Pedro J. Torres,Alan Twaddle,Mary Ann Ugochi Ibekwe,Nicolás A. Villagra,Stephen Wandro,Bryan A. White,Andrew S. Whiteley,Katrine Whiteson,Cisca Wijmenga,María Mercedes Zambrano,Henrike Zschach,Bas E. Dutilh,Bas E. Dutilh +118 more
TL;DR: It is concluded that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.