Yoshiki Vázquez-Baeza

Yoshiki Vázquez-Baeza

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Yoshiki Vázquez-Baeza

Yoshiki Vázquez-Baeza

Publications by authors named "Yoshiki Vázquez-Baeza"

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Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam Rivers Michael S Robeson Patrick Rosenthal Nicola Segata Michael Shaffer Arron Shiffer Rashmi Sinha Se Jin Song John R Spear Austin D Swafford Luke R Thompson Pedro J Torres Pauline Trinh Anupriya Tripathi Peter J Turnbaugh Sabah Ul-Hasan Justin J J van der Hooft Fernando Vargas Yoshiki Vázquez-Baeza Emily Vogtmann Max von Hippel William Walters Yunhu Wan Mingxun Wang Jonathan Warren Kyle C Weber Charles H D Williamson Amy D Willis Zhenjiang Zech Xu Jesse R Zaneveld Yilong Zhang Qiyun Zhu Rob Knight J Gregory Caporaso

Nat Biotechnol 2019 Sep;37(9):1091

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0252-6DOI Listing
September 2019

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam Rivers Michael S Robeson Patrick Rosenthal Nicola Segata Michael Shaffer Arron Shiffer Rashmi Sinha Se Jin Song John R Spear Austin D Swafford Luke R Thompson Pedro J Torres Pauline Trinh Anupriya Tripathi Peter J Turnbaugh Sabah Ul-Hasan Justin J J van der Hooft Fernando Vargas Yoshiki Vázquez-Baeza Emily Vogtmann Max von Hippel William Walters Yunhu Wan Mingxun Wang Jonathan Warren Kyle C Weber Charles H D Williamson Amy D Willis Zhenjiang Zech Xu Jesse R Zaneveld Yilong Zhang Qiyun Zhu Rob Knight J Gregory Caporaso

Nat Biotechnol 2019 08;37(8):852-857

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0209-9DOI Listing
August 2019

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.

Clin Gastroenterol Hepatol 2019 01 18;17(2):218-230. Epub 2018 Sep 18.

Department of Pediatrics, University of California San Diego, La Jolla, California; Center for Microbiome Innovation, University of California San Diego, La Jolla, California; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California; Department of Bioengineering, University of California San Diego, La Jolla, California. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15423565183100
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http://dx.doi.org/10.1016/j.cgh.2018.09.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391518PMC
January 2019

Striped UniFrac: enabling microbiome analysis at unprecedented scale.

Nat Methods 2018 11;15(11):847-848

Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41592-018-0187-8DOI Listing
November 2018

Guiding longitudinal sampling in IBD cohorts.

Gut 2018 09 21;67(9):1743-1745. Epub 2017 Oct 21.

Department of Computer Science and Engineering, University of California, San Diego, California, USA.

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http://dx.doi.org/10.1136/gutjnl-2017-315352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109279PMC
September 2018

Are microbiome studies ready for hypothesis-driven research?

Curr Opin Microbiol 2018 08 27;44:61-69. Epub 2018 Jul 27.

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S13695274183005
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http://dx.doi.org/10.1016/j.mib.2018.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153026PMC
August 2018

Creating a 3D microbial and chemical snapshot of a human habitat.

Sci Rep 2018 02 27;8(1):3669. Epub 2018 Feb 27.

Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.

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http://www.nature.com/articles/s41598-018-21541-4
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http://dx.doi.org/10.1038/s41598-018-21541-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829137PMC
February 2018

Impacts of the Human Gut Microbiome on Therapeutics.

Annu Rev Pharmacol Toxicol 2018 01 2;58:253-270. Epub 2017 Oct 2.

Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA; email:

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http://dx.doi.org/10.1146/annurev-pharmtox-042017-031849DOI Listing
January 2018

Bringing the Dynamic Microbiome to Life with Animations.

Cell Host Microbe 2017 Jan;21(1):7-10

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093-0404, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2016.12.009DOI Listing
January 2017

Balance Trees Reveal Microbial Niche Differentiation.

mSystems 2017 Jan-Feb;2(1). Epub 2017 Jan 17.

Department of Pediatrics, University of California San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1128/mSystems.00162-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264246PMC
January 2017

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks.

Nat Microbiol 2016 Oct 3;1:16177. Epub 2016 Oct 3.

Department of Computer Science and Engineering, University of California, San Diego 92093, USA.

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http://dx.doi.org/10.1038/nmicrobiol.2016.177DOI Listing
October 2016

Tiny microbes, enormous impacts: what matters in gut microbiome studies?

Genome Biol 2016 10 19;17(1):217. Epub 2016 Oct 19.

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1186/s13059-016-1086-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072314PMC
October 2016

From Sample to Multi-Omics Conclusions in under 48 Hours.

mSystems 2016 Mar-Apr;1(2). Epub 2016 Apr 26.

Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, California, USA; Department of Pediatrics, University of California, San Diego, San Diego, California, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA; Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA.

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http://dx.doi.org/10.1128/mSystems.00038-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069746PMC
April 2016

Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project.

J Microbiol Biol Educ 2016 Mar 1;17(1):46-50. Epub 2016 Mar 1.

Department of Pediatrics, University of California, San Diego, CA 92110; Department of Computer Science and Engineering, University of California, San Diego, CA 92093-0404.

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http://dx.doi.org/10.1128/jmbe.v17i1.1034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798814PMC
March 2016

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.

Microbiome 2015 30;3:10. Epub 2015 Mar 30.

Department of Soil, Water, and Climate, and Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN USA ; BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA.

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http://dx.doi.org/10.1186/s40168-015-0070-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378022PMC
March 2015

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water.

Water Res 2015 Feb 13;69:30-39. Epub 2014 Nov 13.

National Risk Management Research Laboratory, US. Environmental Protection Agency, Cincinnati, USA. Electronic address:

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http://dx.doi.org/10.1016/j.watres.2014.11.003DOI Listing
February 2015

Longitudinal analysis of microbial interaction between humans and the indoor environment.

Science 2014 Aug;345(6200):1048-52

Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1126/science.1254529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337996PMC
August 2014

SnapShot: the human microbiome.

Cell 2014 Jul;158(3):690-690.e1

BioFrontiers Institute, University of Colorado, Boulder, CO 80309-0596, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309-0596, USA.

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http://dx.doi.org/10.1016/j.cell.2014.07.019DOI Listing
July 2014

EMPeror: a tool for visualizing high-throughput microbial community data.

Gigascience 2013 Nov 26;2(1):16. Epub 2013 Nov 26.

BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO 80309, USA.

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http://dx.doi.org/10.1186/2047-217X-2-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076506PMC
November 2013

Meta-analyses of studies of the human microbiota.

Genome Res 2013 Oct 16;23(10):1704-14. Epub 2013 Jul 16.

Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA;

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http://dx.doi.org/10.1101/gr.151803.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787266PMC
October 2013

From molecules to dynamic biological communities.

Biol Philos 2013 Mar 5;28(2):241-259. Epub 2013 Feb 5.

Department of Computer Science, University of Colorado at Boulder, Boulder, CO USA ; BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO USA.

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http://dx.doi.org/10.1007/s10539-013-9364-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586164PMC
March 2013