Rob Knight

Rob Knight

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Rob Knight

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Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi.

Am J Primatol 2019 Oct 20;81(10-11):e22989. Epub 2019 May 20.

Anthropology, Northwestern University, Evanston, Illinois.

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http://dx.doi.org/10.1002/ajp.22989DOI Listing
October 2019

Species abundance information improves sequence taxonomy classification accuracy.

Nat Commun 2019 Oct 11;10(1):4643. Epub 2019 Oct 11.

Research School of Biology, Australian National University, Canberra, Australia.

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http://dx.doi.org/10.1038/s41467-019-12669-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789115PMC
October 2019

Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced Obesity.

Mol Cell Proteomics 2019 Sep 1;18(9):1864-1879. Epub 2019 Jul 1.

‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA

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http://dx.doi.org/10.1074/mcp.RA119.001623DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731084PMC
September 2019

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

Expanding the scope and scale of microbiome research.

Genome Biol 2019 09 5;20(1):191. Epub 2019 Sep 5.

Department of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s13059-019-1804-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6729039PMC
September 2019

Challenges in the construction of knowledge bases for human microbiome-disease associations.

Microbiome 2019 Sep 5;7(1):129. Epub 2019 Sep 5.

Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1186/s40168-019-0742-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728997PMC
September 2019

Gut microbiome in serious mental illnesses: A systematic review and critical evaluation.

Schizophr Res 2019 Sep 5. Epub 2019 Sep 5.

Department of Psychiatry, University of California San Diego, CA, United States of America; Center for Microbiome Innovation, University of California San Diego, CA, United States of America; Department of Neurosciences, University of California San Diego, CA, United States of America; Sam and Rose Stein Institute for Research on Aging, University of California San Diego, CA, United States of America.

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http://dx.doi.org/10.1016/j.schres.2019.08.026DOI 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

Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy".

MBio 2019 Aug 6;10(4). Epub 2019 Aug 6.

Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China

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http://dx.doi.org/10.1128/mBio.01234-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686038PMC
August 2019

A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children.

mSystems 2019 Aug 20;4(4). Epub 2019 Aug 20.

Single-Cell Center and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China

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http://dx.doi.org/10.1128/mSystems.00293-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6702293PMC
August 2019

Red Sea SAR11 and Single-Cell Genomes Reflect Globally Distributed Pangenomes.

Appl Environ Microbiol 2019 Jul 17;85(13). Epub 2019 Jun 17.

Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

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http://aem.asm.org/lookup/doi/10.1128/AEM.00369-19
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http://dx.doi.org/10.1128/AEM.00369-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581160PMC
July 2019

Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary.

Biotechniques 2019 Jul 24;67(1):29-32. Epub 2019 May 24.

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

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https://www.future-science.com/doi/10.2144/btn-2018-0192
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http://dx.doi.org/10.2144/btn-2018-0192DOI Listing
July 2019

Is there convergence of gut microbes in blood-feeding vertebrates?

Philos Trans R Soc Lond B Biol Sci 2019 Jul 3;374(1777):20180249. Epub 2019 Jun 3.

15 Department of Ecology and Evolutionary Biology, University of Colorado Boulder , Boulder, CO 80309 , USA.

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http://dx.doi.org/10.1098/rstb.2018.0249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6560276PMC
July 2019

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.

PLoS Comput Biol 2019 Jul 25;15(7):e1007007. Epub 2019 Jul 25.

Data Science Hub, San Diego Supercomputer Center, UC San Diego, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657818PMC
July 2019

Role of the microbiome in human development.

Gut 2019 06 22;68(6):1108-1114. Epub 2019 Jan 22.

Department of Medicine, New York University Langone Medical Center, New York City, New York, USA.

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http://dx.doi.org/10.1136/gutjnl-2018-317503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580755PMC
June 2019

Establishing microbial composition measurement standards with reference frames.

Nat Commun 2019 06 20;10(1):2719. Epub 2019 Jun 20.

Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1038/s41467-019-10656-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586903PMC
June 2019

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research.

mSystems 2019 Jun 25;4(4). Epub 2019 Jun 25.

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

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http://dx.doi.org/10.1128/mSystems.00186-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6593221PMC
June 2019

redbiom: a Rapid Sample Discovery and Feature Characterization System.

mSystems 2019 Jun 25;4(4). Epub 2019 Jun 25.

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

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http://dx.doi.org/10.1128/mSystems.00215-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6593222PMC
June 2019

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue.

J Forensic Sci 2019 May 8;64(3):791-798. Epub 2018 Nov 8.

City and County of Honolulu Department of the Medical Examiner, 835 Iwilei Street, Honolulu, 96817, HI.

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http://dx.doi.org/10.1111/1556-4029.13949DOI Listing
May 2019

Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults.

mSystems 2019 Jul-Aug;4(4). Epub 2019 May 14.

Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1128/mSystems.00261-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6517691PMC
May 2019

Engineering the microbiome for animal health and conservation.

Exp Biol Med (Maywood) 2019 Apr 18;244(6):494-504. Epub 2019 Feb 18.

1 Department of Pediatrics, University of California, San Diego, CA 92093, USA.

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http://dx.doi.org/10.1177/1535370219830075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547002PMC
April 2019

Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects.

Schizophr Res 2019 02 26;204:23-29. Epub 2018 Sep 26.

Department of Psychiatry, University of California San Diego, CA, United States of America; Sam and Rose Stein Institute for Research on Aging, University of California San Diego, CA, United States of America; Center for Microbiome Innovation, University of California San Diego, CA, United States of America; Department of Neurosciences, University of California San Diego, CA, United States of America. Electronic address:

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http://dx.doi.org/10.1016/j.schres.2018.09.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755901PMC
February 2019

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations.

Trends Microbiol 2019 02 26;27(2):105-117. Epub 2018 Nov 26.

Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA, Australia.

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http://dx.doi.org/10.1016/j.tim.2018.11.003DOI Listing
February 2019

FXR Regulates Intestinal Cancer Stem Cell Proliferation.

Cell 2019 Feb;176(5):1098-1112.e18

Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.01.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6701863PMC
February 2019

A Novel Sparse Compositional Technique Reveals Microbial Perturbations.

mSystems 2019 Jan-Feb;4(1). Epub 2019 Feb 12.

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

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http://dx.doi.org/10.1128/mSystems.00016-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372836PMC
February 2019

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month.

Microbiome 2019 02 27;7(1):34. Epub 2019 Feb 27.

Department of Environmental Exposure and Epidemiology, Infection Control and Environmental Health, Norwegian Institute of Public Health, PO Box 222, Skøyen, 0213, Oslo, Norway.

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http://dx.doi.org/10.1186/s40168-019-0645-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393990PMC
February 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

Comparison of Oral Collection Methods for Studies of Microbiota.

Cancer Epidemiol Biomarkers Prev 2019 01 27;28(1):137-143. Epub 2018 Sep 27.

Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland.

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http://dx.doi.org/10.1158/1055-9965.EPI-18-0312DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324947PMC
January 2019

Disease-modifying therapies alter gut microbial composition in MS.

Neurol Neuroimmunol Neuroinflamm 2019 01 26;6(1):e517. Epub 2018 Oct 26.

Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York.

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http://dx.doi.org/10.1212/NXI.0000000000000517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278850PMC
January 2019

Calour: an Interactive, Microbe-Centric Analysis Tool.

mSystems 2019 Jan-Feb;4(1). Epub 2019 Jan 29.

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

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http://dx.doi.org/10.1128/mSystems.00269-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351725PMC
January 2019

Publisher Correction: The gut-liver axis and the intersection with the microbiome.

Nat Rev Gastroenterol Hepatol 2018 12;15(12):785

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

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http://dx.doi.org/10.1038/s41575-018-0031-8DOI Listing
December 2018

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

Identifying and Predicting Novelty in Microbiome Studies.

MBio 2018 11 13;9(6). Epub 2018 Nov 13.

Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China

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http://dx.doi.org/10.1128/mBio.02099-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234870PMC
November 2018

Evaluating the Information Content of Shallow Shotgun Metagenomics.

mSystems 2018 Nov-Dec;3(6). Epub 2018 Nov 13.

Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA.

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http://msystems.asm.org/lookup/doi/10.1128/mSystems.00069-18
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http://dx.doi.org/10.1128/mSystems.00069-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234283PMC
November 2018

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus.

BMC Microbiol 2018 11 26;18(1):197. Epub 2018 Nov 26.

Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, MC 0760, La Jolla, CA, 92093-0760, USA.

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https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s128
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http://dx.doi.org/10.1186/s12866-018-1341-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260558PMC
November 2018

Preserving microbial diversity.

Science 2018 Oct;362(6410):33-34

Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, NY 10016, USA.

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http://www.sciencemag.org/lookup/doi/10.1126/science.aau8816
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http://dx.doi.org/10.1126/science.aau8816DOI Listing
October 2018

Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis.

Eur Psychiatry 2018 09 2;53:37-45. Epub 2018 Jun 2.

Department of Psychiatry, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Mental Health Institute of Central South University, Changsha, Hunan 410011, China; China National Clinical Research Center on Mental Disorders (Xiangya), Changsha, Hunan 410011, China; China National Technology Institute on Mental Disorders, Changsha, Hunan 410011, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09249338183010
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http://dx.doi.org/10.1016/j.eurpsy.2018.05.011DOI Listing
September 2018

Author Correction: Inflammation-induced IgA cells dismantle anti-liver cancer immunity.

Nature 2018 09;561(7721):E1

Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, California, 92093, USA.

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http://dx.doi.org/10.1038/s41586-018-0304-yDOI Listing
September 2018

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics.

Genome Biol Evol 2018 08 1;10(8):1927-1939. Epub 2018 Aug 1.

Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst.

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http://dx.doi.org/10.1093/gbe/evy133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101598PMC
August 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

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota.

Nat Commun 2018 07 19;9(1):2832. Epub 2018 Jul 19.

State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China.

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http://dx.doi.org/10.1038/s41467-018-05284-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053391PMC
July 2018

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism.

Nat Commun 2018 07 20;9(1):2872. Epub 2018 Jul 20.

Regulatory Biology Laboratory, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1038/s41467-018-05336-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054678PMC
July 2018

Methods for phylogenetic analysis of microbiome data.

Nat Microbiol 2018 06 24;3(6):652-661. Epub 2018 May 24.

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

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http://dx.doi.org/10.1038/s41564-018-0156-0DOI Listing
June 2018

The gut microbiome of nonhuman primates: Lessons in ecology and evolution.

Am J Primatol 2018 06 4;80(6):e22867. Epub 2018 Jun 4.

Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota.

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http://dx.doi.org/10.1002/ajp.22867DOI Listing
June 2018

Ancient Diet: Gut Microbiota, Immunity, and Health.

Yale J Biol Med 2018 06 28;91(2):177-184. Epub 2018 Jun 28.

Department of Food Science, The Pennsylvania State University, University Park, PA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020729PMC
June 2018

Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas.

Cell Syst 2018 05 16;6(5):579-592.e4. Epub 2018 May 16.

Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.04.010DOI Listing
May 2018

Bacterial community changes in an industrial algae production system.

Algal Res 2018 Apr 21;31:147-156. Epub 2018 Feb 21.

Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523-1005 USA.

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http://dx.doi.org/10.1016/j.algal.2017.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959032PMC
April 2018