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Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance.
Published in:
eLife, 2015, p. 1, doi. 10.7554/eLife.04634.001
By:
- Bokulich, Nicholas A.;
- Mills, David A.;
- Bergsveinson, Jordyn;
- Ziola, Barry
Publication type:
Article
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Published in:
2019
By:
- Bolyen, Evan;
- Rideout, Jai Ram;
- Dillon, Matthew R.;
- Bokulich, Nicholas A.;
- Abnet, Christian C.;
- Al-Ghalith, Gabriel A.;
- Alexander, Harriet;
- Alm, Eric J.;
- Arumugam, Manimozhiyan;
- Asnicar, Francesco;
- Bai, Yang;
- Bisanz, Jordan E.;
- Bittinger, Kyle;
- Brejnrod, Asker;
- Brislawn, Colin J.;
- Brown, C. Titus;
- Callahan, Benjamin J.;
- Caraballo-Rodríguez, Andrés Mauricio;
- Chase, John;
- Cope, Emily K.
Publication type:
Correction Notice
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Published in:
2019
By:
- Bolyen, Evan;
- Rideout, Jai Ram;
- Dillon, Matthew R.;
- Bokulich, Nicholas A.;
- Abnet, Christian C.;
- Al-Ghalith, Gabriel A.;
- Alexander, Harriet;
- Alm, Eric J.;
- Arumugam, Manimozhiyan;
- Asnicar, Francesco;
- Bai, Yang;
- Bisanz, Jordan E.;
- Bittinger, Kyle;
- Brejnrod, Asker;
- Brislawn, Colin J.;
- Brown, C. Titus;
- Callahan, Benjamin J.;
- Caraballo-Rodríguez, Andrés Mauricio;
- Chase, John;
- Cope, Emily K.
Publication type:
Letter
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.
Published in:
Nature Methods, 2013, v. 10, n. 1, p. 57, doi. 10.1038/nmeth.2276
By:
- Bokulich, Nicholas A;
- Subramanian, Sathish;
- Faith, Jeremiah J;
- Gevers, Dirk;
- Gordon, Jeffrey I;
- Knight, Rob;
- Mills, David A;
- Caporaso, J Gregory
Publication type:
Article
Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue.
Published in:
Bioinformatics, 2022, v. 38, n. 22, p. 5081, doi. 10.1093/bioinformatics/btac639
By:
- Ziemski, Michal;
- Adamov, Anja;
- Kim, Lina;
- Flörl, Lena;
- Bokulich, Nicholas A
Publication type:
Article
Monitoring Seasonal Changes in Winery-Resident Microbiota.
Published in:
PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0066437
By:
- Bokulich, Nicholas A.;
- Ohta, Moe;
- Richardson, Paul M.;
- Mills, David A.
Publication type:
Article
Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice.
Published in:
PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0047416
By:
- Ma, Betty W.;
- Bokulich, Nicholas A.;
- Castillo, Patricia A.;
- Kananurak, Anchasa;
- Underwood, Mark A.;
- Mills, David A.;
- Bevins, Charles L.
Publication type:
Article
Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine.
Published in:
PLoS ONE, 2012, v. 7, n. 5, p. 1, doi. 10.1371/journal.pone.0036357
By:
- Bokulich, Nicholas A.;
- Joseph, C. M. Lucy;
- Allen, Greg;
- Benson, Andrew K.;
- Mills, David A.
Publication type:
Article
Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale.
Published in:
PLoS ONE, 2012, v. 7, n. 4, p. 1, doi. 10.1371/journal.pone.0035507
By:
- Bokulich, Nicholas A.;
- Bamforth, Charles W.;
- Mills, David A.
Publication type:
Article
Editorial: Genomics and metagenomics approaches for food value chain quality, safety, and product development.
Published in:
Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.1056796
By:
- Barretto, Caroline;
- Combrisson, Jerome;
- Bokulich, Nicholas
Publication type:
Article
Species abundance information improves sequence taxonomy classification accuracy.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-12669-6
By:
- Kaehler, Benjamin D.;
- Bokulich, Nicholas A.;
- McDonald, Daniel;
- Knight, Rob;
- Caporaso, J. Gregory;
- Huttley, Gavin A.
Publication type:
Article
Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment.
Published in:
PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009876
By:
- Bokulich, Nicholas A.;
- Łaniewski, Paweł;
- Adamov, Anja;
- Chase, Dana M.;
- Caporaso, J. Gregory;
- Herbst-Kralovetz, Melissa M.
Publication type:
Article
RESCRIPt: Reproducible sequence taxonomy reference database management.
Published in:
PLoS Computational Biology, 2021, v. 17, n. 11, p. 1, doi. 10.1371/journal.pcbi.1009581
By:
- Robeson II, Michael S.;
- O'Rourke, Devon R.;
- Kaehler, Benjamin D.;
- Ziemski, Michal;
- Dillon, Matthew R.;
- Foster, Jeffrey T.;
- Bokulich, Nicholas A.
Publication type:
Article
Oral microbial community composition is associated with pancreatic cancer: A case‐control study in Iran.
Published in:
Cancer Medicine, 2020, v. 9, n. 2, p. 797, doi. 10.1002/cam4.2660
By:
- Vogtmann, Emily;
- Han, Yongli;
- Caporaso, J. Gregory;
- Bokulich, Nicholas;
- Mohamadkhani, Ashraf;
- Moayyedkazemi, Alireza;
- Hua, Xing;
- Kamangar, Farin;
- Wan, Yunhu;
- Suman, Shalabh;
- Zhu, Bin;
- Hutchinson, Amy;
- Dagnall, Casey;
- Jones, Kristine;
- Hicks, Belynda;
- Shi, Jianxin;
- Malekzadeh, Reza;
- Abnet, Christian C.;
- Pourshams, Akram
Publication type:
Article
Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development.
Published in:
Cancer Medicine, 2019, v. 8, n. 2, p. 617, doi. 10.1002/cam4.1965
By:
- Pearson, Talima;
- Caporaso, J. Gregory;
- Yellowhair, Monica;
- Bokulich, Nicholas A.;
- Padi, Megha;
- Roe, Denise J.;
- Wertheim, Betsy C.;
- Linhart, Mark;
- Martinez, Jessica A.;
- Bilagody, Cherae;
- Hornstra, Heidie;
- Alberts, David S.;
- Lance, Peter;
- Thompson, Patricia A.
Publication type:
Article
Loss of HDAC6 alters gut microbiota and worsens obesity.
Published in:
FASEB Journal, 2019, v. 33, n. 1, p. 1098, doi. 10.1096/fj.201701586R
By:
- Lieber, Arnon D.;
- Beier, Ulf H.;
- Haiyan Xiao;
- Wilkins, Benjamin J.;
- Jing Jiao;
- Li, Xinmin S.;
- Schugar, Rebecca C.;
- Strauch, Christopher M.;
- Zeneng Wang;
- Brown, J. Mark;
- Hazen, Stanley L.;
- Bokulich, Nicholas A.;
- Ruggles, Kelly V.;
- Akimova, Tatiana;
- Hancock, Wayne W.;
- Blaser, Martin J.
Publication type:
Article
Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women.
Published in:
2018
By:
- Alemán, José O.;
- Bokulich, Nicholas A.;
- Swann, Jonathan R.;
- Walker, Jeanne M.;
- De Rosa, Joel Correa;
- Battaglia, Thomas;
- Costabile, Adele;
- Pechlivanis, Alexandros;
- Liang, Yupu;
- Breslow, Jan L.;
- Blaser, Martin J.;
- Holt, Peter R.;
- Alemán, José O
Publication type:
journal article
Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment.
Published in:
Nature Communications, 2015, v. 6, n. 6, p. 7486, doi. 10.1038/ncomms8486
By:
- Nobel, Yael R.;
- Cox, Laura M.;
- Kirigin, Francis F.;
- Bokulich, Nicholas A.;
- Yamanishi, Shingo;
- Teitler, Isabel;
- Chung, Jennifer;
- Sohn, Jiho;
- Barber, Cecily M.;
- Goldfarb, David S.;
- Raju, Kartik;
- Abubucker, Sahar;
- Zhou, Yanjiao;
- Ruiz, Victoria E.;
- Li, Huilin;
- Mitreva, Makedonka;
- Alekseyenko, Alexander V.;
- Weinstock, George M.;
- Sodergren, Erica;
- Blaser, Martin J.
Publication type:
Article
Antibiotics, birth mode, and diet shape microbiome maturation during early life.
Published in:
Science Translational Medicine, 2016, v. 8, n. 343, p. 1, doi. 10.1126/scitranslmed.aad7121
By:
- Bokulich, Nicholas A.;
- Chung, Jennifer;
- Battaglia, Thomas;
- Henderson, Nora;
- Jay, Melanie;
- Huilin Li;
- Lieber, Arnon D.;
- Fen Wu;
- Perez-Perez, Guillermo I.;
- Yu Chen;
- Schweizer, William;
- Xuhui Zheng;
- Contreras, Monica;
- Dominguez-Bello, Maria Gloria;
- Blaser, Martin J.
Publication type:
Article
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum.
Published in:
NPJ Biofilms & Microbiomes, 2023, v. 9, n. 1, p. 1, doi. 10.1038/s41522-023-00404-5
By:
- Shin, Hakdong;
- Martinez II, Keith A.;
- Henderson, Nora;
- Jay, Melanie;
- Schweizer, William;
- Bogaert, Debby;
- Park, Gwoncheol;
- Bokulich, Nicholas A.;
- Blaser, Martin J.;
- Dominguez-Bello, Maria Gloria
Publication type:
Article
Prebiotic oligosaccharides in premature infants.
Published in:
2014
By:
- Underwood, Mark A;
- Kalanetra, Karen M;
- Bokulich, Nicholas A;
- Mirmiran, Majid;
- Barile, Daniela;
- Tancredi, Daniel J;
- German, J Bruce;
- Lebrilla, Carlito B;
- Mills, David A
Publication type:
Journal Article
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.
Published in:
Microbiome, 2018, v. 6, n. 1, p. N.PAG, doi. 10.1186/s40168-018-0470-z
By:
- Bokulich, Nicholas A.;
- Kaehler, Benjamin D.;
- Rideout, Jai Ram;
- Dillon, Matthew;
- Bolyen, Evan;
- Knight, Rob;
- Huttley, Gavin A.;
- Gregory Caporaso, J.
Publication type:
Article
Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences.
Published in:
Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.644487
By:
- Ziemski, Michal;
- Wisanwanichthan, Treepop;
- Bokulich, Nicholas A.;
- Kaehler, Benjamin D.
Publication type:
Article
Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.
Published in:
Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2021.673810
By:
- Griggs, Reid G.;
- Steenwerth, Kerri L.;
- Mills, David A.;
- Cantu, Dario;
- Bokulich, Nicholas A.
Publication type:
Article
Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?
Published in:
Evolutionary Applications, 2020, v. 13, n. 8, p. 1984, doi. 10.1111/eva.12956
By:
- Kaplan, Ian;
- Bokulich, Nicholas A.;
- Caporaso, J. Gregory;
- Enders, Laramy S.;
- Ghanem, Wadih;
- Ingerslew, Kathryn S.
Publication type:
Article
Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet.
Published in:
Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0297-9
By:
- Mahana, Douglas;
- Trent, Chad M.;
- Kurtz, Zachary D.;
- Bokulich, Nicholas A.;
- Battaglia, Thomas;
- Chung, Jennifer;
- Müller, Christian L.;
- Huilin Li;
- Bonneau, Richard A.;
- Blaser, Martin J.
Publication type:
Article
A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses.
Published in:
Ecology & Evolution (20457758), 2020, v. 10, n. 18, p. 9721, doi. 10.1002/ece3.6594
By:
- O'Rourke, Devon R.;
- Bokulich, Nicholas A.;
- Jusino, Michelle A.;
- MacManes, Matthew D.;
- Foster, Jeffrey T.
Publication type:
Article
Infant behavioral state and stool microbiome in infants receiving Lactocaseibacillus rhamnosus GG in formula: randomized controlled trial.
Published in:
2022
By:
- Shulman, Robert J.;
- Chichlowski, Maciej;
- Orozco, Fabiola Gutierrez;
- Harris, Cheryl L.;
- Wampler, Jennifer L.;
- Bokulich, Nicholas A.;
- Berseth, Carol Lynn
Publication type:
journal article

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