| Year |
Citation |
Score |
| 2021 |
Ziemski M, Wisanwanichthan T, Bokulich NA, Kaehler BD. Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences. Frontiers in Microbiology. 12: 644487. PMID 34220738 DOI: 10.3389/fmicb.2021.644487 |
0.612 |
|
| 2021 |
Dillon MR, Bolyen E, Adamov A, Belk A, Borsom E, Burcham Z, Debelius JW, Deel H, Emmons A, Estaki M, Herman C, Keefe CR, Morton JT, Oliveira RRM, Sanchez A, ... Bokulich NA, et al. Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. Plos Computational Biology. 17: e1009056. PMID 34166363 DOI: 10.1371/journal.pcbi.1009056 |
0.589 |
|
| 2021 |
Chichlowski M, Bokulich N, Harris CL, Wampler JL, Li F, Berseth CL, Rudolph C, Wu SS. Effect of Bovine Milk Fat Globule Membrane and Lactoferrin in Infant Formula on Gut Microbiome and Metabolome at 4 Months of Age. Current Developments in Nutrition. 5: nzab027. PMID 33981943 DOI: 10.1093/cdn/nzab027 |
0.616 |
|
| 2021 |
Griggs RG, Steenwerth KL, Mills DA, Cantu D, Bokulich NA. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing. Frontiers in Microbiology. 12: 673810. PMID 33927711 DOI: 10.3389/fmicb.2021.673810 |
0.724 |
|
| 2021 |
Morton JT, McDonald D, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, et al. Reply to: Examining microbe-metabolite correlations by linear methods. Nature Methods. PMID 33398188 DOI: 10.1038/s41592-020-01007-0 |
0.589 |
|
| 2020 |
Bolyen E, Dillon MR, Bokulich NA, Ladner JT, Larsen BB, Hepp CM, Lemmer D, Sahl JW, Sanchez A, Holdgraf C, Sewell C, Choudhury AG, Stachurski J, McKay M, Engelthaler DM, et al. Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity. F1000research. 9: 657. PMID 33500774 DOI: 10.12688/F1000Research.24751.1 |
0.605 |
|
| 2020 |
Bokulich NA, Ziemski M, Robeson MS, Kaehler BD. Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. Computational and Structural Biotechnology Journal. 18: 4048-4062. PMID 33363701 DOI: 10.1016/j.csbj.2020.11.049 |
0.634 |
|
| 2020 |
O'Rourke DR, Bokulich NA, Jusino MA, MacManes MD, Foster JT. A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses. Ecology and Evolution. 10: 9721-9739. PMID 33005342 DOI: 10.1002/Ece3.6594 |
0.659 |
|
| 2020 |
Kaplan I, Bokulich NA, Caporaso JG, Enders LS, Ghanem W, Ingerslew KS. Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? Evolutionary Applications. 13: 1984-1999. PMID 32908599 DOI: 10.1111/Eva.12956 |
0.621 |
|
| 2020 |
Ladner JT, Larsen BB, Bowers JR, Hepp CM, Bolyen E, Folkerts M, Sheridan K, Pfeiffer A, Yaglom H, Lemmer D, Sahl JW, Kaelin EA, Maqsood R, Bokulich NA, Quirk G, et al. An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona. Mbio. 11. PMID 32887735 DOI: 10.1128/Mbio.02107-20 |
0.64 |
|
| 2020 |
Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R. QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data. Current Protocols in Bioinformatics. 70: e100. PMID 32343490 DOI: 10.1002/Cpbi.100 |
0.652 |
|
| 2019 |
Vogtmann E, Han Y, Caporaso JG, Bokulich N, Mohamadkhani A, Moayyedkazemi A, Hua X, Kamangar F, Wan Y, Suman S, Zhu B, Hutchinson A, Dagnall C, Jones K, Hicks B, et al. Oral microbial community composition is associated with pancreatic cancer: A case-control study in Iran. Cancer Medicine. PMID 31750624 DOI: 10.1002/Cam4.2660 |
0.605 |
|
| 2019 |
Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, et al. Learning representations of microbe-metabolite interactions. Nature Methods. PMID 31686038 DOI: 10.1038/S41592-019-0616-3 |
0.622 |
|
| 2019 |
Kaehler BD, Bokulich NA, McDonald D, Knight R, Caporaso JG, Huttley GA. Species abundance information improves sequence taxonomy classification accuracy. Nature Communications. 10: 4643. PMID 31604942 DOI: 10.1038/s41467-019-12669-6 |
0.611 |
|
| 2019 |
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, et al. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. PMID 31399723 DOI: 10.1038/S41587-019-0252-6 |
0.577 |
|
| 2019 |
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. PMID 31341288 DOI: 10.1038/S41587-019-0209-9 |
0.573 |
|
| 2019 |
Bokulich NA, Maldonado J, Kang DW, Krajmalnik-Brown R, Caporaso JG. Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles. Msphere. 4. PMID 30971445 DOI: 10.1128/mSphere.00208-19 |
0.644 |
|
| 2019 |
Pearson T, Caporaso JG, Yellowhair M, Bokulich NA, Padi M, Roe DJ, Wertheim BC, Linhart M, Martinez JA, Bilagody C, Hornstra H, Alberts DS, Lance P, Thompson PA. Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development. Cancer Medicine. PMID 30652422 DOI: 10.1002/Cam4.1965 |
0.631 |
|
| 2018 |
Bokulich NA, Dillon MR, Bolyen E, Kaehler BD, Huttley GA, Caporaso JG. q2-sample-classifier: machine-learning tools for microbiome classification and regression. Journal of Open Research Software. 3. PMID 31552137 DOI: 10.21105/joss.00934 |
0.59 |
|
| 2018 |
Bokulich NA, Dillon MR, Zhang Y, Rideout JR, Bolyen E, Li H, Albert PS, Caporaso JG. q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data. Msystems. 3. PMID 30505944 DOI: 10.1128/mSystems.00219-18 |
0.618 |
|
| 2018 |
Alemán JO, Bokulich NA, Swann JR, Walker JM, De Rosa JC, Battaglia T, Costabile A, Pechlivanis A, Liang Y, Breslow JL, Blaser MJ, Holt PR. Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women. Journal of Translational Medicine. 16: 244. PMID 30176893 DOI: 10.1186/S12967-018-1619-Z |
0.59 |
|
| 2018 |
Lieber AD, Beier UH, Xiao H, Wilkins BJ, Jiao J, Li XS, Schugar RC, Strauch CM, Wang Z, Brown JM, Hazen SL, Bokulich NA, Ruggles KV, Akimova T, Hancock WW, et al. Loss of HDAC6 alters gut microbiota and worsens obesity. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. fj201701586R. PMID 30102568 DOI: 10.1096/Fj.201701586R |
0.606 |
|
| 2018 |
Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome. 6: 90. PMID 29773078 DOI: 10.1186/s40168-018-0470-z |
0.607 |
|
| 2017 |
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, ... Bokulich NA, et al. A communal catalogue reveals Earth's multiscale microbial diversity. Nature. PMID 29088705 DOI: 10.1038/Nature24621 |
0.677 |
|
| 2016 |
Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. Msystems. 1. PMID 27822553 DOI: 10.1128/mSystems.00062-16 |
0.66 |
|
| 2016 |
Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, D Lieber A, Wu F, Perez-Perez GI, Chen Y, Schweizer W, Zheng X, Contreras M, Dominguez-Bello MG, Blaser MJ. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Science Translational Medicine. 8: 343ra82. PMID 27306664 DOI: 10.1126/Scitranslmed.Aad7121 |
0.628 |
|
| 2016 |
Bokulich NA, Collins TS, Masarweh C, Allen G, Heymann H, Ebeler SE, Mills DA. Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics. Mbio. 7. PMID 27302757 DOI: 10.1128/Mbio.00631-16 |
0.721 |
|
| 2016 |
Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Medicine. 8: 48. PMID 27124954 DOI: 10.1186/S13073-016-0297-9 |
0.596 |
|
| 2016 |
Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine. PMID 26828196 DOI: 10.1038/Nm.4039 |
0.629 |
|
| 2016 |
Bokulich NA, Lewis ZT, Boundy-Mills K, Mills DA. A new perspective on microbial landscapes within food production. Current Opinion in Biotechnology. 37: 182-189. PMID 26773388 DOI: 10.1016/j.copbio.2015.12.008 |
0.7 |
|
| 2016 |
Walker GA, Hjelmeland A, Bokulich NA, Mills DA, Ebeler SE, Bisson LF. Impact of the [GAR+] prion on fermentation and bacterial community composition with saccharomyces cerevisiae UCD932 American Journal of Enology and Viticulture. 67: 296-307. DOI: 10.5344/Ajev.2016.15092 |
0.502 |
|
| 2015 |
Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, et al. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nature Communications. 6: 7486. PMID 26123276 DOI: 10.1038/Ncomms8486 |
0.651 |
|
| 2015 |
Bokulich NA, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K, Gagelidze N, Sadunishvili T, Goginyan V, Kvesitadze G, Torok T, Mills DA. Microbial biogeography of the transnational fermented milk matsoni. Food Microbiology. 50: 12-9. PMID 25998810 DOI: 10.1016/j.fm.2015.01.018 |
0.729 |
|
| 2015 |
Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S, van der Lelie D, Gilbert JA. The soil microbiome influences grapevine-associated microbiota. Mbio. 6. PMID 25805735 DOI: 10.1128/Mbio.02527-14 |
0.694 |
|
| 2015 |
Bokulich NA, Bergsveinson J, Ziola B, Mills DA. Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance. Elife. 4. PMID 25756611 DOI: 10.7554/eLife.04634 |
0.721 |
|
| 2015 |
De Leoz ML, Kalanetra KM, Bokulich NA, Strum JS, Underwood MA, German JB, Mills DA, Lebrilla CB. Human milk glycomics and gut microbial genomics in infant feces show a correlation between human milk oligosaccharides and gut microbiota: a proof-of-concept study. Journal of Proteome Research. 14: 491-502. PMID 25300177 DOI: 10.1021/Pr500759E |
0.733 |
|
| 2015 |
Bokulich NA, Bergsveinson J, Ziola B, Mills DA. Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance Elife. 2015: e04634. DOI: 10.7554/eLife.04634 |
0.417 |
|
| 2015 |
Bokulich NA, Swadener M, Sakamoto K, Mills DA, Bisson LF. Sulfur dioxide treatment alters wine microbial diversity and fermentation progression in a dose-dependent fashion American Journal of Enology and Viticulture. 66: 73-79. DOI: 10.5344/Ajev.2014.14096 |
0.485 |
|
| 2015 |
De Leoz MLA, Kalanetra KM, Bokulich NA, Strum JS, Underwood MA, German JB, Mills DA, Lebrilla CB. Human milk glycomics and gut microbial genomics in infant feces show a correlation between human milk oligosaccharides and gut microbiota: A proof-of-concept study Journal of Proteome Research. 14: 491-502. DOI: 10.1021/pr500759e |
0.491 |
|
| 2015 |
Bokulich NA, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K, Gagelidze N, Sadunishvili T, Goginyan V, Kvesitadze G, Torok T, Mills DA. Microbial biogeography of the transnational fermented milk matsoni Food Microbiology. 50: 12-19. DOI: 10.1016/j.fm.2015.01.018 |
0.512 |
|
| 2014 |
Bokulich NA, Blaser MJ. A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome. Cell Metabolism. 20: 701-3. PMID 25440050 DOI: 10.1016/J.Cmet.2014.10.012 |
0.642 |
|
| 2014 |
Bokulich NA, Ohta M, Lee M, Mills DA. Indigenous bacteria and fungi drive traditional kimoto sake fermentations. Applied and Environmental Microbiology. 80: 5522-9. PMID 24973064 DOI: 10.1128/AEM.00663-14 |
0.721 |
|
| 2014 |
Bokulich NA, Thorngate JH, Richardson PM, Mills DA. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proceedings of the National Academy of Sciences of the United States of America. 111: E139-48. PMID 24277822 DOI: 10.1073/pnas.1317377110 |
0.728 |
|
| 2014 |
Underwood MA, Kalanetra KM, Bokulich NA, Mirmiran M, Barile D, Tancredi DJ, German JB, Lebrilla CB, Mills DA. Prebiotic oligosaccharides in premature infants. Journal of Pediatric Gastroenterology and Nutrition. 58: 352-60. PMID 24135979 DOI: 10.1097/Mpg.0000000000000211 |
0.685 |
|
| 2013 |
Underwood MA, Kalanetra KM, Bokulich NA, Lewis ZT, Mirmiran M, Tancredi DJ, Mills DA. A comparison of two probiotic strains of bifidobacteria in premature infants. The Journal of Pediatrics. 163: 1585-1591.e9. PMID 23993139 DOI: 10.1016/j.jpeds.2013.07.017 |
0.684 |
|
| 2013 |
Bokulich NA, Ohta M, Richardson PM, Mills DA. Monitoring Seasonal Changes in Winery-Resident Microbiota. Plos One. 8: e66437. PMID 23840468 DOI: 10.1371/journal.pone.0066437 |
0.709 |
|
| 2013 |
Bokulich NA, Mills DA. Facility-specific "house" microbiome drives microbial landscapes of artisan cheesemaking plants. Applied and Environmental Microbiology. 79: 5214-23. PMID 23793641 DOI: 10.1128/AEM.00934-13 |
0.731 |
|
| 2013 |
Bokulich NA, Mills DA, Underwood MA. Surface microbes in the neonatal intensive care unit: changes with routine cleaning and over time. Journal of Clinical Microbiology. 51: 2617-24. PMID 23740726 DOI: 10.1128/JCM.00898-13 |
0.703 |
|
| 2013 |
Bokulich NA, Bamforth CW. The microbiology of malting and brewing. Microbiology and Molecular Biology Reviews : Mmbr. 77: 157-72. PMID 23699253 DOI: 10.1128/MMBR.00060-12 |
0.621 |
|
| 2013 |
Ellis CL, Bokulich NA, Kalanetra KM, Mirmiran M, Elumalai J, Haapanen L, Schegg T, Rutledge JC, Raff G, Mills DA, Underwood MA. Probiotic administration in congenital heart disease: A pilot study Journal of Perinatology. 33: 691-697. PMID 23599119 DOI: 10.1038/jp.2013.41 |
0.437 |
|
| 2013 |
Bokulich NA, Mills DA. Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities. Applied and Environmental Microbiology. 79: 2519-26. PMID 23377949 DOI: 10.1128/AEM.03870-12 |
0.717 |
|
| 2013 |
Lewis ZT, Bokulich NA, Kalanetra KM, Ruiz-Moyano S, Underwood MA, Mills DA. Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities. Anaerobe. 19: 62-9. PMID 23261904 DOI: 10.1016/j.anaerobe.2012.12.005 |
0.715 |
|
| 2013 |
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods. 10: 57-9. PMID 23202435 DOI: 10.1038/Nmeth.2276 |
0.692 |
|
| 2013 |
Ma BW, Bokulich NA, Castillo PA, Kananurak A, Underwood MA, Mills DA, Bevins CL. Correction: Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice Plos One. 8. DOI: 10.1371/annotation/7e4429bf-b5a6-43d6-8b03-1457e01450e3 |
0.434 |
|
| 2013 |
Bokulich NA, Joseph CML, Allen G, Benson AK, Mills DA. Correction: Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine Plos One. 8. DOI: 10.1371/Annotation/4D347090-Bca1-4184-A5D5-Bc2D38Baec7D |
0.439 |
|
| 2013 |
Bokulich N, Bamforth C, Mills D. A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine Cerevisia. 38: 56. DOI: 10.1016/J.CERVIS.2013.09.021 |
0.486 |
|
| 2012 |
Ma BW, Bokulich NA, Castillo PA, Kananurak A, Underwood MA, Mills DA, Bevins CL. Routine habitat change: a source of unrecognized transient alteration of intestinal microbiota in laboratory mice. Plos One. 7: e47416. PMID 23082164 DOI: 10.1371/Journal.Pone.0047416 |
0.721 |
|
| 2012 |
Bokulich NA, Mills DA. Next-generation approaches to the microbial ecology of food fermentations. Bmb Reports. 45: 377-89. PMID 22831972 |
0.703 |
|
| 2012 |
Bokulich NA, Joseph CM, Allen G, Benson AK, Mills DA. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. Plos One. 7: e36357. PMID 22563494 DOI: 10.1371/Journal.Pone.0036357 |
0.737 |
|
| 2012 |
Bokulich NA, Bamforth CW, Mills DA. Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale. Plos One. 7: e35507. PMID 22530036 DOI: 10.1371/journal.pone.0035507 |
0.723 |
|
| 2012 |
Bokulich NA, Mills DA. Differentiation of mixed lactic acid bacteria communities in beverage fermentations using targeted terminal restriction fragment length polymorphism. Food Microbiology. 31: 126-32. PMID 22475950 DOI: 10.1016/j.fm.2012.02.007 |
0.71 |
|
| 2012 |
Bokulich NA, Bamforth CW, Mills DA. A review of molecular methods for microbial community profiling of beer and wine Journal of the American Society of Brewing Chemists. 70: 150-162. DOI: 10.1094/ASBCJ-2012-0709-01 |
0.536 |
|
| 2011 |
Bokulich NA, Hwang C, Liu S, Boundy-Mills KL, Mills DA. Profiling the Yeast Communities of Wine Fermentations Using Terminal Restriction Fragment Length Polymorphism Analysis American Journal of Enology and Viticulture. 63: 185-194. DOI: 10.5344/ajev.2011.11077 |
0.476 |
|
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