PubMed

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, Dorrestein PC, Knight R.

Nat Methods. 2019 Dec;16(12):1306-1314. doi: 10.1038/s41592-019-0616-3. Epub 2019 Nov 4.

Kaehler BD, Bokulich NA, McDonald D, Knight R, Caporaso JG, Huttley GA.

Nat Commun. 2019 Oct 11;10(1):4643. doi: 10.1038/s41467-019-12669-6.

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, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

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, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091.

Bokulich NA, Maldonado J, Kang DW, Krajmalnik-Brown R, Caporaso JG.

mSphere. 2019 Apr 10;4(2). pii: e00208-19. doi: 10.1128/mSphere.00208-19.

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.

Cancer Med. 2019 Feb;8(2):617-628. doi: 10.1002/cam4.1965. Epub 2019 Jan 16.

Bokulich NA, Dillon MR, Zhang Y, Rideout JR, Bolyen E, Li H, Albert PS, Caporaso JG.

mSystems. 2018 Nov 20;3(6). pii: e00219-18. doi: 10.1128/mSystems.00219-18. eCollection 2018 Nov-Dec.

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.

J Transl Med. 2018 Sep 3;16(1):244. doi: 10.1186/s12967-018-1619-z.

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, Blaser MJ.

FASEB J. 2019 Jan;33(1):1098-1109. doi: 10.1096/fj.201701586R. Epub 2018 Aug 13.

Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J.

Microbiome. 2018 May 17;6(1):90. doi: 10.1186/s40168-018-0470-z.

Bokulich NA, Dillon MR, Bolyen E, Kaehler BD, Huttley GA, Caporaso JG.

J Open Res Softw. 2018;3(30). pii: 934. doi: 10.21105/joss.00934. Epub 2018 Oct 23.

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, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.

Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG.

mSystems. 2016 Oct 18;1(5). pii: e00062-16. eCollection 2016 Sep-Oct.

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.

Sci Transl Med. 2016 Jun 15;8(343):343ra82. doi: 10.1126/scitranslmed.aad7121.

Bokulich NA, Collins TS, Masarweh C, Allen G, Heymann H, Ebeler SE, Mills DA.

MBio. 2016 Jun 14;7(3). pii: e00631-16. doi: 10.1128/mBio.00631-16.

Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ.

Genome Med. 2016 Apr 27;8(1):48.

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.

Nat Med. 2016 Mar;22(3):250-3. doi: 10.1038/nm.4039. Epub 2016 Feb 1.

Bokulich NA, Battaglia T, Aleman JO, Walker JM, Blaser MJ, Holt PR.

Clin Microbiol Infect. 2016 May;22(5):464-5. doi: 10.1016/j.cmi.2016.01.013. Epub 2016 Jan 22. No abstract available.

Bokulich NA, Lewis ZT, Boundy-Mills K, Mills DA.

Curr Opin Biotechnol. 2016 Feb;37:182-189. doi: 10.1016/j.copbio.2015.12.008. Epub 2016 Jan 11. Review.

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, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ.

Nat Commun. 2015 Jun 30;6:7486. doi: 10.1038/ncomms8486.

Bokulich NA, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K, Gagelidze N, Sadunishvili T, Goginyan V, Kvesitadze G, Torok T, Mills DA.

Food Microbiol. 2015 Sep;50:12-9. doi: 10.1016/j.fm.2015.01.018. Epub 2015 Feb 10.

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.

MBio. 2015 Mar 24;6(2). pii: e02527-14. doi: 10.1128/mBio.02527-14.

Bokulich NA, Bergsveinson J, Ziola B, Mills DA.

Elife. 2015 Mar 10;4. doi: 10.7554/eLife.04634.

Bokulich NA, Blaser MJ.

Cell Metab. 2014 Nov 4;20(5):701-703. doi: 10.1016/j.cmet.2014.10.012. Epub 2014 Nov 4.

De Leoz ML, Kalanetra KM, Bokulich NA, Strum JS, Underwood MA, German JB, Mills DA, Lebrilla CB.

J Proteome Res. 2015 Jan 2;14(1):491-502. doi: 10.1021/pr500759e. Epub 2014 Oct 28.

Bokulich NA, Ohta M, Lee M, Mills DA.

Appl Environ Microbiol. 2014 Sep;80(17):5522-9. doi: 10.1128/AEM.00663-14. Epub 2014 Jun 27.

Bokulich NA, Thorngate JH, Richardson PM, Mills DA.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):E139-48. doi: 10.1073/pnas.1317377110. Epub 2013 Nov 25.

Underwood MA, Kalanetra KM, Bokulich NA, Mirmiran M, Barile D, Tancredi DJ, German JB, Lebrilla CB, Mills DA.

J Pediatr Gastroenterol Nutr. 2014 Mar;58(3):352-60. doi: 10.1097/MPG.0000000000000211.

Underwood MA, Kalanetra KM, Bokulich NA, Lewis ZT, Mirmiran M, Tancredi DJ, Mills DA.

J Pediatr. 2013 Dec;163(6):1585-1591.e9. doi: 10.1016/j.jpeds.2013.07.017. Epub 2013 Aug 29.

Bokulich NA, Ohta M, Richardson PM, Mills DA.

PLoS One. 2013 Jun 19;8(6):e66437. doi: 10.1371/journal.pone.0066437. Print 2013.

Bokulich NA, Mills DA.

Appl Environ Microbiol. 2013 Sep;79(17):5214-23. doi: 10.1128/AEM.00934-13. Epub 2013 Jun 21.

Bokulich NA, Mills DA, Underwood MA.

J Clin Microbiol. 2013 Aug;51(8):2617-24. doi: 10.1128/JCM.00898-13. Epub 2013 Jun 5.

Bokulich NA, Bamforth CW.

Microbiol Mol Biol Rev. 2013 Jun;77(2):157-72. doi: 10.1128/MMBR.00060-12. Review.

Ellis CL, Bokulich NA, Kalanetra KM, Mirmiran M, Elumalai J, Haapanen L, Schegg T, Rutledge JC, Raff G, Mills DA, Underwood MA.

J Perinatol. 2013 Sep;33(9):691-7. doi: 10.1038/jp.2013.41. Epub 2013 Apr 18.

Bokulich NA, Mills DA.

Appl Environ Microbiol. 2013 Apr;79(8):2519-26. doi: 10.1128/AEM.03870-12. Epub 2013 Feb 1.

Lewis ZT, Bokulich NA, Kalanetra KM, Ruiz-Moyano S, Underwood MA, Mills DA.

Anaerobe. 2013 Feb;19:62-9. doi: 10.1016/j.anaerobe.2012.12.005. Epub 2012 Dec 20.

Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG.

Nat Methods. 2013 Jan;10(1):57-9. doi: 10.1038/nmeth.2276. Epub 2012 Dec 2.

Ma BW, Bokulich NA, Castillo PA, Kananurak A, Underwood MA, Mills DA, Bevins CL.

PLoS One. 2012;7(10):e47416. doi: 10.1371/journal.pone.0047416. Epub 2012 Oct 17.

Bokulich NA, Mills DA.

BMB Rep. 2012 Jul;45(7):377-89.

Bokulich NA, Joseph CM, Allen G, Benson AK, Mills DA.

PLoS One. 2012;7(5):e36357. doi: 10.1371/journal.pone.0036357. Epub 2012 May 1.

Bokulich NA, Bamforth CW, Mills DA.

PLoS One. 2012;7(4):e35507. doi: 10.1371/journal.pone.0035507. Epub 2012 Apr 18.

Bokulich NA, Mills DA.

Food Microbiol. 2012 Aug;31(1):126-32. doi: 10.1016/j.fm.2012.02.007. Epub 2012 Feb 21.