Refereed publications

  • Amir A*, McDonald D*, Navas-Molina JA, Kopylova E, Morton J, Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, Knight R. (2016) Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems (in press)

  • Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D’Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK. (2016). Dynamics of the human gut microbiome in Inflammatory Bowel Disease. Nature Microbiology. (in press).

  • McDonald D, Ackermann G, Khailova L, Baird C, Heyland D, Kozar R, Lemieux M, Derenski K, King J, Vis-Kampen C, Knight R, Wischmeyer PE. (2016) Extreme Dysbiosis of the Microbiome in Critical Illness. mSphere 1(4):e00199-16. DOI: 10.1128/mSphere.00199-16

  • Debelius JW*, McDonald D*, Ackermann G, Dunn RR, Fahimpour AK, Gaffney J, Gilbert JA, Green JL, Gonzalez A, Gogul G, Hugenholtz P, Humphrey G, Huttenhower C, Hyde E, Jackson MA, Kelley ST, Knights D, Ladau J, Leach J, Metcalf JL, Morgan XC, Morton JT, Navas-Molina J, Montassier E, Rahnavard G, Robbins-Pianka A, Pollard KS, Sangwan N, Shorenstein J, Spector T, Thompson LR, Thackray VG, Wischmeyer P, Wolfe E, Vazquez-Baeza Y, The American Gut Consortium, Knight R. (2016) American Gut: an Open Platform for Citizen-Science Microbiome Research (submitted) *These authors contributed equally

  • Gonzalez A, Vazquez-Baeza Y, Pettengill J, Ottesen A, McDonald D, Knight R. (2016) Avoiding pandemic fears in the subway and conquering the platypus. mSystems (in press)

  • McDonald D, Birmingham A, Knight R. (2015) Context, and the human microbiome. Microbiome 3:52 PMID: 26530830

  • Debelius JW, Vázquez-Baeza Y, McDonald D, Zhenjiang X, Wolfe E, and Knight R. (2016) Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project. Journal of Microbiology and Biology Education 17(1):46-50 PMID: 27047589

  • Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, and Kelley ST. (2016) ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome 4(1):11 PMID: 26905735

  • Mandal S, Godfre KM, McDonald D, Treuren WV, Bjørnholt JV, Midtvedt T, Moen B, Rudi K, Knight R, Peddada SD, Brantsaeter AL, Eggesbø M. (2015) Intake of specific fats and vitamins during pregnancy is associated with a pro-inflammatory maternal gut microbiota. Microbial Ecology in Health and Disease (submitted)

  • Bokulich NA, Rideout JR, Kopylova E, Bolyen E, Patnode J, Ellett Z, McDonald D, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG. (2015) A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments. Microbiome (submitted)

  • McDonald D, Hornig M, Lozupone C, Debelius J, Gilbert JA, Knight R. (2015) “Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients.” Microbial Ecology in Health and Disease 26:26555 PMID: 25758371

  • Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, The Scientists for Advancement of Microbiome Research*, White O. (2014) “Advancing the Microbiome Research Community.” Cell 159(2):227–230 PMID: 25303518 *signee of the scientists for advancement of microbiome

  • Knights D, Ward TL, McKinlay CE, Miller H, Gonzalez A, McDonald D, Knight R. (2014) ‘Rethinking “Enterotypes”.’ Cell Host Microbe 16(4):433–437 PMID: 25299329

  • Integrative HMP (iHMP) Research Network Consortium. (2014) “The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.” Cell Host Microbe 16(3):276-89 PMID: 25211071

  • Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG. (2014) “Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.” Peerj Aug 21 2:e545 PMID: 25177538

  • Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ. (2014) “The treatment-naive microbiome in new-onset Crohn’s disease.” Cell Host Microbe 15(3):382-92 PMID: 24629344

  • Ursell LK, Gunawardana M, Chang S, Mullen M, Moss JA, Herold BC, Keller MJ, McDonald D, González A, Knight R, Baum MM. (2013) “Comparison of the Vaginal Microbial Communities in Women with Recurrent Genital HSV Receiving Acyclovir Intravaginal Rings.” Antiviral research 102:87-94. PMID: 24361269

  • Langille MGI, Zaneveld, J, Caporaso, JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R, Beiko RG, and Huttenhower C. (2013) “Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.” Nature Biotechnology 31(9):814-821. PMID: 23975157

  • McDonald D, Vázquez-Baeza Y, Walters WA, Caporaso JG, and Knight R. (2013) “From molecules to dynamic biological communities.” Biology and Philosophy 28(2):241-259. PMID: 23483075

  • Ragan-Kelley B*, Walters W*, McDonald D*, Riley J, Granger BE, Knight R, Perez F and Caporaso JG. (2012) “Collaborative cloud-enabled tools allow rapid, reproducible biological insights.” ISME Journal 7:461–464 Oct. 25. PMID: 23096404 *these authors contributed equally

  • Metcalf J, Love Stowell S, Kennedy C, Rogers K, McDonald D, Keepers K, Epp J, Cooper A, Austin J, and Martin A. (2012). “Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout.” Molecular Ecology 21(21):5194-207. PMID: 22998121

  • Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld J and Knight R. (2012). “RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs.” RNA 18(7):1319-27. PMID: 22645380

  • Harris JK*, Caporaso JG*, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR. (2012). “Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.” ISME Journal Epub Jul 26. PMID: 22832344 *these authors contributed equally

  • Human Microbiome Project Consortium. (2012). “Structure, Function and Diversity of the Human Microbiome in an Adult Reference Population.” Nature 486(7402):207-214. PMID: 22699609

  • Human Microbiome Project Consortium. (2012). “A framework for human microbiome research.” Nature 486(7402):215-221. PMID: 22699610

  • McDonald D*, Clemente J*, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R and Caporaso JG. (2012). “The Biological Observation Matrix (BIOM) Format or: How I Learned To Stop Worrying and Love the Ome-ome.” GigaScience 1:7. PMID: 23587224 *these authors contributed equally

  • Fierer N, Ferrenberg S, Flores GE, González A, Kueneman J, Legg T, Lynch RC, McDonald D, Mihaljevic JR, O’Neill SP, Rhodes ME, Song S, Walters WA. (2012). “From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome.” Annual Review of Ecology, Evolution and Systematics Vol. 43 pp137-155 DOI: 10.1146/annurev-ecolsys-110411-160307

  • Almodovar S, Knight R, Allshouse A, Roemer S, Lozupone C, McDonald D, Widmann J, Voelkel NF, Shelton RJ, Suarez EB, Hammer KW, Goujard C, Petrosillo N, Simonneau G, Hsue PY, Humbert M, Flores SC. (2012). “Human Immunodeficiency Virus nef Signature Sequences are Associated with Pulmonary Hypertension.” AIDS Research and Human Retroviruses Jun;28(6):607-18. PMID: 22066947

  • McDonald D, Price M, Goodrich J, Nawrocki E, DeSantis T, Anderson G, Eddy S, Arkin A, Knight R, Hugenholtz P. (2012). “An improved greengenes taxonomy for bacteria and archaea with explicit ranks.” ISME Journal Mar;6(3):610-8. PMID: 22134646

  • Stombaugh J, Widmann J, McDonald D, Knight R. (2011). “Boulder ALignment Editor (ALE): a web-based RNA alignment tool.” Bioinformatics 27(12):1706-7. PMID: 21546392

  • Hansen E, Lozupone C, Rey F, Wu M, Guruge J, Narra A, Goodfellow J, Zaneveld J, McDonald D, Goodrich J, Heath A, Knight R, Gordon J. (2011) “Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii: a study in twins.” Proceedings of the National Academy of Sciences 1:4599-606. PMID: 21317366

  • Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R. (2010). “Microbial community resemblance methods differ in their ability to detect biologically relevant patterns.” Nature Methods 7(10):813-9. PMID: 20818378

  • Majerfeld I, Chocholousova J, Malaiya V, Widmann J, McDonald D, Reeder J, Iyer M, Illangasekare M, Yarus M, Knight R. (2010). “Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.” RNA 16(10):1915-24. PMID: 20699302

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. (2010). “QIIME allows analysis of high-throughput community sequencing data.” Nat Methods 7(5):335-6. PMID: 20383131

  • Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. (2010). “Forensic identification using skin bacterial communities.” Proc Natl Acad Sci 107(14):6477-81. PMID: 20231444

  • Marshall P, Woitaszek M, Tufo HM, Knight R, McDonald D, Goodrich J, Widmann J. (2009). “Ensemble Dispatching on a Blue Gene/L for a Bioinformatics Knowledge Environment”, Proceedings of the Second ACM Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS), Portland, Oregon, November 2009. ACMID: 1646481.

  • McDonald D, Waterbury L, Knight R, Betterton MD. (2008). “Activating and inhibiting connections in biological network dynamics.” Biol Direct 3:49. PMID: 19055800

  • Oscamou M, McDonald D, Yap VB, Huttley GA, Lladser ME, Knight R. (2008). “Comparison of methods for estimating the nucleotide substitution matrix.” BMC Bioinformatics 9:511. PMID: 19046431

  • Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. (2007). “PyCogent: a toolkit for making sense from sequence.” Genome Biol. 8(8):R171. PMID: 17708774

Non-refereed publications

  • Wischmeyer P, McDonald D, Knight R. (2016) Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness. Current Opinion Critical Care. PMID: 27327243

  • McDonald D, Glusman G, Price N. (2016) From digital medicine to personalized nutrition. Nature Biotechnology 34(2):152-4 PMID: 26849520

  • McDonald D, Xu Z, Hyde ER, Knight R. (2015) Ribosomal RNA, the lens into life. RNA 21(4):692-4. PMID: 25780194

  • Knight R and McDonald D. “Our Second Genome”. Imagine Sept/Oct 2013: 26-29