TitleAuthor(s)Venueyear
Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic InfectionMcCall L.I., Morton J.T., Bernatchez J.A., Siquiera-Neto J.L., Knight R., Dorrestein P.C., McKerrow J.H. Anal Chem. 2017
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of TanzaniaSmits S.A., Leach J., Sonnenburg E.D., Gonzalez C.G., Lichtman J.S., Reid G., Knight R., Manjurano A., Changalucha J., Elias J.E., Dominguez-Bello M.G., Sonnenburg J.L. Science: Vol. 357, Issue 6353, pp. 802-8062017
Genetic influences on the human oral microbiomeDemmitt B.A., Corley R.P., Huibregtse B.M., Keller M.C., Hewitt J.K., McQueen M.B., Knight R., McDermott I., Krauter K.S. BMC Genomics 201718:6592017
The sponge microbiome projectMoitinho-Silva L., Nielsen S., Amir A., Gonzalez A., Ackermann G., Cerrano C., Astudillo-Garcia C., Easson C., Sipkema D., Liu F., Steinert G., Kotoulas G., McCormack G.P., Feng G., Bell J.J., Vicente J., Björk J.R., Montoya J.M., Olson J.B., Reveillaud J., Steindler L., Pineda M., Marra M.V., Ilan M., Taylor M.W., Polymenakou P., Erwin P.M., Schupp P.J., Simister R.L., Knight R., Thacker R.W., Costa R., Hill R.T., Lopez-Legentil S., Dailianis T., Ravasi T., Hentschel U., Li Z., Webster N.S., Thomas T.GigaScience2017
Leukotriene B4-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progressionJala V.R., Maturu P., Bodduluri S.R., Krishnan E., Mathis S., Subbarao K., Wang M., Jenson A.B., Proctor M.L., Rouchka E.C., Knight R., Haribabu B.OncoImmunology2017
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. R. M. Bowers, N. C. Kypides, R. Stepanauskas, M. Harmon-Smith, D. Doud, T. B. K. Reddy, F. Schulz, J. Jarett, A. R. Rivers, E. A Eloe-Fadrosh, S. G. Tringe, N. N. Ivanova, A. Copeland, A. Clum, E. D. Becraft, R. R. Malstrom, B. Birren, M. Podar, P. Bork, G. M. Weinstock, G. M. Garrity, J. A. Dodsworth, S. Yooseph, G. Sutton, F. O. Glöckner, J. A. Gilbert, W. C. Nelson, S. J. Hallam, S. P. Jungbluth, T. J. G. Ettema, S. Tighe, K. T. Konstantinidis, W. Liu, B. J. Baker, T. Rattei, J. A. Eisen, B. Hedlund, K. D. McMahon, N. Fierer, R. Knight, R. Finn, G. Cochrane, I. Karsch-Mizrachi, G. W. Tyson, C. Rinke, A. Lapidus, F. Meyer, P. Yilmaz, D. H. Parks, A. M. Eren, L. Schriml, J. F. Banfield, P. Hugenholtz, T. WolkeNat Biotechnol2017
Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey SpeciesV. L. Hale, C. L. Tan, K. Niu, Y. Yang, R. Knight, Q. Zhang, D. Cui and K. R. AmatoMicrob Ecol 2017
The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory StudyS. M. J. Hemmings, S. Malan-Muller, L. L. van den Heuvel, B. A. Demmitt, M. A. Stanislawski, D. G. Smith, A. D. Bohr, C. E. Stamper, E. R. Hyde, J. T. Morton, C. A. Marotz, P. H. Siebler, M. Braspenning, W. Van Criekinge, A. J. Hoisington, L. A. Brenner, T. T. Postolache, M. B. McQueen, K. S. Krauter, R. Knight, S. Seedat and C. A. LowryPsychosom Med 2017
Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes"A. M. Linz, B. C. Crary, A. Shade, S. Owens, J. A. Gilbert, R. Knight and K. D. McMahonmSphere 2, (4) 2017
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal SamplesA. V. Melnik, R. R. da Silva, E. R. Hyde, A. A. Aksenov, F. Vargas, A. Bouslimani, I. Protsyuk, A. K. Jarmusch, A. Tripathi, T. Alexandrov, R. Knight and P. C. DorresteinAnal Chem 89, (14) 7549-75592017
Intermittent Hypoxia and Hypercapnia Accelerate Atherosclerosis, Partially via Trimethylamine-OxideJ. Xue, D. Zhou, O. Poulsen, T. Imamura, Y. H. Hsiao, T. H. Smith, A. Malhotra, P. Dorrestein, R. Knight and G. G. HaddadAm J Respir Cell Mol Biol 20172017
Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin ResistanceV. Charepalli, L. Reddivari, S. Radhakrishnan, E. Eriksson, X. Xiao, S. W. Kim, F. Shen, M. Vijay-Kumar, Q. Li, V. B. Bhat, R. Knight and J. K. P. Vanamala Cancer Prev Res (Phila) 2017
The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory StudyS. M. J. Hemmings, S. Malan-Muller, L. L. van den Heuvel, B. A. Demmitt, M. A. Stanislawski, D. G. Smith, A. D. Bohr, C. E. Stamper, E. R. Hyde, J. T. Morton, C. A. Marotz, P. H. Siebler, M. Braspenning, W. Van Criekinge, A. J. Hoisington, L. A. Brenner, T. T. Postolache, M. B. McQueen, K. S. Krauter, R. Knight, S. Seedat and C. A. LowryPsychosom Med2017
Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog LakesA. M. Linz, B. C. Crary, A. Shade, S. Owens, J. A. Gilbert, R. Knight and K. D. McMahonmSphere 2, (3) 2017
DNA extraction for streamlined metagenomics of diverse environmental samplesC. Marotz, A. Amir, G. Humphrey, J. Gaffney, G. Gogul and R. KnightBiotechniques 62, (6) 290-2932017
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal SamplesA. V. Melnik, R. R. da Silva, E. R. Hyde, A. A. Aksenov, F. Vargas, A. Bouslimani, I. Protsyuk, A. K. Jarmusch, A. Tripathi, T. Alexandrov, R. Knight and P. C. DorresteinAnal Chem 2017
Significant Impacts of Increasing Aridity on the Arid Soil MicrobiomeJ. W. Neilson, K. Califf, C. Cardona, A. Copeland, W. van Treuren, K. L. Josephson, R. Knight, J. A. Gilbert, J. Quade, J. G. Caporaso and R. M. MaiermSystems 2, (3) 22017
Bacterial colonization and succession in a newly opened hospitalS. Lax, N. Sangwan, D. Smith, P. Larsen, K. M. Handley, M. Richardson, K. Guyton, M. Krezalek, B. D. Shogan, J. Defazio, I. Flemming, B. Shakhsheer, S. Weber, E. Landon, S. Garcia-Houchins, J. Siegel, J. Alverdy, R. Knight, B. Stephens and J. A. GilbertScience Translational Medicine 9(391)2017
Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big DataJ. Xu, B. Ma, X. Su, S. Huang, X. Xu, X. Zhou, W. E. Huang and R. KnightEngineering 3, (1) 66-702017
Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping A. Amir, D. McDonald, J. A. Navas-Molina, J. Debelius, J. T. Morton, E. Hyde, A. Robbins-Pianka and R. Knight mSystems 2, (2) 2017
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns A. Amir, D. McDonald, J. A. Navas-Molina, E. Kopylova, J. T. Morton, Z. Zech Xu, E. P. Kightley, L. R. Thompson, E. R. Hyde, A. Gonzalez and R. Knight mSystems 2, (2)2017
Mass Spectrometry Based Molecular 3D-Cartography of Plant Metabolites D. J. Floros, D. Petras, C. A. Kapono, A. V. Melnik, T. J. Ling, R. Knight and P. C. Dorrestein Front Plant Sci 8, 4292017
A Microbiome Foundation for the Study of Crohn's Disease D. Gevers, S. Kugathasan, D. Knights, A. D. Kostic, R. Knight and R. J. Xavier Cell Host Microbe 21, (3) 301-3042017
Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome E. M. Hill-Burns, J. W. Debelius, J. T. Morton, W. T. Wissemann, M. R. Lewis, Z. D. Wallen, S. D. Peddada, S. A. Factor, E. Molho, C. P. Zabetian, R. Knight and H. Payami Mov Disord 32, (5) 739-7492017
Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease S. Khanna, Y. Vazquez-Baeza, A. Gonzalez, S. Weiss, B. Schmidt, D. A. Muniz-Pedrogo, J. F. Rainey, 3rd, P. Kammer, H. Nelson, M. Sadowsky, A. Khoruts, S. L. Farrugia, R. Knight, D. S. Pardi and P. C. Kashyap Microbiome 5, (1) 552017
Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape H. C. King, T. Khera-Butler, P. James, B. B. Oakley, G. Erenso, A. Aseffa, R. Knight, E. M. Wellington and O. Courtenay PLoS One 12, (3) e01738112017
The Microbiome and Human Biology R. Knight, C. Callewaert, C. Marotz, E. R. Hyde, J. W. Debelius, D. McDonald and M. L. Sogin Annu Rev Genomics Hum Genet 2017
Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algaeT. Luzzatto Knaan, N. Garg, M. Wang, E. Glukhov, Y. Peng, G. Ackermann, A. Amir, B. M. Duggan, S. Ryazanov, L. Gerwick, R. Knight, T. Alexandrov, N. Bandeira, W. H. Gerwick and P. C. Dorrestein Elife 62017
Microbiome Tools for Forensic Science J. L. Metcalf, Z. Z. Xu, A. Bouslimani, P. Dorrestein, D. O. Carter and R. Knight Trends Biotechnol 2017
Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus E. Novakova, D. C. Woodhams, S. M. Rodriguez-Ruano, R. M. Brucker, J. W. Leff, A. Maharaj, A. Amir, R. Knight and J. Scott Front Microbiol 8, 5262017
Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh E. Vogtmann, J. Chen, M. G. Kibriya, Y. Chen, T. Islam, M. Eunes, A. Ahmed, J. Naher, A. Rahman, A. Amir, J. Shi, C. C. Abnet, H. Nelson, R. Knight, N. Chia, H. Ahsan and R. Sinha Appl Environ Microbiol 83, (10) 2017
An Elegan(t) Screen for Drug-Microbe Interactions A. Vrbanac, J. W. Debelius, L. Jiang, J. T. Morton, P. Dorrestein and R. Knight Cell Host Microbe 21, (5) 555-5562017
Normalization and microbial differential abundance strategies depend upon data characteristics S. Weiss, Z. Z. Xu, S. Peddada, A. Amir, K. Bittinger, A. Gonzalez, C. Lozupone, J. R. Zaneveld, Y. Vazquez-Baeza, A. Birmingham, E. R. Hyde and R. Knight Microbiome 5, (1) 272017
Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical PrimateK. R. Amato, S. Van Belle, A. Di Fiore, A. Estrada, R. Stumpf, B. White, K. E. Nelson, R. Knight and S. R. LeighMicrobial Ecology 1-92017
Dynamics of the human gut microbiome in inflammatory bowel diseaseJ. Halfvarson, C. J. Brislawn, R. Lamendella, Y. Vázquez-Baeza, W. A. Walters, L. M. Bramer, M. D'Amato, F. Bonfiglio, D. McDonald and A. GonzalezNature Microbiology 2, 170042017
Origin of microbial biomineralization and magnetotaxis during the ArcheanW. Lin, G. A. Paterson, Q. Zhu, Y. Wang, E. Kopylova, Y. Li, R. Knight, D. A. Bazylinski, R. Zhu and J. L. KirschvinkProceedings of the National Academy of Sciences 2016146542017
Balance Trees Reveal Microbial Niche DifferentiationJ. T. Morton, J. Sanders, R. A. Quinn, D. McDonald, A. Gonzalez, Y. Vázquez-Baeza, J. A. Navas-Molina, S. J. Song, J. L. Metcalf and E. R. HydemSystems 2, (1) e00162-162017
Uncovering the Horseshoe Effect in Microbial AnalysesJ. T. Morton, L. Toran, A. Edlund, J. L. Metcalf, C. Lauber and R. KnightmSystems 2, (1) e00166-162017
Gut Instinct: Creating scientific theories with online learnersV. Pandey, A. Amir, J. Debelius, E. R. Hyde, T. Kosciolek, R. Knight and S. Klemmer2017
Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopesL. R. Thompson, K. Nikolakakis, S. Pan, J. Reed, R. Knight and E. G. RubyEnvironmental Microbiology2017
Bringing the Dynamic Microbiome to Life with AnimationsY. Vázquez-Baeza, A. Gonzalez, L. Smarr, D. McDonald, J. T. Morton, J. A. Navas-Molina and R. KnightCell Host Microbe 21, (1) 7-102017
Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD riskN. Bergeron, P. T. Williams, R. Lamendella, N. Faghihnia, A. Grube, X. Li, Z. Wang, R. Knight, J. K. Jansson, S. L. Hazen and R. M. KraussBr J Nutr 116, (12) 2020-20292016
Lifestyle chemistries from phones for individual profilingA. Bouslimani, A. V. Melnik, Z. Xu, A. Amir, R. R. da Silva, M. Wang, N. Bandeira, T. Alexandrov, R. Knight and P. C. DorresteinProceedings of the National Academy of Sciences 113, (48) E7645-E76542016
Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co‐utilization in Escherichia coliJ. Groot, S. C. Cepress‐Mclean, A. Robbins‐Pianka, R. Knight and R. T. GillBiotechnology and Bioengineering2016
Antibiotic discovery is a walk in the parkL.-F. Nothias, R. Knight and P. C. DorresteinProceedings of the National Academy of Sciences 113, (51) 14477-144792016
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s DiseaseT. R. Sampson, J. W. Debelius, T. Thron, S. Janssen, G. G. Shastri, Z. E. Ilhan, C. Challis, C. E. Schretter, S. Rocha and V. GradinaruCell 167, (6) 1469-1480. e122016
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's DiseaseT. R. Sampson, J. W. Debelius, T. Thron, S. Janssen, G. G. Shastri, Z. E. Ilhan, C. Challis, C. E. Schretter, S. Rocha, V. Gradinaru, M. F. Chesselet, A. Keshavarzian, K. M. Shannon, R. Krajmalnik-Brown, P. Wittung-Stafshede, R. Knight and S. K. MazmanianCell 167, (6) 1469-1480.e122016
Intestinal adaptation in proximal and distal segments: Two epithelial responses diverge after intestinal separationK. Schall, K. Holoyda, M. Isani, C. Schlieve, T. Salisbury, T. Khuu, J. Debelius, R. Moats, H. Pollack and C. LienSurgery2016
Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha DiversityR. S. Thompson, R. Roller, A. Mika, B. N. Greenwood, R. Knight, M. Chichlowski, B. M. Berg and M. FleshnerFront Behav Neurosci 10, 2402016
Comparison of collection methods for fecal samples in microbiome studiesE. Vogtmann, J. Chen, A. Amir, J. Shi, C. C. Abnet, H. Nelson, R. Knight, N. Chia and R. SinhaAmerican Journal of Epidemiology2016
Using machine learning to identify major shifts in human gut microbiome protein family abundance in diseaseM. Yazdani, B. C. Taylor, J. W. Debelius, W. Li, R. Knight and L. SmarrBig Data (Big Data), 2016 IEEE International Conference on2016
Using the gut microbiota as a novel tool for examining colobine primate GI healthK. R. Amato, J. L. Metcalf, S. J. Song, V. L. Hale, J. Clayton, G. Ackermann, G. Humphrey, K. Niu, D. Cui and H. ZhaoGlobal Ecology and Conservation 7, 225-2372016
Heritable components of the human fecal microbiome are associated with visceral fatM. Beaumont, J. K. Goodrich, M. A. Jackson, I. Yet, E. R. Davenport, S. Vieira-Silva, J. Debelius, T. Pallister, M. Mangino and J. RaesGenome Biol 17, (1) 1892016
Precision Medicine in Alcoholic and Non-Alcoholic Fatty Liver Disease via Modulating the Gut MicrobiotaS. Bluemel, B. Williams, R. Knight and B. SchnablAmerican Journal of Physiology-Gastrointestinal and Liver Physiology ajpgi. 00245.20162016
Tiny microbes, enormous impacts: what matters in gut microbiome studies?J. Debelius, S. J. Song, Y. Vazquez-Baeza, Z. Z. Xu, A. Gonzalez and R. KnightGenome Biol 17, (1) 2172016
Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project CohortA. Gonzalez, E. Hyde, N. Sangwan, J. A. Gilbert, E. Viirre and R. KnightmSystems 1, (5) e00105-162016
Effects of field conditions on fecal microbiotaV. L. Hale, C. L. Tan, K. Niu, Y. Yang, D. Cui, H. Zhao, R. Knight and K. R. AmatoJ Microbiol Methods 130, 180-1882016
The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their HabitatE. R. Hyde, J. A. Navas-Molina, S. J. Song, J. G. Kueneman, G. Ackermann, C. Cardona, G. Humphrey, D. Boyer, T. Weaver and J. R. MendelsonmSystems 1, (4) e00046-162016
Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivityJ. G. Kueneman, D. C. Woodhams, R. Harris, H. M. Archer, R. Knight and V. J. McKenzieProc. R. Soc. B2016
Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic StudiesE. Loftfield, E. Vogtmann, J. N. Sampson, S. C. Moore, H. Nelson, R. Knight, N. Chia and R. SinhaCancer Epidemiology and Prevention Biomarkers2016
Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intakeS. Mandal, K. M. Godfrey, D. McDonald, W. V. Treuren, J. V. Bjørnholt, T. Midtvedt, B. Moen, K. Rudi, R. Knight and A. L. BrantsæterMicrobiome 4, (1) 552016
Culturing: Looking it up in our gutC. Marotz and R. KnightNature Microbiology 1, 161692016
Let researchers try new pathsT. Oni, F. Sciarrino, G. Adesso and R. KnightNature 538, (7626) 451-4532016
Integrating citizen science with online learning to ask better questionsV. Pandey, S. Klemmer, A. Amir, J. Debelius, E. R. Hyde, T. Kosciolek and R. KnightarXiv preprint arXiv:1609.057632016
Mass Spectrometry-Based Visualization of Molecules Associated with Human HabitatsD. Petras, L.-F. Nothias, R. A. Quinn, T. Alexandrov, N. Bandeira, A. Bouslimani, G. Castro-Falcón, L. Chen, T. Dang and D. J. FlorosAnalytical Chemistry2016
Prevalence and genetic diversity of Blastocystis in family units living in the United StatesP. D. Scanlan, R. Knight, S. J. Song, G. Ackermann and P. D. CotterInfection, Genetics and Evolution 45, 95-972016
Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networksY. Vázquez-Baeza, E. R. Hyde, J. S. Suchodolski and R. KnightNature Microbiology 1, 161772016
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular NetworkingM. Wang, J. J. Carver, V. V. Phelan, L. M. Sanchez, N. Garg, Y. Peng, D. D. Nguyen, J. Watrous, C. A. Kapono and T. Luzzatto-KnaanNat Biotechnol 34, (8) 828-8372016
Role of the microbiome, probiotics, and ‘dysbiosis therapy’in critical illnessP. E. Wischmeyer, D. McDonald and R. KnightCurrent Opinion in Critical Care 22, (4) 347-3532016
Microbiome-wide association studies link dynamic microbial consortia to diseaseJ. A. Gilbert, R. A. Quinn, J. Debelius, Z. Z. Xu, J. Morton, N. Garg, J. K. Jansson, P. C. Dorrestein and R. KnightNature 535, (7610) 94-1032016
The Microbiota, Immunoregulation, and Mental Health: Implications for Public HealthC. A. Lowry, D. G. Smith, P. H. Siebler, D. Schmidt, C. E. Stamper, J. E. Hassell, Jr., P. S. Yamashita, J. H. Fox, S. O. Reber, L. A. Brenner, A. J. Hoisington, T. T. Postolache, K. A. Kinney, D. Marciani, M. Hernandez, S. M. Hemmings, S. Malan-Muller, K. P. Wright, R. Knight, C. L. Raison and G. A. RookCurr Environ Health Rep2016
Microbiology of deathJ. L. Metcalf, D. O. Carter and R. KnightCurrent Biology 26, (13) R561-R5632016
Metagenomic covariation along densely sampled environmental gradients in the Red SeaL. R. Thompson, G. J. Williams, M. F. Haroon, A. Shibl, P. Larsen, J. Shorenstein, R. Knight and U. StinglIsme journal2016
THE ICU MICROBIOME PROJECT: CRITICAL ILLNESS ASSOCIATES WITH LOSS OF MICROBIAL DIVERSITY AND ALTERATIONS IN METAGENOMICSP. Wischmeyer, D. Mcdonald, C. Baird, D. Heyland and R. KnightLIPPINCOTT WILLIAMS & WILKINS2016
Host age, social group, and habitat type influence the gut microbiota of wild ring?tailed lemurs (Lemur catta)G. Bennett, M. Malone, M. L. Sauther, F. P. Cuozzo, B. White, K. E. Nelson, R. M. Stumpf, R. Knight, S. R. Leigh and K. R. AmatoAmerican Journal of Primatology 20162016
Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century ChallengesM. J. Blaser, Z. G. Cardon, M. K. Cho, J. L. Dangl, T. J. Donohue, J. L. Green, R. Knight, M. E. Maxon, T. R. Northen and K. S. PollardMBio 7, (3) e00714-162016
mockrobiota: a public resource for microbiome bioinformatics benchmarkingN. A. Bokulich, J. R. Rideout, W. G. Mercurio, B. Wolfe, C. F. Maurice, R. J. Dutton, P. J. Turnbaugh, R. Knight and J. G. CaporasoPeerJ Preprints2016
Microbial Skin Inhabitants: Friends ForeverP. C. Dorrestein, R. L. Gallo and R. KnightCell 165, (4) 771-7722016
Avoiding Pandemic Fears in the Subway and Conquering the PlatypusA. Gonzalez, Y. Vázquez-Baeza, J. Pettengill, A. Ottesen, D. McDonald and R. KnightmSystems 1, (3) e00050-162016
Genetic Determinants of the Gut Microbiome in UK TwinsJ. K. Goodrich, E. R. Davenport, M. Beaumont, M. A. Jackson, R. Knight, C. Ober, T. D. Spector, J. T. Bell, A. G. Clark and R. E. LeyCell Host Microbe 19, (5) 731-432016
Stress response, gut microbial diversity and sexual signals correlate with social interactionsI. I. Levin, D. M. Zonana, B. K. Fosdick, S. J. Song, R. Knight and R. J. SafranBiology Letters 12, (6) 201603522016
Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in miceS. O. Reber, P. H. Siebler, N. C. Donner, J. T. Morton, D. G. Smith, J. M. Kopelman, K. R. Lowe, K. J. Wheeler, J. H. Fox and J. E. HassellProceedings of the National Academy of Sciences 2016003242016
Fecal Microbiome in Epidemiologic Studies—ResponseR. Sinha, E. Vogtmann, J. Chen, A. Amir, J. Shi, J. Sampson, R. Flores, R. Knight and N. ChiaCancer Epidemiology Biomarkers & Prevention 25, (5) 870-8712016
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field StudiesS. J. Song, A. Amir, J. L. Metcalf, K. R. Amato, Z. Z. Xu, G. Humphrey and R. KnightmSystems 1, (3) e00021-162016
Diversity, structure and convergent evolution of the global sponge microbiomeT. Thomas, L. Moitinho-Silva, M. Lurgi, J. R. Bjork, C. Easson, C. Astudillo-Garcia, J. B. Olson, P. M. Erwin, S. Lopez-Legentil, H. Luter, A. Chaves-Fonnegra, R. Costa, P. J. Schupp, L. Steindler, D. Erpenbeck, J. Gilbert, R. Knight, G. Ackermann, J. Victor Lopez, M. W. Taylor, R. W. Thacker, J. M. Montoya, U. Hentschel and N. S. WebsterNat Commun 7, 118702016
The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic diseaseM. M. Wieck, J. W. Debelius, R. G. Spurrier, A. Trecartin, R. Knight and T. C. GrikscheitSurgery2016
Role of the microbiome, probiotics, and ‘dysbiosis therapy’in critical illnessP. E. Wischmeyer, D. McDonald and R. KnightCurrent Opinion in Critical Care 22, (4) 347-3532016
From Sample to Multi-Omics Conclusions in under 48 HoursR. A. Quinn, J. A. Navas-Molina, E. R. Hyde, S. J. Song, Y. Vázquez-Baeza, G. Humphrey, J. Gaffney, J. J. Minich, A. V. Melnik and J. HerschendmSystems 1, (2)2016
Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate speciesK. R. Amato, R. Martinez-Mota, N. Righini, M. Raguet-Schofield, F. P. Corcione, E. Marini, G. Humphrey, G. Gogul, J. Gaffney, E. Lovelace, L. Williams, A. Luong, M. G. Dominguez-Bello, R. M. Stumpf, B. White, K. E. Nelson, R. Knight and S. R. LeighOecologia 180, (3) 717-332016
The impact of kinship and social contact on the gut microbiota of wild, black howler monkeys (Alouatta pigra)K. R. Amato, S. Van Belle, A. Di Fiore, A. Estrada, R. Stumpf, B. White, K. Nelson, R. Knight and S. R. LeighJ Microbiol Biol Educ. 2016 Mar; 17(1): 46–50.2016
Tools for the Microbiome: Nano and BeyondJ. S. Biteen, P. C. Blainey, Z. G. Cardon, M. Chun, G. M. Church, P. C. Dorrestein, S. E. Fraser, J. A. Gilbert, J. K. Jansson, R. Knight, J. F. Miller, A. Ozcan, K. A. Prather, S. R. Quake, E. G. Ruby, P. A. Silver, S. Taha, G. van den Engh, P. S. Weiss, G. C. Wong, A. T. Wright and T. D. YoungACS Nano 10, (1) 6-372016
Geography and location are the primary drivers of office microbiome compositionJ. H. Chase, J. Fouquier, M. Zare, D. L. Sonderegger, R. Knight, S. Kelley, J. A. Siegel and J. G. CaporasoPeerJ Preprints2016
Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut ProjectJ. W. Debelius, Y. Vazquez-Baeza, D. McDonald, Z. Xu, E. Wolfe and R. KnightJ Microbiol Biol Educ 17, (1) 46-502016
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transferM. G. Dominguez-Bello, K. M. De Jesus-Laboy, N. Shen, L. M. Cox, A. Amir, A. Gonzalez, N. A. Bokulich, S. J. Song, M. Hoashi, J. I. Rivera-Vinas, K. Mendez, R. Knight and J. C. ClementeNat Med 22, (3) 250-32016
ghost-tree: creating hybrid-gene phylogenetic trees for diversity analysesJ. Fouquier, J. R. Rideout, E. Bolyen, J. Chase, A. Shiffer, D. McDonald, R. Knight, J. G. Caporaso and S. T. KelleyMicrobiome 4, (1) 112016
Les grands pouvoirs des bactériesR. Knight and B. BuhlerMarabout2016
Open-Source Sequence Clustering Methods Improve the State Of the ArtE. Kopylova, J. A. Navas-Molina, C. Mercier, Z. Z. Xu, F. Mahé, Y. He, H.-W. Zhou, T. Rognes, J. G. Caporaso and R. KnightmSystems 1, (1)3-152016
Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas)J. G. Kueneman, D. C. Woodhams, W. Van Treuren, H. M. Archer, R. Knight and V. J. McKenzieIsme j 10, (4) 934-442016
Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander SkinA. H. Loudon, A. Venkataraman, W. Van Treuren, D. C. Woodhams, L. W. Parfrey, V. J. McKenzie, R. Knight, T. M. Schmidt and R. N. HarrisFront Microbiol 72016
Microbial community assembly and metabolic function during mammalian corpse decompositionJ. L. Metcalf, Z. Z. Xu, S. Weiss, S. Lax, W. Van Treuren, E. R. Hyde, S. J. Song, A. Amir, P. Larsen, N. Sangwan, D. Haarmann, G. C. Humphrey, G. Ackermann, L. R. Thompson, C. Lauber, A. Bibat, C. Nicholas, M. J. Gebert, J. F. Petrosino, S. C. Reed, J. A. Gilbert, A. M. Lynne, S. R. Bucheli, D. O. Carter and R. KnightScience 351, (6269) 158-622016
Keemei: cloud-based validation of tabular bioinformatics file formats in Google SheetsJ. R. Rideout, J. H. Chase, E. Bolyen, G. Ackermann, A. Gonzalez, R. Knight and J. G. CaporasoPeerJ PrePrints 42016
Walls talk: Microbial biogeography of homes spanning urbanizationJ. F. Ruiz-Calderon, H. Cavallin, S. J. Song, A. Novoselac, L. R. Pericchi, J. N. Hernandez, R. Rios, O. H. Branch, H. Pereira, L. C. Paulino, M. J. Blaser, R. Knight and M. G. Dominguez-BelloSci Adv 2, (2)2016
"Fecal microbiome in epidemiologic studies" - ResponseR. Sinha, E. Vogtmann, J. Chen, A. Amir, J. Shi, J. N. Sampson, R. Flores, R. Knight and N. ChiaCancer Epidemiol Biomarkers Prev2016
Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon EnvironmentsL. K. Ursell, A. Robbins-Pianka, N. Scott, A. Gonzalez, D. Knights, J. R. Rideout, A. Kshatriya, J. G. Caporaso and R. KnightSpringer Protocols Handbooks2016
Carcass mass has little influence on the structure of gravesoil microbial communitiesS. Weiss, D. O. Carter, J. L. Metcalf and R. KnightInt J Legal Med 130, (1) 253-2632016
Correlation detection strategies in microbial data sets vary widely in sensitivity and precisionS. Weiss, W. Van Treuren, C. Lozupone, K. Faust, J. Friedman, Y. Deng, L. C. Xia, Z. Z. Xu, L. Ursell, E. J. Alm, A. Birmingham, J. A. Cram, J. A. Fuhrman, J. Raes, F. Sun, J. Zhou and R. KnightIsme Journal2016
Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coliS. J. Weiss, T. J. Mansell, P. Mortazavi, R. Knight and R. T. GillPLoS One 11(1)2016
Associations between human milk oligosaccharides and infant body composition in the first 6 mo of lifeT. L. Alderete, C. Autran, B. E. Brekke, R. Knight, L. Bode, M. I. Goran and D. A. FieldsAm J Clin Nutr 102, (6) 1381-82015
MICROBIOME. A unified initiative to harness Earth's microbiomesA. P. Alivisatos, M. J. Blaser, E. L. Brodie, M. Chun, J. L. Dangl, T. J. Donohue, P. C. Dorrestein, J. A. Gilbert, J. L. Green, J. K. Jansson, R. Knight, M. E. Maxon, M. J. McFall-Ngai, J. F. Miller, K. S. Pollard, E. G. Ruby and S. A. TahaScience 350, (6260) 507-82015
Determinants of the gut microbiota of Mesoamerican howler monkeys (Alouatta pigra and A. palliata)K. R. Amato, M. Raguet-Schofield, N. Righini, R. Martinez-Mota, R. Knight, R. M. Stumpf, K. E. Nelson, B. A. White and S. R. LeighAmerican Journal of Physical Anthropology2015
Variable responses of human and non-human primate gut microbiomes to a Western dietK. R. Amato, C. J. Yeoman, G. Cerda, C. A. Schmitt, J. D. Cramer, M. E. Miller, A. Gomez, T. R. Turner, B. A. Wilson, R. M. Stumpf, K. E. Nelson, B. A. White, R. Knight and S. R. LeighMicrobiome 3, 532015
Microbiome Studies of Carrion DecompositionM. E. Benbow, J. K. Tomberlin, A. M. Tarone, J. L. Metcalf, D. O. Carter and R. KnightCarrion Ecology, Evolution, and Their Applications2015
Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic YogurtJ. E. Bisanz, M. K. Enos, G. PrayGod, S. Seney, J. M. Macklaim, S. Chilton, D. Willner, R. Knight, C. Fusch, G. Fusch, G. B. Gloor, J. P. Burton and G. ReidAppl Environ Microbiol 81, (15) 4965-752015
Molecular cartography of the human skin surface in 3DA. Bouslimani, C. Porto, C. M. Rath, M. Wang, Y. Guo, A. Gonzalez, D. Berg-Lyon, G. Ackermann, G. J. Moeller Christensen, T. Nakatsuji, L. Zhang, A. W. Borkowski, M. J. Meehan, K. Dorrestein, R. L. Gallo, N. Bandeira, R. Knight, T. Alexandrov and P. C. DorresteinProc Natl Acad Sci U S A 112, (17)2015
Seasonal variation of postmortem microbial communitiesD. O. Carter, J. L. Metcalf, A. Bibat and R. KnightForensic Sci Med Pathol 11, (2) 202-72015
The microbiome of uncontacted AmerindiansJ. C. Clemente, E. C. Pehrsson, M. J. Blaser, K. Sandhu, Z. Gao, B. Wang, M. Magris, G. Hidalgo, M. Contreras, O. Noya-Alarcon, O. Lander, J. McDonald, M. Cox, J. Walter, P. L. Oh, J. F. Ruiz, S. Rodriguez, N. Shen, S. J. Song, J. Metcalf, R. Knight, G. Dantas and M. G. Dominguez-BelloSci Adv 1, (3)2015
Short Course in the MicrobiomeK. Falana, R. Knight, C. R. Martin, R. Goldszmid, K. L. Greathouse, J. Gere, H. Young and W. P. KuoJournal of Circulating Biomarkers2015
Cross-biome comparison of microbial association networksK. Faust, G. Lima-Mendez, J.-S. Lerat, J. F. Sathirapongsasuti, R. Knight, C. Huttenhower, T. Lenaerts and J. RaesFront Microbiol 62015
Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial TraitsE. F. Freed, J. D. Winkler, S. J. Weiss, A. D. Garst, V. K. Mutalik, A. P. Arkin, R. Knight and R. T. GillACS Synth Biol 4, (11) 1244-532015
Conceptualizing a Genomics Software Institute (GSI)J. A. Gilbert, C. Catlett, N. Desai, R. Knight, O. White, R. Robbins, R. Sankaran, S.-A. Sansone, D. Field and F. MeyerStandards in genomic sciences 6, (1) 1362015
Euphorbia plant latex is inhabited by diverse microbial communitiesM. Gunawardana, E. R. Hyde, S. Lahmeyer, B. L. Dorsey, T. P. La Val, M. Mullen, J. Yoo, R. Knight and M. M. BaumAm J Bot 102, (12) 1966-19772015
Microbiota and Host Nutrition across Plant and Animal KingdomsS. Hacquard, R. Garrido-Oter, A. Gonzalez, S. Spaepen, G. Ackermann, S. Lebeis, A. C. McHardy, J. L. Dangl, R. Knight, R. Ley and P. Schulze-LefertCell Host Microbe 17, (5) 603-162015
Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8weeksV. L. Hale, C. L. Tan, R. Knight and K. R. AmatoJ Microbiol Methods 113, 16-262015
Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversityY. He, J. G. Caporaso, X.-T. Jiang, H.-F. Sheng, S. M. Huse, J. R. Rideout, R. C. Edgar, E. Kopylova, W. A. Walters and R. KnightMicrobiome 3, (1) 12015
Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversityY. He, J. G. Caporaso, X. T. Jiang, H. F. Sheng, S. M. Huse, J. R. Rideout, R. C. Edgar, E. Kopylova, W. A. Walters, R. Knight and H. W. Zhou2015
Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidisW. M. Holden, S. M. Hanlon, D. C. Woodhams, T. M. Chappell, H. L. Wells, S. M. Glisson, V. J. McKenzie, R. Knight, M. J. Parris and L. A. Rollins-SmithBiological Conservation 187, 91-1022015
Why microbiome treatments could pay off soonR. KnightNature 5182015
Follow Your Gut: The Enormous Impact of Tiny MicrobesR. KnightSimon and Schuster2015
Wir sind viele: TED BooksR. Knight and B. BuhlerS. Fischer Verlag2015
Microbiome based systems, Apparatus and methods for the exploration and production of HydrocarbonsR. Knight, A. Kshatriya, J. Ely, J. Prestidge Jr, P. Henshaw, C. Lauber, G. J. Caporaso, D. Knights, R. Gill and J. Moxley2015
Microbiome based systems, Apparatus and methods for monitoring and controlling industrial processes and systemsR. Knight, A. Kshatriya, C. Lauber, G. J. Caporaso, D. Knights, R. Gill and J. Moxley2015
New Tools for Understanding, Composition and Dynamics of Microbial Communities, ProjectR. Knight, M. E. Lladser, A. P. Martin and S. E. BrennerEncyclopedia of Metagenomics: Environmental Metagenomics 457-4572015
Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river waterA. Korajkic, L. W. Parfrey, B. R. McMinn, Y. V. Baeza, W. VanTeuren, R. Knight and O. C. ShanksWater Res 69, 30-392015
Satellite remote sensing data can be used to model marine microbial metabolite turnoverP. E. Larsen, N. Scott, A. F. Post, D. Field, R. Knight, Y. Hamada and J. A. GilbertIsme Journal 9, (1) 166-1792015
The unifrac significance test is sensitive to tree topologyC. A. Lozupone and R. KnightBMC Bioinformatics 16, (1) 2112015
ConStrains identifies microbial strains in metagenomic datasetsC. Luo, R. Knight, H. Siljander, M. Knip, R. J. Xavier and D. GeversNat Biotechnol 33, (10) 1045-10522015
Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experimentC. A. Macdonald, M. J. Crawley, D. J. Wright, J. Kuczynski, L. Robinson, R. Knight, W. A. Al-Soud, S. J. Sorensen, Y. Deng, J. Zhou and B. K. SinghEnviron Microbiol 17, (3) 841-542015
Changes in vaginal microbiota following antimicrobial and probiotic therapyJ. M. Macklaim, J. C. Clemente, R. Knight, G. B. Gloor and G. ReidMicrob Ecol Health Dis 262015
Analysis of composition of microbiomes: a novel method for studying microbial compositionS. Mandal, W. Van Treuren, R. A. White, M. Eggesbo, R. Knight and S. D. PeddadaMicrob Ecol Health Dis 262015
Context and the human microbiomeD. McDonald, A. Birmingham and R. KnightMicrobiome 3, (1) 1-82015
Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patientsD. McDonald, M. Hornig, C. Lozupone, J. Debelius, J. A. Gilbert and R. KnightMicrob Ecol Health Dis 262015
Ribosomal RNA, the lens into lifeD. McDonald, Z. Xu, E. R. Hyde and R. KnightRna 21, (4) 692-6942015
Microbiome Studies of Carrion DecompositionJ. L. Metcalf, D. O. Carter and R. KnightCarrion Ecology, Evolution, and Their Applications 4212015
Exercise is more effective at altering gut microbial composition and producing stable changes in lean mass in juvenile versus adult male F344 ratsA. Mika, W. Van Treuren, A. González, J. J. Herrera, R. Knight and M. FleshnerPLoS One 10, (5)2015
Microbial endocrinology: the interplay between the microbiota and the endocrine systemH. Neuman, J. W. Debelius, R. Knight and O. KorenFEMS Microbiol Rev2015
Subsistence strategies in traditional societies distinguish gut microbiomesA. J. Obregon-Tito, R. Y. Tito, J. Metcalf, K. Sankaranarayanan, J. C. Clemente, L. K. Ursell, Z. Z. Xu, W. Van Treuren, R. Knight and P. M. GaffneyNature Communications 62015
Genetic and environmental control of host-gut microbiota interactionsE. Org, B. W. Parks, J. W. J. Joo, B. Emert, W. Schwartzman, E. Y. Kang, M. Mehrabian, C. Pan, R. Knight and R. GunsalusGenome Res 25, (10) 1558-15692015
The gut microbiota in human energy homeostasis and obesityM. Rosenbaum, R. Knight and R. L. LeibelTrends in Endocrinology & Metabolism 26, (9) 493-5012015
The MS Microbiome Consortium (MSMC): an academic multi-disciplinary collaborative effort to elucidate the role of the gut microbiota in MS (P2. 205)I. K. Sand, S. Baranzini, R. Knight, R. S. Farber, Y. Bencosme, R. Kanner, R. Gomez, S. Mazmanian, P. Casaccia and B. CreeNeurology 84, (14 Supplement) P2. 2052015
The microbiome quality control project: baseline study design and future directionsR. Sinha, C. C. Abnet, O. White, R. Knight and C. HuttenhowerGenome Biol 16, (1) 1-62015
Collecting Fecal Samples for Microbiome Analyses in Epidemiology StudiesR. Sinha, J. Chen, A. Amir, E. Vogtmann, K. S. Inman, R. Flores-Munguia, J. N. Sampson, R. Knight and N. ChiaCancer Epidemiology Biomarkers & Prevention2015
Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiotaC. C. Smith, L. K. Snowberg, J. G. Caporaso, R. Knight and D. I. BolnickIsme Journal2015
Faecal transplantsT. Spector and R. Knight2015
Authors' reply to Mawer and Wilcox and Mullish and WilliamsT. Spector and R. KnightBmj 3512015
Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral MicrobiotaF. Teng, F. Yang, S. Huang, C. Bo, Z. Z. Xu, A. Amir, R. Knight, J. Ling and J. XuCell Host Microbe 18, (3) 296-3062015
Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and SexW. Van Treuren, L. Ponnusamy, R. J. Brinkerhoff, A. Gonzalez, C. M. Parobek, J. J. Juliano, T. G. Andreadis, R. C. Falco, L. B. Ziegler, N. Hathaway, C. Keeler, M. Emch, J. A. Bailey, R. M. Roe, C. S. Apperson, R. Knight and S. R. MeshnickAppl Environ Microbiol 81, (18) 6200-92015
Can Your Microbiome Tell You What to Eat?J. K. Vanamala, R. Knight and T. D. SpectorCell Metab 22, (6) 960-12015
Dynamic changes in short-and long-term bacterial composition following fecal microbiota transplantation for recurrent infectionA. Weingarden, A. González, Y. Vázquez-Baeza, S. Weiss, G. Humphry, D. Berg-Lyons, D. Knights, T. Unno, A. Bobr and J. KangMicrobiome 3, (1) 12015
Dietary effects on human gut microbiome diversityZ. Xu and R. KnightBritish Journal of Nutrition 113, S1-S52015
Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversityD. I. Bolnick, L. K. Snowberg, J. G. Caporaso, C. Lauber, R. Knight and W. E. StutzMol Ecol 23, (19) 4831-452014
Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)D. I. Bolnick, L. K. Snowberg, P. E. Hirsch, C. L. Lauber, R. Knight, J. G. Caporaso and R. SvanbäckEcol Lett 17, (8) 979-9872014
Individual diet has sex-dependent effects on vertebrate gut microbiotaD. I. Bolnick, L. K. Snowberg, P. E. Hirsch, C. L. Lauber, E. Org, B. Parks, A. J. Lusis, R. Knight, J. G. Caporaso and R. SvanbäckNature Communications 52014
The human microbiome: getting personalK. Califf, A. Gonzalez, R. Knight and J. G. CaporasoMicrobe 9, 410-4152014
The founding charter of the Genomic Observatories NetworkN. Davies, D. Field, L. Amaral-Zettler, M. S. Clark, J. Deck, A. Drummond, D. P. Faith, J. Geller, J. Gilbert, F. O. Glockner, P. R. Hirsch, J. A. Leong, C. Meyer, M. Obst, S. Planes, C. Scholin, A. P. Vogler, R. D. Gates, R. Toonen, V. Berteaux-Lecellier, M. Barbier, K. Barker, S. Bertilsson, M. Bicak, M. J. Bietz, J. Bobe, L. Bodrossy, A. Borja, J. Coddington, J. Fuhrman, G. Gerdts, R. Gillespie, K. Goodwin, P. C. Hanson, J. M. Hero, D. Hoekman, J. Jansson, C. Jeanthon, R. Kao, A. Klindworth, R. Knight, R. Kottmann, M. S. Koo, G. Kotoulas, A. J. Lowe, V. T. Marteinsson, F. Meyer, N. Morrison, D. D. Myrold, E. Pafilis, S. Parker, J. J. Parnell, P. N. Polymenakou, S. Ratnasingham, G. K. Roderick, N. Rodriguez-Ezpeleta, K. Schonrogge, N. Simon, N. J. Valette-Silver, Y. P. Springer, G. N. Stone, S. Stones-Havas, S. A. Sansone, K. M. Thibault, P. Wecker, A. Wichels, J. C. Wooley, T. Yahara, A. Zingone and G. O. COS2014
Convergence of gut microbiomes in myrmecophagous mammalsF. Delsuc, J. L. Metcalf, L. Wegener Parfrey, S. J. Song, A. González and R. KnightMol Ecol 23, (6) 1301-13172014
Finding the missing links among metabolites, microbes, and the hostP. C. Dorrestein, S. K. Mazmanian and R. KnightImmunity 40, (6) 824-322014
From microbiomess to metabolomes to function during host-microbial interactionsP. C. Dorrestein, S. K. Mazmanian and R. KnightImmunity 40, (6) 8242014
Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptationsO. Eilam, R. Zarecki, M. Oberhardt, L. K. Ursell, M. Kupiec, R. Knight, U. Gophna and E. RuppinMBio 5, (4)2014
pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soilsY. Feng, P. Grogan, J. G. Caporaso, H. Zhang, X. Lin, R. Knight and H. ChuSoil Biology and Biochemistry 74, 193-2002014
Temporal variability is a personalized feature of the human microbiomeG. E. Flores, J. G. Caporaso, J. B. Henley, J. R. Rideout, D. Domogala, J. Chase, J. W. Leff, Y. Vazquez-Baeza, A. Gonzalez, R. Knight, R. R. Dunn and N. FiererGenome Biol 15, (12) 5312014
Bacterial phylogeny structures soil resistomes across habitatsK. J. Forsberg, S. Patel, M. K. Gibson, C. L. Lauber, R. Knight, N. Fierer and G. DantasNature 509, (7502) 612-62014
The treatment-naive microbiome in new-onset Crohn's diseaseD. Gevers, S. Kugathasan, L. A. Denson, Y. Vazquez-Baeza, W. Van Treuren, B. Ren, E. Schwager, D. Knights, S. J. Song, M. Yassour, X. C. Morgan, A. D. Kostic, C. Luo, A. Gonzalez, D. McDonald, Y. Haberman, T. Walters, S. Baker, J. Rosh, M. Stephens, M. Heyman, J. Markowitz, R. Baldassano, A. Griffiths, F. Sylvester, D. Mack, S. Kim, W. Crandall, J. Hyams, C. Huttenhower, R. Knight and R. J. XavierCell Host Microbe 15, (3) 382-922014
The Earth Microbiome project: successes and aspirationsJ. A. Gilbert, J. K. Jansson and R. KnightBMC Biol 12, 692014
SnapShot: the human microbiomeA. Gonzalez, Y. Vazquez-Baeza and R. KnightCell 158, (3) 690-690.e12014
Conducting a microbiome studyJ. K. Goodrich, S. C. Di Rienzi, A. C. Poole, O. Koren, W. A. Walters, J. G. Caporaso, R. Knight and R. E. LeyCell 158, (2) 250-622014
Human genetics shape the gut microbiomeJ. K. Goodrich, J. L. Waters, A. C. Poole, J. L. Sutter, O. Koren, R. Blekhman, M. Beaumont, W. Van Treuren, R. Knight, J. T. Bell, T. D. Spector, A. G. Clark and R. E. LeyCell 159, (4) 789-992014
Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samplesH. C. Green, R. A. Haugland, M. Varma, H. T. Millen, M. A. Borchardt, K. G. Field, W. A. Walters, R. Knight, M. Sivaganesan and C. A. KeltyAppl Environ Microbiol 80, (10) 3086-30942014
Predictive modeling of gingivitis severity and susceptibility via oral microbiotaS. Huang, R. Li, X. Zeng, T. He, H. Zhao, A. Chang, C. Bo, J. Chen, F. Yang, R. Knight, J. Liu, C. Davis and J. XuIsme j 8, (9) 1768-802014
Advancing the microbiome research communityC. Huttenhower, R. Knight, C. T. Brown, J. G. Caporaso, J. C. Clemente, D. Gevers, E. A. Franzosa, S. T. Kelley, D. Knights, R. E. Ley, A. Mahurkar, J. Ravel and O. WhiteCell 159, (2) 227-302014
Rethinking “Enterotypes”D. Knights, T. L. Ward, C. E. McKinlay, H. Miller, A. Gonzalez, D. McDonald and R. KnightCell Host Microbe 16, (4) 433-4372014
The amphibian skin‐associated microbiome across species, space and life history stagesJ. G. Kueneman, L. W. Parfrey, D. C. Woodhams, H. M. Archer, R. Knight and V. J. McKenzieMol Ecol 23, (6) 1238-12502014
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strainsN. C. Kyrpides, P. Hugenholtz, J. A. Eisen, T. Woyke, M. Goker, C. T. Parker, R. Amann, B. J. Beck, P. S. Chain, J. Chun, R. R. Colwell, A. Danchin, P. Dawyndt, T. Dedeurwaerdere, E. F. DeLong, J. C. Detter, P. De Vos, T. J. Donohue, X. Z. Dong, D. S. Ehrlich, C. Fraser, R. Gibbs, J. Gilbert, P. Gilna, F. O. Glockner, J. K. Jansson, J. D. Keasling, R. Knight, D. Labeda, A. Lapidus, J. S. Lee, W. J. Li, J. Ma, V. Markowitz, E. R. Moore, M. Morrison, F. Meyer, K. E. Nelson, M. Ohkuma, C. A. Ouzounis, N. Pace, J. Parkhill, N. Qin, R. Rossello-Mora, J. Sikorski, D. Smith, M. Sogin, R. Stevens, U. Stingl, K. Suzuki, D. Taylor, J. M. Tiedje, B. Tindall, M. Wagner, G. Weinstock, J. Weissenbach, O. White, J. Wang, L. Zhang, Y. G. Zhou, D. Field, W. B. Whitman, G. M. Garrity and H. P. KlenkPLoS Biol 12, (8)2014
Vertebrate decomposition is accelerated by soil microbesC. L. Lauber, J. L. Metcalf, K. Keepers, G. Ackermann, D. O. Carter and R. KnightAppl Environ Microbiol 80, (16) 4920-49292014
Longitudinal analysis of microbial interaction between humans and the indoor environmentS. Lax, D. P. Smith, J. Hampton-Marcell, S. M. Owens, K. M. Handley, N. M. Scott, S. M. Gibbons, P. Larsen, B. D. Shogan, S. Weiss, J. L. Metcalf, L. K. Ursell, Y. Vazquez-Baeza, W. Van Treuren, N. A. Hasan, M. K. Gibson, R. Colwell, G. Dantas, R. Knight and J. A. GilbertScience 345, (6200) 1048-522014
HLA-B27 and human beta2-microglobulin affect the gut microbiota of transgenic ratsP. Lin, M. Bach, M. Asquith, A. Y. Lee, L. Akileswaran, P. Stauffer, S. Davin, Y. Pan, E. D. Cambronne, M. Dorris, J. W. Debelius, C. L. Lauber, G. Ackermann, Y. V. Baeza, T. Gill, R. Knight, R. A. Colbert, J. D. Taurog, R. N. Van Gelder and J. T. RosenbaumPLoS One 9, (8) e1056842014
Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)A. H. Loudon, D. C. Woodhams, L. W. Parfrey, H. Archer, R. Knight, V. McKenzie and R. N. HarrisIsme j 8, (4) 830-8402014
Anal gas evacuation and colonic microbiota in patients with flatulence: effect of dietC. Manichanh, A. Eck, E. Varela, J. Roca, J. C. Clemente, A. González, D. Knights, R. Knight, S. Estrella and C. HernandezGut 63, (3) 401-4082014
Gut Microbes and the Brain: Paradigm Shift in NeuroscienceE. A. Mayer, R. Knight, S. K. Mazmanian, J. F. Cryan and K. TillischThe Journal of Neuroscience 34, (46) 15490-154962014
Ancient human oral plaque preserves a wealth of biological dataJ. L. Metcalf, L. K. Ursell and R. KnightNat Genet 46, (4)2014
Multilevel research strategies and biological systemsM. A. O’Malley, I. Brigandt, A. C. Love, J. W. Crawford, J. A. Gilbert, R. Knight, S. D. Mitchell and F. RohwerPhilosophy of Science 81, (5) 811-8282014
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversityL. W. Parfrey, W. A. Walters, C. L. Lauber, J. C. Clemente, D. Berg-Lyons, C. Teiling, C. Kodira, M. Mohiuddin, J. Brunelle, M. Driscoll, N. Fierer, J. A. Gilbert and R. KnightFront Microbiol 5, 2982014
Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow NestsJ. M. Peralta-Sánchez, J. J. Soler, A. M. Martín-Platero, R. Knight, M. Martínez-Bueno and A. P. MøllerMicrobial ecology 67, (2) 480-4872014
The promise of the microbiome: Function and dysfunction in humans and beyondD. A. Relman, J. A. Gilbert and R. KnightScience 345, (6193) 226-2262014
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequencesJ. R. Rideout, Y. He, J. A. Navas-Molina, W. A. Walters, L. K. Ursell, S. M. Gibbons, J. Chase, D. McDonald, A. Gonzalez, A. Robbins-Pianka, J. C. Clemente, J. A. Gilbert, S. M. Huse, H. W. Zhou, R. Knight and J. G. CaporasoPeerJ 2, e5452014
Bacteria from diverse habitats colonize and compete in the mouse gutH. Seedorf, N. W. Griffin, V. K. Ridaura, A. Reyes, J. Cheng, F. E. Rey, M. I. Smith, G. M. Simon, R. H. Scheffrahn, D. Woebken, A. M. Spormann, W. Van Treuren, L. K. Ursell, M. Pirrung, A. Robbins-Pianka, B. L. Cantarel, V. Lombard, B. Henrissat, R. Knight and J. I. GordonCell 159, (2) 253-662014
Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial DiversityA. Shade, S. E. Jones, J. G. Caporaso, J. Handelsman, R. Knight, N. Fierer and J. A. GilbertMBio 5, (4)2014
Specialized Metabolites from the Microbiome in Health and DiseaseG. Sharon, N. Garg, J. Debelius, R. Knight, P. C. Dorrestein and S. K. MazmanianCell Metab 20, (5) 719-7302014
Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forestN. Tas, E. Prestat, J. W. McFarland, K. P. Wickland, R. Knight, A. A. Berhe, T. Jorgenson, M. P. Waldrop and J. K. JanssonIsme j 8, (9) 1904-192014
Structural basis for diversity in the SAM clan of riboswitchesJ. J. Trausch, Z. Xu, A. L. Edwards, F. E. Reyes, P. E. Ross, R. Knight and R. T. BateyProceedings of the National Academy of Sciences 111, (18) 6624-66292014
The Intestinal Metabolome: An Intersection Between Microbiota and HostL. K. Ursell, H. J. Haiser, W. Van Treuren, N. Garg, L. Reddivari, J. Vanamala, P. C. Dorrestein, P. J. Turnbaugh and R. KnightGastroenterology 146, (6) 1470-14762014
Meta-analyses of human gut microbes associated with obesity and IBDW. A. Walters, Z. Xu and R. KnightFEBS Lett 588, (22) 4223-42332014
Tracking down the sources of experimental contamination in microbiome studiesS. Weiss, A. Amir, E. R. Hyde, J. L. Metcalf, S. J. Song and R. KnightGenome Biol 15, (12) 1-32014
Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectivenessD. C. Woodhams, H. Brandt, S. Baumgartner, J. Kielgast, E. Kupfer, U. Tobler, L. R. Davis, B. R. Schmidt, C. Bel, S. Hodel, R. Knight and V. McKenziePLoS One 9, (4)2014
Which is more important for classifying microbial communities: who’s there or what they can doZ. Xu, D. Malmer, M. G. Langille, S. F. Way and R. KnightIsme j 8, (12) 2357-23592014
Toward Effective Probiotics for Autism and Other Neurodevelopmental DisordersJ. A. Gilbert, R. Krajmalnik-Brown, D. L. Porazinska, S. J. Weiss and R. KnightCell 155, (7) 1446-14482013
Supplementary Material Cross-biome comparison of microbial association networksK. Faust, G. Lima-Mendez, J.-S. Lerat, J. Fah, R. K. Sathirapongsasuti, C. Huttenhower, T. Lenaerts and J. Raes
Microbiota Restoration: Natural and Supplemented Recovery of Human Microbial CommunitiesH. C. Younes, G. B. Gloor, R. Knight and H. J. Busscher
Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal ringsLK Ursell, M Gunawardana, S Chang, M Mullen, JA Moss, BC Herold, ...Antiviral research 102, 87-942014
What Is the Value of a Food and Drug Administration Investigational New Drug Application for Fecal Microbiota Transplantation to Treat Clostridium difficile Infection?GA Hecht, MJ Blaser, J Gordon, LM Kaplan, R Knight, L Laine, R Peek, ...Clinical gastroenterology and hepatology: the official clinical practice ...2014
Genomic Standards Consortium ProjectsD Field, P Sterk, R Kottmann, W De Smet, L Amaral-Zettler, G Cochrane, ...Standards in Genomic Sciences 9 (3)2014
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spillOU Mason, NM Scott, A Gonzalez, A Robbins-Pianka, J Bælum, J Kimbrel, ...The ISME Journal2014
Technology and Techniques for Microbial Ecology via DNA SequencingWA Walters, R KnightAnnals of the American Thoracic Society 11 (Supplement 1), S16-S202014
Diversity of Rickettsiales in the Microbiome of the Lone Star Tick, Amblyomma americanumL Ponnusamy, A Gonzalez, W Van Treuren, S Weiss, CM Parobek, ...Applied and environmental microbiology 80 (1), 354-3592014
Toward Effective Probiotics for Autism and Other Neurodevelopmental DisordersJA Gilbert, R Krajmalnik-Brown, DL Porazinska, SJ Weiss, R KnightCell 155 (7), 1446-14482013
Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)AH Loudon, DC Woodhams, LW Parfrey, H Archer, R Knight, V McKenzie, ...The ISME Journal2013
EMPeror: a tool for visualizing high-throughput microbial community dataY Vázquez-Baeza, M Pirrung, A Gonzalez, R KnightGigaScience 2 (1), 1-42013
A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel DiseaseM Tong, X Li, LW Parfrey, B Roth, A Ippoliti, B Wei, J Borneman, ...PLOS ONE 8 (11)2013
Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United StatesN Fierer, J Ladau, JC Clemente, JW Leff, SM Owens, KS Pollard, R Knight, ...Science 342 (6158), 621-6242013
MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environmentEM Glass, Y Dribinsky, P Yilmaz, H Levin, R Van Pelt, D Wendel, A Wilke, ...The ISME Journal2013
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiotaPC Kashyap, A Marcobal, LK Ursell, SA Smits, ED Sonnenburg, ...Proceedings of the National Academy of Sciences 110 (42), 17059-170642013
A microbial clock provides an accurate estimate of the postmortem interval in a mouse model systemJL Metcalf, L Wegener Parfrey, A Gonzalez, CL Lauber, D Knights, ...eLife 22013
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiotaPC Kashyap, A Marcobal, LK Ursell, SA Smits, ED Sonnenburg, ...Proceedings of the National Academy of Sciences 110 (42), 17059-170642013
The amphibian skin‐associated microbiome across species, space and life history stagesJG Kueneman, LW Parfrey, DC Woodhams, HM Archer, R Knight, ...Molecular Ecology2013
Meta-analyses of studies of the human microbiotaCA Lozupone, J Stombaugh, A Gonzalez, G Ackermann, D Wendel, ...Genome research 23 (10), 1704-17142013
Alterations in the Gut Microbiota Associated with HIV-1 InfectionCA Lozupone, M Li, TB Campbell, SC Flores, D Linderman, MJ Gebert, ...Cell Host & Microbe 14 (3), 329-3392013
Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato PhyllosphereAR Ottesen, A Gonzalez, R Bell, C Arce, S Rideout, M Allard, P Evans, ...PLOS ONE 8 (9)2013
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in MiceVK Ridaura, JJ Faith, FE Rey, J Cheng, AE Duncan, AL Kau, NW Griffin, ...Science 341 (6150)2013
Replenishing our defensive microbesLK Ursell, WV Treuren, JL Metcalf, M Pirrung, A Gewirtz, R KnightBioEssays 35 (9), 810-8172013
Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and ColonAA Devine, A Gonzalez, KE Speck, R Knight, M Helmrath, PK Lund, ...PLOS ONE 8 (8)2013
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequencesMGI Langille, J Zaneveld, JG Caporaso, D McDonald, D Knights, ...Nature biotechnology 31 (9), 814-8212013
Convergence of gut microbiomes in myrmecophagous mammalsF Delsuc, JL Metcalf, L Wegener Parfrey, SJ Song, A González, R KnightMolecular Ecology2013
The Long-Term Stability of the Human Gut MicrobiotaJJ Faith, JL Guruge, M Charbonneau, S Subramanian, H Seedorf, ...Science 341 (6141)2013
The Ecology of Microbial Communities Associated with Macrocystis pyriferaVK Michelou, JG Caporaso, R Knight, SR PalumbiPLOS ONE 8 (6)2013
Anal gas evacuation and colonic microbiota in patients with flatulence: effect of dietC Manichanh, A Eck, E Varela, J Roca, JC Clemente, A González, ...Gut2013
Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized micePC Kashyap, A Marcobal, LK Ursell, M Larauche, H Duboc, KA Earle, ...Gastroenterology 144 (5), 967-9772013
Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitchCD Stoddard, J Widmann, JJ Trausch, JG Marcano-Velázquez, R Knight, ...Journal of molecular biology 425 (10), 1596-16112013
Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)AR Ottesen, AG Peña, JR White, JB Pettengill, C Li, S Allard, S Rideout, ...BMC Microbiology 13 (1), 1142013
Widespread Colonization of the Lung by Tropheryma whipplei in HIV InfectionC Lozupone, A Cota-Gomez, BE Palmer, DJ Linderman, ES Charlson, ...American journal of respiratory and critical care medicine 187 (10), 1110-11172013
The 15th Genomic Standards Consortium meetingL Schriml, I Mizrachi, P Sterl, D Field, L Hirschman, T Tatusova, ...Standards in Genomic Sciences 8 (1)2013
Cohabiting family members share microbiota with one another and with their dogsSJ Song, C Lauber, EK Costello, CA Lozupone, G Humphrey, ...eLife 22013
Meeting Report: Fungal ITS Workshop (October 2012)ST Bates, S Ahrendt, HM Bik, TD Bruns, JG Caporaso, J Cole, M Dwan, ...Standards in genomic sciences 8 (1), 1182013
The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012D Smith, J Alverdy, G An, M Coleman, S Garcia-Houchins, J Green, ...Standards in genomic sciences 8 (1), 1122013
A meta-analysis of changes in bacterial and archaeal communities with timeA Shade, JG Caporaso, J Handelsman, R Knight, N FiererThe ISME journal2013
Translating the human microbiomeJ Brown, WM de Vos, PS DiStefano, J Doré, C Huttenhower, R Knight, ...Nature biotechnology 31 (4), 304-82013
Biphasic assembly of the murine intestinal microbiota during early developmentIG Pantoja-Feliciano, JC Clemente, EK Costello, ME Perez, MJ Blaser, ...The ISME journal 7 (6), 1112-11152013
Evidence for a persistent microbial seed bank throughout the global oceanSM Gibbons, JG Caporaso, M Pirrung, D Field, R Knight, JA GilbertProceedings of the National Academy of Sciences 110 (12), 4651-46552013
Xenobiotics and the Human Gut Microbiome: Metatranscriptomics Reveal the Active PlayersLK Ursell, R KnightCell Metabolism 17 (3), 317-3182013
How delivery mode and feeding can shape the bacterial community in the infant gut.SJ Song, MG Dominguez-Bello, R KnightCMAJ: Canadian Medical Association journal= journal de l'Association ...2013
Global biogeography of highly diverse protistan communities in soilST Bates, JC Clemente, GE Flores, WA Walters, LW Parfrey, R Knight, ...The ISME journal 7 (3), 652-6592013
Collaborative cloud-enabled tools allow rapid, reproducible biological insightsB Ragan-Kelley, WA Walters, D McDonald, J Riley, BE Granger, ...The ISME journal 7 (3), 4612013
From molecules to dynamic biological communitiesD McDonald, Y Vázquez-Baeza, WA Walters, JG Caporaso, R KnightBiology & philosophy 28 (2), 241-2592013
Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial CommunitiesS Kittelmann, H Seedorf, WA Walters, JC Clemente, R Knight, JI Gordon, ...PloS one 8 (2), e478792013
The microbiome explored: recent insights and future challengesM Blaser, P Bork, C Fraser, R Knight, J WangNature Reviews Microbiology 11 (3), 213-2172013
Diversity, distribution and sources of bacteria in residential kitchensGE Flores, ST Bates, JG Caporaso, CL Lauber, JW Leff, R Knight, N FiererEnvironmental microbiology 15 (2), 588-5962013
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor.MI Smith, T Yatsunenko, MJ Manary, I Trehan, R Mkakosya, J Cheng, ...Science (New York, NY) 339 (6119), 548-5542013
Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)KM Hewitt, FL Mannino, A Gonzalez, JH Chase, JG Caporaso, R Knight, ...PloS one 8 (1)2013
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome DatasetsO Koren, D Knights, A Gonzalez, L Waldron, N Segata, R Knight, ...PLoS computational biology 9 (1)2013
Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in miceBW Parks, E Nam, E Kostem, F Norheim, ST Hui, C Pan, M Civelek, ...Cell metabolism 17 (1), 141-1522013
What's the Value of an FDA IND for Fecal Microbiota Transplantation in Clostridium difficile Infection?GA Hecht, MJ Blaser, J Gordon, LM Kaplan, R Knight, L Laine, R Peek, ...Clinical gastroenterology and hepatology: the official clinical practice ...2013
Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow NestsJM Peralta-Sánchez, JJ Soler, AM Martín-Platero, R Knight, ...Microbial Ecology, 1-82013
Advancing Our Understanding of the Human Microbiome Using QIIMEJA Navas-Molina, JM Peralta-Sánchez, A González, PJ McMurdie, ...Methods in enzymology 531, 371-4442013
Mathematical Approaches for Describing Microbial Populations: Practice and Theory for Extrapolation of Rich EnvironmentsME Lladser, R KnightThe Human Microbiota: How Microbial Communities Affect Health and Disease ...2013
Correction: Commensal Bacteria and MAMPs Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1T Maslanik, K Tannura, L Mahaffey, AB Loughridge, L Benninson, L Ursell, ...PloS one 8 (8)2013
Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycleHV Carey, WA Walters, R KnightAmerican Journal of Physiology-Regulatory, Integrative and Comparative ...2013
Crystal ball–2013T Curtis, JM Daran, JT Pronk, J Frey, JK Jansson, A Robbins‐Pianka, ...Microbial Biotechnology 6 (1), 3-162013
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residentsMJ Blaser, MG Dominguez-Bello, M Contreras, M Magris, G Hidalgo, ...The ISME journal 7 (1), 85-952013
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencingNA Bokulich, S Subramanian, JJ Faith, D Gevers, JI Gordon, R Knight, ...Nature methods 10 (1), 57-592013
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial matJK Harris, JG Caporaso, JJ Walker, JR Spear, NJ Gold, CE Robertson, ...The ISME journal 7 (1), 50-602013
Insights from characterizing extinct human gut microbiomesRY Tito, D Knights, J Metcalf, AJ Obregon-Tito, L Cleeland, F Najar, B Roe, ...PloS one 7 (12), e511462012
Commensal Bacteria and MAMPs Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1T Maslanik, K Tannura, L Mahaffey, AB Loughridge, L Benninson, L Ursell, ...PloS one 7 (12), e506362012
Colitis in TLR5‐deficiency Mice: Role of the Microbiota: P‐259 YIF Carvalho, O Koren, B Chassaing, A Darfeuille-Michaud, R Knight, R Ley, ...Inflammatory Bowel Diseases 18, S113-S1142012
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial CommunitiesJ Kuczynski, J Stombaugh, WA Walters, A González, JG Caporaso, ...Current protocols in microbiology, 1E. 5.1-1E. 5.202012
Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthoodSS Stahringer, JC Clemente, RP Corley, J Hewitt, D Knights, WA Walters, ...Genome research 22 (11), 2146-21522012
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbiontsC Lozupone, K Faust, J Raes, JJ Faith, DN Frank, J Zaneveld, JI Gordon, ...Genome research 22 (10), 1974-19842012
Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the ZebrafishI Semova, JD Carten, J Stombaugh, LC Mackey, R Knight, SA Farber, ...Cell Host & Microbe 12 (3), 277-2882012
Diversity, stability and resilience of the human gut microbiotaCA Lozupone, JI Stombaugh, JI Gordon, JK Jansson, R KnightNature 489 (7415), 220-2302012
Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan PlateauJ Xiong, Y Liu, X Lin, H Zhang, J Zeng, J Hou, Y Yang, T Yao, R Knight, ...Environmental microbiology 14 (9), 2457-24662012
Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient miceFA Carvalho, O Koren, JK Goodrich, MEV Johansson, I Nalbantoglu, ...Cell host & microbe 12 (2), 139-1522012
Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic SyndromeML Zupancic, BL Cantarel, Z Liu, EF Drabek, KA Ryan, S Cirimotich, ...PloS one 7 (8), e430522012
The Human Microbiome Project: A Community Resource for the Healthy Human MicrobiomeD Gevers, R Knight, JF Petrosino, K Huang, AL McGuire, BW Birren, ...PLoS biology 10 (8), e10013772012
Host Remodeling of the Gut Microbiome and Metabolic Changes during PregnancyO Koren, JK Goodrich, TC Cullender, A Spor, K Laitinen, H Kling Bäckhed, ...Cell 150 (3), 470-4802012
Defining the human microbiomeLK Ursell, JL Metcalf, LW Parfrey, R KnightNutrition Reviews 70 (s1), S38-S442012
Discussion from the 24th Marabou Symposium: Nutrition and the human microbiomeD Ehrlich, R Knight, R Ley, J Nielsen, G Hansson, W de Vos, J Nielsen, ...NUTRITION REVIEWS 70, S57-S862012
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-omeD McDonald, JC Clemente, J Kuczynski, JR Rideout, J Stombaugh, ...GigaScience 1 (1), 72012
RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAsJ Widmann, J Stombaugh, D McDonald, J Chocholousova, P Gardner, ...RNA 18 (7), 1319-13272012
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequencesX Wang, Y Cai, Y Sun, R Knight, V MaiThe ISME journal 6 (7), 12772012
Environmental and ecological factors that shape the gut bacterial communities of fish: a meta‐analysisKE Sullam, SD Essinger, CA Lozupone, MP O’CONNOR, GL Rosen, ...Molecular Ecology 21 (13), 3363-33782012
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveysJJ Werner, D Zhou, JG Caporaso, R Knight, LT AngenentThe ISME journal 6 (7), 1273-12762012
Characterizing microbial communities through space and timeA Gonzalez, A King, MS Robeson II, S Song, A Shade, JL Metcalf, ...Current opinion in biotechnology 23 (3), 431-4362012
Lake microbial communities are resilient after a whole-ecosystem disturbanceA Shade, JS Read, ND Youngblut, N Fierer, R Knight, TK Kratz, NR Lottig, ...The ISME journal 6 (12), 2153-21672012
A framework for human microbiome researchHuman Microbiome Project ConsortiumNature 486 (7402), 215-2212012
Structure, function and diversity of the healthy human microbiomeHuman Microbiome Project ConsortiumNature 486 (7402), 207-2142012
Unlocking the potential of metagenomics through replicated experimental designR Knight, J Jansson, D Field, N Fierer, N Desai, JA Fuhrman, ...Nature biotechnology 30 (6), 513-5202012
The identification of environmental parameters which could influence soil bacterial community composition on the Antarctic Peninsula-a statistical approachCW Chong, DA Pearce, P Convey, IKP TanAntarctic Science 24 (03), 249-2582012
Human Immunodeficiency Virus nef Signature Sequences Are Associated with Pulmonary HypertensionS Almodovar, R Knight, AA Allshouse, S Roemer, C Lozupone, ...AIDS Research and Human Retroviruses 28 (6), 607-6182012
The Western English Channel contains a persistent microbial seed bankJG Caporaso, K Paszkiewicz, D Field, R Knight, JA GilbertThe ISME journal 6 (6), 1089-10932012
Su1926 Defining a Mosaic of Functional Microbial Communities at the Human Mucosal Surface, and Their Association With IBDM Tong, XX Li, LW Parfrey, A Ippoliti, B Wei, DP McGovern, D Frank, E Li, ...Gastroenterology 142 (5), S-5382012
Su1991 Diet-Induced Change in Gastrointestinal Transit Significantly Alters Distal Gut Microbial CommunitiesPC Kashyap, S Higginbottom, L Ursell, PJ Pasricha, R Knight, G Farrugia, ...Gastroenterology 142 (5), S-554-S-5552012
Spatial and temporal variability of the human microbiotaLW Parfrey, R KnightClinical Microbiology and Infection 18 (s4), 8-112012
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sitesLK Ursell, JC Clemente, JR Rideout, D Gevers, JG Caporaso, R KnightJournal of Allergy and Clinical Immunology 129 (5), 1204-12082012
Human gut microbiome viewed across age and geographyT Yatsunenko, FE Rey, MJ Manary, I Trehan, MG Dominguez-Bello, ...Nature 486 (7402), 222-2272012
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradientsN Fierer, CL Lauber, KS Ramirez, J Zaneveld, MA Bradford, R KnightThe ISME journal 6 (5), 1007-10172012
Sequencing our way towards understanding global eukaryotic biodiversityHM Bik, DL Porazinska, S Creer, JG Caporaso, R Knight, WK ThomasTrends in ecology & evolution 27 (4), 233-2432012
Hibernation alters the gut microbial community in ground squirrelsHV Carey, WA Walters, R KnightFASEB JOURNAL 262012
Broad patterns in the diversity of eukaryotic microbesWL Parfrey, R KnightINTEGRATIVE AND COMPARATIVE BIOLOGY 52, E188-E1882012
Responses of gut microbiota to diet composition and weight loss in lean and obese miceY Ravussin, O Koren, A Spor, C LeDuc, R Gutman, J Stombaugh, ...Obesity 20 (4), 738-7472012
Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquiferX Lin, J McKinley, CT Resch, R Kaluzny, CL Lauber, J Fredrickson, ...The ISME Journal 6 (9), 1665-16762012
Conceptualizing a Genomics Software Institute (GSI)JA Gilbert, C Catlett, N Desai, R Knight, O White, R Robbins, R Sankaran, ...Standards in Genomic Sciences 6 (1)2012
The impact of the gut microbiota on human health: an integrative viewJC Clemente, LK Ursell, LW Parfrey, R KnightCell 148 (6), 1258-12702012
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platformsJG Caporaso, CL Lauber, WA Walters, D Berg-Lyons, J Huntley, N Fierer, ...The ISME journal 6 (8), 1621-16242012
Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitisFA Carvalho, I Nalbantoglu, S Ortega-Fernandez, JD Aitken, Y Su, ...Gut 61 (3), 373-3842012
Co-habiting amphibian species harbor unique skin bacterial communities in wild populationsVJ McKenzie, RM Bowers, N Fierer, R Knight, CL LauberThe ISME journal 6 (3), 588-5962012
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaeaD McDonald, MN Price, J Goodrich, EP Nawrocki, TZ DeSantis, A Probst, ...The ISME journal 6 (3), 610-6182012
Advancing analytical algorithms and pipelines for billions of microbial sequencesA Gonzalez, R KnightCurrent opinion in biotechnology 23 (1), 64-712012
SitePainter: a tool for exploring biogeographical patternsA Gonzalez, J Stombaugh, CL Lauber, N Fierer, R KnightBioinformatics 28 (3), 436-4382012
Defining seasonal marine microbial community dynamicsJA Gilbert, JA Steele, JG Caporaso, L Steinbrück, J Reeder, B Temperton, ...The ISME journal 6 (2), 298-3082012
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequencesDAW Soergel, N Dey, R Knight, SE BrennerThe ISME journal 6 (7), 1440-14442012
List of participants from the 24th Marabou Symposium: Nutrition and the Human MicrobiomeB Angelin, A Berstad, R Black, P Brandtzaeg, F Bäckhed, W de Vos, ...Nutrition Reviews 70 (1), S952012
Evidence for a persistent microbial community in the Western English ChannelJG Caporaso, D Field, K Paszkiewicz, R Knight, J GilbertISME Journal 6 (ANL/CLS/JA-69610)2012
Gene discovery from a pilot study of the transcriptomes from three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetrasporaJR Grant, DJG Lahr, FE Rey, JG Burleigh, JI Gordon, R Knight, ...Protist Genomics 1, 3-182012
Community Page-The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome-e1001377D Gevers, R Knight, JF Petrosino, K Huang, AL McGuire, BW Birren, ...PLoS-Biology 10 (8), 14822012
A preliminary survey of lichen associated eukaryotes using pyrosequencingST Bates, D Berg-Lyons, CL Lauber, WA Walters, R Knight, N FiererThe Lichenologist 44 (01), 137-1462012
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysisY Sun, Y Cai, SM Huse, R Knight, WG Farmerie, X Wang, V MaiBriefings in bioinformatics 13 (1), 107-1212012
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveysJJ Werner, O Koren, P Hugenholtz, TZ DeSantis, WA Walters, ...The ISME journal 6 (1), 94-1032012
Composition of human skin microbiota affects attractiveness to malaria mosquitoesNO Verhulst, YT Qiu, H Beijleveld, C Maliepaard, D Knights, S Schulz, ...PloS one 6 (12), e289912011
Experimental and analytical tools for studying the human microbiomeJ Kuczynski, CL Lauber, WA Walters, LW Parfrey, JC Clemente, D Gevers, ...Nature Reviews Genetics 13 (1), 47-582011
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial CommunitiesJ Kuczynski, J Stombaugh, WA Walters, A González, JG Caporaso, ...Current Protocols in Bioinformatics, 10.7. 1-10.7. 202011
The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011JA Gilbert, M Bailey, D Field, N Fierer, JA Fuhrman, B Hu, J Jansson, ...Standards in Genomic Sciences 5 (2), 2432011
Microbial biogeography of public restroom surfacesGE Flores, ST Bates, D Knights, CL Lauber, J Stombaugh, R Knight, ...PLoS One 6 (11), e281322011
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences: Supplementary MaterialsDAW Soergel, N Dey, R Knight, SE Brenner2011
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadataM Pirrung, R Kennedy, JG Caporaso, J Stombaugh, D Wendel, R KnightBioinformatics 27 (21), 3067-30692011
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptationJRR Zaneveld, LW Parfrey, W Van Treuren, C Lozupone, JC Clemente, ...Trends in microbiology 19 (10), 472-4822011
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twinsNP McNulty, T Yatsunenko, A Hsiao, JJ Faith, BD Muegge, AL Goodman, ...Science translational medicine 3 (106)2011
Linking long-term dietary patterns with gut microbial enterotypesGD Wu, J Chen, C Hoffmann, K Bittinger, YY Chen, SA Keilbaugh, ...Science 334 (6052), 105-1082011
Human-Associated Microbial Signatures: Examining Their Predictive ValueD Knights, LW Parfrey, J Zaneveld, C Lozupone, R KnightCell host & microbe 10 (4), 292-2962011
The genomic standards consortium: bringing standards to life for microbial ecologyP Yilmaz, JA Gilbert, R Knight, L Amaral-Zettler, I Karsch-Mizrachi, ...The ISME journal 5 (10), 15652011
Sources of bacteria in outdoor air across cities in the midwestern United StatesRM Bowers, AP Sullivan, EK Costello, JL Collett, R Knight, N FiererApplied and environmental microbiology 77 (18), 6350-63562011
ANALYSIS OF TRANSCRIPTOMES FROM THREE MICROBIAL EUKARYOTESJR Grant, DJ Lahr, F Rey, R Knight, LA Katz, J GordonJOURNAL OF PHYCOLOGY 47, S74-S752011
UCHIME improves sensitivity and speed of chimera detectionRC Edgar, BJ Haas, JC Clemente, C Quince, R KnightBioinformatics 27 (16), 2194-22002011
The under-recognized dominance of< i> Verrucomicrobia</i> in soil bacterial communitiesGT Bergmann, ST Bates, KG Eilers, CL Lauber, JG Caporaso, WA Walters, ...Soil Biology and Biochemistry 43 (7), 1450-14552011
Bayesian community-wide culture-independent microbial source trackingD Knights, J Kuczynski, ES Charlson, J Zaneveld, MC Mozer, RG Collman, ...nature methods 8 (9), 761-7632011
Our microbial selves: what ecology can teach usA Gonzalez, JC Clemente, A Shade, JL Metcalf, S Song, B Prithiviraj, ...EMBO reports 12 (8), 775-7842011
Sharing and archiving nucleic acid structure mapping dataP Rocca-Serra, S Bellaousov, A Birmingham, C Chen, P Cordero, R Das, ...RNA 17 (7), 1204-12122011
Boulder ALignment Editor (ALE): a web-based RNA alignment toolJ Stombaugh, J Widmann, D McDonald, R KnightBioinformatics 27 (12), 1706-17072011
The genomic standards consortiumD Field, L Amaral-Zettler, G Cochrane, JR Cole, P Dawyndt, GM Garrity, ...PLoS biology 9 (6)2011
Controlled Feeding Experiments Demonstrate the Impact of Diet on the Composition of the Human Gut MicrobiomeGD Wu, M Bewtra, C Hoffmann, YY Chen, SA Keilbaugh, K Bittinger, ...Gastroenterology 140 (5), S-472011
Development of the human gastrointestinal microbiota and insights from high-throughput sequencingMG Dominguez-Bello, MJ Blaser, RE Ley, R KnightGastroenterology 140 (6), 1713-17192011
Moving pictures of the human microbiomeJG Caporaso, CL Lauber, EK Costello, D Berg-Lyons, A Gonzalez, ...Genome Biol 12 (5), R502011
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humansBD Muegge, J Kuczynski, D Knights, JC Clemente, A González, ...Science 332 (6032), 970-9742011
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specificationsP Yilmaz, R Kottmann, D Field, R Knight, JR Cole, L Amaral-Zettler, ...Nature biotechnology 29 (5), 415-4202011
Examining the global distribution of dominant archaeal populations in soilST Bates, D Berg-Lyons, JG Caporaso, WA Walters, R Knight, N FiererThe ISME journal 5 (5), 908-9172011
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primersWA Walters, JG Caporaso, CL Lauber, D Berg-Lyons, N Fierer, R KnightBioinformatics 27 (8), 1159-11612011
New Insight into the Diversity of Life's Building Blocks: Evenness, Not VarianceJG Caporaso, R KnightAstrobiology 11 (3), 197-1982011
Meeting report of the RNA Ontology Consortium January 8-9, 2011A Birmingham, JC Clemente, N Desai, J Gilbert, A Gonzalez, N Kyrpides, ...Standards in genomic sciences 4 (2), 252-2562011
Supervised classification of microbiota mitigates mislabeling errorsD Knights, J Kuczynski, O Koren, RE Ley, D Field, R Knight, TZ DeSantis, ...The ISME journal 5 (4), 5702011
Microbes do not follow the elevational diversity patterns of plants and animalsN Fierer, CM McCain, P Meir, M Zimmermann, JM Rapp, MR Silman, ...Ecology 92 (4), 797-8042011
Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environmentsRM Bowers, S McLetchie, R Knight, N FiererThe ISME journal 5 (4), 601-6122011
Spatially and Temporally Resolved Studies of the Human Microbiome (2011 JGI User Meeting)R KnightDOE Joint Genome Institute (JGI), LBNL (Lawrence Berkeley National ...2011
Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twinsEE Hansen, CA Lozupone, FE Rey, M Wu, JL Guruge, A Narra, ...Proceedings of the National Academy of Sciences 108 (Supplement 1), 4599-46062011
Human oral, gut, and plaque microbiota in patients with atherosclerosisO Koren, A Spor, J Felin, F Fåk, J Stombaugh, V Tremaroli, CJ Behre, ...Proceedings of the National Academy of Sciences 108 (Supplement 1), 4592-45982011
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sampleJG Caporaso, CL Lauber, WA Walters, D Berg-Lyons, CA Lozupone, ...Proceedings of the National Academy of Sciences 108 (Supplement 1), 4516-45222011
Succession of microbial consortia in the developing infant gut microbiomeJE Koenig, A Spor, N Scalfone, AD Fricker, J Stombaugh, R Knight, ...Proceedings of the National Academy of Sciences 108 (Supplement 1), 4578-45852011
Bacterial community structures are unique and resilient in full-scale bioenergy systemsJJ Werner, D Knights, ML Garcia, NB Scalfone, S Smith, K Yarasheski, ...Proceedings of the National Academy of Sciences 108 (10), 4158-41632011
The mind-body-microbial continuumA Gonzalez, J Stombaugh, C Lozupone, PJ Turnbaugh, JI Gordon, ...Dialogues in clinical neuroscience 13 (1), 552011
Supervised classification of human microbiotaD Knights, EK Costello, R KnightFEMS microbiology reviews 35 (2), 343-3592011
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR ampliconsBJ Haas, D Gevers, AM Earl, M Feldgarden, DV Ward, G Giannoukos, ...Genome research 21 (3), 494-5042011
Host-associated and free-living phage communities differ profoundly in phylogenetic compositionJG Caporaso, R Knight, ST KelleyPloS one 6 (2)2011
Bacterial communities associated with the lichen symbiosisST Bates, GWG Cropsey, JG Caporaso, R Knight, N FiererApplied and environmental microbiology 77 (4), 1309-13142011
UniFrac: an effective distance metric for microbial community comparisonC Lozupone, ME Lladser, D Knights, J Stombaugh, R KnightThe ISME journal 5 (2), 1692011
641: Depth of 16S rRNA sequencing required for characterization of microbial composition in the vaginal, oral, and rectal compartments in pregnancyO Cohavy, J Acuna, I Solt, J Reeder, M Kim, I Lebovics, B Paster, R Knight, ...American Journal of Obstetrics and Gynecology 204 (1), S2542011
257: Preliminary observations on the microbial phylogeny of the oral, vaginal, and rectal microbiome in gestational diabetes and healthy pregnanciesJ Acuna, O Cohavy, I Solt, J Reeder, M Kim, I Lebovics, B Paster, R Knight, ...American Journal of Obstetrics and Gynecology 204 (1), S109-S1102011
Closure of the NCBI SRA and implications for the long-term future of genomics data storageGBE TeamGenome biology 12 (3), 4022011
Community Page-The Genomic Standards ConsortiumD Field, L Amaral-Zettler, G Cochrane, JR Cole, P Dawyndt, GM Garrity, ...PLoS-Biology 9 (6), 11892011
Analytic Strategies for Understanding Host-Associated Microbial CommunitiesJ Kuczynski, R KnightMicrobe 6 (9), 3892011
Microbial eukaryotes in the human microbiome: ecology, evolution, and future directionsLW Parfrey, WA Walters, R KnightFrontiers in microbiology 22011
The RNA Ontology (RNAO): an ontology for integrating RNA sequence and structure dataR Hoehndorf, C Batchelor, T Bittner, M Dumontier, K Eilbeck, R Knight, ...Applied Ontology 6 (1), 53-892011
Global patterns in the biogeography of bacterial taxaDR Nemergut, EK Costello, M Hamady, C Lozupone, L Jiang, SK Schmidt, ...Environmental microbiology 13 (1), 135-1442011
Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010JA Gilbert, F Meyer, R Knight, D Field, N Kyrpides, P Yilmaz, J WooleyStandards in genomic sciences 3 (3), 2352010
The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.JA Gilbert, F Meyer, J Jansson, J Gordon, N Pace, J Tiedje, R Ley, ...Standards in genomic sciences 3 (3), 2492010
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome projectJ Gilbert, F Meyer, DA Antonopoulos, P Balaji, CT Brown, CT Brown, ...Standards in genomic sciences 3 (3), 243-2482010
Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systemsKS Ramirez, CL Lauber, R Knight, MA Bradford, N FiererEcology 91 (12), 3463-34702010
Microbiota restoration: natural and supplemented recovery of human microbial communitiesG Reid, JA Younes, HC Van der Mei, GB Gloor, R Knight, HJ BusscherNature Reviews Microbiology 9 (1), 27-382010
The “Minimum Information about an ENvironmental Sequence”(MIENS) specificationP Yilmaz, R Kottmann, D Field, R Knight, JR Cole, L Amaral-Zettler, ...Nature Publishing Group2010
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leavesAJ Redford, RM Bowers, R Knight, Y Linhart, N FiererEnvironmental microbiology 12 (11), 2885-28932010
Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomesH Chu, N Fierer, CL Lauber, JG Caporaso, R Knight, P GroganEnvironmental Microbiology 12 (11), 2998-30062010
The bacterial microbiota in the oral mucosa of rural AmerindiansM Contreras, EK Costello, G Hidalgo, M Magris, R Knight, ...Microbiology 156 (11), 3282-32872010
Changes through time: integrating microorganisms into the study of successionN Fierer, D Nemergut, R Knight, JM CraineResearch in microbiology 161 (8), 635-6422010
Reply to Putignani et al.: Vagina as a major source of natural inoculum for the newbornMG Dominguez-Bello, EK Costello, R KnightProceedings of the National Academy of Sciences 107 (42), E160-E1602010
A data analysis and coordination center for the human microbiome projectJ Wortman, M Giglio, H Creasy, A Chen, K Liolios, K Chu, N Davidovics, ...Genome Biology 11 (Suppl 1), O132010
Translational medicine and the human microbiomeR KnightGenome Biology 11 (Suppl 1), I152010
Loss of toll-like receptor-5 changes gut microbiota and results in metabolic syndromeM Vijay-Kumar, J Aitken, F Carvalho, T Cullendar, S Mwangi, S Srinivasan, ...DIABETES OBESITY & METABOLISM 12, 44-442010
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNAI Majerfeld, J Chocholousova, V Malaiya, J Widmann, D McDonald, ...RNA 16 (10), 1915-19242010
Reshaping the gut microbiome with bacterial transplantation and antibiotic intakeC Manichanh, J Reeder, P Gibert, E Varela, M Llopis, M Antolin, R Guigo, ...Genome research 20 (10), 1411-14192010
Estimate of the abundance of cardiomyopathic mutations in the β-myosin geneM Hamady, M Buvoli, LA Leinwand, R KnightInternational journal of cardiology 144 (1), 124-1262010
Microbial community resemblance methods differ in their ability to detect biologically relevant patternsJ Kuczynski, Z Liu, C Lozupone, D McDonald, N Fierer, R KnightNature methods 7 (10), 813-8192010
Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distributionJ Reeder, R KnightNature methods 7 (9), 6682010
Biogeography and habitat modelling of high-alpine bacteriaAJ King, KR Freeman, KF McCormick, RC Lynch, C Lozupone, R Knight, ...Nature Communications 1, 532010
OOS 31-5: Using phylogenetic β diversity measures to understand the factors structuring microbial diversity over large and fine scalesC Lozupone, R KnightThe 95th ESA Annual Meeting2010
OOS 31-9: Soil bacterial diversity in the Arctic is not fundamentally different from other biomesH Chu, N Fierer, C Lauber, JG Caporaso, R Knight, P GroganThe 95th ESA Annual Meeting2010
Stable tRNA-based phylogenies using only 76 nucleotidesJ Widmann, JK Harris, C Lozupone, A Wolfson, R KnightRNA 16 (8), 1469-14772010
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tagsGD Wu, JD Lewis, C Hoffmann, YY Chen, R Knight, K Bittinger, J Hwang, ...BMC microbiology 10 (1), 2062010
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relativesJR Zaneveld, C Lozupone, JI Gordon, R KnightNucleic acids research 38 (12), 3869-38792010
Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soilKG Eilers, CL Lauber, R Knight, N FiererSoil Biology and Biochemistry 42 (6), 896-9032010
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newbornsMG Dominguez-Bello, EK Costello, M Contreras, M Magris, G Hidalgo, ...Proceedings of the National Academy of Sciences 107 (26), 11971-119752010
Postprandial remodeling of the gut microbiota in Burmese pythonsEK Costello, JI Gordon, SM Secor, R KnightThe ISME journal 4 (11), 1375-13852010
279 Altered Gut Microbiota in Toll-Like Receptor-5 (TLR5) Deficient Mice Results in Metabolic SyndromeM Vijay-Kumar, JD Aitken, FA Carvalho, TC Cullender, SM Mwangi, ...Gastroenterology 138 (5), S-522010
Soil bacterial and fungal communities across a pH gradient in an arable soilJ Rousk, E Bååth, PC Brookes, CL Lauber, C Lozupone, JG Caporaso, ...The ISME journal 4 (10), 1340-13512010
Direct sequencing of the human microbiome readily reveals community differencesJ Kuczynski, EK Costello, DR Nemergut, J Zaneveld, CL Lauber, ...Genome Biol 11 (5), 2102010
Bioinformatics assessment of beta-myosin mutations reveals myosin's high sensitivity to mutations (vol 18, pg 141, 2008)M Buvoli, M Hamady, LA Leinwand, R KnightTRENDS IN CARDIOVASCULAR MEDICINE 20 (4), 141-1412010
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twinsPJ Turnbaugh, C Quince, JJ Faith, AC McHardy, T Yatsunenko, F Niazi, ...Proceedings of the National Academy of Sciences 107 (16), 7503-75082010
QIIME allows analysis of high-throughput community sequencing dataJG Caporaso, J Kuczynski, J Stombaugh, K Bittinger, FD Bushman, ...Nature methods 7 (5), 335-3362010
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5M Vijay-Kumar, JD Aitken, FA Carvalho, TC Cullender, S Mwangi, ...Science 328 (5975), 228-2312010
Forensic identification using skin bacterial communitiesN Fierer, CL Lauber, N Zhou, D McDonald, EK Costello, R KnightProceedings of the National Academy of Sciences 107 (14), 6477-64812010
Simple, recurring RNA binding sites for L-arginineT Janas, JJ Widmann, R Knight, M YarusRNA 16 (4), 805-8162010
Effect of storage conditions on the assessment of bacterial community structure in soil and human‐associated samplesCL Lauber, N Zhou, JI Gordon, R Knight, N FiererFEMS microbiology letters 307 (1), 80-862010
Natural and artificial RNAs occupy the same restricted region of sequence spaceR Kennedy, ME Lladser, Z Wu, C Zhang, M Yarus, H De Sterck, R KnightRNA 16 (2), 280-2892010
Bacterial communities of disease vectors sampled across time, space, and speciesRT Jones, R Knight, AP MartinThe ISME journal 4 (2), 223-2312010
Methods and Compositions for Using Error-Detecting and/or Error-Correcting Barcodes in Nucleic Acid Amplification ProcessML Hamady, RD KnightUS Patent App. 12/693,6122010
PyNAST: a flexible tool for aligning sequences to a template alignmentJG Caporaso, K Bittinger, FD Bushman, TZ DeSantis, GL Andersen, ...Bioinformatics 26 (2), 266-2672010
HIV-1 Nef Signature Sequences Are A Feature Of HIV-related Pulmonary Hypertension: A Genetic Translational Tool?A Allshouse, R Knight, S Roemer, NF Voelkel, P Hsue, MJC Humbert, ...America 1, 22010
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip dataM Hamady, C Lozupone, R KnightThe ISME journal 4 (1), 17-272010
Bacterial community variation in human body habitats across space and timeEK Costello, CL Lauber, M Hamady, N Fierer, JI Gordon, R KnightScience 326 (5960), 1694-16972009
High-fat diet determines the composition of the murine gut microbiome independently of obesityMA Hildebrandt, C Hoffmann, SA Sherrill–Mix, SA Keilbaugh, M Hamady, ...Gastroenterology 137 (5), 1716-1724. e22009
Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environmentP Marshall, M Woitaszek, HM Tufo, R Knight, D McDonald, J GoodrichProceedings of the 2nd Workshop on Many-Task Computing on Grids and ...2009
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic micePJ Turnbaugh, VK Ridaura, JJ Faith, FE Rey, R Knight, JI GordonScience translational medicine 1 (6)2009
The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology’s “phylogenetic beta diversity” frameworkDP Faith, CA Lozupone, D Nipperess, R KnightInternational journal of molecular sciences 10 (11), 4723-47412009
RNA–amino acid binding: A stereochemical era for the genetic codeM Yarus, JJ Widmann, R KnightJournal of molecular evolution 69 (5), 406-4292009
Identifying genetic determinants needed to establish a human gut symbiont in its habitatAL Goodman, NP McNulty, Y Zhao, D Leip, RD Mitra, CA Lozupone, ...Cell host & microbe 6 (3), 279-2892009
The RNA structure alignment ontologyJW Brown, A Birmingham, PE Griffiths, F Jossinet, R Kachouri-Lafond, ...RNA 15 (9), 1623-16312009
The ‘rare biosphere’: a reality checkJ Reeder, R KnightNature Methods 6 (9), 636-6372009
Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nucleiRM Bowers, CL Lauber, C Wiedinmyer, M Hamady, AG Hallar, R Fall, ...Applied and environmental microbiology 75 (15), 5121-51302009
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scaleCL Lauber, M Hamady, R Knight, N FiererApplied and environmental microbiology 75 (15), 5111-51202009
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure dataC Batchelor, T Bittner, K Eilbeck, C Mungall, J Richardson, R Knight, ...Proceedings of the International Conference on Biomedical Ontologies, 7-102009
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivationPA Crawford, JR Crowley, N Sambandam, BD Muegge, EK Costello, ...Proceedings of the National Academy of Sciences 106 (27), 11276-112812009
Life Through A Microbial LensS Spath, M O’Malley, J Zaneveld, R Knight, C ZimmerMetascience 18 (2), 179-2052009
Systems Biology: Understanding function from genes to networksR Singh, R KnightCurrent Proteomics 6 (2), 93-1032009
Microbial community profiling for human microbiome projects: Tools, techniques, and challengesM Hamady, R KnightGenome research 19 (7), 1141-11522009
Soil pH as a predictor of soil bacterial community structure at the continental scale: a pyrosequencing-based assessmentCL Lauber, M Hamady, R Knight, N FiererApplied and Environmental Microbiology2009
662 High Fat Diet Determines the Composition of the Gut Microbiome Independent of Host Genotype and PhenotypeMA Hildebrandt, C Hoffmann, M Hamady, YY Chen, R Knight, ...Gastroenterology 136 (5), A-1022009
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomesM Hamady, SA Wilson, J Zaneveld, N Sueoka, R KnightBioinformatics 25 (10), 1331-13322009
RNA structure prediction from evolutionary patterns of nucleotide compositionS Smit, R Knight, J HeringaNucleic acids research 37 (5), 1378-13862009
A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteinsCY Yen, K Meyer-Arendt, B Eichelberger, S Sun, S Houel, WM Old, ...Molecular & Cellular Proteomics 8 (4), 857-8692009
A core gut microbiome in obese and lean twinsPJ Turnbaugh, M Hamady, T Yatsunenko, BL Cantarel, A Duncan, RE Ley, ...Nature 457 (7228), 480-4842009
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analysesRT Jones, MS Robeson, CL Lauber, M Hamady, R Knight, N FiererThe ISME journal 3 (4), 442-4532009
Biogeography of bacterial diversity and function across a heterogeneous alpine landscape.AJ King, KR Freeman, KF McCormick, M Hamady, C Lozupone, R Knight, ...Aspects of Applied Biology, 213-2152009
Codonexplorer: an interactive online database for the analysis of codon usage and sequence compositionJ Zaneveld, M Hamady, N Sueoka, R KnightBioinformatics for DNA Sequence Analysis, 207-2322009
Pathological rate matrices: from primates to pathogensHW Schranz, VB Yap, S Easteal, R Knight, GA HuttleyBMC bioinformatics 9 (1), 5502008
Activating and inhibiting connections in biological network dynamicsD McDonald, L Waterbury, R Knight, MD BettertonBiology direct 3 (1), 492008
Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metricsJG Caporaso, S Smit, BC Easton, L Hunter, GA Huttley, R KnightBMC evolutionary biology 8 (1), 3272008
Fine-Scale Physical Structure and Microbial Composition of Soil AggregatesVL Bailey, L McCue, MI Boyanov, F de Carlo, N Fierer, ML Hamady, ...AGU Fall Meeting Abstracts 1, 052008
Comparison of methods for estimating the nucleotide substitution matrixM Oscamou, D McDonald, GAH Von Bing Yap, ME Lladser, R KnightBMC bioinformatics 9 (1), 5112008
The influence of sex, handedness, and washing on the diversity of hand surface bacteriaN Fierer, M Hamady, CL Lauber, R KnightProceedings of the National Academy of Sciences 105 (46), 17994-179992008
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencersZ Liu, TZ DeSantis, GL Andersen, R KnightNucleic acids research 36 (18), e120-e1202008
Worlds within worlds: evolution of the vertebrate gut microbiotaRE Ley, CA Lozupone, M Hamady, R Knight, JI GordonNature Reviews Microbiology 6 (10), 776-7882008
The convergence of carbohydrate active gene repertoires in human gut microbesCA Lozupone, M Hamady, BL Cantarel, PM Coutinho, B Henrissat, ...Proceedings of the National Academy of Sciences 105 (39), 15076-150812008
MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifsM Hamady, J Widmann, SD Copley, R KnightGenome biology 9 (8), R1282008
Evolution of mammals and their gut microbesRE Ley, M Hamady, C Lozupone, PJ Turnbaugh, RR Ramey, JS Bircher, ...Science 320 (5883), 1647-16512008
Bioinformatics Assessment of β-Myosin Mutations Reveals Myosin High Sensitivity to MutationsM Buvoli, M Hamady, LA Leinwand, R KnightTrends in cardiovascular medicine 18 (4), 141-1492008
Insights and inferences about integron evolution from genomic dataDR Nemergut, MS Robeson, RF Kysela, AP Martin, SK Schmidt, R KnightBMC genomics 9 (1), 2612008
Information, probability, and the abundance of the simplest RNA active sitesR Kennedy, ME Lladser, M Yarus, R KnightFront Biosci 13, 6060-60712008
Species divergence and the measurement of microbial diversityCA Lozupone, R KnightFEMS microbiology reviews 32 (4), 557-5782008
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removalS Smit, K Rother, J Heringa, R KnightRNA 14 (3), 410-4162008
Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplexM Hamady, JJ Walker, JK Harris, NJ Gold, R KnightNature methods 5 (3), 2352008
Host-bacterial coevolution and the search for new drug targetsJ Zaneveld, PJ Turnbaugh, C Lozupone, RE Ley, M Hamady, JI Gordon, ...Current opinion in chemical biology 12 (1), 109-1142008
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitisP McKenna, C Hoffmann, N Minkah, PP Aye, A Lackner, Z Liu, ...PLoS pathogens 4 (2), e202008
Database-driven grid computing and distributed web applications: A comparisonH De Sterck, A Papo, C Zhang, M Hamady, R KnightGrid Computing for Bioinformatics and Computational Biology, 2472008
Multiple pattern matching: A Markov chain approachME Lladser, MD Betterton, R KnightJournal of mathematical biology 56 (1-2), 51-922008
Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patternsJR Zaneveld, DR Nemergut, R KnightMicrobiology 154 (1), 1-152008
Short-term temporal variability in airborne bacterial and fungal populationsN Fierer, Z Liu, M Rodríguez-Hernández, R Knight, M Henn, ...Applied and environmental microbiology 74 (1), 200-2072008
New Tools For Understanding Microbial Diversity Using High-throughput Sequence DataR Knight, M Hamady, Z Liu, C LozuponeAGU Fall Meeting Abstracts 1, 012007
Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soilN Fierer, M Breitbart, J Nulton, P Salamon, C Lozupone, R Jones, ...Applied and environmental microbiology 73 (21), 7059-70662007
The human microbiome project: exploring the microbial part of ourselves in a changing worldPJ Turnbaugh, RE Ley, M Hamady, C Fraser-Liggett, R Knight, JI GordonNature 449 (7164), 8042007
Short pyrosequencing reads suffice for accurate microbial community analysisZ Liu, C Lozupone, M Hamady, FD Bushman, R KnightNucleic acids research 35 (18), e1202007
PyCogent: a toolkit for making sense from sequenceR Knight, P Maxwell, A Birmingham, J Carnes, JG Caporaso, BC Easton, ...Genome Biol 8 (8), R1712007
Global patterns in bacterial diversityCA Lozupone, R KnightProceedings of the National Academy of Sciences 104 (27), 11436-114402007
Evolution of symbiotic bacteria in the distal human intestineJ Xu, MA Mahowald, RE Ley, CA Lozupone, M Hamady, EC Martens, ...PLoS biology 5 (7), e1562007
Evolutionary rates vary among rRNA structural elementsS Smit, J Widmann, R KnightNucleic acids research 35 (10), 3339-33542007
Reports of the death of the gene are greatly exaggeratedR KnightBiology & Philosophy 22 (2), 293-3062007
Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communitiesCA Lozupone, M Hamady, ST Kelley, R KnightApplied and environmental microbiology 73 (5), 1576-15852007
The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecologyRE Ley, R Knight, JI GordonEnvironmental microbiology 9 (1), 3-42007
Selfish Genes-The Eunuchs of SelectionRD Knight, PE Griffiths2007
Using the nucleotide substitution rate matrix to detect horizontal gene transferM Hamady, MD Betterton, R KnightBMC bioinformatics 7 (1), 4762006
UniFrac–an online tool for comparing microbial community diversity in a phylogenetic contextC Lozupone, M Hamady, R KnightBMC bioinformatics 7 (1), 3712006
DivergentSet, a tool for picking non-redundant sequences from large sequence collectionsJ Widmann, M Hamady, R KnightMolecular & Cellular Proteomics 5 (8), 1520-15322006
Parallel evolution of the genetic code in arthropod mitochondrial genomesF Abascal, D Posada, RD Knight, R ZardoyaPLoS biology 4 (5), e1272006
Analysis of membrane proteins from human chronic myelogenous leukemia cells: comparison of extraction methods for multidimensional LC-MS/MSMC Ruth, WM Old, MA Emrick, K Meyer-Arendt, LD Aveline-Wolf, ...Journal of proteome research 5 (3), 709-7192006
Fast-Find: a novel computational approach to analyzing combinatorial motifsM Hamady, E Peden, R Knight, R SinghBMC bioinformatics 7 (1), 12006
Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categoriesS Smit, M Yarus, R KnightRNA 12 (1), 1-142006
UniFrac: a new phylogenetic method for comparing microbial communitiesC Lozupone, R KnightApplied and environmental microbiology 71 (12), 8228-82352005
Error minimization and coding triplet/binding site associations are independent features of the canonical genetic codeJG Caporaso, M Yarus, R KnightJournal of molecular evolution 61 (5), 597-6072005
Size, constant sequences, and optimal selectionM Legiewicz, C Lozupone, ROB Knight, M YarusRna 11 (11), 1701-17092005
Do universal codon-usage patterns minimize the effects of mutation and translation error?R Marquez, S Smit, R KnightGenome biology 6 (11), R912005
tRNA creation by hairpin duplicationJ Widmann, M Di Giulio, M Yarus, R KnightJournal of molecular evolution 61 (4), 524-5302005
Obesity alters gut microbial ecologyRE Ley, F Bäckhed, P Turnbaugh, CA Lozupone, RD Knight, JI GordonProceedings of the National Academy of Sciences of the United States of ...2005
Origins of the genetic code: the escaped triplet theoryM Yarus, JG Caporaso, R KnightAnnu. Rev. Biochem. 74, 179-1982005
Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acidsA Wolfson, R KnightFEBS letters 579 (17), 3467-34722005
32 TaskSpaces: A Software Framework for Parallel Bioinformatics on Computational GridsH De Sterck, R Markel, R Knight2005
A lightweight, scalable grid computing framework for parallel bioinformatics applicationsH De Sterck, R Markel, R KnightHigh Performance Computing Systems and Applications, 2005. HPCS 2005. 19th ...2005
MEDICINE AND BIOLOGYM Hamady, THT Cheung, K Resing, KJ Cios, R Knight, RE Ison, ...IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE, 22005
The Scope of SelectionM Yarus, R KnightEurekah Bioscience 1 (1), 9-182005
Does protein structure influence trypsin miscleavage?M Hamady, THT Cheung, H Tufo, R KnightEngineering in Medicine and Biology Magazine, IEEE 24 (3), 58-662005
Key challenges in proteomics and proteoinformaticsM Hamady, THT Cheung, K Resing, KJ Cios, R KnightEngineering in Medicine and Biology Magazine, IEEE 24 (3), 34-402005
Published online November 27, 2005R Knight, H De Sterck, R Markel, S Smit, A Oshmyansky, M Yarus, S Smit, ...Nucleic Acids Research 33 (20), 5924-59352005
Artificial Selection: Finding Function amongst Randomized SequencesI de Zwart, C Lozupone, R Knight, A Birmingham, M Illangasekare, ...Handbook of RNA Biochemistry, 783-8062005
Abundance of correctly folded RNA motifs in sequence space, calculated on computational gridsR Knight, H De Sterck, R Markel, S Smit, A Oshmyansky, M YarusNucleic acids research 33 (18), 5924-59352005
How biologists conceptualize genes: an empirical studyK Stotz, PE Griffiths, R KnightStudies in History and Philosophy of Science Part C: Studies in History and ...2004
BayesFold: rational 2 folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequencesR Knight, A Birmingham, M YarusRna 10 (9), 1323-13362004
Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomicsKA Resing, K Meyer-Arendt, AM Mendoza, LD Aveline-Wolf, KR Jonscher, ...Analytical chemistry 76 (13), 3556-35682004
Adaptive evolution of the genetic codeRD Knight, SJ Freeland, LF LandweberThe Genetic Code and the Origin of Life, 201-2202004
Analyzing partially randomized nucleic acid pools: straight dope on dopingR Knight, M YarusNucleic acids research 31 (6), e30-e302003
Finding specific RNA motifs: Function in a zeptomole world?R Knight, M YarusRna 9 (2), 218-2302003
Tests of a stereochemical genetic codeRD Knight, L Landweber, M YarusTranslation mechanisms, 115-1282003
Genetic code evolution in the RNA world and beyondRD KnightEvolution as Computation, 160-1782002
How mitochondria redefine the codeRD Knight, LF Landweber, M YarusJournal of molecular evolution 53 (4), 299-3132001
FACULTY OF PRINCETON UNIVERSITY IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHYRD Knight2001
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomesRD Knight, SJ Freeland, LF LandweberGenome biology 2 (4), research00102001
The molecular basis of nuclear genetic code change in ciliatesCA Lozupone, RD Knight, LF LandweberCurrent Biology 11 (2), 65-742001
The origin and evolution of the genetic code: statistical and experimental investigationsRD KnightPrinceton University2001
Rewiring the keyboard: evolvability of the genetic codeRD Knight, SJ Freeland, LF LandweberNature Reviews Genetics 2 (1), 49-582001
The early evolution of the genetic codeRD Knight, LF LandweberCell 101 (6), 569-5722000
Guilt by association: the arginine case revisited.RD Knight, LF LandweberRna 6 (4), 499-5102000
Early fixation of an optimal genetic codeSJ Freeland, RD Knight, LF Landweber, LD HurstMolecular Biology and Evolution 17 (4), 511-5182000
Measuring adaptation within the genetic codeSJ Freeland, RD Knight, LF LandweberTrends in Biochemical Sciences 25 (2), 44-452000
HAS NATURAL SHAPED THE GENETIC CODE?SJ Freeland, RD Knight, LD Hurst, LF LandweberORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE 30 (2/4), 308-3092000
Do proteins predate DNA?SJ Freeland, RD Knight, LF LandweberScience 286 (5440), 690-6921999
Selection, history and chemistry: the three faces of the genetic codeRD Knight, SJ Freeland, LF LandweberTrends in biochemical sciences 24 (6), 241-2471999
Is the genetic code really a frozen accident? New evidence from in vitro selectionRD Knight, LF LandweberAnnals of the New York Academy of Sciences 870 (1), 408-4101999
Do Proteins Predate DNA?RD Knight, SJ FreelandScience 286 (5440), 680-6821999
Rhyme or reason: RNA-arginine interactions and the genetic codeRD Knight, LF LandweberChemistry & biology 5 (9), R215-R2201998
What is the developmentalist challenge?PE Griffiths, RD KnightPhilosophy of Science 65 (2), 253-2581998
Frontiers: Microbial eukaryotes in the human microbiome: ecology, evolution, and future directionsLW Parfrey, WA Walters, R KnightFrontiers in Cellular And Infection Microbiology
L'obésité altère l'écologie microbienne intestinaleRE Ley, F Bäckhed, P Turnbaugh, CA Lozupone, RD Knight, JI Gordon
Soil bacterial diversity in the Arctic is not fundamentally different from other biomesH Chu, N Fierer, C Lauber, JG Caporaso, R Knight, P Grogan
Evolutionary patterns of nucleotide composition reveal RNA structure qualityS Smit, R Knight, J HeringaRNA in Formation: Computational Studies on RNA Structure and Evolution, 97
Generating a continental scale, systems model to explore scalar interactions within and between NEON terrestrial observation sitesJA Gilbert, P Larsen, J Parnel, N Fierer, R Knight, JK Jansson, B Drewniak, ...
Using Structural Properties to Predict Behavior of Related Proteins: Does Protein Structure Influence Trypsin Miscleavage?M Hamady, T Cheung, H Tufo, R Knight
Other Human MicrobiotaG Reid, JA Younes, HC Van der Mei, GB Gloor, R KnightMetagenomics Research Review 17, 24