Works by Knight, Rob

Results: 361

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome.

Published in:

PLoS Biology, 2012, v. 10, n. 8, p. 1, doi. 10.1371/journal.pbio.1001377

By:

Gevers, Dirk;
Knight, Rob;
Petrosino, Joseph F.;
Huang, Katherine;
McGuire, Amy L.;
Birren, Bruce W.;
Nelson, Karen E.;
White, Owen;
Methé, Barbara A.;
Huttenhower, Curtis

Publication type:

Article

The Genomic Standards Consortium.

Published in:

PLoS Biology, 2011, v. 9, n. 6, p. 1, doi. 10.1371/journal.pbio.1001088

By:

Field, Dawn;
Amaral-Zettler, Linda;
Cochrane, Guy;
Cole, James R.;
Dawyndt, Peter;
Garrity, George M.;
Gilbert, Jack;
Glöckner, Frank Oliver;
Hirschman, Lynette;
Karsch-Mizrachi, Ilene;
Klenk, Hans-Peter;
Knight, Rob;
Kottmann, Renzo;
Kyrpides, Nikos;
Meyer, Folker;
Gil, Inigo San;
Sansone, Susanna-Assunta;
Schriml, Lynn M.;
Sterk, Peter;
Tatusova, Tatiana

Publication type:

Article

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Published in:

Microbial Ecology, 2018, v. 75, n. 2, p. 515, doi. 10.1007/s00248-017-1041-8

By:

Hale, Vanessa L.;
Tan, Chia L.;
Niu, Kefeng;
Yang, Yeqin;
Knight, Rob;
Zhang, Qikun;
Cui, Duoying;
Amato, Katherine R.

Publication type:

Article

Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Published in:

2018

By:

Hale, Vanessa L.;
Tan, Chia L.;
Niu, Kefeng;
Yang, Yeqin;
Knight, Rob;
Zhang, Qikun;
Cui, Duoying;
Amato, Katherine R.

Publication type:

Erratum

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate.

Published in:

Microbial Ecology, 2017, v. 74, n. 1, p. 250, doi. 10.1007/s00248-017-0938-6

By:

Amato, Katherine;
Van Belle, Sarie;
Di Fiore, Anthony;
Estrada, Alejandro;
Stumpf, Rebecca;
White, Bryan;
Nelson, Karen;
Knight, Rob;
Leigh, Steven

Publication type:

Article

Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow Nests.

Published in:

Microbial Ecology, 2014, v. 67, n. 2, p. 480, doi. 10.1007/s00248-013-0338-5

By:

Peralta-Sánchez, Juan;
Soler, Juan;
Martín-Platero, Antonio;
Knight, Rob;
Martínez-Bueno, Manuel;
Møller, Anders

Publication type:

Article

A preliminary survey of lichen associated eukaryotes using pyrosequencing.

Published in:

Lichenologist, 2012, v. 44, n. 1, p. 137, doi. 10.1017/S0024282911000648

By:

BATES, Scott T.;
BERG-LYONS, Donna;
LAUBER, Christian L.;
WALTERS, William A.;
KNIGHT, Rob;
FIERER, Noah

Publication type:

Article

Associations between gut microbiota and incident fractures in the FINRISK cohort.

Published in:

NPJ Biofilms & Microbiomes, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41522-024-00530-8

By:

Grahnemo, Louise;
Kambur, Oleg;
Lahti, Leo;
Jousilahti, Pekka;
Niiranen, Teemu;
Knight, Rob;
Salomaa, Veikko;
Havulinna, Aki S.;
Ohlsson, Claes

Publication type:

Article

Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS.

Published in:

NPJ Biofilms & Microbiomes, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41522-022-00289-w

By:

Marotz, Clarisse;
Molinsky, Rebecca;
Martino, Cameron;
Bohn, Bruno;
Roy, Sumith;
Rosenbaum, Michael;
Desvarieux, Moïse;
Yuzefpolskaya, Melana;
Paster, Bruce J.;
Jacobs, David R.;
Colombo, Paolo C.;
Papapanou, Panos N.;
Knight, Rob;
Demmer, Ryan T.

Publication type:

Article

Optimizing campus-wide COVID-19 test notifications with interpretable wastewater time-series features using machine learning models.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-47859-2

By:

Lin, Tuo;
Karthikeyan, Smruthi;
Satterlund, Alysson;
Schooley, Robert;
Knight, Rob;
De Gruttola, Victor;
Martin, Natasha;
Zou, Jingjing

Publication type:

Article

Genomic Standards Consortium Projects.

Published in:

Standards in Genomic Sciences, 2014, v. 9, n. 3, p. 599, doi. 10.4056/sigs.5559680

By:

Field, Dawn;
Sterk, Peter;
Kottmann, Renzo;
Smet, J.;
Amaral-Zettler, Linda;
Cochrane, Guy;
Cole, James;
Davies, Neil;
Dawyndt, Peter;
Garrity, George;
Gilbert, Jack;
Glöckner, Frank;
Hirschman, Lynette;
Klenk, Hans-Peter;
Knight, Rob;
Kyrpides, Nikos;
Meyer, Folker;
Karsch-Mizrachi, Ilene;
Morrison, Norman;
Robbins, Robert

Publication type:

Article

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 2012.

Published in:

Standards in Genomic Sciences, 2013, v. 8, n. 1, p. 112, doi. 10.4056/sigs.3717348

By:

Smith, Daniel;
Alverdy, John;
An, Gary;
Coleman, Maureen;
Garcia-Houchins, Sylvia;
Green, Jessica;
Keegan, Kevin;
Kelley, Scott;
Kirkup, Benjamin;
Kociolek, Larry;
Levin, Hal;
Landon, Emily;
Olsiewski, Paula;
Knight, Rob;
Siegel, Jeffrey;
Weber, Stephen;
Gilbert, Jack

Publication type:

Article

Meeting Report: Fungal ITS Workshop (October 2012).

Published in:

Standards in Genomic Sciences, 2013, v. 8, n. 1, p. 118, doi. 10.4056/sigs.3737409

By:

Bates, Scott;
Ahrendt, Steven;
Bik, Holly;
Bruns, Thomas;
Caporaso, J.;
Cole, James;
Dwan, Michael;
Fierer, Noah;
Gu, Dai;
Houston, Shawn;
Knight, Rob;
Leff, Jon;
Lewis, Christopher;
Maestre, Juan;
McDonald, Daniel;
Nilsson, R.;
Porras-Alfaro, Andrea;
Robert, Vincent;
Schoch, Conrad;
Scott, James

Publication type:

Article

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).

Published in:

Ecology Letters, 2014, v. 17, n. 8, p. 979, doi. 10.1111/ele.12301

By:

Bolnick, Daniel I.;
Snowberg, Lisa K.;
Hirsch, Philipp E.;
Lauber, Christian L.;
Knight, Rob;
Caporaso, J. Gregory;
Svanbäck, Richard;
Post, David

Publication type:

Article

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 12, p. 3869, doi. 10.1093/nar/gkq066

By:

Zaneveld, Jesse R.;
Lozupone, Catherine;
Gordon, Jeffrey I.;
Knight, Rob

Publication type:

Article

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 18, p. e120, doi. 10.1093/nar/gkn491

By:

Liu, Zongzhi;
DeSantis, Todd Z.;
Andersen, Gary L.;
Knight, Rob

Publication type:

Article

Short pyrosequencing reads suffice for accurate microbial community analysis.

Published in:

Nucleic Acids Research, 2007, v. 35, n. 18, p. e120, doi. 10.1093/nar/gkm541

By:

Liu, Zongzhi;
Lozupone, Catherine;
Hamady, Micah;
Bushman, Frederic D.;
Knight, Rob

Publication type:

Article

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 18, p. 5924, doi. 10.1093/nar/gki886

By:

Knight, Rob;
De Sterck, Hans;
Markel, Rob;
Smit, Sandra;
Oshmyansky, Alexander;
Yarus, Michael

Publication type:

Article

Analyzing partially randomized nucleic acid pools: straight dope on doping.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 6, p. e30, doi. 10.1093/nar/gng030

By:

Knight, Rob;
Yarus, Michael

Publication type:

Article

Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-47072-3

By:

Tatsuya Dokoshi;
Yang Chen;
Cavagnero, Kellen J.;
Rahman, Gibraan;
Hakim, Daniel;
Brinton, Samantha;
Schwarz, Hana;
Brown, Elizabeth A.;
O’Neill, Alan;
Yoshiyuki Nakamura;
Fengwu Li;
Salzman, Nita H.;
Knight, Rob;
Gallo, Richard L.

Publication type:

Article

Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38558-7

By:

Tap, Julien;
Lejzerowicz, Franck;
Cotillard, Aurélie;
Pichaud, Matthieu;
McDonald, Daniel;
Song, Se Jin;
Knight, Rob;
Veiga, Patrick;
Derrien, Muriel

Publication type:

Article

Sequence-structure-function relationships in the microbial protein universe.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37896-w

By:

Koehler Leman, Julia;
Szczerbiak, Pawel;
Renfrew, P. Douglas;
Gligorijevic, Vladimir;
Berenberg, Daniel;
Vatanen, Tommi;
Taylor, Bryn C.;
Chandler, Chris;
Janssen, Stefan;
Pataki, Andras;
Carriero, Nick;
Fisk, Ian;
Xavier, Ramnik J.;
Knight, Rob;
Bonneau, Richard;
Kosciolek, Tomasz

Publication type:

Article

Tracking down the sources of experimental contamination in microbiome studies.

Published in:

Genome Biology, 2014, v. 15, n. 12, p. 564, doi. 10.1186/s13059-014-0564-2

By:

Weiss, Sophie;
Amir, Amnon;
Hyde, Embriette R;
Metcalf, Jessica L;
Se Jin Song;
Knight, Rob

Publication type:

Article

Temporal variability is a personalized feature of the human microbiome.

Published in:

Genome Biology, 2014, v. 15, n. 12, p. 531, doi. 10.1186/s13059-014-0531-y

By:

Flores, Gilberto E;
Caporaso, J Gregory;
Henley, Jessica B;
Rideout, Jai Ram;
Domogala, Daniel;
Chase, John;
Leff, Jonathan W;
Vázquez-Baeza, Yoshiki;
Gonzalez, Antonio;
Knight, Rob;
Dunn, Robert R;
Fierer, Noah

Publication type:

Article

Moving pictures of the human microbiome.

Published in:

Genome Biology, 2011, v. 12, n. 5, p. 1, doi. 10.1186/gb-2011-12-5-r50

By:

Caporaso, J. Gregory;
Lauber, Christian L.;
Costello, Elizabeth K.;
Berg-Lyons, Donna;
Gonzalez, Antonio;
Stombaugh, Jesse;
Knights, Dan;
Gajer, Pawel;
Ravel, Jacques;
Fierer, Noah;
Gordon, Jeffrey I.;
Knight, Rob

Publication type:

Article

Observed Mask Wearing and Presence of SARS-CoV-2 in School Wastewater, San Diego County, CA, 2022.

Published in:

American Journal of Public Health, 2025, v. 115, n. 4, p. 519, doi. 10.2105/AJPH.2024.307925

By:

Fielding-Miller, Rebecca;
Gaines, Tommi;
Hassani, Ashkan;
Le, Tina;
Omaleki, Vinton;
Flores, Marlene;
Majnoonian, Araz;
Wijaya, F. Carrissa;
Knight, Rob;
Karthikeyan, Smruthi;
Garfein, Richard S.

Publication type:

Article

Crystal ball - 2013.

Published in:

Microbial Biotechnology, 2013, v. 6, n. 1, p. 3, doi. 10.1111/1751-7915.12014

By:

Curtis, Tom;
Daran, Jean-Marc;
Pronk, Jack T.;
Frey, Joachim;
Jansson, Janet K.;
Robbins-Pianka, Adam;
Knight, Rob;
Schnürer, Anna;
Smets, Barth F.;
Smid, E. J.;
Abee, T.;
Vicente, Miguel;
Zengler, Karsten

Publication type:

Article

Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.

Published in:

Biological Reviews, 2025, v. 100, n. 2, p. 748, doi. 10.1111/brv.13161

By:

Degregori, Samuel;
Wang, Xiaolin;
Kommala, Akhil;
Schulhof, Noah;
Moradi, Sadaf;
MacDonald, Allison;
Eblen, Kaitlin;
Jukovich, Sophia;
Smith, Emma;
Kelleher, Emily;
Suzuki, Kota;
Hall, Zoey;
Knight, Rob;
Amato, Katherine Ryan

Publication type:

Article

Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults.

Published in:

2022

By:

Ruuskanen, Matti O.;
Erawijantari, Pande P.;
Havulinna, Aki S.;
Yang Liu;
Méric, Guillaume;
Tuomilehto, Jaakko;
Inouye, Michael;
Jousilahti, Pekka;
Salomaa, Veikko;
Jain, Mohit;
Knight, Rob;
Lahti, Leo;
Niiranen, Teemu J.;
Liu, Yang

Publication type:

journal article

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus.

Published in:

BMC Microbiology, 2018, v. 18, n. 1, p. N.PAG, doi. 10.1186/s12866-018-1341-2

By:

Vrbanac, Alison;
Riestra, Angelica M.;
Coady, Alison;
Knight, Rob;
Nizet, Victor;
Patras, Kathryn A.

Publication type:

Article

The microbiome explored: recent insights and future challenges.

Published in:

Nature Reviews Microbiology, 2013, v. 11, n. 3, p. 213, doi. 10.1038/nrmicro2973

By:

Blaser, Martin;
Bork, Peer;
Fraser, Claire;
Knight, Rob;
Wang, Jun

Publication type:

Article

Microbiota restoration: natural and supplemented recovery of human microbial communities.

Published in:

Nature Reviews Microbiology, 2011, v. 9, n. 1, p. 27, doi. 10.1038/nrmicro2473

By:

Reid, Gregor;
Younes, Jessica A.;
Van der Mei, Henny C.;
Gloor, Gregory B.;
Knight, Rob;
Busscher, Henk J.

Publication type:

Article

RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code.

Published in:

Journal of Molecular Evolution, 2009, v. 69, n. 5, p. 406, doi. 10.1007/s00239-009-9270-1

By:

Yarus, Michael;
Widmann, Jeremy Joseph;
Knight, Rob

Publication type:

Article

Error Minimization and Coding Triplet/Binding Site Associations Are Independent Features of the Canonical Genetic Code.

Published in:

Journal of Molecular Evolution, 2005, v. 61, n. 5, p. 597, doi. 10.1007/s00239-004-0314-2

By:

Caporaso, J. Gregory;
Yarus, Michael;
Knight, Rob

Publication type:

Article

tRNA Creation by Hairpin Duplication.

Published in:

Journal of Molecular Evolution, 2005, v. 61, n. 4, p. 524, doi. 10.1007/s00239-004-0315-1

By:

Widmann, Jeremy;
Di Giulio, Massimo;
Yarus, Michael;
Knight, Rob;
Lehman, Niles

Publication type:

Article

Integrating clinical research into electronic health record workflows to support a learning health system.

Published in:

JAMIA Open, 2024, v. 7, n. 2, p. 1, doi. 10.1093/jamiaopen/ooae023

By:

Goldhaber, Nicole H;
Jacobs, Marni B;
Laurent, Louise C;
Knight, Rob;
Zhu, Wenhong;
Pham, Dean;
Tran, Allen;
Patel, Sandip P;
Hogarth, Michael;
Longhurst, Christopher A

Publication type:

Article

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.

Published in:

Briefings in Bioinformatics, 2012, v. 13, n. 1, p. 107, doi. 10.1093/bib/bbr009

By:

Sun, Yijun;
Cai, Yunpeng;
Huse, Susan M.;
Knight, Rob;
Farmerie, William G.;
Wang, Xiaoyu;
Mai, Volker

Publication type:

Article

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).

Published in:

MicrobiologyOpen, 2018, v. 7, n. 6, p. N.PAG, doi. 10.1002/mbo3.716

By:

Minich, Jeremiah J.;
Zhu, Qiyun;
Xu, Zhenjiang Zech;
Amir, Amnon;
Ngochera, Maxon;
Simwaka, Moses;
Allen, Eric E.;
Zidana, Hastings;
Knight, Rob

Publication type:

Article

Evolving approaches to profiling the microbiome in skin disease.

Published in:

Frontiers in Immunology, 2023, v. 14, p. 01, doi. 10.3389/fimmu.2023.1151527

By:

Yang Chen;
Knight, Rob;
Gallo, Richard L.

Publication type:

Article

Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort.

Published in:

European Journal of Nutrition, 2025, v. 64, n. 4, p. 1, doi. 10.1007/s00394-025-03668-z

By:

Koponen, Kari;
McDonald, Daniel;
Jousilahti, Pekka;
Meric, Guillaume;
Inouye, Michael;
Lahti, Leo;
Niiranen, Teemu;
Männistö, Satu;
Havulinna, Aki;
Knight, Rob;
Salomaa, Veikko

Publication type:

Article

Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults.

Published in:

European Journal of Nutrition, 2024, v. 63, n. 6, p. 2247, doi. 10.1007/s00394-024-03406-x

By:

Maukonen, Mirkka;
Koponen, Kari K;
Havulinna, Aki S;
Kaartinen, Niina E;
Niiranen, Teemu;
Méric, Guillaume;
Pajari, Anne-Maria;
Knight, Rob;
Salomaa, Veikko;
Männistö, Satu

Publication type:

Article

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism.

Published in:

Nature Communications, 2018, v. 9, p. 1, doi. 10.1038/s41467-018-05336-9

By:

Zarrinpar, Amir;
Chaix, Amandine;
Xu, Zhenjiang Z.;
Chang, Max W.;
Marotz, Clarisse A.;
Saghatelian, Alan;
Knight, Rob;
Panda, Satchidananda

Publication type:

Article

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05284-4

By:

Zheng-Shuang Hua;
Yan-Ni Qu;
Qiyun Zhu;
En-Min Zhou;
Yan-Ling Qi;
Yi-Rui Yin;
Yang-Zhi Rao;
Ye Tian;
Yu-Xian Li;
Lan Liu;
Castelle, Cindy J.;
Hedlund, Brian P.;
Wen-Sheng Shu;
Knight, Rob;
Wen-Jun Li

Publication type:

Article

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-04409-z

By:

Michaud, Jennifer M.;
Thompson, Luke R.;
Kaul, Drishti;
Espinoza, Josh L.;
Richter, R. Alexander;
Zhenjiang Zech Xu;
Lee, Christopher;
Pham, Kevin M.;
Beall, Charlotte M.;
Malfatti, Francesca;
Azam, Farooq;
Knight, Rob;
Burkart, Michael D.;
Dupont, Christopher L.;
Prather, Kimberly A.

Publication type:

Article

Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution.

Published in:

BioEssays, 2022, v. 44, n. 5, p. 1, doi. 10.1002/bies.202100252

By:

Sepich‐Poore, Gregory D.;
Guccione, Caitlin;
Laplane, Lucie;
Pradeu, Thomas;
Curtius, Kit;
Knight, Rob

Publication type:

Article

A multi-study analysis enables identification of potential microbial features associated with skin aging signs.

Published in:

Frontiers in Aging Neuroscience, 2024, p. 1, doi. 10.3389/fragi.2023.1304705

By:

Myers, Tyler;
Bouslimani, Amina;
Shi Huang;
Hansen, Shalisa T.;
Clavaud, Cécile;
Azouaoui, Anissa;
Ott, Alban;
Gueniche, Audrey;
Bouez, Charbel;
Qian Zheng;
Aguilar, Luc;
Knight, Rob;
Moreau, Magali;
Se Jin Song

Publication type:

Article

A multi-study analysis enables identification of potential microbial features associated with skin aging signs.

Published in:

Frontiers in Aging Neuroscience, 2024, p. 1, doi. 10.3389/fragi.2023.1304705

By:

Myers, Tyler;
Bouslimani, Amina;
Huang, Shi;
Hansen, Shalisa T.;
Clavaud, Cécile;
Azouaoui, Anissa;
Ott, Alban;
Gueniche, Audrey;
Bouez, Charbel;
Qian Zheng;
Aguilar, Luc;
Knight, Rob;
Moreau, Magali;
Se Jin Song

Publication type:

Article

Euphorbia plant latex is inhabited by diverse microbial communities.

Published in:

American Journal of Botany, 2015, v. 102, n. 12, p. 1966, doi. 10.3732/ajb.1500223

By:

Gunawardana, Manjula;
Hyde, Embriette R.;
Lahmeyer, Sean;
Dorsey, Brian L.;
La Val, Taylor P.;
Mullen, Madeline;
Yoo, Jennifer;
Knight, Rob;
Baum, Marc M.

Publication type:

Article

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘Omics.

Published in:

Genome Biology & Evolution, 2018, v. 10, n. 8, p. 1927, doi. 10.1093/gbe/evy133

By:

Maurer-Alcalá, Xyrus X;
Yan, Ying;
Pilling, Olivia A;
Knight, Rob;
Katz, Laura A

Publication type:

Article

The Earth Microbiome project: successes and aspirations.

Published in:

BMC Biology, 2014, v. 12, n. 1, p. 69, doi. 10.1186/s12915-014-0069-1

By:

Gilbert, Jack A;
Jansson, Janet K;
Knight, Rob

Publication type:

Article