Recent Publications

The under-recognized dominance of Verrucomicrobia in soil bacterial communities.

Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N

2011 Jul . PMID: 22267877

GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease.

Haft DH, Varghese N

PLoS ONE 2011 . PMID: 22194940

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

Schloss PD, Gevers D, Westcott SL

PLoS ONE 2011 . PMID: 22194782

IMG: the Integrated Microbial Genomes database and comparative analysis system.

Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC

Nucleic Acids Res. 2012 Jan . PMID: 22194640

Experimental and analytical tools for studying the human microbiome.

Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R

Nat. Rev. Genet. 2012 Jan . PMID: 22179717

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R

Curr Protoc Bioinformatics 2011 Dec . PMID: 22161565

CharProtDB: a database of experimentally characterized protein annotations.

Madupu R, Richter A, Dodson RJ, Brinkac L, Harkins D, Durkin S, Shrivastava S, Sutton G, Haft D

Nucleic Acids Res. 2012 Jan . PMID: 22140108

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.

Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC

Nucleic Acids Res. 2012 Jan . PMID: 22135293

Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.

Cantarel BL, Erickson AR, VerBerkmoes NC, Erickson BK, Carey PA, Pan C, Shah M, Mongodin EF, Jansson JK, Fraser-Liggett CM, Hettich RL

PLoS ONE 2011 . PMID: 22132090

Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment.

Ye Y

Proceedings (IEEE Int Conf Bioinformatics Biomed) 2011 Feb 4. PMID: 22102981

Astrovirus MLB2 viremia in febrile child.

Holtz LR, Wylie KM, Sodergren E, Jiang Y, Franz CJ, Weinstock GM, Storch GA, Wang D

Emerging Infect. Dis. 2011 Nov . PMID: 22099095

IMG/M: the integrated metagenome data management and comparative analysis system.

Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, Liolios K, Pagani I, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC

Nucleic Acids Res. 2012 Jan . PMID: 22086953

Epigenetic priors for identifying active transcription factor binding sites.

Cuellar-Partida G, Buske FA, McLeay RC, Whitington T, Noble WS, Bailey TL

Bioinformatics 2012 Jan 1. PMID: 22072382

ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.

Basu MK, Selengut JD, Haft DH

BMC Bioinformatics 2011 . PMID: 22070167

Saying privacy, meaning confidentiality.

Schwab AP, Frank L, Gligorov N

Am J Bioeth 2011 Nov . PMID: 22047127

De minimis risk: a proposal for a new category of research risk.

Rhodes R, Azzouni J, Baumrin SB, Benkov K, Blaser MJ, Brenner B, Dauben JW, Earle WJ, Frank L, Gligorov N, Goldfarb J, Hirschhorn K, Hirschhorn R, Holzman I, Indyk D, Jabs EW, Lackey DP, Moros DA, Philpott S, Rhodes ME, Richardson LD, Sacks HS, Schwab A, Sperling R, Trusko B, Zweig A

Am J Bioeth 2011 Nov . PMID: 22047112

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.

Zhao Y, Tang H, Ye Y

Bioinformatics 2012 Jan 1. PMID: 22039206

Graph accordance of next-generation sequence assemblies.

Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM

Bioinformatics 2012 Jan 1. PMID: 22025481

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.

Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M

BMC Genomics 2011 . PMID: 21989143

Microbiome and malignancy.

Plottel CS, Blaser MJ

Cell Host Microbe 2011 Oct 20. PMID: 22018233

Fluorescent labeling of antibody fragments using split GFP.

Ferrara F, Listwan P, Waldo GS, Bradbury AR

PLoS ONE 2011 . PMID: 21998685

Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data.

Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C

Bioinformatics 2011 Dec 1. PMID: 21984758

Bambus 2: scaffolding metagenomes.

Koren S, Treangen TJ, Pop M

Bioinformatics 2011 Nov 1. PMID: 21926123

The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.

Sczesnak A, Segata N, Qin X, Gevers D, Petrosino JF, Huttenhower C, Littman DR, Ivanov II

Cell Host Microbe 2011 Sep 15. PMID: 21925113

Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

Youssef NH, Blainey PC, Quake SR, Elshahed MS

Appl. Environ. Microbiol. 2011 Nov . PMID: 21908640

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.

Pirrung M, Kennedy R, Caporaso JG, Stombaugh J, Wendel D, Knight R

Bioinformatics 2011 Nov 1. PMID: 21903626

Genetic basis for in vivo daptomycin resistance in enterococci.

Arias CA, Panesso D, McGrath DM, Qin X, Mojica MF, Miller C, Diaz L, Tran TT, Rincon S, Barbu EM, Reyes J, Roh JH, Lobos E, Sodergren E, Pasqualini R, Arap W, Quinn JP, Shamoo Y, Murray BE, Weinstock GM

N. Engl. J. Med. 2011 Sep 8. PMID: 21899450

Linking long-term dietary patterns with gut microbial enterotypes.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD

Science 2011 Oct 7. PMID: 21885731

Antibiotic effects on bacterial profile in osteonecrosis of the jaw.

Ji X, Pushalkar S, Li Y, Glickman R, Fleisher K, Saxena D

Oral Dis 2012 Jan . PMID: 21883710

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.

Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R

Trends Microbiol. 2011 Oct . PMID: 21872475

Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.

Ahn J, Yang L, Paster BJ, Ganly I, Morris L, Pei Z, Hayes RB

PLoS ONE 2011 . PMID: 21829515

Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization.

Chen CH, Cho SH, Chiang HI, Tsai F, Zhang K, Lo YH

Anal. Chem. 2011 Oct 1. PMID: 21809842

Bayesian community-wide culture-independent microbial source tracking.

Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST

Nat. Methods 2011 Sep . PMID: 21765408

Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH).

Liu P, Meagher RJ, Light YK, Yilmaz S, Chakraborty R, Arkin AP, Hazen TC, Singh AK

Lab Chip 2011 Aug 21. PMID: 21755095

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.

Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J

Gastroenterology 2011 Nov . PMID: 21741921

Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown.

Lladser ME, Gouet R, Reeder J

PLoS ONE 2011 . PMID: 21738613

DNACLUST: accurate and efficient clustering of phylogenetic marker genes.

Ghodsi M, Liu B, Pop M

BMC Bioinformatics 2011 . PMID: 21718538

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.

Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE

ISME J 2012 Jan . PMID: 21716311

How patients view probiotics: findings from a multicenter study of patients with inflammatory bowel disease and irritable bowel syndrome.

Mercer M, Brinich MA, Geller G, Harrison K, Highland J, James K, Marshall P, McCormick JB, Tilburt J, Achkar JP, Farrell RM, Sharp RR

J. Clin. Gastroenterol. 2012 Feb . PMID: 21716123

UCHIME improves sensitivity and speed of chimera detection.

Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R

Bioinformatics 2011 Aug 15. PMID: 21700674

Bacterial DNA content in the intestinal wall from infants with necrotizing enterocolitis.

Bucher BT, McDuffie LA, Shaikh N, Tarr PI, Warner BB, Hamvas A, White FV, Erwin CR, Warner BW

J. Pediatr. Surg. 2011 Jun . PMID: 21683193

Moving pictures of the human microbiome.

Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R

Genome Biol. 2011 . PMID: 21624126

Mammalian Cell Sorting using μFACS.

Cho SH, Chen CH, Tsai FS, Godin J, Lo YH

Conf Lasers Electro Optics 2010 May 16. PMID: 21614147

The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens.

Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry JD, Van der Pol B

PLoS ONE 2011 . PMID: 21603636

RAPSearch: a fast protein similarity search tool for short reads.

Ye Y, Choi JH, Tang H

BMC Bioinformatics 2011 . PMID: 21575167

Evolution and classification of the CRISPR-Cas systems.

Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV

Nat. Rev. Microbiol. 2011 Jun . PMID: 21552286

Boulder ALignment Editor (ALE): a web-based RNA alignment tool.

Stombaugh J, Widmann J, McDonald D, Knight R

Bioinformatics 2011 Jun 15. PMID: 21546392

Brief communication: DNA from early Holocene American dog.

Tito RY, Belknap SL, Sobolik KD, Ingraham RC, Cleeland LM, Lewis CM

Am. J. Phys. Anthropol. 2011 Aug . PMID: 21541929

Development of the human gastrointestinal microbiota and insights from high-throughput sequencing.

Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R

Gastroenterology 2011 May . PMID: 21530737

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

Sun Y, Cai Y, Huse SM, Knight R, Farmerie WG, Wang X, Mai V

Brief. Bioinformatics 2012 Jan . PMID: 21525143

Simrank: Rapid and sensitive general-purpose k-mer search tool.

DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N

BMC Ecol. 2011 . PMID: 21524302

Reliability and validity of a modified Bristol Stool Form Scale for children.

Lane MM, Czyzewski DI, Chumpitazi BP, Shulman RJ

J. Pediatr. 2011 Sep . PMID: 21489557

The mind-body-microbial continuum.

Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R

Dialogues Clin Neurosci 2011 . PMID: 21485746

Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.

Haft DH, Basu MK

J. Bacteriol. 2011 Jun . PMID: 21478363

Overview of the development of personalized genomic medicine and surgery.

Brunicardi FC, Gibbs RA, Wheeler DA, Nemunaitis J, Fisher W, Goss J, Chen C

World J Surg 2011 Aug . PMID: 21424870

Unravelling the effects of the environment and host genotype on the gut microbiome.

Spor A, Koren O, Ley R

Nat. Rev. Microbiol. 2011 Apr . PMID: 21407244

The skin microbiome.

Grice EA, Segre JA

Nat. Rev. Microbiol. 2011 Apr . PMID: 21407241

Next generation sequence assembly with AMOS.

Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M

Curr Protoc Bioinformatics 2011 Mar . PMID: 21400694

Beyond natural antibodies: the power of in vitro display technologies.

Bradbury AR, Sidhu S, Dübel S, McCafferty J

Nat. Biotechnol. 2011 Mar . PMID: 21390033

A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.

Wu YW, Ye Y

J. Comput. Biol. 2011 Mar . PMID: 21385052

Host-associated and free-living phage communities differ profoundly in phylogenetic composition.

Caporaso JG, Knight R, Kelley ST

PLoS ONE 2011 . PMID: 21383980

Skin microbiome: genomics-based insights into the diversity and role of skin microbes.

Kong HH

Trends Mol Med 2011 Jun . PMID: 21376666

Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.

Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR

PLoS ONE 2011 . PMID: 21364937

The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer.

Hu S, Dong TS, Dalal SR, Wu F, Bissonnette M, Kwon JH, Chang EB

PLoS ONE 2011 . PMID: 21283757

The age of necrotizing enterocolitis onset: an application of Sartwell's incubation period model.

González-Rivera R, Culverhouse RC, Hamvas A, Tarr PI, Warner BB

J Perinatol 2011 Aug . PMID: 21273988

Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice.

Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J, Smith CW

FASEB J. 2011 May . PMID: 21228220

Building a comprehensive genomic program for hepatocellular carcinoma.

Harring TR, Guiteau JJ, Nguyen NT, Cotton RT, Gingras MC, Wheeler DA, O'Mahony CA, Gibbs RA, Brunicardi FC, Goss JA

World J Surg 2011 Aug . PMID: 21225260

Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners.

Haft DH

BMC Genomics 2011 . PMID: 21223593

A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfalls.

Nguyen NT, Cotton RT, Harring TR, Guiteau JJ, Gingras MC, Wheeler DA, O'Mahony CA, Gibbs RA, Brunicardi FC, Goss JA

World J Surg 2011 Aug . PMID: 21221581

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.

Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Petrosino JF, Knight R, Birren BW

Genome Res. 2011 Mar . PMID: 21212162

Microbial diversity in saliva of oral squamous cell carcinoma.

Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D

FEMS Immunol. Med. Microbiol. 2011 Apr . PMID: 21205002

Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth.

Zhou X, Brotman RM, Gajer P, Abdo Z, Schüette U, Ma S, Ravel J, Forney LJ

Infect Dis Obstet Gynecol 2010 . PMID: 21197076

Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection.

Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD

PLoS ONE 2010 . PMID: 21124791

Probiotics, enteric and diarrheal diseases, and global health.

Preidis GA, Hill C, Guerrant RL, Ramakrishna BS, Tannock GW, Versalovic J

Gastroenterology 2011 Jan . PMID: 21075108

Digital MDA for enumeration of total nucleic acid contamination.

Blainey PC, Quake SR

Nucleic Acids Res. 2011 Mar . PMID: 21071419

Regional mucosa-associated microbiota determine physiological expression of TLR2 and TLR4 in murine colon.

Wang Y, Devkota S, Musch MW, Jabri B, Nagler C, Antonopoulos DA, Chervonsky A, Chang EB

PLoS ONE 2010 . PMID: 21042588

SmashCell: a software framework for the analysis of single-cell amplified genome sequences.

Harrington ED, Arumugam M, Raes J, Bork P, Relman DA

Bioinformatics 2010 Dec 1. PMID: 20966005

A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.

Krentz BD, Mulheron HJ, Semrau JD, Dispirito AA, Bandow NL, Haft DH, Vuilleumier S, Murrell JC, McEllistrem MT, Hartsel SC, Gallagher WH

Biochemistry 2010 Nov 30. PMID: 20961038

Human oral, gut, and plaque microbiota in patients with atherosclerosis.

Koren O, Spor A, Felin J, Fåk F, Stombaugh J, Tremaroli V, Behre CJ, Knight R, Fagerberg B, Ley RE, Bäckhed F

Proc. Natl. Acad. Sci. U.S.A. 2011 Mar 15. PMID: 20937873

Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era.

Frank DN

J. Anim. Sci. 2011 Mar . PMID: 20935136

Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon.

Wang Y, Antonopoulos DA, Zhu X, Harrell L, Hanan I, Alverdy JC, Meyer F, Musch MW, Young VB, Chang EB

Appl. Microbiol. Biotechnol. 2010 Dec . PMID: 20931185

Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.

Yeoman CJ, Yildirim S, Thomas SM, Durkin AS, Torralba M, Sutton G, Buhay CJ, Ding Y, Dugan-Rocha SP, Muzny DM, Qin X, Gibbs RA, Leigh SR, Stumpf R, White BA, Highlander SK, Nelson KE, Wilson BA

PLoS ONE 2010 . PMID: 20865041

Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins.

Hu S, Wang Y, Lichtenstein L, Tao Y, Musch MW, Jabri B, Antonopoulos D, Claud EC, Chang EB

Am. J. Physiol. Gastrointest. Liver Physiol. 2010 Dec . PMID: 20864653

Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases.

Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H, Zhu W, Sartor RB, Boedeker EC, Harpaz N, Pace NR, Li E

Inflamm. Bowel Dis. 2011 Jan . PMID: 20839241

An algorithm for automated closure during assembly.

Koren S, Miller JR, Walenz BP, Sutton G

BMC Bioinformatics 2010 . PMID: 20831800

Creation and initial evaluation of a Stool Form Scale for children.

Chumpitazi BP, Lane MM, Czyzewski DI, Weidler EM, Swank PR, Shulman RJ

J. Pediatr. 2010 Oct . PMID: 20826285

Molecular microbiological methods in the diagnosis of neonatal sepsis.

Venkatesh M, Flores A, Luna RA, Versalovic J

Expert Rev Anti Infect Ther 2010 Sep . PMID: 20818947

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns.

Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R

Nat. Methods 2010 Oct . PMID: 20818378

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome.

Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, Desantis TZ, Brodie EL, Malamud D, Poles MA, Pei Z

World J. Gastroenterol. 2010 Sep 7. PMID: 20806429

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.

Reeder J, Knight R

Nat. Methods 2010 Sep . PMID: 20805793

FragGeneScan: predicting genes in short and error-prone reads.

Rho M, Tang H, Ye Y

Nucleic Acids Res. 2010 Nov . PMID: 20805240

METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.

Goll J, Rusch DB, Tanenbaum DM, Thiagarajan M, Li K, Methé BA, Yooseph S

Bioinformatics 2010 Oct 15. PMID: 20798169

Quantitation of major human cutaneous bacterial and fungal populations.

Gao Z, Perez-Perez GI, Chen Y, Blaser MJ

J. Clin. Microbiol. 2010 Oct . PMID: 20702672

Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.

Marri PR, Paniscus M, Weyand NJ, Rendón MA, Calton CM, Hernández DR, Higashi DL, Sodergren E, Weinstock GM, Rounsley SD, So M

PLoS ONE 2010 . PMID: 20676376

Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.

Selengut JD, Haft DH

J. Bacteriol. 2010 Nov . PMID: 20675471

Probiotics-host communication: Modulation of signaling pathways in the intestine.

Thomas CM, Versalovic J

Gut Microbes . PMID: 20672012

Rapid fluctuation of the vaginal microbiota measured by Gram stain analysis.

Brotman RM, Ravel J, Cone RA, Zenilman JM

Sex Transm Infect 2010 Aug . PMID: 20660593

The right to ignore genetic status of late onset genetic disease in the genomic era; Prenatal testing for Huntington disease as a paradigm.

Erez A, Plunkett K, Sutton VR, McGuire AL

Am. J. Med. Genet. A 2010 Jul . PMID: 20583190

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.

Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R

Proc. Natl. Acad. Sci. U.S.A. 2010 Jun 29. PMID: 20566857

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves.

Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N

Environ. Microbiol. 2010 Nov . PMID: 20545741

Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies.

Harwich MD, Alves JM, Buck GA, Strauss JF, Patterson JL, Oki AT, Girerd PH, Jefferson KK

BMC Genomics 2010 . PMID: 20540756

Vaginal microbiome of reproductive-age women.

Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ

Proc. Natl. Acad. Sci. U.S.A. 2011 Mar 15. PMID: 20534435

Postprandial remodeling of the gut microbiota in Burmese pythons.

Costello EK, Gordon JI, Secor SM, Knight R

ISME J 2010 Nov . PMID: 20520652

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family.

Haft DH, Basu MK, Mitchell DA

BMC Biol. 2010 . PMID: 20500830

A catalog of reference genomes from the human microbiome.

Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D

Science 2010 May 21. PMID: 20489017

Informed consent in genomics and genetic research.

McGuire AL, Beskow LM

Annu Rev Genomics Hum Genet 2010 Sep 22. PMID: 20477535

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes.

Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC

Nat. Methods 2010 Jun . PMID: 20436475

Diversity of 16S rRNA genes within individual prokaryotic genomes.

Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P, Yang L, Poles M, Brown SM, Sotero S, Desantis T, Brodie E, Nelson K, Pei Z

Appl. Environ. Microbiol. 2010 Jun . PMID: 20418441

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples.

Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N

FEMS Microbiol. Lett. 2010 Jun . PMID: 20412303

QIIME allows analysis of high-throughput community sequencing data.

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R

Nat. Methods 2010 May . PMID: 20383131

Personal genome research : what should the participant be told?

McGuire AL, Lupski JR

Trends Genet. 2010 May . PMID: 20381895

Human mammalian cell sorting using a highly integrated micro-fabricated fluorescence-activated cell sorter (microFACS).

Cho SH, Chen CH, Tsai FS, Godin JM, Lo YH

Lab Chip 2010 Jun 21. PMID: 20379604

Role of the gut microbiota in defining human health.

Fujimura KE, Slusher NA, Cabana MD, Lynch SV

Expert Rev Anti Infect Ther 2010 Apr . PMID: 20377338

Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.

Wang GP, Sherrill-Mix SA, Chang KM, Quince C, Bushman FD

J. Virol. 2010 Jun . PMID: 20375170

Harnessing the power of the human microbiome.

Blaser MJ

Proc. Natl. Acad. Sci. U.S.A. 2010 Apr 6. PMID: 20360554

Alignment and clustering of phylogenetic markers--implications for microbial diversity studies.

White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M

BMC Bioinformatics 2010 . PMID: 20334679

Ironing out the wrinkles in the rare biosphere through improved OTU clustering.

Huse SM, Welch DM, Morrison HG, Sogin ML

Environ. Microbiol. 2010 Jul . PMID: 20236171

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

Zaneveld JR, Lozupone C, Gordon JI, Knight R

Nucleic Acids Res. 2010 Jul . PMID: 20197316

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Helping patients make informed choices about probiotics: a need for research.

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

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