Recent Publications
Aagaard, K. et al.
The FASEB Journal (19 November 2012)
Jiao D, Ye Y, Tang H
PLoS Comput. Biol. 2013 Mar . PMID: 23555216
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.
Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M
Proc. Natl. Acad. Sci. U.S.A. 2013 Apr 2. PMID: 23509275
Wu X, Berkow K, Frank DN, Li E, Gulati AS, Zhu W
BMC Bioinformatics 2013 . PMID: 23497007
Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases.
Leone V, Chang EB, Devkota S
J. Gastroenterol. 2013 Mar . PMID: 23475322
Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players.
Ursell LK, Knight R
Cell Metab. 2013 Mar 5. PMID: 23473028
Munch EM, Harris RA, Mohammad M, Benham AL, Pejerrey SM, Showalter L, Hu M, Shope CD, Maningat PD, Gunaratne PH, Haymond M, Aagaard K
PLoS ONE 2013 . PMID: 23418415
Shallow breathing: bacterial life at low O(2).
Morris RL, Schmidt TM
Nat. Rev. Microbiol. 2013 Mar . PMID: 23411864
The human gut microbiome and body metabolism: implications for obesity and diabetes.
Devaraj S, Hemarajata P, Versalovic J
Clin. Chem. 2013 Apr . PMID: 23401286
Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M
Environ. Microbiol. 2013 Jan 18. PMID: 23387867
Single cell microRNA analysis using microfluidic flow cytometry.
Wu M, Piccini M, Koh CY, Lam KS, Singh AK
PLoS ONE 2013 . PMID: 23383050
Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis.
Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, Smith RD, Adkins JN, Grundner C, Wright AT
Chem. Biol. 2013 Jan 24. PMID: 23352146
Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne.
Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, Modlin RL, Miller JF, Sodergren E, Craft N, Weinstock GM, Li H
J. Invest. Dermatol. 2013 Jan 21. PMID: 23337890
Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE
PLoS Comput. Biol. 2013 Jan . PMID: 23326225
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences.
Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A
BMC Bioinformatics 2012 . PMID: 23320832
An analysis of online messages about probiotics.
Brinich MA, Mercer MB, Sharp RR
BMC Gastroenterol 2013 . PMID: 23311418
Blaser MJ
Trans. Am. Clin. Climatol. Assoc. 2012 . PMID: 23303990
Species-level classification of the vaginal microbiome.
Fettweis JM, Serrano MG, Sheth NU, Mayer CM, Glascock AL, Brooks JP, Jefferson KK, Buck GA
BMC Genomics 2012 . PMID: 23282177
Genomic sequence analysis and characterization of Sneathia amnii sp. nov.
Harwich MD, Serrano MG, Fettweis JM, Alves JM, Reimers MA, Buck GA, Jefferson KK
BMC Genomics 2012 . PMID: 23281612
Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men.
Redel H, Gao Z, Li H, Alekseyenko AV, Zhou Y, Perez-Perez GI, Weinstock G, Sodergren E, Blaser MJ
J. Infect. Dis. 2013 Apr . PMID: 23300163
The future is now: single-cell genomics of bacteria and archaea.
Blainey PC
FEMS Microbiol. Rev. 2013 May . PMID: 23298390
Hypothesis testing and power calculations for taxonomic-based human microbiome data.
La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, Wang Q, Sodergren E, Weinstock G, Shannon WD
PLoS ONE 2012 . PMID: 23284876
Insights from characterizing extinct human gut microbiomes.
Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S, Foster M, Spicer P, Knight R, Lewis CM
PLoS ONE 2012 . PMID: 23251439
Increased prevalence of anellovirus in pediatric patients with fever.
McElvania TeKippe E, Wylie KM, Deych E, Sodergren E, Weinstock G, Storch GA
PLoS ONE 2012 . PMID: 23226428
Genomic variation landscape of the human gut microbiome.
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P
Nature 2013 Jan 3. PMID: 23222524
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.
Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK
PLoS ONE 2012 . PMID: 23209564
Bioinformatics for the Human Microbiome Project.
Gevers D, Pop M, Schloss PD, Huttenhower C
PLoS Comput. Biol. 2012 . PMID: 23209389
Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome.
Kontur WS, Schackwitz WS, Ivanova N, Martin J, Labutti K, Deshpande S, Tice HN, Pennacchio C, Sodergren E, Weinstock GM, Noguera DR, Donohue TJ
J. Bacteriol. 2012 Dec . PMID: 23209255
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG
Nat. Methods 2013 Jan . PMID: 23202435
TIGRFAMs and Genome Properties in 2013.
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E
Nucleic Acids Res. 2013 Jan . PMID: 23197656
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 Microbiol 2012 Nov . PMID: 23184592
Aagaard K, Petrosino J, Keitel W, Watson M, Katancik J, Garcia N, Patel S, Cutting M, Madden T, Hamilton H, Harris E, Gevers D, Simone G, McInnes P, Versalovic J
FASEB J. 2013 Mar . PMID: 23165986
Statistical object data analysis of taxonomic trees from human microbiome data.
La Rosa PS, Shands B, Deych E, Zhou Y, Sodergren E, Weinstock G, Shannon WD
PLoS ONE 2012 . PMID: 23152838
Estimation of distribution overlap of urn models.
Hampton J, Lladser ME
PLoS ONE 2012 . PMID: 23139734
Tran TT, Panesso D, Gao H, Roh JH, Munita JM, Reyes J, Diaz L, Lobos EA, Shamoo Y, Mishra NN, Bayer AS, Murray BE, Weinstock GM, Arias CA
Antimicrob. Agents Chemother. 2013 Jan . PMID: 23114757
Slashinski MJ, McCurdy SA, Achenbaum LS, Whitney SN, McGuire AL
BMC Med Ethics 2012 . PMID: 23110633
Dietary issues in recurrent abdominal pain.
Shulman RJ
J. Pediatr. Gastroenterol. Nutr. 2012 Nov . PMID: 23103654
Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa.
Williams TM, Loman NJ, Ebruke C, Musher DM, Adegbola RA, Pallen MJ, Weinstock GM, Antonio M
PLoS ONE 2012 . PMID: 23082106
Chen J, Bushman FD, Lewis JD, Wu GD, Li H
Biostatistics 2013 Apr . PMID: 23074263
Species-level analysis of DNA sequence data from the NIH Human Microbiome Project.
Conlan S, Kong HH, Segre JA
PLoS ONE 2012 . PMID: 23071716
Peterfreund GL, Vandivier LE, Sinha R, Marozsan AJ, Olson WC, Zhu J, Bushman FD
PLoS ONE 2012 . PMID: 23071679
The L1-norm best-fit hyperplane problem.
Brooks JP, Dulá JH
Appl Math Lett 2012 Jan 1. PMID: 23024460
Blainey PC, Milla CE, Cornfield DN, Quake SR
Sci Transl Med 2012 Sep 26. PMID: 23019655
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.
Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C
Genome Biol. 2012 . PMID: 23013615
Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, Forney LJ, Carlton JM, Abdo Z, Ravel J
Sex Transm Dis 2012 Oct . PMID: 23007708
Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish.
Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF
Cell Host Microbe 2012 Sep 13. PMID: 22980325
Genomic approaches to studying the human microbiota.
Weinstock GM
Nature 2012 Sep 13. PMID: 22972298
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.
Wu YW, Rho M, Doak TG, Ye Y
Bioinformatics 2012 Sep 15. PMID: 22962453
Current technology in the diagnosis of developmentally related lung disorders.
Hamvas A
Neonatology 2012 . PMID: 22940625
Madan JC, Koestler DC, Stanton BA, Davidson L, Moulton LA, Housman ML, Moore JH, Guill MF, Morrison HG, Sogin ML, Hampton TH, Karagas MR, Palumbo PE, Foster JA, Hibberd PL, O'Toole GA
MBio 2012 . PMID: 22911969
Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome.
Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan KA, Cirimotich S, Jones C, Knight R, Walters WA, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM
PLoS ONE 2012 . PMID: 22905200
The Human Microbiome Project: a community resource for the healthy human microbiome.
Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methé BA, Huttenhower C
PLoS Biol. 2012 . PMID: 22904687
Conservation of gene cassettes among diverse viruses of the human gut.
Minot S, Wu GD, Lewis JD, Bushman FD
PLoS ONE 2012 . PMID: 22900013
Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R
ISME J 2013 Jan . PMID: 22895161
Defining the human microbiome.
Ursell LK, Metcalf JL, Parfrey LW, Knight R
Nutr. Rev. 2012 Aug . PMID: 22861806
Perspectives on human microbiome research ethics.
McGuire AL, Achenbaum LS, Whitney SN, Slashinski MJ, Versalovic J, Keitel WA, McCurdy SA
J Empir Res Hum Res Ethics 2012 Jul . PMID: 22850139
The "most wanted" taxa from the human microbiome for whole genome sequencing.
Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM
PLoS ONE 2012 . PMID: 22848458
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal.
Trimble WL, Keegan KP, D'Souza M, Wilke A, Wilkening J, Gilbert J, Meyer F
BMC Bioinformatics 2012 . PMID: 22839106
Pushalkar S, Ji X, Li Y, Estilo C, Yegnanarayana R, Singh B, Li X, Saxena D
BMC Microbiol. 2012 . PMID: 22817758
Microbial co-occurrence relationships in the human microbiome.
Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C
PLoS Comput. Biol. 2012 . PMID: 22807668
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project.
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Jacob B, Ratner A, Liolios K, Pagani I, Huntemann M, Mavromatis K, Ivanova NN, Kyrpides NC
PLoS ONE 2012 . PMID: 22792232
Harrison KL, Geller G, Marshall P, Tilburt J, Mercer M, Brinich MA, Highland J, Farrell RM, Sharp RR
AJOB Prim Res 2012 Jul 1. PMID: 22773953
Qin X, Galloway-Peña JR, Sillanpaa J, Roh JH, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Muzny DM, Buhay CJ, Ding Y, Dugan-Rocha S, Liu W, Kovar C, Sodergren E, Highlander S, Petrosino JF, Worley KC, Gibbs RA, Weinstock GM, Murray BE
BMC Microbiol. 2012 . PMID: 22769602
Diversity of 5S rRNA genes within individual prokaryotic genomes.
Pei A, Li H, Oberdorf WE, Alekseyenko AV, Parsons T, Yang L, Gerz EA, Lee P, Xiang C, Nossa CW, Pei Z
FEMS Microbiol. Lett. 2012 Oct . PMID: 22765222
Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine.
Ma ZS, Abdo Z, Forney LJ
Per Med 2011 Nov . PMID: 22754581
Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, Morrison HG, Paster BJ, O'Toole GA
J. Bacteriol. 2012 Sep . PMID: 22753064
Vaginal microbiome: rethinking health and disease.
Ma B, Forney LJ, Ravel J
Annu. Rev. Microbiol. 2012 . PMID: 22746335
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice.
Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB
Nature 2012 Jul 5. PMID: 22722865
Evaluation of 16S rDNA-based community profiling for human microbiome research.
PLoS ONE 2012 . PMID: 22720093
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.
Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J
PLoS ONE 2012 . PMID: 22719832
Martin J, Sykes S, Young S, Kota K, Sanka R, Sheth N, Orvis J, Sodergren E, Wang Z, Weinstock GM, Mitreva M
PLoS ONE 2012 . PMID: 22719831
Novel bacterial taxa in the human microbiome.
Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS
PLoS ONE 2012 . PMID: 22719826
A core human microbiome as viewed through 16S rRNA sequence clusters.
Huse SM, Ye Y, Zhou Y, Fodor AA
PLoS ONE 2012 . PMID: 22719824
Analyses of the microbial diversity across the human microbiome.
Li K, Bihan M, Yooseph S, Methé BA
PLoS ONE 2012 . PMID: 22719823
Zhang T, DeSimone RA, Jiao X, Rohlf FJ, Zhu W, Gong QQ, Hunt SR, Dassopoulos T, Newberry RD, Sodergren E, Weinstock G, Robertson CE, Frank DN, Li E
PLoS ONE 2012 . PMID: 22719822
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BA
PLoS ONE 2012 . PMID: 22719821
Complex carbohydrate utilization by the healthy human microbiome.
Cantarel BL, Lombard V, Henrissat B
PLoS ONE 2012 . PMID: 22719820
Sequence analysis of the human virome in febrile and afebrile children.
Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA
PLoS ONE 2012 . PMID: 22719819
Li E, Hamm CM, Gulati AS, Sartor RB, Chen H, Wu X, Zhang T, Rohlf FJ, Zhu W, Gu C, Robertson CE, Pace NR, Boedeker EC, Harpaz N, Yuan J, Weinstock GM, Sodergren E, Frank DN
PLoS ONE 2012 . PMID: 22719818
Diverse CRISPRs evolving in human microbiomes.
Rho M, Wu YW, Tang H, Doak TG, Ye Y
PLoS Genet. 2012 . PMID: 22719260
Metabolic reconstruction for metagenomic data and its application to the human microbiome.
Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C
PLoS Comput. Biol. 2012 . PMID: 22719234
Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H
Bioinformatics 2012 Aug 15. PMID: 22711789
A framework for human microbiome research.
Nature 2012 Jun 14. PMID: 22699610
Structure, function and diversity of the healthy human microbiome.
Nature 2012 Jun 14. PMID: 22699609
Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J
Genome Biol. 2012 . PMID: 22698087
Wang M, Ye Y, Tang H
J. Comput. Biol. 2012 Jun . PMID: 22697249
Host genetic and environmental effects on mouse intestinal microbiota.
Campbell JH, Foster CM, Vishnivetskaya T, Campbell AG, Yang ZK, Wymore A, Palumbo AV, Chesler EJ, Podar M
ISME J 2012 Nov . PMID: 22695862
mcaGUI: microbial community analysis R-Graphical User Interface (GUI).
Copeland WK, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z
Bioinformatics 2012 Aug 15. PMID: 22692220
Stabilization of the murine gut microbiome following weaning.
Schloss PD, Schubert AM, Zackular JP, Iverson KD, Young VB, Petrosino JF
Gut Microbes . PMID: 22688727
Emerging view of the human virome.
Wylie KM, Weinstock GM, Storch GA
Transl Res 2012 Oct . PMID: 22683423
Understanding vaginal microbiome complexity from an ecological perspective.
Hickey RJ, Zhou X, Pierson JD, Ravel J, Forney LJ
Transl Res 2012 Oct . PMID: 22683415
Deep sequencing of the oral microbiome reveals signatures of periodontal disease.
Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S
PLoS ONE 2012 . PMID: 22675498
Spatial and temporal variability of the human microbiota.
Parfrey LW, Knight R
Clin. Microbiol. Infect. 2012 Jul . PMID: 22647040
Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R
Genome Res. 2012 Oct . PMID: 22665442
Comparison of storage conditions for human vaginal microbiome studies.
Bai G, Gajer P, Nandy M, Ma B, Yang H, Sakamoto J, Blanchard MH, Ravel J, Brotman RM
PLoS ONE 2012 . PMID: 22655031
'Omics' of the mammalian gut--new insights into function.
Lamendella R, VerBerkmoes N, Jansson JK
Curr. Opin. Biotechnol. 2012 Jun . PMID: 22626866
Zhang T, Song B, Zhu W, Xu X, Gong QQ, Morando C, Dassopoulos T, Newberry RD, Hunt SR, Li E
PLoS ONE 2012 . PMID: 22606341
Bacterial communities of the coronal sulcus and distal urethra of adolescent males.
Nelson DE, Dong Q, Van der Pol B, Toh E, Fan B, Katz BP, Mi D, Rong R, Weinstock GM, Sodergren E, Fortenberry JD
PLoS ONE 2012 . PMID: 22606251
Britton RA, Young VB
Trends Microbiol. 2012 Jul . PMID: 22595318
A new era of the vaginal microbiome: advances using next-generation sequencing.
Fettweis JM, Serrano MG, Girerd PH, Jefferson KK, Buck GA
Chem. Biodivers. 2012 May . PMID: 22589096
Food and the gut microbiota in inflammatory bowel diseases: a critical connection.
Albenberg LG, Lewis JD, Wu GD
Curr. Opin. Gastroenterol. 2012 Jul . PMID: 22573192
Temporal dynamics of the human vaginal microbiota.
Gajer P, Brotman RM, Bai G, Sakamoto J, Schütte UM, Zhong X, Koenig SS, Fu L, Ma ZS, Zhou X, Abdo Z, Forney LJ, Ravel J
Sci Transl Med 2012 May 2. PMID: 22553250
We are what we eat: how the diet of infants affects their gut microbiome.
Pop M
Genome Biol. 2012 . PMID: 22546514
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.
Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R
J. Allergy Clin. Immunol. 2012 May . PMID: 22541361
Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism.
Pathak DT, Wei X, Bucuvalas A, Haft DH, Gerloff DL, Wall D
PLoS Genet. 2012 . PMID: 22511878
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.
Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A
Genome Biol. 2012 . PMID: 22455878
Decade-long bacterial community dynamics in cystic fibrosis airways.
Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ, Young VB, LiPuma JJ
Proc. Natl. Acad. Sci. U.S.A. 2012 Apr 10. PMID: 22451929
Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation.
Hill DA, Siracusa MC, Abt MC, Kim BS, Kobuley D, Kubo M, Kambayashi T, Larosa DF, Renner ED, Orange JS, Bushman FD, Artis D
Nat. Med. 2012 Apr . PMID: 22447074
AntiFam: a tool to help identify spurious ORFs in protein annotation.
Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A
Database (Oxford) 2012 . PMID: 22434837
Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC
Genome Res. 2012 Jun . PMID: 22434425
The human microbiome: at the interface of health and disease.
Cho I, Blaser MJ
Nat. Rev. Genet. 2012 Apr . PMID: 22411464
Experiences of patients with chronic gastrointestinal conditions: in their own words.
McCormick JB, Hammer RR, Farrell RM, Geller G, James KM, Loftus EV, Mercer MB, Tilburt JC, Sharp RR
Health Qual Life Outcomes 2012 . PMID: 22401607
Harrell L, Wang Y, Antonopoulos D, Young V, Lichtenstein L, Huang Y, Hanauer S, Chang E
PLoS ONE 2012 . PMID: 22389708
Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.
Thompson JD, Shibahara G, Rajan S, Pel J, Marziali A
PLoS ONE 2012 . PMID: 22355378
Hypervariable loci in the human gut virome.
Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD
Proc. Natl. Acad. Sci. U.S.A. 2012 Mar 6. PMID: 22355105
Yang L, Francois F, Pei Z
Clin. Cancer Res. 2012 Apr 15. PMID: 22344232
Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice.
Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Barrish JP, Finegold MJ, Petrosino JF, Guerrant RL, Conner ME, Versalovic J
J. Pediatr. Gastroenterol. Nutr. 2012 Sep . PMID: 22343914
Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice.
Mei J, Liu Y, Dai N, Hoffmann C, Hudock KM, Zhang P, Guttentag SH, Kolls JK, Oliver PM, Bushman FD, Worthen GS
J. Clin. Invest. 2012 Mar 1. PMID: 22326959
Significance of the microbiome in obstructive lung disease.
Han MK, Huang YJ, Lipuma JJ, Boushey HA, Boucher RC, Cookson WO, Curtis JL, Erb-Downward J, Lynch SV, Sethi S, Toews GB, Young VB, Wolfgang MC, Huffnagle GB, Martinez FJ
Thorax 2012 May . PMID: 22318161
Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD, Murray PR, Turner ML, Segre JA
Genome Res. 2012 May . PMID: 22310478
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
Soil Biol. Biochem. 2011 Jul . PMID: 22267877
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine.
Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Finegold MJ, Petrosino JF, Conner ME, Versalovic J
FASEB J. 2012 May . PMID: 22267340
Ozok AR, Persoon IF, Huse SM, Keijser BJ, Wesselink PR, Crielaard W, Zaura E
Int Endod J 2012 Jun . PMID: 22251411
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.
Soergel DA, Dey N, Knight R, Brenner SE
ISME J 2012 Jul . PMID: 22237546
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.
Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M
Brief. Bioinformatics 2013 Mar . PMID: 22199379
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
Human microbiome and HIV/AIDS.
Saxena D, Li Y, Yang L, Pei Z, Poles M, Abrams WR, Malamud D
Curr HIV/AIDS Rep 2012 Mar . PMID: 22193889
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
Zhang Q, Doak TG, Ye Y
Pac Symp Biocomput 2012 . PMID: 22174281
Advancing analytical algorithms and pipelines for billions of microbial sequences.
Gonzalez A, Knight R
Curr. Opin. Biotechnol. 2012 Feb . PMID: 22172529
SitePainter: a tool for exploring biogeographical patterns.
Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R
Bioinformatics 2012 Feb 1. PMID: 22171330
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.
Wang X, Cai Y, Sun Y, Knight R, Mai V
ISME J 2012 Jul . PMID: 22170430
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
Characterizing microbial communities through space and time.
Gonzalez A, King A, Robeson MS, Song S, Shade A, Metcalf JL, Knight R
Curr. Opin. Biotechnol. 2012 Jun . PMID: 22154467
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA
Genome Res. 2012 Mar . PMID: 22147368
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
Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC
Nucleic Acids Res. 2012 Jan . PMID: 22135293
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P
ISME J 2012 Mar . PMID: 22134646
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
The Human Microbiome Project: lessons from human genomics.
Lewis CM, Obregón-Tito A, Tito RY, Foster MW, Spicer PG
Trends Microbiol. 2012 Jan . PMID: 22112388
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
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
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
Fluorescent labeling of antibody fragments using split GFP.
Ferrara F, Listwan P, Waldo GS, Bradbury AR
PLoS ONE 2011 . PMID: 21998685
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
Sczesnak A, Segata N, Qin X, Gevers D, Petrosino JF, Huttenhower C, Littman DR, Ivanov II
Cell Host Microbe 2011 Sep 15. PMID: 21925113
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
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
Chen CH, Cho SH, Chiang HI, Tsai F, Zhang K, Lo YH
Anal. Chem. 2011 Oct 1. PMID: 21809842
He Z, Piceno Y, Deng Y, Xu M, Lu Z, Desantis T, Andersen G, Hobbie SE, Reich PB, Zhou J
ISME J 2012 Feb . PMID: 21796217
Investigating the biological and clinical significance of human dysbioses.
Frank DN, Zhu W, Sartor RB, Li E
Trends Microbiol. 2011 Sep . PMID: 21775143
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
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
Carvalho FA, Nalbantoglu I, Ortega-Fernandez S, Aitken JD, Su Y, Koren O, Walters WA, Knight R, Ley RE, Vijay-Kumar M, Gewirtz AT
Gut 2012 Mar . PMID: 21646247
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
Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry JD, Van der Pol B
PLoS ONE 2011 . PMID: 21603636
Responses of gut microbiota to diet composition and weight loss in lean and obese mice.
Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE, Leibel RL
Obesity (Silver Spring) 2012 Apr . PMID: 21593810
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
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO
Nat. Biotechnol. 2011 May . PMID: 21552244
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
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
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
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
Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR
PLoS ONE 2011 . PMID: 21364937
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
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
Dielectrophoresis of Caenorhabditis elegans.
Chuang HS, Raizen DM, Lamb A, Dabbish N, Bau HH
Lab Chip 2011 Feb 21. PMID: 21225036
Haft DH
BMC Genomics 2011 . PMID: 21223593
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
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
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.
Shah N, Tang H, Doak TG, Ye Y
Pac Symp Biocomput 2011 . PMID: 21121044
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
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
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
Frank DN
J. Anim. Sci. 2011 Mar . PMID: 20935136
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
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
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
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
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
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
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
Erez A, Plunkett K, Sutton VR, McGuire AL
Am. J. Med. Genet. A 2010 Jul . PMID: 20583190
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
Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N
Environ. Microbiol. 2010 Nov . PMID: 20545741
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
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
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
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
Selengut JD, Rusch DB, Haft DH
BMC Bioinformatics 2010 . PMID: 20102603
Micro-fabricated fluorescence-activated cell sorter.
Cho SH, Chen CH, Tsai FS, Lo YH
Conf Proc IEEE Eng Med Biol Soc 2009 . PMID: 19965141
Searching for SNPs with cloud computing.
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL
Genome Biol. 2009 . PMID: 19930550
PyNAST: a flexible tool for aligning sequences to a template alignment.
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R
Bioinformatics 2010 Jan 15. PMID: 19914921
What are the consequences of the disappearing human microbiota?
Blaser MJ, Falkow S
Nat. Rev. Microbiol. 2009 Dec . PMID: 19898491
Inexact Local Alignment Search over Suffix Arrays.
Ghodsi M, Pop M
Proceedings (IEEE Int Conf Bioinformatics Biomed) 2009 Nov 1. PMID: 21278916
Frank DN
BMC Bioinformatics 2009 . PMID: 19874596
Bacterial communities of disease vectors sampled across time, space, and species.
Jones RT, Knight R, Martin AP
ISME J 2010 Feb . PMID: 19865184
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Osterås M, Schrenzel J, François P
J. Microbiol. Methods 2009 Dec . PMID: 19796657
Hamady M, Lozupone C, Knight R
ISME J 2010 Jan . PMID: 19710709
High-fat diet determines the composition of the murine gut microbiome independently of obesity.
Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD
Gastroenterology 2009 Nov . PMID: 19706296
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
Ye Y, Doak TG
PLoS Comput. Biol. 2009 Aug . PMID: 19680427
A method for isolating and analyzing human mRNA from newborn stool.
Bennett WE, González-Rivera R, Shaikh N, Magrini V, Boykin M, Warner BB, Hamvas A, Tarr PI
J. Immunol. Methods 2009 Sep 30. PMID: 19660464
Microfluidic cell sorter with integrated piezoelectric actuator.
Chen CH, Cho SH, Tsai F, Erten A, Lo YH
Biomed Microdevices 2009 Dec . PMID: 19649710
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.
Brady A, Salzberg SL
Nat. Methods 2009 Sep . PMID: 19648916
An ORFome assembly approach to metagenomics sequences analysis.
Ye Y, Tang H
J Bioinform Comput Biol 2009 Jun . PMID: 19507285
Genome assembly reborn: recent computational challenges.
Pop M
Brief. Bioinformatics 2009 Jul . PMID: 19482960
Diversity of 23S rRNA genes within individual prokaryotic genomes.
Pei A, Nossa CW, Chokshi P, Blaser MJ, Yang L, Rosmarin DM, Pei Z
PLoS ONE 2009 . PMID: 19415112
Yang L, Lu X, Nossa CW, Francois F, Peek RM, Pei Z
Gastroenterology 2009 Aug . PMID: 19394334
Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, Antonopoulos DA, Chang EB, Claud EC
ISME J 2009 Aug . PMID: 19369970
Statistical methods for detecting differentially abundant features in clinical metagenomic samples.
White JR, Nagarajan N, Pop M
PLoS Comput. Biol. 2009 Apr . PMID: 19360128
Helping patients make informed choices about probiotics: a need for research.
Sharp RR, Achkar JP, Brinich MA, Farrell RM
Am. J. Gastroenterol. 2009 Apr . PMID: 19343022
Metagenomic pyrosequencing and microbial identification.
Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J
Clin. Chem. 2009 May . PMID: 19264858
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL
Genome Biol. 2009 . PMID: 19261174
Metagenomics: Facts and Artifacts, and Computational Challenges*
Wooley JC, Ye Y
J Comput Sci Technol 2009 Jan . PMID: 20648230
