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Items: 1 to 50 of 121

1.

Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, Nguyen H, Zhou X, Albright B, Hong BY, Petersen L, Bautista E, Hanson B, Chen L, Spakowicz D, Bahmani A, Salins D, Leopold B, Ashland M, Dagan-Rosenfeld O, Rego S, Limcaoco P, Colbert E, Allister C, Perelman D, Craig C, Wei E, Chaib H, Hornburg D, Dunn J, Liang L, Rose SMS, Kukurba K, Piening B, Rost H, Tse D, McLaughlin T, Sodergren E, Weinstock GM, Snyder M.

Nature. 2019 May;569(7758):663-671. doi: 10.1038/s41586-019-1236-x. Epub 2019 May 29.

PMID:
31142858
2.

A longitudinal big data approach for precision health.

Schüssler-Fiorenza Rose SM, Contrepois K, Moneghetti KJ, Zhou W, Mishra T, Mataraso S, Dagan-Rosenfeld O, Ganz AB, Dunn J, Hornburg D, Rego S, Perelman D, Ahadi S, Sailani MR, Zhou Y, Leopold SR, Chen J, Ashland M, Christle JW, Avina M, Limcaoco P, Ruiz C, Tan M, Butte AJ, Weinstock GM, Slavich GM, Sodergren E, McLaughlin TL, Haddad F, Snyder MP.

Nat Med. 2019 May;25(5):792-804. doi: 10.1038/s41591-019-0414-6. Epub 2019 May 8.

PMID:
31068711
3.

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.

Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S, Goncharenko-Foster I, Minx P, Sodergren E, Weinstock G, Rokhsar DS, McFall-Ngai M, Simakov O, Foster JS, Nyholm SV.

Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3030-3035. doi: 10.1073/pnas.1817322116. Epub 2019 Jan 11.

4.

Effects of diet on the childhood gut microbiome and its implications for atopic dermatitis.

Mahdavinia M, Rasmussen HE, Botha M, Binh Tran TD, Van den Berg JP, Sodergren E, Davis E, Engen K, Gray C, Lunjani N, Hlela C, Preite NZ, Basera W, Hobane L, Watkins A, Engen P, Mankahla A, Gaunt B, Thomas F, Tobin MC, Landay A, Weinstock GM, Keshavarzian A, Levin ME.

J Allergy Clin Immunol. 2019 Apr;143(4):1636-1637.e5. doi: 10.1016/j.jaci.2018.11.034. Epub 2018 Dec 19. No abstract available.

PMID:
30578881
5.

Diet during Pregnancy and Infancy and the Infant Intestinal Microbiome.

Savage JH, Lee-Sarwar KA, Sordillo JE, Lange NE, Zhou Y, O'Connor GT, Sandel M, Bacharier LB, Zeiger R, Sodergren E, Weinstock GM, Gold DR, Weiss ST, Litonjua AA.

J Pediatr. 2018 Dec;203:47-54.e4. doi: 10.1016/j.jpeds.2018.07.066. Epub 2018 Aug 30.

PMID:
30173873
6.

Extensive Gene Amplification as a Mechanism for Piperacillin-Tazobactam Resistance in Escherichia coli.

Schechter LM, Creely DP, Garner CD, Shortridge D, Nguyen H, Chen L, Hanson BM, Sodergren E, Weinstock GM, Dunne WM Jr, van Belkum A, Leopold SR.

MBio. 2018 Apr 24;9(2). pii: e00583-18. doi: 10.1128/mBio.00583-18.

7.

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP.

Cell Syst. 2018 Feb 28;6(2):157-170.e8. doi: 10.1016/j.cels.2017.12.013. Epub 2018 Jan 17.

8.

An Analysis of the Epidemic of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae: Convergence of Two Evolutionary Mechanisms Creates the "Perfect Storm".

Rojas LJ, Weinstock GM, De La Cadena E, Diaz L, Rios R, Hanson BM, Brown JS, Vats P, Phillips DS, Nguyen H, Hujer KM, Correa A, Adams MD, Perez F, Sodergren E, Narechania A, Planet PJ, Villegas MV, Bonomo RA, Arias CA.

J Infect Dis. 2017 Dec 27;217(1):82-92. doi: 10.1093/infdis/jix524.

9.

Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology.

Kwambana-Adams B, Hanson B, Worwui A, Agbla S, Foster-Nyarko E, Ceesay F, Ebruke C, Egere U, Zhou Y, Ndukum M, Sodergren E, Barer M, Adegbola R, Weinstock G, Antonio M.

Sci Rep. 2017 Aug 15;7(1):8127. doi: 10.1038/s41598-017-08717-0.

10.

Community characteristics of the gut microbiomes of competitive cyclists.

Petersen LM, Bautista EJ, Nguyen H, Hanson BM, Chen L, Lek SH, Sodergren E, Weinstock GM.

Microbiome. 2017 Aug 10;5(1):98. doi: 10.1186/s40168-017-0320-4.

11.

A prospective microbiome-wide association study of food sensitization and food allergy in early childhood.

Savage JH, Lee-Sarwar KA, Sordillo J, Bunyavanich S, Zhou Y, O'Connor G, Sandel M, Bacharier LB, Zeiger R, Sodergren E, Weinstock GM, Gold DR, Weiss ST, Litonjua AA.

Allergy. 2018 Jan;73(1):145-152. doi: 10.1111/all.13232. Epub 2017 Aug 2.

12.

Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis.

Robinson LS, Perry J, Lek S, Wollam A, Sodergren E, Weinstock G, Lewis WG, Lewis AL.

Genome Announc. 2016 Sep 29;4(5). pii: e00879-16. doi: 10.1128/genomeA.00879-16.

13.

Household air pollution and the lung microbiome of healthy adults in Malawi: a cross-sectional study.

Rylance J, Kankwatira A, Nelson DE, Toh E, Day RB, Lin H, Gao X, Dong Q, Sodergren E, Weinstock GM, Heyderman RS, Twigg HL 3rd, Gordon SB.

BMC Microbiol. 2016 Aug 11;16(1):182. doi: 10.1186/s12866-016-0803-7.

14.

Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study.

Hanson B, Zhou Y, Bautista EJ, Urch B, Speck M, Silverman F, Muilenberg M, Phipatanakul W, Weinstock G, Sodergren E, Gold DR, Sordillo JE.

Environ Sci Process Impacts. 2016 Jun 15;18(6):713-24. doi: 10.1039/c5em00639b. Epub 2016 May 23.

15.

Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study.

Warner BB, Deych E, Zhou Y, Hall-Moore C, Weinstock GM, Sodergren E, Shaikh N, Hoffmann JA, Linneman LA, Hamvas A, Khanna G, Rouggly-Nickless LC, Ndao IM, Shands BA, Escobedo M, Sullivan JE, Radmacher PG, Shannon WD, Tarr PI.

Lancet. 2016 May 7;387(10031):1928-36. doi: 10.1016/S0140-6736(16)00081-7. Epub 2016 Mar 9.

16.

Effect of Advanced HIV Infection on the Respiratory Microbiome.

Twigg HL 3rd, Knox KS, Zhou J, Crothers KA, Nelson DE, Toh E, Day RB, Lin H, Gao X, Dong Q, Mi D, Katz BP, Sodergren E, Weinstock GM.

Am J Respir Crit Care Med. 2016 Jul 15;194(2):226-35. doi: 10.1164/rccm.201509-1875OC.

17.

Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains.

Rodriguez M, Hogan PG, Satola SW, Crispell E, Wylie T, Gao H, Sodergren E, Weinstock GM, Burnham CA, Fritz SA.

Medicine (Baltimore). 2015 Sep;94(37):e1534. doi: 10.1097/MD.0000000000001534.

18.

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

Beck JM, Schloss PD, Venkataraman A, Twigg H 3rd, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2015 Dec 1;192(11):1335-44. doi: 10.1164/rccm.201501-0128OC.

19.

Correction: Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis.

Zhang Y, Rowehl L, Krumsiek JM, Orner EP, Shaikh N, Tarr PI, Sodergren E, Weinstock GM, Boedeker EC, Xiong X, Parkinson J, Frank DN, Li E, Gathungu G.

PLoS One. 2015 Jul 28;10(7):e0134759. doi: 10.1371/journal.pone.0134759. eCollection 2015. No abstract available.

20.

Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis.

Zhang Y, Rowehl L, Krumsiek JM, Orner EP, Shaikh N, Tarr PI, Sodergren E, Weinstock GM, Boedeker EC, Xiong X, Parkinson J, Frank DN, Li E, Gathungu G.

PLoS One. 2015 Jun 30;10(6):e0130902. doi: 10.1371/journal.pone.0130902. eCollection 2015. Erratum in: PLoS One. 2015;10(7):e0134759.

21.

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment.

Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ.

Nat Commun. 2015 Jun 30;6:7486. doi: 10.1038/ncomms8486.

22.

Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study.

Zhou Y, Shan G, Sodergren E, Weinstock G, Walker WA, Gregory KE.

PLoS One. 2015 Mar 5;10(3):e0118632. doi: 10.1371/journal.pone.0118632. eCollection 2015.

23.

Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis.

Shi B, Chang M, Martin J, Mitreva M, Lux R, Klokkevold P, Sodergren E, Weinstock GM, Haake SK, Li H.

MBio. 2015 Feb 17;6(1):e01926-14. doi: 10.1128/mBio.01926-14.

24.

Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes.

Staudová B, Strouhal M, Zobaníková M, Cejková D, Fulton LL, Chen L, Giacani L, Centurion-Lara A, Bruisten SM, Sodergren E, Weinstock GM, Smajs D.

PLoS Negl Trop Dis. 2014 Nov 6;8(11):e3261. doi: 10.1371/journal.pntd.0003261. eCollection 2014.

25.

Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study.

Zhou Y, Burnham CA, Hink T, Chen L, Shaikh N, Wollam A, Sodergren E, Weinstock GM, Tarr PI, Dubberke ER.

J Clin Microbiol. 2014 Dec;52(12):4260-6. doi: 10.1128/JCM.02115-14. Epub 2014 Oct 1.

26.

Metagenomic analysis of double-stranded DNA viruses in healthy adults.

Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM.

BMC Biol. 2014 Sep 10;12:71. doi: 10.1186/s12915-014-0071-7.

27.

Small bowel resection induces long-term changes in the enteric microbiota of mice.

Sommovilla J, Zhou Y, Sun RC, Choi PM, Diaz-Miron J, Shaikh N, Sodergren E, Warner BB, Weinstock GM, Tarr PI, Warner BW.

J Gastrointest Surg. 2015 Jan;19(1):56-64; discussion 64. doi: 10.1007/s11605-014-2631-0. Epub 2014 Sep 3.

28.

Patterned progression of bacterial populations in the premature infant gut.

La Rosa PS, Warner BB, Zhou Y, Weinstock GM, Sodergren E, Hall-Moore CM, Stevens HJ, Bennett WE Jr, Shaikh N, Linneman LA, Hoffmann JA, Hamvas A, Deych E, Shands BA, Shannon WD, Tarr PI.

Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12522-7. doi: 10.1073/pnas.1409497111. Epub 2014 Aug 11. Erratum in: Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17336.

29.

Exploration of bacterial community classes in major human habitats.

Zhou Y, Mihindukulasuriya KA, Gao H, La Rosa PS, Wylie KM, Martin JC, Kota K, Shannon WD, Mitreva M, Sodergren E, Weinstock GM.

Genome Biol. 2014 May 7;15(5):R66. doi: 10.1186/gb-2014-15-5-r66.

30.

Resequencing of Treponema pallidum ssp. pallidum strains Nichols and SS14: correction of sequencing errors resulted in increased separation of syphilis treponeme subclusters.

Pětrošová H, Pospíšilová P, Strouhal M, Čejková D, Zobaníková M, Mikalová L, Sodergren E, Weinstock GM, Šmajs D.

PLoS One. 2013 Sep 10;8(9):e74319. doi: 10.1371/journal.pone.0074319. eCollection 2013.

31.

Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis.

Turabelidze G, Lawrence SJ, Gao H, Sodergren E, Weinstock GM, Abubucker S, Wylie T, Mitreva M, Shaikh N, Gautom R, Tarr PI.

J Clin Microbiol. 2013 Dec;51(12):3950-4. doi: 10.1128/JCM.01930-13. Epub 2013 Sep 18.

32.

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.

Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, Botstein D, Desai MM.

Nature. 2013 Aug 29;500(7464):571-4. doi: 10.1038/nature12344. Epub 2013 Jul 21.

33.

Whole genome sequence of the Treponema Fribourg-Blanc: unspecified simian isolate is highly similar to the yaws subspecies.

Zobaníková M, Strouhal M, Mikalová L, Cejková D, Ambrožová L, Pospíšilová P, Fulton LL, Chen L, Sodergren E, Weinstock GM, Smajs D.

PLoS Negl Trop Dis. 2013 Apr 18;7(4):e2172. doi: 10.1371/journal.pntd.0002172. Print 2013.

34.

Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome.

Tomida S, Nguyen L, Chiu BH, Liu J, Sodergren E, Weinstock GM, Li H.

MBio. 2013 Apr 30;4(3):e00003-13. doi: 10.1128/mBio.00003-13.

35.

Comparison of the respiratory microbiome in healthy nonsmokers and smokers.

Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2013 May 15;187(10):1067-75. doi: 10.1164/rccm.201210-1913OC.

36.

Widespread colonization of the lung by Tropheryma whipplei in HIV infection.

Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2013 May 15;187(10):1110-7. doi: 10.1164/rccm.201211-2145OC.

37.

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 Sep;133(9):2152-60. doi: 10.1038/jid.2013.21. Epub 2013 Jan 21.

38.

Biogeography of the ecosystems of the healthy human body.

Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM.

Genome Biol. 2013 Jan 14;14(1):R1. doi: 10.1186/gb-2013-14-1-r1.

39.

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;207(7):1105-14. doi: 10.1093/infdis/jit005. Epub 2013 Jan 8.

40.

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;7(12):e52078. doi: 10.1371/journal.pone.0052078. Epub 2012 Dec 20.

41.

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;7(11):e50937. doi: 10.1371/journal.pone.0050937. Epub 2012 Nov 30.

42.

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;194(24):7016-7. doi: 10.1128/JB.01214-12.

43.

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;7(11):e48996. doi: 10.1371/journal.pone.0048996. Epub 2012 Nov 9.

44.

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;7(7):e41294. doi: 10.1371/journal.pone.0041294. Epub 2012 Jul 26.

45.

Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes.

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 Jul 7;12:135. doi: 10.1186/1471-2180-12-135.

46.

Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.

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;7(6):e36427. doi: 10.1371/journal.pone.0036427. Epub 2012 Jun 13.

47.

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;7(6):e35294. doi: 10.1371/journal.pone.0035294. Epub 2012 Jun 13.

48.

Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.

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;7(6):e30044. doi: 10.1371/journal.pone.0030044. Epub 2012 Jun 13.

49.

Sequence analysis of the human virome in febrile and afebrile children.

Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA.

PLoS One. 2012;7(6):e27735. doi: 10.1371/journal.pone.0027735. Epub 2012 Jun 13.

50.

Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.

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;7(6):e26284. doi: 10.1371/journal.pone.0026284. Epub 2012 Jun 13.

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