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Items: 1 to 50 of 252

1.

HIV-1 latent reservoir size and diversity are stable following brief treatment interruption.

Salantes DB, Zheng Y, Mampe F, Srivastava T, Beg S, Lai J, Li JZ, Tressler RL, Koup RA, Hoxie J, Abdel-Mohsen M, Sherrill-Mix S, McCormick K, Overton ET, Bushman FD, Learn GH, Siliciano RF, Siliciano JM, Tebas P, Bar KJ.

J Clin Invest. 2018 Jun 18. pii: 120194. doi: 10.1172/JCI120194. [Epub ahead of print]

2.

Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells.

Fraietta JA, Nobles CL, Sammons MA, Lundh S, Carty SA, Reich TJ, Cogdill AP, Morrissette JJD, DeNizio JE, Reddy S, Hwang Y, Gohil M, Kulikovskaya I, Nazimuddin F, Gupta M, Chen F, Everett JK, Alexander KA, Lin-Shiao E, Gee MH, Liu X, Young RM, Ambrose D, Wang Y, Xu J, Jordan MS, Marcucci KT, Levine BL, Garcia KC, Zhao Y, Kalos M, Porter DL, Kohli RM, Lacey SF, Berger SL, Bushman FD, June CH, Melenhorst JJ.

Nature. 2018 Jun;558(7709):307-312. doi: 10.1038/s41586-018-0178-z. Epub 2018 May 30.

PMID:
29849141
3.

Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates.

Taylor JM, Clarke EL, Baker K, Lauder A, Kim D, Bailey A, Wu GD, Collman RG, Doyle-Meyers L, Russell-Lodrigue K, Blanchard J, Bushman FD, Bohm R.

PeerJ. 2018 Apr 11;6:e4612. doi: 10.7717/peerj.4612. eCollection 2018.

4.

Allometry and Ecology of the Bilaterian Gut Microbiome.

Sherrill-Mix S, McCormick K, Lauder A, Bailey A, Zimmerman L, Li Y, Django JN, Bertolani P, Colin C, Hart JA, Hart TB, Georgiev AV, Sanz CM, Morgan DB, Atencia R, Cox D, Muller MN, Sommer V, Piel AK, Stewart FA, Speede S, Roman J, Wu G, Taylor J, Bohm R, Rose HM, Carlson J, Mjungu D, Schmidt P, Gaughan C, Bushman JI, Schmidt E, Bittinger K, Collman RG, Hahn BH, Bushman FD.

MBio. 2018 Mar 27;9(2). pii: e00319-18. doi: 10.1128/mBio.00319-18.

5.

Fully 3D printed integrated reactor array for point-of-care molecular diagnostics.

Kadimisetty K, Song J, Doto AM, Hwang Y, Peng J, Mauk MG, Bushman FD, Gross R, Jarvis JN, Liu C.

Biosens Bioelectron. 2018 Jun 30;109:156-163. doi: 10.1016/j.bios.2018.03.009. Epub 2018 Mar 10.

PMID:
29550739
6.

Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12.

Uribe-Herranz M, Bittinger K, Rafail S, Guedan S, Pierini S, Tanes C, Ganetsky A, Morgan MA, Gill S, Tanyi JL, Bushman FD, June CH, Facciabene A.

JCI Insight. 2018 Feb 22;3(4). pii: 94952. doi: 10.1172/jci.insight.94952. [Epub ahead of print]

7.

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Mar;3(3):388. doi: 10.1038/s41564-018-0114-x.

PMID:
29440750
8.

Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting.

Gijsbers R, Vets S, De Rijck J, Ocwieja KE, Ronen K, Malani N, Bushman FD, Debyser Z.

J Biol Chem. 2018 Jan 5;293(1):114. doi: 10.1074/jbc.W117.001458. No abstract available.

9.

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13;:.

10.

A Pilot Characterization of the Human Chronobiome.

Skarke C, Lahens NF, Rhoades SD, Campbell A, Bittinger K, Bailey A, Hoffmann C, Olson RS, Chen L, Yang G, Price TS, Moore JH, Bushman FD, Greene CS, Grant GR, Weljie AM, FitzGerald GA.

Sci Rep. 2017 Dec 7;7(1):17141. doi: 10.1038/s41598-017-17362-6.

11.

A role for bacterial urease in gut dysbiosis and Crohn's disease.

Ni J, Shen TD, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I, Scott J, Lauder A, Hoffmann C, Rivas G, Albenberg L, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD.

Sci Transl Med. 2017 Nov 15;9(416). pii: eaah6888. doi: 10.1126/scitranslmed.aah6888.

12.

Viral communities of the human gut: metagenomic analysis of composition and dynamics.

Aggarwala V, Liang G, Bushman FD.

Mob DNA. 2017 Oct 3;8:12. doi: 10.1186/s13100-017-0095-y. eCollection 2017. Review.

13.

A Model-Based Approach For Species Abundance Quantification Based On Shotgun Metagenomic Data.

Chen EZ, Bushman FD, Li H.

Stat Biosci. 2017 Jun;9(1):13-27. doi: 10.1007/s12561-016-9148-x. Epub 2016 May 16.

14.

Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples.

Clarke EL, Lauder AP, Hofstaedter CE, Hwang Y, Fitzgerald AS, Imai I, Biernat W, Rękawiecki B, Majewska H, Dubaniewicz A, Litzky LA, Feldman MD, Bittinger K, Rossman MD, Patterson KC, Bushman FD, Collman RG.

Am J Respir Crit Care Med. 2018 Jan 15;197(2):225-234. doi: 10.1164/rccm.201705-0891OC.

PMID:
28846439
15.

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease.

Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD.

Cell Host Microbe. 2017 Aug 9;22(2):247. doi: 10.1016/j.chom.2017.07.011. No abstract available.

PMID:
28799909
16.

Gene therapy for Wiskott-Aldrich syndrome in a severely affected adult.

Morris EC, Fox T, Chakraverty R, Tendeiro R, Snell K, Rivat C, Grace S, Gilmour K, Workman S, Buckland K, Butler K, Chee R, Salama AD, Ibrahim H, Hara H, Duret C, Mavilio F, Male F, Bushman FD, Galy A, Burns SO, Gaspar HB, Thrasher AJ.

Blood. 2017 Sep 14;130(11):1327-1335. doi: 10.1182/blood-2017-04-777136. Epub 2017 Jul 17.

PMID:
28716862
17.

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome.

Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, Adisetiyo H, Zabih S, Lincez PJ, Bittinger K, Bailey A, Bushman FD, Sleasman JW, Aldrovandi GM.

JAMA Pediatr. 2017 Jul 1;171(7):647-654. doi: 10.1001/jamapediatrics.2017.0378.

18.

Optimizing methods and dodging pitfalls in microbiome research.

Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano R, Bushman FD, Bittinger K.

Microbiome. 2017 May 5;5(1):52. doi: 10.1186/s40168-017-0267-5. Review.

19.

A role for glycolipid biosynthesis in severe fever with thrombocytopenia syndrome virus entry.

Drake MJ, Brennan B, Briley K Jr, Bart SM, Sherman E, Szemiel AM, Minutillo M, Bushman FD, Bates P.

PLoS Pathog. 2017 Apr 7;13(4):e1006316. doi: 10.1371/journal.ppat.1006316. eCollection 2017 Apr.

20.

Genome Sequence of a Toxin-Positive Clostridium difficile Strain Isolated from Murine Feces.

Etienne-Mesmin L, Chassaing B, Adekunle O, Mattei LM, Edwards AN, McBride SM, Bushman FD, Gewirtz AT.

Genome Announc. 2017 Apr 6;5(14). pii: e00088-17. doi: 10.1128/genomeA.00088-17.

21.

INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.

Sherman E, Nobles C, Berry CC, Six E, Wu Y, Dryga A, Malani N, Male F, Reddy S, Bailey A, Bittinger K, Everett JK, Caccavelli L, Drake MJ, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD.

Mol Ther Methods Clin Dev. 2016 Dec 18;4:39-49. doi: 10.1016/j.omtm.2016.11.002. eCollection 2017 Mar 17.

22.

INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions.

Berry CC, Nobles C, Six E, Wu Y, Malani N, Sherman E, Dryga A, Everett JK, Male F, Bailey A, Bittinger K, Drake MJ, Caccavelli L, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD.

Mol Ther Methods Clin Dev. 2016 Dec 18;4:17-26. doi: 10.1016/j.omtm.2016.11.003. eCollection 2017 Mar 17.

23.

swga: a primer design toolkit for selective whole genome amplification.

Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D.

Bioinformatics. 2017 Jul 15;33(14):2071-2077. doi: 10.1093/bioinformatics/btx118.

24.

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile.

Etienne-Mesmin L, Chassaing B, Adekunle O, Mattei LM, Bushman FD, Gewirtz AT.

Gut. 2018 May;67(5):860-871. doi: 10.1136/gutjnl-2016-313510. Epub 2017 Feb 20.

PMID:
28219893
25.

Evolutionary and functional implications of hypervariable loci within the skin virome.

Hannigan GD, Zheng Q, Meisel JS, Minot SS, Bushman FD, Grice EA.

PeerJ. 2017 Feb 7;5:e2959. doi: 10.7717/peerj.2959. eCollection 2017.

26.

Human and rat gut microbiome composition is maintained following sleep restriction.

Zhang SL, Bai L, Goel N, Bailey A, Jang CJ, Bushman FD, Meerlo P, Dinges DF, Sehgal A.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1564-E1571. doi: 10.1073/pnas.1620673114. Epub 2017 Feb 8.

27.

Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors.

Chehoud C, Stieh DJ, Bailey AG, Laughlin AL, Allen SA, McCotter KL, Sherrill-Mix SA, Hope TJ, Bushman FD.

AIDS. 2017 Apr 24;31(7):895-904. doi: 10.1097/QAD.0000000000001421.

28.

Miniaturized devices for point of care molecular detection of HIV.

Mauk M, Song J, Bau HH, Gross R, Bushman FD, Collman RG, Liu C.

Lab Chip. 2017 Jan 31;17(3):382-394. doi: 10.1039/c6lc01239f. Review.

29.

Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase.

Gupta K, Turkki V, Sherrill-Mix S, Hwang Y, Eilers G, Taylor L, McDanal C, Wang P, Temelkoff D, Nolte RT, Velthuisen E, Jeffrey J, Van Duyne GD, Bushman FD.

PLoS Biol. 2016 Dec 9;14(12):e1002584. doi: 10.1371/journal.pbio.1002584. eCollection 2016 Dec.

30.

The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction.

Abbas AA, Diamond JM, Chehoud C, Chang B, Kotzin JJ, Young JC, Imai I, Haas AR, Cantu E, Lederer DJ, Meyer KC, Milewski RK, Olthoff KM, Shaked A, Christie JD, Bushman FD, Collman RG.

Am J Transplant. 2017 May;17(5):1313-1324. doi: 10.1111/ajt.14076. Epub 2016 Nov 4.

31.

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota.

Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, Leite R, Elovitz MA, Parry S, Bushman FD.

Microbiome. 2016 Jun 23;4(1):29. doi: 10.1186/s40168-016-0172-3.

32.

Modeling altered T-cell development with induced pluripotent stem cells from patients with RAG1-dependent immune deficiencies.

Brauer PM, Pessach IM, Clarke E, Rowe JH, Ott de Bruin L, Lee YN, Dominguez-Brauer C, Comeau AM, Awong G, Felgentreff K, Zhang YH, Bredemeyer A, Al-Herz W, Du L, Ververs F, Kennedy M, Giliani S, Keller G, Sleckman BP, Schatz DG, Bushman FD, Notarangelo LD, Zúñiga-Pflücker JC.

Blood. 2016 Aug 11;128(6):783-93. doi: 10.1182/blood-2015-10-676304. Epub 2016 Jun 14.

33.

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium.

Shen TC, Chehoud C, Ni J, Hsu E, Chen YY, Bailey A, Laughlin A, Bittinger K, Bushman FD, Wu GD.

PLoS One. 2016 May 13;11(5):e0155620. doi: 10.1371/journal.pone.0155620. eCollection 2016.

34.

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation.

Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD.

MBio. 2016 Mar 29;7(2):e00322. doi: 10.1128/mBio.00322-16.

35.

Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria.

Sundararaman SA, Plenderleith LJ, Liu W, Loy DE, Learn GH, Li Y, Shaw KS, Ayouba A, Peeters M, Speede S, Shaw GM, Bushman FD, Brisson D, Rayner JC, Sharp PM, Hahn BH.

Nat Commun. 2016 Mar 22;7:11078. doi: 10.1038/ncomms11078.

36.

Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis.

Hergott CB, Roche AM, Tamashiro E, Clarke TB, Bailey AG, Laughlin A, Bushman FD, Weiser JN.

Blood. 2016 May 19;127(20):2460-71. doi: 10.1182/blood-2015-10-675173. Epub 2016 Mar 17.

37.

The Competitive Interplay between Allosteric HIV-1 Integrase Inhibitor BI/D and LEDGF/p75 during the Early Stage of HIV-1 Replication Adversely Affects Inhibitor Potency.

Feng L, Dharmarajan V, Serrao E, Hoyte A, Larue RC, Slaughter A, Sharma A, Plumb MR, Kessl JJ, Fuchs JR, Bushman FD, Engelman AN, Griffin PR, Kvaratskhelia M.

ACS Chem Biol. 2016 May 20;11(5):1313-21. doi: 10.1021/acschembio.6b00167. Epub 2016 Mar 2.

38.

Composition and dynamics of the respiratory tract microbiome in intubated patients.

Kelly BJ, Imai I, Bittinger K, Laughlin A, Fuchs BD, Bushman FD, Collman RG.

Microbiome. 2016 Feb 11;4:7. doi: 10.1186/s40168-016-0151-8.

39.

Bidirectional interactions between indomethacin and the murine intestinal microbiota.

Liang X, Bittinger K, Li X, Abernethy DR, Bushman FD, FitzGerald GA.

Elife. 2015 Dec 23;4:e08973. doi: 10.7554/eLife.08973.

40.

Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees.

Barbian HJ, Li Y, Ramirez M, Klase Z, Lipende I, Mjungu D, Moeller AH, Wilson ML, Pusey AE, Lonsdorf EV, Bushman FD, Hahn BH.

Am J Primatol. 2018 Jan;80(1). doi: 10.1002/ajp.22515. Epub 2015 Dec 16.

41.

The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome.

Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA.

MBio. 2015 Oct 20;6(5):e01578-15. doi: 10.1128/mBio.01578-15.

42.

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease.

Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD.

Cell Host Microbe. 2015 Oct 14;18(4):489-500. doi: 10.1016/j.chom.2015.09.008. Erratum in: Cell Host Microbe. 2017 Aug 9;22(2):247.

43.

Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats.

Sherrill-Mix S, Ocwieja KE, Bushman FD.

Retrovirology. 2015 Sep 17;12:79. doi: 10.1186/s12977-015-0205-1.

44.

BIRC2/cIAP1 Is a Negative Regulator of HIV-1 Transcription and Can Be Targeted by Smac Mimetics to Promote Reversal of Viral Latency.

Pache L, Dutra MS, Spivak AM, Marlett JM, Murry JP, Hwang Y, Maestre AM, Manganaro L, Vamos M, Teriete P, Martins LJ, König R, Simon V, Bosque A, Fernandez-Sesma A, Cosford ND, Bushman FD, Young JA, Planelles V, Chanda SK.

Cell Host Microbe. 2015 Sep 9;18(3):345-53. doi: 10.1016/j.chom.2015.08.009.

45.

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts.

Kelsen J, Bittinger K, Pauly-Hubbard H, Posivak L, Grunberg S, Baldassano R, Lewis JD, Wu GD, Bushman FD.

Inflamm Bowel Dis. 2015 Dec;21(12):2797-805. doi: 10.1097/MIB.0000000000000557.

46.

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.

47.

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock.

Liang X, Bushman FD, FitzGerald GA.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10479-84. doi: 10.1073/pnas.1501305112. Epub 2015 Aug 3.

48.

Host Factors in Retroviral Integration and the Selection of Integration Target Sites.

Craigie R, Bushman FD.

Microbiol Spectr. 2014 Dec;2(6). doi: 10.1128/microbiolspec.MDNA3-0026-2014. Review.

49.

Engineering the gut microbiota to treat hyperammonemia.

Shen TC, Albenberg L, Bittinger K, Chehoud C, Chen YY, Judge CA, Chau L, Ni J, Sheng M, Lin A, Wilkins BJ, Buza EL, Lewis JD, Daikhin Y, Nissim I, Yudkoff M, Bushman FD, Wu GD.

J Clin Invest. 2015 Jul 1;125(7):2841-50. doi: 10.1172/JCI79214. Epub 2015 Jun 22.

50.

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.

Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD.

Inflamm Bowel Dis. 2015 Aug;21(8):1948-56. doi: 10.1097/MIB.0000000000000454.

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