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Items: 1 to 50 of 268

1.

Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents.

McGinniss JE, Imai I, Simon-Soro A, Brown MC, Knecht VR, Frye L, Ravindran PM, Dothard MI, Wadell DA, Sohn MB, Li H, Christie JD, Diamond JM, Haas AR, Lanfranco AR, DiBardino DM, Bushman FD, Collman RG.

PLoS One. 2019 May 29;14(5):e0217306. doi: 10.1371/journal.pone.0217306. eCollection 2019.

2.

Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness.

Abbas AA, Taylor LJ, Dothard MI, Leiby JS, Fitzgerald AS, Khatib LA, Collman RG, Bushman FD.

Cell Host Microbe. 2019 May 8;25(5):719-729.e4. doi: 10.1016/j.chom.2019.04.001.

PMID:
31071295
3.

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.

Clarke EL, Taylor LJ, Zhao C, Connell A, Lee JJ, Fett B, Bushman FD, Bittinger K.

Microbiome. 2019 Mar 22;7(1):46. doi: 10.1186/s40168-019-0658-x.

4.

Gene therapy targeting haematopoietic stem cells for inherited diseases: progress and challenges.

Cavazzana M, Bushman FD, Miccio A, André-Schmutz I, Six E.

Nat Rev Drug Discov. 2019 Jun;18(6):447-462. doi: 10.1038/s41573-019-0020-9. Review.

PMID:
30858502
5.

De-Discovery of the Placenta Microbiome.

Bushman FD.

Am J Obstet Gynecol. 2019 Mar;220(3):213-214. doi: 10.1016/j.ajog.2018.11.1093. No abstract available.

PMID:
30832983
6.

A quantitative approach for measuring the reservoir of latent HIV-1 proviruses.

Bruner KM, Wang Z, Simonetti FR, Bender AM, Kwon KJ, Sengupta S, Fray EJ, Beg SA, Antar AAR, Jenike KM, Bertagnolli LN, Capoferri AA, Kufera JT, Timmons A, Nobles C, Gregg J, Wada N, Ho YC, Zhang H, Margolick JB, Blankson JN, Deeks SG, Bushman FD, Siliciano JD, Laird GM, Siliciano RF.

Nature. 2019 Feb;566(7742):120-125. doi: 10.1038/s41586-019-0898-8. Epub 2019 Jan 30.

PMID:
30700913
7.

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana.

Hansen MEB, Rubel MA, Bailey AG, Ranciaro A, Thompson SR, Campbell MC, Beggs W, Dave JR, Mokone GG, Mpoloka SW, Nyambo T, Abnet C, Chanock SJ, Bushman FD, Tishkoff SA.

Genome Biol. 2019 Jan 22;20(1):16. doi: 10.1186/s13059-018-1616-9.

8.

iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity.

Nobles CL, Reddy S, Salas-McKee J, Liu X, June CH, Melenhorst JJ, Davis MM, Zhao Y, Bushman FD.

Genome Biol. 2019 Jan 17;20(1):14. doi: 10.1186/s13059-019-1625-3.

9.

Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit.

Knecht VR, McGinniss JE, Shankar HM, Clarke EL, Kelly BJ, Imai I, Fitzgerald AS, Bittinger K, Bushman FD, Collman RG.

Infect Control Hosp Epidemiol. 2018 Dec 18:1-7. doi: 10.1017/ice.2018.319. [Epub ahead of print]

PMID:
30560753
10.

Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.

Leiby JS, McCormick K, Sherrill-Mix S, Clarke EL, Kessler LR, Taylor LJ, Hofstaedter CE, Roche AM, Mattei LM, Bittinger K, Elovitz MA, Leite R, Parry S, Bushman FD.

Microbiome. 2018 Oct 30;6(1):196. doi: 10.1186/s40168-018-0575-4.

11.

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase.

Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM.

Nat Biotechnol. 2018 Oct 8. doi: 10.1038/nbt.4204. [Epub ahead of print]

12.

Induction of resistance to chimeric antigen receptor T cell therapy by transduction of a single leukemic B cell.

Ruella M, Xu J, Barrett DM, Fraietta JA, Reich TJ, Ambrose DE, Klichinsky M, Shestova O, Patel PR, Kulikovskaya I, Nazimuddin F, Bhoj VG, Orlando EJ, Fry TJ, Bitter H, Maude SL, Levine BL, Nobles CL, Bushman FD, Young RM, Scholler J, Gill SI, June CH, Grupp SA, Lacey SF, Melenhorst JJ.

Nat Med. 2018 Oct;24(10):1499-1503. doi: 10.1038/s41591-018-0201-9. Epub 2018 Oct 1.

13.

T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency.

Clarke EL, Connell AJ, Six E, Kadry NA, Abbas AA, Hwang Y, Everett JK, Hofstaedter CE, Marsh R, Armant M, Kelsen J, Notarangelo LD, Collman RG, Hacein-Bey-Abina S, Kohn DB, Cavazzana M, Fischer A, Williams DA, Pai SY, Bushman FD.

Genome Med. 2018 Sep 28;10(1):70. doi: 10.1186/s13073-018-0580-z.

14.

Long-term remission despite clonal expansion of replication-competent HIV-1 isolates.

Veenhuis RT, Kwaa AK, Garliss CC, Latanich R, Salgado M, Pohlmeyer CW, Nobles CL, Gregg J, Scully EP, Bailey JR, Bushman FD, Blankson JN.

JCI Insight. 2018 Sep 20;3(18). pii: 122795. doi: 10.1172/jci.insight.122795. eCollection 2018 Sep 20.

15.

Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation.

Abbas AA, Young JC, Clarke EL, Diamond JM, Imai I, Haas AR, Cantu E, Lederer DJ, Meyer K, Milewski RK, Olthoff KM, Shaked A, Christie JD, Bushman FD, Collman RG.

Am J Transplant. 2019 Apr;19(4):1086-1097. doi: 10.1111/ajt.15116. Epub 2018 Oct 8.

PMID:
30203917
16.

Sera from Individuals with Narrowly Focused Influenza Virus Antibodies Rapidly Select Viral Escape Mutations In Ovo.

Davis AKF, McCormick K, Gumina ME, Petrie JG, Martin ET, Xue KS, Bloom JD, Monto AS, Bushman FD, Hensley SE.

J Virol. 2018 Sep 12;92(19). pii: e00859-18. doi: 10.1128/JVI.00859-18. Print 2018 Oct 1.

17.

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 Jul 2;128(7):3102-3115. doi: 10.1172/JCI120194. Epub 2018 Jun 18.

18.

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.

19.

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.

20.

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.

21.

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
22.

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. eCollection 2018 Feb 22.

23.

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
24.

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.

25.

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;:.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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