Frederic D. Bushman - Publications

Genomics and Computational Biology University of Pennsylvania, Philadelphia, PA, United States 
Bioinformatics, Molecular Biology, Immunology

270 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD, et al. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host & Microbe. PMID 33440171 DOI: 10.1016/j.chom.2020.12.012  0.36
2020 Abbas A, Taylor LJ, Collman RG, Bushman FD, Ictv Report Consortium. ICTV Virus Taxonomy Profile: . The Journal of General Virology. PMID 33258767 DOI: 10.1099/jgv.0.001526  0.36
2020 Gu CH, Zhao C, Hofstaedter C, Tebas P, Glaser L, Baldassano R, Bittinger K, Mattei LM, Bushman FD. Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly. Plos One. 15: e0236533. PMID 33166284 DOI: 10.1371/journal.pone.0236533  0.36
2020 Smith SA, Ogawa SA, Chau L, Whelan KA, Hamilton KE, Chen J, Tan L, Chen EZ, Keilbaugh S, Fogt F, Bewtra M, Braun J, Xavier RJ, Clish CB, Slaff B, ... ... Bushman FD, et al. Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines. The Journal of Clinical Investigation. PMID 33141762 DOI: 10.1172/JCI133371  0.36
2020 Schrijvers R, Rijck J, Demeulemeester J, Adachi N, Vets S, Ronen K, Christ F, Bushman FD, Debyser Z, Gijsbers R. Correction: LEDGF/p75-Independent HIV-1 Replication Demonstrates a Role for HRP-2 and Remains Sensitive to Inhibition by LEDGINs. Plos Pathogens. 16: e1008894. PMID 32870932 DOI: 10.1371/journal.ppat.1008894  0.4
2020 Eilers G, Gupta K, Allen A, Zhou J, Hwang Y, Cory MB, Bushman FD, Van Duyne G. Influence of the amino-terminal sequence on the structure and function of HIV integrase. Retrovirology. 17: 28. PMID 32867805 DOI: 10.1186/s12977-020-00537-x  0.52
2020 Bushman FD, Conrad M, Ren Y, Zhao C, Gu C, Petucci C, Kim MS, Abbas A, Downes KJ, Devas N, Mattei LM, Breton J, Kelsen J, Marakos S, Galgano A, et al. Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease. Cell Host & Microbe. PMID 32822584 DOI: 10.1016/j.chom.2020.07.020  0.36
2020 Sherrill-Mix S, Connors K, Aldrovandi GM, Brenchley J, Boucher C, Bushman F, Collman R, Dandekar S, Klatt NR, Lagenaur LA, Paredes R, Tachedjian G, Turpin JA, Landay A, Ghosh M. A summary of the fifth annual Virology Education HIV Microbiome workshop. Aids Research and Human Retroviruses. PMID 32777940 DOI: 10.1089/AID.2020.0121  0.4
2020 Liang G, Zhao C, Zhang H, Mattei L, Sherrill-Mix S, Bittinger K, Kessler LR, Wu GD, Baldassano RN, DeRusso P, Ford E, Elovitz MA, Kelly MS, Patel MZ, Mazhani T, ... ... Bushman FD, et al. The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature. 581: 470-474. PMID 32461640 DOI: 10.1038/s41586-020-2192-1  0.4
2020 Rubel MA, Abbas A, Taylor LJ, Connell A, Tanes C, Bittinger K, Ndze VN, Fonsah JY, Ngwang E, Essiane A, Fokunang C, Njamnshi AK, Bushman FD, Tishkoff SA. Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. Genome Biology. 21: 122. PMID 32450885 DOI: 10.1186/s13059-020-02020-4  0.36
2020 Liang G, Conrad MA, Kelsen JR, Kessler LR, Breton J, Albenberg LG, Marakos S, Galgano A, Devas N, Erlichman J, Zhang H, Mattei L, Bittinger K, Baldassano RN, Bushman FD. The dynamics of the stool virome in very early onset inflammatory bowel disease. Journal of Crohn's & Colitis. PMID 32406906 DOI: 10.1093/ecco-jcc/jjaa094  0.36
2020 Liu R, Yeh YJ, Varabyou A, Collora JA, Sherrill-Mix S, Talbot CC, Mehta S, Albrecht K, Hao H, Zhang H, Pollack RA, Beg SA, Calvi RM, Hu J, Durand CM, ... ... Bushman FD, et al. Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target. Science Translational Medicine. 12. PMID 32404504 DOI: 10.1126/scitranslmed.aaz0802  0.4
2020 Bittinger K, Zhao C, Li Y, Ford E, Friedman ES, Ni J, Kulkarni CV, Cai J, Tian Y, Liu Q, Patterson AD, Sarkar D, Chan SHJ, Maranas C, Saha-Shah A, ... ... Bushman FD, et al. Bacterial colonization reprograms the neonatal gut metabolome. Nature Microbiology. PMID 32284564 DOI: 10.1038/s41564-020-0694-0  0.36
2020 Taylor LJ, Abbas A, Bushman FD. grabseqs: Simple downloading of reads and metadata from multiple next-generation sequencing data repositories. Bioinformatics (Oxford, England). PMID 32154830 DOI: 10.1093/bioinformatics/btaa167  0.32
2020 Giron LB, Tanes CE, Schleimann MH, Engen PA, Mattei LM, Anzurez A, Damra M, Zhang H, Bittinger K, Bushman F, Kossenkov A, Denton PW, Tateno H, Keshavarzian A, Landay AL, et al. Sialylation and fucosylation modulate inflammasome-activating eIF2 Signaling and microbial translocation during HIV infection. Mucosal Immunology. PMID 32152415 DOI: 10.1038/s41385-020-0279-5  0.36
2019 Nobles CL, Sherrill-Mix S, Everett JK, Reddy S, Fraietta JA, Porter DL, Frey N, Gill SI, Grupp SA, Maude SL, Siegel DL, Levine BL, June CH, Lacey SF, Melenhorst JJ, ... Bushman FD, et al. CD19-targeting CAR T cell immunotherapy outcomes correlate with genomic modification by vector integration. The Journal of Clinical Investigation. PMID 31845905 DOI: 10.1172/JCI130144  0.4
2019 Uribe-Herranz M, Rafail S, Beghi S, Gil-de-Gómez L, Verginadis I, Bittinger K, Pustylnikov S, Pierini S, Perales-Linares R, Blair IA, Mesaros CA, Snyder NW, Bushman F, Koumenis C, Facciabene A. Gut microbiota modulate dendritic cell antigen presentation and radiotherapy-induced antitumor immune response. The Journal of Clinical Investigation. PMID 31815742 DOI: 10.1172/JCI124332  0.36
2019 Abbas AA, Taylor LJ, Dothard MI, Leiby JS, Fitzgerald AS, Khatib LA, Collman RG, Bushman FD. Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness. Cell Host & Microbe. 26: 297. PMID 31415757 DOI: 10.1016/j.chom.2019.07.015  0.36
2019 Simon-Soro A, Sohn MB, McGinniss JE, Imai I, Brown MC, Knecht VR, Bailey A, Clarke EL, Cantu E, Li H, Bittinger K, Diamond JM, Christie JD, Bushman FD, Collman RG. Upper Respiratory Dysbiosis with a Facultative-Dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant. Annals of the American Thoracic Society. PMID 31415219 DOI: 10.1513/AnnalsATS.201904-299OC  0.36
2019 Bushman FD, McCormick K, Sherrill-Mix S. Virus structures constrain transmission modes. Nature Microbiology. PMID 31358983 DOI: 10.1038/s41564-019-0523-5  0.4
2019 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, ... ... Bushman FD, et al. Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents. Plos One. 14: e0217306. PMID 31141557 DOI: 10.1371/journal.pone.0217306  0.36
2019 Abbas AA, Taylor LJ, Dothard MI, Leiby JS, Fitzgerald AS, Khatib LA, Collman RG, Bushman FD. Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness. Cell Host & Microbe. 25: 719-729.e4. PMID 31071295 DOI: 10.1016/j.chom.2019.04.001  0.36
2019 Clarke EL, Taylor LJ, Zhao C, Connell A, Lee JJ, Fett B, Bushman FD, Bittinger K. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. Microbiome. 7: 46. PMID 30902113 DOI: 10.1186/s40168-019-0658-x  0.36
2018 Knecht VR, McGinniss JE, Shankar HM, Clarke EL, Kelly BJ, Imai I, Fitzgerald AS, Bittinger K, Bushman FD, Collman RG. Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit. Infection Control and Hospital Epidemiology. 1-7. PMID 30560753 DOI: 10.1017/ice.2018.319  0.36
2018 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. Lack of detection of a human placenta microbiome in samples from preterm and term deliveries. Microbiome. 6: 196. PMID 30376898 DOI: 10.1186/s40168-018-0575-4  0.4
2018 Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nature Biotechnology. PMID 30295673 DOI: 10.1038/nbt.4204  0.52
2018 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, ... ... Bushman FD, et al. T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency. Genome Medicine. 10: 70. PMID 30261899 DOI: 10.1186/s13073-018-0580-z  0.52
2018 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. Bidirectional transfer of anelloviridae lineages between graft and host during lung transplantation. American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons. PMID 30203917 DOI: 10.1111/ajt.15116  0.36
2018 Williams B, Boucher C, Bushman F, Carrington-Lawrence S, Collman RG, Dandekar S, Dang Q, Malaspina A, Paredes R, Wilson C, Nowak P, Klatt N, Lagenaur L, Landay A. A summary of the third annual HIV microbiome workshop. Aids Research and Human Retroviruses. PMID 30105916 DOI: 10.1089/AID.2018.0103  0.36
2018 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, et al. HIV-1 latent reservoir size and diversity are stable following brief treatment interruption. The Journal of Clinical Investigation. PMID 29911997 DOI: 10.1172/JCI120194  0.4
2018 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, ... ... Bushman FD, et al. Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells. Nature. PMID 29849141 DOI: 10.1038/s41586-018-0178-z  0.52
2018 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. Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques () and linked microbial community correlates. Peerj. 6: e4612. PMID 29666764 DOI: 10.7717/peerj.4612  0.36
2018 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, ... ... Bushman FD, et al. Allometry and Ecology of the Bilaterian Gut Microbiome. Mbio. 9. PMID 29588401 DOI: 10.1128/mBio.00319-18  0.4
2018 Kadimisetty K, Song J, Doto AM, Hwang Y, Peng J, Mauk MG, Bushman FD, Gross R, Jarvis JN, Liu C. Fully 3D printed integrated reactor array for point-of-care molecular diagnostics. Biosensors & Bioelectronics. 109: 156-163. PMID 29550739 DOI: 10.1016/j.bios.2018.03.009  0.52
2018 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. Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. Jci Insight. 3. PMID 29467322 DOI: 10.1172/jci.insight.94952  0.36
2018 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, et al. Publisher Correction: Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. PMID 29440750 DOI: 10.1038/s41564-018-0114-x  0.36
2018 Gijsbers R, Vets S, De Rijck J, Ocwieja KE, Ronen K, Malani N, Bushman FD, Debyser Z. Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting. The Journal of Biological Chemistry. 293: 114. PMID 29305523 DOI: 10.1074/jbc.W117.001458  0.52
2018 Costea PI, Hildebrand F, Manimozhiyan A, 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, et al. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. 3: 8-16. PMID 29255284 DOI: 10.1038/s41564-017-0072-8  0.36
2017 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, et al. A Pilot Characterization of the Human Chronobiome. Scientific Reports. 7: 17141. PMID 29215023 DOI: 10.1038/s41598-017-17362-6  0.36
2017 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, ... ... Bushman FD, et al. A role for bacterial urease in gut dysbiosis and Crohn's disease. Science Translational Medicine. 9. PMID 29141885 DOI: 10.1126/scitranslmed.aah6888  0.36
2017 Williams B, Ghosh M, Boucher CAB, Bushman F, Carrington-Lawrence S, Collman RG, Dandekar S, Dang Q, Malaspina A, Paredes R, Wilson C, Nowak P, Klatt N, Lagenaur L, Landay A. A summary of the second annual HIV Microbiome workshop. Aids Research and Human Retroviruses. PMID 28899105 DOI: 10.1089/AID.2017.0137  0.36
2017 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, et al. Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples. American Journal of Respiratory and Critical Care Medicine. PMID 28846439 DOI: 10.1164/rccm.201705-0891OC  0.52
2017 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, ... ... Bushman FD, et al. Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Cell Host & Microbe. 22: 247. PMID 28799909 DOI: 10.1016/j.chom.2017.07.011  0.36
2017 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. Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome. Jama Pediatrics. PMID 28492938 DOI: 10.1001/jamapediatrics.2017.0378  0.36
2017 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. Optimizing methods and dodging pitfalls in microbiome research. Microbiome. 5: 52. PMID 28476139 DOI: 10.1186/s40168-017-0267-5  0.4
2017 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, ... ... Bushman FD, et al. INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes. Molecular Therapy. Methods & Clinical Development. 4: 39-49. PMID 28344990 DOI: 10.1016/j.omtm.2016.11.002  0.4
2017 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, ... ... Bushman FD, et al. INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions. Molecular Therapy. Methods & Clinical Development. 4: 17-26. PMID 28344988 DOI: 10.1016/j.omtm.2016.11.003  0.4
2017 Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D. swga: A primer design toolkit for selective whole genome amplification. Bioinformatics (Oxford, England). PMID 28334194 DOI: 10.1093/bioinformatics/btx118  0.32
2017 Mauk M, Song J, Bau HH, Gross R, Bushman FD, Collman RG, Liu C. Miniaturized devices for point of care molecular detection of HIV. Lab On a Chip. PMID 28092381 DOI: 10.1039/c6lc01239f  0.36
2016 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. Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase. Plos Biology. 14: e1002584. PMID 27935939 DOI: 10.1371/journal.pbio.1002584  0.52
2016 Abbas AA, Diamond JM, Chehoud C, Chang B, Kotzin JJ, Young JC, Imai I, Haas AR, Cantu E, Lederer DJ, Meyer K, Milewski RK, Olthoff KM, Shaked A, Christie JD, ... Bushman FD, et al. The Perioperative Lung Transplant Virome: Torque Teno Viruses are Elevated in Donor Lungs and Show Divergent Dynamics In Primary Graft Dysfunction. American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons. PMID 27731934 DOI: 10.1111/ajt.14076  0.36
2016 Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, Leite R, Elovitz MA, Parry S, Bushman FD. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome. 4: 29. PMID 27338728 DOI: 10.1186/s40168-016-0172-3  0.4
2016 Williams B, Mirmonsef P, Boucher CA, Bushman F, Carrington-Lawrence S, Collman RG, Dandekar S, Dang Q, Malaspina A, Paredes R, Stone A, Landay A. A Summary of The First HIV Microbiome Workshop 2015. Aids Research and Human Retroviruses. PMID 27267576 DOI: 10.1089/AID.2016.0034  0.36
2016 Shen TD, Chehoud C, Ni J, Hsu E, Chen YY, Bailey A, Laughlin A, Bittinger K, Bushman FD, Wu GD. Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium. Plos One. 11: e0155620. PMID 27176607 DOI: 10.1371/journal.pone.0155620  0.36
2016 Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD. Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. Mbio. 7. PMID 27025251 DOI: 10.1128/mBio.00322-16  1
2016 Li H, Hwang Y, Perry K, Bushman F, Van Duyne GD. Structure and metal-binding properties of a poxvirus resolvase. The Journal of Biological Chemistry. PMID 27013661 DOI: 10.1074/jbc.M115.709139  1
2016 Kelly BJ, Imai I, Bittinger K, Laughlin A, Fuchs BD, Bushman FD, Collman RG. Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome. 4: 7. PMID 26865050 DOI: 10.1186/s40168-016-0151-8  0.36
2015 Liang X, Bittinger K, Li X, Abernethy DR, Bushman FD, FitzGerald GA. Bidirectional interactions between indomethacin and the murine intestinal microbiota. Elife. 4: e08973. PMID 26701907 DOI: 10.7554/eLife.08973  0.36
2015 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, ... ... Bushman FD, et al. Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Cell Host & Microbe. 18: 489-500. PMID 26468751 DOI: 10.1016/j.chom.2015.09.008  1
2015 Sherrill-Mix S, Ocwieja KE, Bushman FD. Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. Retrovirology. 12: 79. PMID 26377088 DOI: 10.1186/s12977-015-0205-1  1
2015 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, ... ... Bushman FD, et al. BIRC2/cIAP1 Is a Negative Regulator of HIV-1 Transcription and Can Be Targeted by Smac Mimetics to Promote Reversal of Viral Latency. Cell Host & Microbe. 18: 345-53. PMID 26355217 DOI: 10.1016/j.chom.2015.08.009  0.52
2015 Kelsen J, Bittinger K, Pauly-Hubbard H, Posivak L, Grunberg S, Baldassano R, Lewis JD, Wu GD, Bushman FD. Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts. Inflammatory Bowel Diseases. PMID 26288001 DOI: 10.1097/MIB.0000000000000557  1
2015 Beck JM, Schloss PD, Venkataraman A, Twigg H, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, et al. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. American Journal of Respiratory and Critical Care Medicine. 192: 1335-44. PMID 26247840 DOI: 10.1164/rccm.201501-0128OC  0.36
2015 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, ... ... Bushman FD, et al. Engineering the gut microbiota to treat hyperammonemia. The Journal of Clinical Investigation. 125: 2841-50. PMID 26098218 DOI: 10.1172/JCI79214  1
2015 Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD. Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Inflammatory Bowel Diseases. 21: 1948-56. PMID 26083617 DOI: 10.1097/MIB.0000000000000454  0.36
2015 Bryson AL, Hwang Y, Sherrill-Mix S, Wu GD, Lewis JD, Black L, Clark TA, Bushman FD. Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. Mbio. 6. PMID 26081634 DOI: 10.1128/mBio.00648-15  1
2015 Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Compher C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu GD, Lewis JD. Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. Inflammatory Bowel Diseases. 21: 1786-93. PMID 25970545 DOI: 10.1097/MIB.0000000000000426  0.36
2015 Aiyer S, Rossi P, Malani N, Schneider WM, Chandar A, Bushman FD, Montelione GT, Roth MJ. Structural and sequencing analysis of local target DNA recognition by MLV integrase. Nucleic Acids Research. 43: 5647-63. PMID 25969444 DOI: 10.1093/nar/gkv410  1
2015 Corrigan-Curay J, O'Reilly M, Kohn DB, Cannon PM, Bao G, Bushman FD, Carroll D, Cathomen T, Joung JK, Roth D, Sadelain M, Scharenberg AM, von Kalle C, Zhang F, Jambou R, et al. Genome editing technologies: defining a path to clinic. Molecular Therapy : the Journal of the American Society of Gene Therapy. 23: 796-806. PMID 25943494 DOI: 10.1038/mt.2015.54  1
2015 Hacein-Bey Abina S, Gaspar HB, Blondeau J, Caccavelli L, Charrier S, Buckland K, Picard C, Six E, Himoudi N, Gilmour K, McNicol AM, Hara H, Xu-Bayford J, Rivat C, Touzot F, ... ... Bushman FD, et al. Outcomes following gene therapy in patients with severe Wiskott-Aldrich syndrome. Jama. 313: 1550-63. PMID 25898053 DOI: 10.1001/jama.2015.3253  1
2015 Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics (Oxford, England). PMID 25819674 DOI: 10.1093/bioinformatics/btv183  0.4
2015 Ocwieja KE, Sherrill-Mix S, Liu C, Song J, Bau H, Bushman FD. A reverse transcription loop-mediated isothermal amplification assay optimized to detect multiple HIV subtypes. Plos One. 10: e0117852. PMID 25675344 DOI: 10.1371/journal.pone.0117852  1
2015 Young JC, Chehoud C, Bittinger K, Bailey A, Diamond JM, Cantu E, Haas AR, Abbas A, Frye L, Christie JD, Bushman FD, Collman RG. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 15: 200-9. PMID 25403800 DOI: 10.1111/ajt.13031  1
2015 Bushman M, Zimmerman L, Bushman F. HIV Replication in LEGO Mosaic Aids Research and Human Retroviruses. 31: 772-773. DOI: 10.1089/aid.2015.0007  1
2014 Craigie R, Bushman FD. Host Factors in Retroviral Integration and the Selection of Integration Target Sites. Microbiology Spectrum. 2. PMID 26104434 DOI: 10.1128/microbiolspec.MDNA3-0026-2014  1
2014 Liu C, Sadik MM, Mauk MG, Edelstein PH, Bushman FD, Gross R, Bau HH. Nuclemeter: a reaction-diffusion based method for quantifying nucleic acids undergoing enzymatic amplification. Scientific Reports. 4: 7335. PMID 25477046 DOI: 10.1038/srep07335  1
2014 Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie AM, Flint HJ, Metz DC, Bennett MJ, ... ... Bushman FD, et al. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut. PMID 25431456 DOI: 10.1136/gutjnl-2014-308209  1
2014 Bittinger K, Charlson ES, Loy E, Shirley DJ, Haas AR, Laughlin A, Yi Y, Wu GD, Lewis JD, Frank I, Cantu E, Diamond JM, Christie JD, Collman RG, Bushman FD. Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome Biology. 15: 487. PMID 25344286 DOI: 10.1186/s13059-014-0487-y  0.36
2014 Hacein-Bey-Abina S, Pai SY, Gaspar HB, Armant M, Berry CC, Blanche S, Bleesing J, Blondeau J, de Boer H, Buckland KF, Caccavelli L, Cros G, De Oliveira S, Fernández KS, Guo D, ... ... Bushman FD, et al. A modified γ-retrovirus vector for X-linked severe combined immunodeficiency. The New England Journal of Medicine. 371: 1407-17. PMID 25295500 DOI: 10.1056/NEJMoa1404588  0.4
2014 Osborne LC, Monticelli LA, Nice TJ, Sutherland TE, Siracusa MC, Hepworth MR, Tomov VT, Kobuley D, Tran SV, Bittinger K, Bailey AG, Laughlin AL, Boucher JL, Wherry EJ, Bushman FD, et al. Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation. Science (New York, N.Y.). 345: 578-82. PMID 25082704 DOI: 10.1126/science.1256942  1
2014 Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, Thom SR, Bushman FD, Vinogradov SA, Wu GD. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology. 147: 1055-63.e8. PMID 25046162 DOI: 10.1053/j.gastro.2014.07.020  1
2014 Margolis D, Bushman F. Persistence by proliferation? Science. 345: 143-144. PMID 25013050 DOI: 10.1126/science.1257426  1
2014 Gupta K, Brady T, Dyer BM, Malani N, Hwang Y, Male F, Nolte RT, Wang L, Velthuisen E, Jeffrey J, Van Duyne GD, Bushman FD. Allosteric inhibition of human immunodeficiency virus integrase: late block during viral replication and abnormal multimerization involving specific protein domains. The Journal of Biological Chemistry. 289: 20477-88. PMID 24904063 DOI: 10.1074/jbc.M114.551119  1
2014 Sharma A, Slaughter A, Jena N, Feng L, Kessl JJ, Fadel HJ, Malani N, Male F, Wu L, Poeschla E, Bushman FD, Fuchs JR, Kvaratskhelia M. A new class of multimerization selective inhibitors of HIV-1 integrase. Plos Pathogens. 10: e1004171. PMID 24874515 DOI: 10.1371/journal.ppat.1004171  1
2014 Bushman FD. Engineering the human genome: reflections on the beginning. Human Gene Therapy. 25: 395-400. PMID 24848314 DOI: 10.1089/hum.2014.2524  1
2014 Manganaro L, Pache L, Herrmann T, Marlett J, Hwang Y, Murry J, Miorin L, Ting AT, König R, García-Sastre A, Bushman FD, Chanda SK, Young JA, Fernandez-Sesma A, Simon V. Tumor suppressor cylindromatosis (CYLD) controls HIV transcription in an NF-κB-dependent manner. Journal of Virology. 88: 7528-40. PMID 24760882 DOI: 10.1128/JVI.00239-14  1
2014 Aiyer S, Swapna GV, Malani N, Aramini JM, Schneider WM, Plumb MR, Ghanem M, Larue RC, Sharma A, Studamire B, Kvaratskhelia M, Bushman FD, Montelione GT, Roth MJ. Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction. Nucleic Acids Research. 42: 5917-28. PMID 24623816 DOI: 10.1093/nar/gku175  1
2014 Larue RC, Plumb MR, Crowe BL, Shkriabai N, Sharma A, DiFiore J, Malani N, Aiyer SS, Roth MJ, Bushman FD, Foster MP, Kvaratskhelia M. Bimodal high-affinity association of Brd4 with murine leukemia virus integrase and mononucleosomes. Nucleic Acids Research. 42: 4868-81. PMID 24520112 DOI: 10.1093/nar/gku135  1
2014 Petersen J, Drake MJ, Bruce EA, Riblett AM, Didigu CA, Wilen CB, Malani N, Male F, Lee FH, Bushman FD, Cherry S, Doms RW, Bates P, Briley K. The major cellular sterol regulatory pathway is required for Andes virus infection. Plos Pathogens. 10: e1003911. PMID 24516383 DOI: 10.1371/journal.ppat.1003911  1
2014 Berry CC, Ocwieja KE, Malani N, Bushman FD. Comparing DNA integration site clusters with scan statistics. Bioinformatics (Oxford, England). 30: 1493-500. PMID 24489369 DOI: 10.1093/bioinformatics/btu035  1
2014 Korn LL, Thomas HL, Hubbeling HG, Spencer SP, Sinha R, Simkins HM, Salzman NH, Bushman FD, Laufer TM. Conventional CD4+ T cells regulate IL-22-producing intestinal innate lymphoid cells. Mucosal Immunology. 7: 1045-57. PMID 24448096 DOI: 10.1038/mi.2013.121  1
2014 Wu GD, Bushman FD, Lewis JD. 'Corrigendum to "Diet, the human gut microbiota, and IBD" [Anaerobe 24, (2013, Dec) 117-20], 10.1016/j.anaerobe.2013.03.011. Anaerobe. 30: 181. DOI: 10.1016/j.anaerobe.2014.08.004  1
2014 Ravel J, Blaser MJ, Braun J, Brown E, Bushman FD, Chang EB, Davies J, Dewey KG, Dinan T, Dominguez-Bello M, Erdman SE, Finlay BB, Garrett WS, Huffnagle GB, Huttenhower C, et al. Human microbiome science: Vision for the future, Bethesda, MD, July 24 to 26, 2013 Microbiome. 2.  1
2013 Alenghat T, Osborne LC, Saenz SA, Kobuley D, Ziegler CG, Mullican SE, Choi I, Grunberg S, Sinha R, Wynosky-Dolfi M, Snyder A, Giacomin PR, Joyce KL, Hoang TB, Bewtra M, ... ... Bushman FD, et al. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature. 504: 153-7. PMID 24185009 DOI: 10.1038/nature12687  1
2013 De Rijck J, de Kogel C, Demeulemeester J, Vets S, El Ashkar S, Malani N, Bushman FD, Landuyt B, Husson SJ, Busschots K, Gijsbers R, Debyser Z. The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites. Cell Reports. 5: 886-94. PMID 24183673 DOI: 10.1016/j.celrep.2013.09.040  1
2013 Bushman FD, Lewis JD, Wu GD. Diet, gut enterotypes and health: is there a link? Nestlé Nutrition Institute Workshop Series. 77: 65-73. PMID 24107497 DOI: 10.1159/000351385  1
2013 Liu C, Mauk M, Gross R, Bushman FD, Edelstein PH, Collman RG, Bau HH. Membrane-based, sedimentation-assisted plasma separator for point-of-care applications. Analytical Chemistry. 85: 10463-70. PMID 24099566 DOI: 10.1021/ac402459h  1
2013 Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, Cuff C, Lewis JD, Wu GD, Bushman FD. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. Plos One. 8: e71806. PMID 23977147 DOI: 10.1371/journal.pone.0071806  1
2013 Sherrill-Mix S, Lewinski MK, Famiglietti M, Bosque A, Malani N, Ocwieja KE, Berry CC, Looney D, Shan L, Agosto LM, Pace MJ, Siliciano RF, O'Doherty U, Guatelli J, Planelles V, ... Bushman FD, et al. HIV latency and integration site placement in five cell-based models. Retrovirology. 10: 90. PMID 23953889 DOI: 10.1186/1742-4690-10-90  1
2013 Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD. Rapid evolution of the human gut virome. Proceedings of the National Academy of Sciences of the United States of America. 110: 12450-5. PMID 23836644 DOI: 10.1073/pnas.1300833110  1
2013 Sharma A, Larue RC, Plumb MR, Malani N, Male F, Slaughter A, Kessl JJ, Shkriabai N, Coward E, Aiyer SS, Green PL, Wu L, Roth MJ, Bushman FD, Kvaratskhelia M. BET proteins promote efficient murine leukemia virus integration at transcription start sites. Proceedings of the National Academy of Sciences of the United States of America. 110: 12036-41. PMID 23818621 DOI: 10.1073/pnas.1307157110  1
2013 Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. Plos One. 8: e66019. PMID 23799070 DOI: 10.1371/journal.pone.0066019  1
2013 Han D, Walsh MC, Cejas PJ, Dang NN, Kim YF, Kim J, Charrier-Hisamuddin L, Chau L, Zhang Q, Bittinger K, Bushman FD, Turka LA, Shen H, Reizis B, Defranco AL, et al. Dendritic cell expression of the signaling molecule TRAF6 is critical for gut microbiota-dependent immune tolerance. Immunity. 38: 1211-22. PMID 23791643 DOI: 10.1016/j.immuni.2013.05.012  0.36
2013 Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCray PB, Bushman FD, Sinn PL, Craig NL. piggyBac transposase tools for genome engineering. Proceedings of the National Academy of Sciences of the United States of America. 110: E2279-87. PMID 23723351 DOI: 10.1073/pnas.1305987110  1
2013 Bushman FD, Barton S, Bailey A, Greig C, Malani N, Bandyopadhyay S, Young J, Chanda S, Krogan N. Bringing it all together: big data and HIV research. Aids (London, England). 27: 835-8. PMID 23719353 DOI: 10.1097/QAD.0b013e32835cb785  1
2013 Hepworth MR, Monticelli LA, Fung TC, Ziegler CG, Grunberg S, Sinha R, Mantegazza AR, Ma HL, Crawford A, Angelosanto JM, Wherry EJ, Koni PA, Bushman FD, Elson CO, Eberl G, et al. Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature. 498: 113-7. PMID 23698371 DOI: 10.1038/nature12240  1
2013 Wojcechowskyj JA, Didigu CA, Lee JY, Parrish NF, Sinha R, Hahn BH, Bushman FD, Jensen ST, Seeholzer SH, Doms RW. Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry. Cell Host & Microbe. 13: 613-23. PMID 23684312 DOI: 10.1016/j.chom.2013.04.011  1
2013 Schneider WM, Brzezinski JD, Aiyer S, Malani N, Gyuricza M, Bushman FD, Roth MJ. Viral DNA tethering domains complement replication-defective mutations in the p12 protein of MuLV Gag. Proceedings of the National Academy of Sciences of the United States of America. 110: 9487-92. PMID 23661057 DOI: 10.1073/pnas.1221736110  1
2013 Zhong L, Malani N, Li M, Brady T, Xie J, Bell P, Li S, Jones H, Wilson JM, Flotte TR, Bushman FD, Gao G. Recombinant adeno-associated virus integration sites in murine liver after ornithine transcarbamylase gene correction. Human Gene Therapy. 24: 520-5. PMID 23621841 DOI: 10.1089/hum.2012.112  1
2013 Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, ... ... Bushman FD, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature Medicine. 19: 576-85. PMID 23563705 DOI: 10.1038/nm.3145  1
2013 Vets S, De Rijck J, Brendel C, Grez M, Bushman F, Debyser Z, Gijsbers R. Transient Expression of an LEDGF/p75 Chimera Retargets Lentivector Integration and Functionally Rescues in a Model for X-CGD. Molecular Therapy. Nucleic Acids. 2: e77. PMID 23462964 DOI: 10.1038/mtna.2013.4  1
2013 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, ... ... Bushman FD, et al. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. American Journal of Respiratory and Critical Care Medicine. 187: 1110-7. PMID 23392441 DOI: 10.1164/rccm.201211-2145OC  1
2013 Brady T, Kelly BJ, Male F, Roth S, Bailey A, Malani N, Gijsbers R, O'Doherty U, Bushman FD. Quantitation of HIV DNA integration: effects of differential integration site distributions on Alu-PCR assays. Journal of Virological Methods. 189: 53-7. PMID 23348058 DOI: 10.1016/j.jviromet.2013.01.004  1
2013 Tebas P, Stein D, Binder-Scholl G, Mukherjee R, Brady T, Rebello T, Humeau L, Kalos M, Papasavvas E, Montaner LJ, Schullery D, Shaheen F, Brennan AL, Zheng Z, Cotte J, ... ... Bushman FD, et al. Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV. Blood. 121: 1524-33. PMID 23264589 DOI: 10.1182/blood-2012-07-447250  1
2013 Li X, Ewis H, Hice RH, Malani N, Parker N, Zhou L, Feschotte C, Bushman FD, Atkinson PW, Craig NL. A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture. Proceedings of the National Academy of Sciences of the United States of America. 110: E478-87. PMID 23091042 DOI: 10.1073/pnas.1121543109  1
2013 Chen J, Bushman FD, Lewis JD, Wu GD, Li H. Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis. Biostatistics (Oxford, England). 14: 244-58. PMID 23074263 DOI: 10.1093/biostatistics/kxs038  1
2012 Woodard LE, Li X, Malani N, Kaja A, Hice RH, Atkinson PW, Bushman FD, Craig NL, Wilson MH. Comparative analysis of the recently discovered hAT transposon TcBuster in human cells. Plos One. 7: e42666. PMID 23166581 DOI: 10.1371/journal.pone.0042666  1
2012 Peterfreund GL, Vandivier LE, Sinha R, Marozsan AJ, Olson WC, Zhu J, Bushman FD. Succession in the Gut Microbiome following Antibiotic and Antibody Therapies for Clostridium difficile Plos One. 7. PMID 23071679 DOI: 10.1371/journal.pone.0046966  1
2012 Schrijvers R, Vets S, De Rijck J, Malani N, Bushman FD, Debyser Z, Gijsbers R. HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells. Retrovirology. 9: 84. PMID 23046603 DOI: 10.1186/1742-4690-9-84  1
2012 Gupta K, Curtis JE, Krueger S, Hwang Y, Cherepanov P, Bushman FD, Van Duyne GD. Solution conformations of prototype foamy virus integrase and its stable synaptic complex with U5 viral DNA. Structure (London, England : 1993). 20: 1918-28. PMID 23000384 DOI: 10.1016/j.str.2012.08.023  1
2012 Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. Plos One. 7: e42786. PMID 22970118 DOI: 10.1371/journal.pone.0042786  1
2012 Ocwieja KE, Sherrill-Mix S, Mukherjee R, Custers-Allen R, David P, Brown M, Wang S, Link DR, Olson J, Travers K, Schadt E, Bushman FD. Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing. Nucleic Acids Research. 40: 10345-55. PMID 22923523 DOI: 10.1093/nar/gks753  1
2012 Pace MJ, Graf EH, Agosto LM, Mexas AM, Male F, Brady T, Bushman FD, O'Doherty U. Directly infected resting CD4+T cells can produce HIV Gag without spreading infection in a model of HIV latency. Plos Pathogens. 8: e1002818. PMID 22911005 DOI: 10.1371/journal.ppat.1002818  1
2012 Minot S, Wu GD, Lewis JD, Bushman FD. Conservation of gene cassettes among diverse viruses of the human gut. Plos One. 7: e42342. PMID 22900013 DOI: 10.1371/journal.pone.0042342  1
2012 Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, Bushman FD, Collman RG. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. American Journal of Respiratory and Critical Care Medicine. 186: 536-45. PMID 22798321 DOI: 10.1164/rccm.201204-0693OC  1
2012 Craigie R, Bushman FD. HIV DNA integration. Cold Spring Harbor Perspectives in Medicine. 2: a006890. PMID 22762018 DOI: 10.1101/cshperspect.a006890  1
2012 Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biology. 13: R60. PMID 22759449 DOI: 10.1186/gb-2012-13-7-r60  1
2012 Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics (Oxford, England). 28: 2106-13. PMID 22711789 DOI: 10.1093/bioinformatics/bts342  1
2012 Sonnenberg GF, Monticelli LA, Alenghat T, Fung TC, Hutnick NA, Kunisawa J, Shibata N, Grunberg S, Sinha R, Zahm AM, Tardif MR, Sathaliyawala T, Kubota M, Farber DL, Collman RG, ... ... Bushman FD, et al. Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science (New York, N.Y.). 336: 1321-5. PMID 22674331 DOI: 10.1126/science.1222551  1
2012 Corrigan-Curay J, Cohen-Haguenauer O, O'Reilly M, Ross SR, Fan H, Rosenberg N, Somia N, King N, Friedmann T, Dunbar C, Aiuti A, Naldini L, Baum C, von Kalle C, Kiem HP, ... ... Bushman F, et al. Challenges in vector and trial design using retroviral vectors for long-term gene correction in hematopoietic stem cell gene therapy. Molecular Therapy : the Journal of the American Society of Gene Therapy. 20: 1084-94. PMID 22652996 DOI: 10.1038/mt.2012.93  1
2012 Culyba M, Hwang Y, Attar S, Madrid PB, Bupp J, Huryn D, Sanchez L, Grobler J, Miller MD, Bushman FD. Bulged DNA substrates for identifying poxvirus resolvase inhibitors. Nucleic Acids Research. 40: e124. PMID 22581770 DOI: 10.1093/nar/gks325  1
2012 Scholler J, Brady TL, Binder-Scholl G, Hwang WT, Plesa G, Hege KM, Vogel AN, Kalos M, Riley JL, Deeks SG, Mitsuyasu RT, Bernstein WB, Aronson NE, Levine BL, Bushman FD, et al. Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Science Translational Medicine. 4: 132ra53. PMID 22553251 DOI: 10.1126/scitranslmed.3003761  1
2012 Hill DA, Siracusa MC, Abt MC, Kim BS, Kobuley D, Kubo M, Kambayashi T, Larosa DF, Renner ED, Orange JS, Bushman FD, Artis D. Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Nature Medicine. 18: 538-46. PMID 22447074 DOI: 10.1038/nm.2657  1
2012 Schrijvers R, De Rijck J, Demeulemeester J, Adachi N, Vets S, Ronen K, Christ F, Bushman FD, Debyser Z, Gijsbers R. LEDGF/p75-independent HIV-1 replication demonstrates a role for HRP-2 and remains sensitive to inhibition by LEDGINs. Plos Pathogens. 8: e1002558. PMID 22396646 DOI: 10.1371/journal.ppat.1002558  1
2012 Lehman DA, Wamalwa DC, McCoy CO, Matsen FA, Langat A, Chohan BH, Benki-Nugent S, Custers-Allen R, Bushman FD, John-Stewart GC, Overbaugh J. Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment. Journal of Acquired Immune Deficiency Syndromes (1999). 60: 225-33. PMID 22395670 DOI: 10.1097/QAI.0b013e3182515730  1
2012 Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD. Hypervariable loci in the human gut virome. Proceedings of the National Academy of Sciences of the United States of America. 109: 3962-6. PMID 22355105 DOI: 10.1073/pnas.1119061109  1
2012 Mei J, Liu Y, Dai N, Hoffmann C, Hudock KM, Zhang P, Guttentag SH, Kolls JK, Oliver PM, Bushman FD, Worthen GS. Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. The Journal of Clinical Investigation. 122: 974-86. PMID 22326959 DOI: 10.1172/JCI60588  1
2012 Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Estimating abundances of retroviral insertion sites from DNA fragment length data. Bioinformatics (Oxford, England). 28: 755-62. PMID 22238265 DOI: 10.1093/bioinformatics/bts004  1
2012 Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, ... ... Bushman FD, et al. Global landscape of HIV-human protein complexes. Nature. 481: 365-70. PMID 22190034 DOI: 10.1038/nature10719  1
2012 Sadelain M, Papapetrou EP, Bushman FD. Safe harbours for the integration of new DNA in the human genome. Nature Reviews. Cancer. 12: 51-8. PMID 22129804 DOI: 10.1038/nrc3179  1
2011 Schaller T, Ocwieja KE, Rasaiyaah J, Price AJ, Brady TL, Roth SL, Hué S, Fletcher AJ, Lee K, KewalRamani VN, Noursadeghi M, Jenner RG, James LC, Bushman FD, Towers GJ. HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency Plos Pathogens. 7. PMID 22174692 DOI: 10.1371/journal.ppat.1002439  1
2011 Gijsbers R, Vets S, De Rijck J, Ocwieja KE, Ronen K, Malani N, Bushman FD, Debyser Z. Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting. The Journal of Biological Chemistry. 286: 41812-25. PMID 21987578 DOI: 10.1074/jbc.M111.255711  1
2011 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, ... ... Bushman FD, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science (New York, N.Y.). 334: 105-8. PMID 21885731 DOI: 10.1126/science.1208344  1
2011 Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. The human gut virome: inter-individual variation and dynamic response to diet. Genome Research. 21: 1616-25. PMID 21880779 DOI: 10.1101/gr.122705.111  1
2011 Mukherjee R, Jensen ST, Male F, Bittinger K, Hodinka RL, Miller MD, Bushman FD. Switching between raltegravir resistance pathways analyzed by deep sequencing. Aids (London, England). 25: 1951-9. PMID 21832937 DOI: 10.1097/QAD.0b013e32834b34de  1
2011 Meylan S, Groner AC, Ambrosini G, Malani N, Quenneville S, Zangger N, Kapopoulou A, Kauzlaric A, Rougemont J, Ciuffi A, Bushman FD, Bucher P, Trono D. A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. Bmc Genomics. 12: 378. PMID 21791101 DOI: 10.1186/1471-2164-12-378  1
2011 Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. Bayesian community-wide culture-independent microbial source tracking Nature Methods. 8: 761-765. PMID 21765408 DOI: 10.1038/nmeth.1650  1
2011 Li H, Haurigot V, Doyon Y, Li T, Wong SY, Bhagwat AS, Malani N, Anguela XM, Sharma R, Ivanciu L, Murphy SL, Finn JD, Khazi FR, Zhou S, Paschon DE, ... ... Bushman FD, et al. In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature. 475: 217-21. PMID 21706032 DOI: 10.1038/nature10177  1
2011 Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, Bushman FD, Collman RG. Topographical continuity of bacterial populations in the healthy human respiratory tract. American Journal of Respiratory and Critical Care Medicine. 184: 957-63. PMID 21680950 DOI: 10.1164/rccm.201104-0655OC  1
2011 Roth SL, Malani N, Bushman FD. Gammaretroviral integration into nucleosomal target DNA in vivo. Journal of Virology. 85: 7393-401. PMID 21561906 DOI: 10.1128/JVI.00635-11  1
2011 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, ... ... Bushman FD, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29: 415-20. PMID 21552244 DOI: 10.1038/nbt.1823  1
2011 Wilen CB, Wang J, Tilton JC, Miller JC, Kim KA, Rebar EJ, Sherrill-Mix SA, Patro SC, Secreto AJ, Jordan AP, Lee G, Kahn J, Aye PP, Bunnell BA, Lackner AA, ... ... Bushman FD, et al. Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases. Plos Pathogens. 7: e1002020. PMID 21533216 DOI: 10.1371/journal.ppat.1002020  1
2011 Brady T, Bushman FD. Nondividing cells: a safer bet for integrating vectors? Molecular Therapy : the Journal of the American Society of Gene Therapy. 19: 640-1. PMID 21455211 DOI: 10.1038/mt.2011.40  1
2011 Negre O, Fusil F, Colomb C, Roth S, Gillet-Legrand B, Henri A, Beuzard Y, Bushman F, Leboulch P, Payen E. Correction of murine β-thalassemia after minimal lentiviral gene transfer and homeostatic in vivo erythroid expansion Blood. 117: 5321-5331. PMID 21436071 DOI: 10.1182/blood-2010-01-263582  1
2011 Ocwieja KE, Brady TL, Ronen K, Huegel A, Roth SL, Schaller T, James LC, Towers GJ, Young JA, Chanda SK, König R, Malani N, Berry CC, Bushman FD. HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2. Plos Pathogens. 7: e1001313. PMID 21423673 DOI: 10.1371/journal.ppat.1001313  1
2011 Brady T, Roth SL, Malani N, Wang GP, Berry CC, Leboulch P, Hacein-Bey-Abina S, Cavazzana-Calvo M, Papapetrou EP, Sadelain M, Savilahti H, Bushman FD. A method to sequence and quantify DNA integration for monitoring outcome in gene therapy. Nucleic Acids Research. 39: e72. PMID 21415009 DOI: 10.1093/nar/gkr140  1
2011 Ronen K, Negre O, Roth S, Colomb C, Malani N, Denaro M, Brady T, Fusil F, Gillet-Legrand B, Hehir K, Beuzard Y, Leboulch P, Down JD, Payen E, Bushman FD. Distribution of lentiviral vector integration sites in mice following therapeutic gene transfer to treat β-thalassemia. Molecular Therapy : the Journal of the American Society of Gene Therapy. 19: 1273-86. PMID 21386821 DOI: 10.1038/mt.2011.20  1
2011 Cavazzana-Calvo M, Fischer A, Bushman FD, Payen E, Hacein-Bey-Abina S, Leboulch P. Is normal hematopoiesis maintained solely by long-term multipotent stem cells? Blood. 117: 4420-4. PMID 21304104 DOI: 10.1182/blood-2010-09-255679  1
2011 Gillet NA, Malani N, Melamed A, Gormley N, Carter R, Bentley D, Berry C, Bushman FD, Taylor GP, Bangham CR. The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood. 117: 3113-22. PMID 21228324 DOI: 10.1182/blood-2010-10-312926  1
2011 Papapetrou EP, Lee G, Malani N, Setty M, Riviere I, Tirunagari LM, Kadota K, Roth SL, Giardina P, Viale A, Leslie C, Bushman FD, Studer L, Sadelain M. Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells. Nature Biotechnology. 29: 73-8. PMID 21151124 DOI: 10.1038/nbt.1717  1
2011 Li H, Malani N, Hamilton SR, Schlachterman A, Bussadori G, Edmonson SE, Shah R, Arruda VR, Mingozzi F, Wright JF, Bushman FD, High KA. Assessing the potential for AAV vector genotoxicity in a murine model. Blood. 117: 3311-9. PMID 21106988 DOI: 10.1182/blood-2010-08-302729  1
2011 Ciuffi A, Bushman F. Retroviral Integration Target Site Selection Hiv-1 Integrase: Mechanism and Inhibitor Design. 51-65. DOI: 10.1002/9781118015377.ch5  1
2010 Cattoglio C, Maruggi G, Bartholomae C, Malani N, Pellin D, Cocchiarella F, Magnani Z, Ciceri F, Ambrosi A, Von Kalle C, Bushman FD, Bonini C, Schmidt M, Mavilio F, Recchia A. High-definition mapping of retroviral integration sites defines the fate of allogeneic t cells after donor lymphocyte infusion Plos One. 5. PMID 21203516 DOI: 10.1371/journal.pone.0015688  1
2010 Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG. Disordered microbial communities in the upper respiratory tract of cigarette smokers. Plos One. 5: e15216. PMID 21188149 DOI: 10.1371/journal.pone.0015216  1
2010 Tilton JC, Wilen CB, Didigu CA, Sinha R, Harrison JE, Agrawal-Gamse C, Henning EA, Bushman FD, Martin JN, Deeks SG, Doms RW. A maraviroc-resistant HIV-1 with narrow cross-resistance to other CCR5 antagonists depends on both N-terminal and extracellular loop domains of drug-bound CCR5. Journal of Virology. 84: 10863-76. PMID 20702642 DOI: 10.1128/JVI.01109-10  1
2010 Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. Bmc Microbiology. 10: 206. PMID 20673359 DOI: 10.1186/1471-2180-10-206  1
2010 Hacein-Bey-Abina S, Hauer J, Lim A, Picard C, Wang GP, Berry CC, Martinache C, Rieux-Laucat F, Latour S, Belohradsky BH, Leiva L, Sorensen R, Debré M, Casanova JL, Blanche S, ... ... Bushman FD, et al. Efficacy of gene therapy for X-linked severe combined immunodeficiency. The New England Journal of Medicine. 363: 355-64. PMID 20660403 DOI: 10.1056/NEJMoa1000164  1
2010 Gupta K, Diamond T, Hwang Y, Bushman F, Van Duyne GD. Structural properties of HIV integrase. Lens epithelium-derived growth factor oligomers. The Journal of Biological Chemistry. 285: 20303-15. PMID 20406807 DOI: 10.1074/jbc.M110.114413  1
2010 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, et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. 7: 335-6. PMID 20383131 DOI: 10.1038/nmeth.f.303  1
2010 Culyba MJ, Hwang Y, Hu JY, Minkah N, Ocwieja KE, Bushman FD. Metal cofactors in the structure and activity of the fowlpox resolvase. Journal of Molecular Biology. 399: 182-95. PMID 20380839 DOI: 10.1016/j.jmb.2010.03.054  1
2010 Wang GP, Sherrill-Mix SA, Chang KM, Quince C, Bushman FD. Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. Journal of Virology. 84: 6218-28. PMID 20375170 DOI: 10.1128/JVI.02271-09  1
2010 Wang GP, Berry CC, Malani N, Leboulch P, Fischer A, Hacein-Bey-Abina S, Cavazzana-Calvo M, Bushman FD. Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood. 115: 4356-66. PMID 20228274 DOI: 10.1182/blood-2009-12-257352  1
2010 Gijsbers R, Ronen K, Vets S, Malani N, De Rijck J, McNeely M, Bushman FD, Debyser Z. LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin. Molecular Therapy : the Journal of the American Society of Gene Therapy. 18: 552-60. PMID 20195265 DOI: 10.1038/mt.2010.36  1
2010 Perry K, Hwang Y, Bushman FD, Van Duyne GD. Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic. Structure (London, England : 1993). 18: 127-37. PMID 20152159 DOI: 10.1016/j.str.2009.10.020  1
2010 Mukherjee R, Plesa G, Sherrill-Mix S, Richardson MW, Riley JL, Bushman FD. HIV sequence variation associated with env antisense adoptive T-cell therapy in the hNSG mouse model. Molecular Therapy : the Journal of the American Society of Gene Therapy. 18: 803-11. PMID 20104212 DOI: 10.1038/mt.2009.316  1
2010 Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D, Kirn TJ, Bushman FD, Artis D. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunology. 3: 148-58. PMID 19940845 DOI: 10.1038/mi.2009.132  1
2010 Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (Oxford, England). 26: 266-7. PMID 19914921 DOI: 10.1093/bioinformatics/btp636  1
2009 Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology. 137: 1716-24.e1-2. PMID 19706296 DOI: 10.1053/j.gastro.2009.08.042  0.36
2009 Hoffmann C, Hill DA, Minkah N, Kirn T, Troy A, Artis D, Bushman F. Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing. Infection and Immunity. 77: 4668-78. PMID 19635824 DOI: 10.1128/IAI.00493-09  1
2009 Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, et al. Host cell factors in HIV replication: meta-analysis of genome-wide studies. Plos Pathogens. 5: e1000437. PMID 19478882 DOI: 10.1371/journal.ppat.1000437  1
2009 Brady T, Lee YN, Ronen K, Malani N, Berry CC, Bieniasz PD, Bushman FD. Integration target site selection by a resurrected human endogenous retrovirus. Genes & Development. 23: 633-42. PMID 19270161 DOI: 10.1101/gad.1762309  1
2009 Wang GP, Levine BL, Binder GK, Berry CC, Malani N, McGarrity G, Tebas P, June CH, Bushman FD. Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells. Molecular Therapy : the Journal of the American Society of Gene Therapy. 17: 844-50. PMID 19259065 DOI: 10.1038/mt.2009.16  1
2009 Ciuffi A, Ronen K, Brady T, Malani N, Wang G, Berry CC, Bushman FD. Methods for integration site distribution analyses in animal cell genomes. Methods (San Diego, Calif.). 47: 261-8. PMID 19038346 DOI: 10.1016/j.ymeth.2008.10.028  1
2009 Culyba MJ, Hwang Y, Minkah N, Bushman FD. DNA binding and cleavage by the fowlpox virus resolvase. The Journal of Biological Chemistry. 284: 1190-201. PMID 19004818 DOI: 10.1074/jbc.M807864200  1
2008 Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomäki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H. Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Research. 36: e148. PMID 18953026 DOI: 10.1093/nar/gkn801  1
2008 König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, ... ... Bushman FD, et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 135: 49-60. PMID 18854154 DOI: 10.1016/j.cell.2008.07.032  1
2008 Hacein-Bey-Abina S, Garrigue A, Wang GP, Soulier J, Lim A, Morillon E, Clappier E, Caccavelli L, Delabesse E, Beldjord K, Asnafi V, MacIntyre E, Dal Cortivo L, Radford I, Brousse N, ... ... Bushman FD, et al. Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. The Journal of Clinical Investigation. 118: 3132-42. PMID 18688285 DOI: 10.1172/JCI35700  1
2008 Bushman FD, Hoffmann C, Ronen K, Malani N, Minkah N, Rose HM, Tebas P, Wang GP. Massively parallel pyrosequencing in HIV research. Aids (London, England). 22: 1411-5. PMID 18614863 DOI: 10.1097/QAD.0b013e3282fc972e  1
2008 Wang GP, Garrigue A, Ciuffi A, Ronen K, Leipzig J, Berry C, Lagresle-Peyrou C, Benjelloun F, Hacein-Bey-Abina S, Fischer A, Cavazzana-Calvo M, Bushman FD. DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Research. 36: e49. PMID 18411205 DOI: 10.1093/nar/gkn125  1
2008 Barr SD, Smiley JR, Bushman FD. The interferon response inhibits HIV particle production by induction of TRIM22. Plos Pathogens. 4: e1000007. PMID 18389079 DOI: 10.1371/journal.ppat.1000007  1
2008 Meekings KN, Leipzig J, Bushman FD, Taylor GP, Bangham CR. HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP. Plos Pathogens. 4: e1000027. PMID 18369476 DOI: 10.1371/journal.ppat.1000027  1
2008 McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, Lozupone CA, Hamady M, Knight R, Bushman FD. The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. Plos Pathogens. 4: e20. PMID 18248093 DOI: 10.1371/journal.ppat.0040020  1
2007 Marshall HM, Ronen K, Berry C, Llano M, Sutherland H, Saenz D, Bickmore W, Poeschla E, Bushman FD. Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting. Plos One. 2: e1340. PMID 18092005 DOI: 10.1371/journal.pone.0001340  1
2007 Culyba MJ, Minkah N, Hwang Y, Benhamou OM, Bushman FD. DNA branch nuclease activity of vaccinia A22 resolvase. The Journal of Biological Chemistry. 282: 34644-52. PMID 17890227 DOI: 10.1074/jbc.M705322200  1
2007 Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Research. 35: e120. PMID 17881377 DOI: 10.1093/nar/gkm541  1
2007 Bushman FD. Retroviral integration and human gene therapy. The Journal of Clinical Investigation. 117: 2083-6. PMID 17671645 DOI: 10.1172/JCI32949  1
2007 Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, Bushman FD. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Research. 35: e91. PMID 17576693 DOI: 10.1093/nar/gkm435  1
2007 Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Research. 17: 1186-94. PMID 17545577 DOI: 10.1101/gr.6286907  1
2007 Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD. Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Virology. 365: 60-9. PMID 17462694 DOI: 10.1016/j.virol.2007.02.037  1
2007 Ren G, Gao K, Bushman FD, Yeager M. Single-particle Image Reconstruction of a Tetramer of HIV Integrase Bound to DNA Journal of Molecular Biology. 366: 286-294. PMID 17157316 DOI: 10.1016/j.jmb.2006.11.029  1
2006 Berry C, Hannenhalli S, Leipzig J, Bushman FD. Selection of target sites for mobile DNA integration in the human genome. Plos Computational Biology. 2: e157. PMID 17166054 DOI: 10.1371/journal.pcbi.0020157  1
2006 Levine BL, Humeau LM, Boyer J, MacGregor RR, Rebello T, Lu X, Binder GK, Slepushkin V, Lemiale F, Mascola JR, Bushman FD, Dropulic B, June CH. Gene transfer in humans using a conditionally replicating lentiviral vector. Proceedings of the National Academy of Sciences of the United States of America. 103: 17372-7. PMID 17090675 DOI: 10.1073/pnas.0608138103  1
2006 Diamond TL, Bushman FD. Role of metal ions in catalysis by HIV integrase analyzed using a quantitative PCR disintegration assay Nucleic Acids Research. 34: 6116-6125. PMID 17085478 DOI: 10.1093/nar/gkl862  1
2006 Hwang Y, Minkah N, Perry K, Van Duyne GD, Bushman FD. Regulation of catalysis by the smallpox virus topoisomerase. The Journal of Biological Chemistry. 281: 38052-60. PMID 17032643 DOI: 10.1074/jbc.M608858200  1
2006 Ciuffi A, Diamond TL, Hwang Y, Marshall HM, Bushman FD. Modulating target site selection during human immunodeficiency virus DNA integration in vitro with an engineered tethering factor Human Gene Therapy. 17: 960-967. PMID 16972764 DOI: 10.1089/hum.2006.17.960  1
2006 Perry K, Hwang Y, Bushman FD, Van Duyne GD. Structural basis for specificity in the poxvirus topoisomerase. Molecular Cell. 23: 343-54. PMID 16885024 DOI: 10.1016/j.molcel.2006.06.015  1
2006 Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: viral and cellular determinants of target-site selection. Plos Pathogens. 2: e60. PMID 16789841 DOI: 10.1371/journal.ppat.0020060  1
2006 Culyba MJ, Harrison JE, Hwang Y, Bushman FD. DNA cleavage by the A22R resolvase of vaccinia virus. Virology. 352: 466-76. PMID 16781759 DOI: 10.1016/j.virol.2006.05.007  1
2006 Ciuffi A, Bushman FD. Retroviral DNA integration: HIV and the role of LEDGF/p75 Trends in Genetics. 22: 388-395. PMID 16730094 DOI: 10.1016/j.tig.2006.05.006  1
2006 Barr SD, Ciuffi A, Leipzig J, Shinn P, Ecker JR, Bushman FD. HIV Integration Site Selection: Targeting in Macrophages and the Effects of Different Routes of Viral Entry Molecular Therapy. 14: 218-225. PMID 16647883 DOI: 10.1016/j.ymthe.2006.03.012  1
2006 Wang GP, Bushman FD. A statistical method for comparing viral growth curves. Journal of Virological Methods. 135: 118-23. PMID 16564579 DOI: 10.1016/j.jviromet.2006.02.008  1
2006 Yoder K, Sarasin A, Kraemer K, McIlhatton M, Bushman F, Fishel R. The DNA repair genes XPB and XPD defend cells from retroviral infection. Proceedings of the National Academy of Sciences of the United States of America. 103: 4622-7. PMID 16537383 DOI: 10.1073/pnas.0509828103  1
2006 Ciuffi A, Mitchell RS, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman FD. Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts. Molecular Therapy : the Journal of the American Society of Gene Therapy. 13: 366-73. PMID 16325473 DOI: 10.1016/j.ymthe.2005.10.009  1
2005 Ciuffi A, Llano M, Poeschla E, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman F. A role for LEDGF/p75 in targeting HIV DNA integration Nature Medicine. 11: 1287-1289. PMID 16311605 DOI: 10.1038/nm1329  1
2005 Diamond TL, Bushman FD. Division of labor within human immunodeficiency virus integrase complexes: Determinants of catalysis and target DNA capture Journal of Virology. 79: 15376-15387. PMID 16306609 DOI: 10.1128/JVI.79.24.15376-15387.2005  1
2005 Lewinski MK, Bushman FD. Retroviral DNA integration--mechanism and consequences. Advances in Genetics. 55: 147-81. PMID 16291214 DOI: 10.1016/S0065-2660(05)55005-3  1
2005 Bisgrove D, Lewinski M, Bushman F, Verdin E. Molecular mechanisms of HIV-1 proviral latency. Expert Review of Anti-Infective Therapy. 3: 805-14. PMID 16207172 DOI: 10.1586/14787210.3.5.805  1
2005 Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C. Genome-wide analysis of retroviral DNA integration. Nature Reviews. Microbiology. 3: 848-58. PMID 16175173 DOI: 10.1038/nrmicro1263  1
2005 Barr SD, Leipzig J, Shinn P, Ecker JR, Bushman FD. Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome Journal of Virology. 79: 12035-12044. PMID 16140779 DOI: 10.1128/JVI.79.18.12035-12044.2005  1
2005 Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. Journal of Virology. 79: 6610-9. PMID 15890899 DOI: 10.1128/JVI.79.11.6610-6619.2005  1
2004 Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. Plos Biology. 2: E234. PMID 15314653 DOI: 10.1371/journal.pbio.0020234  1
2004 Hu WY, Bushman FD, Siva AC. RNA interference against retroviruses. Virus Research. 102: 59-64. PMID 15068881 DOI: 10.1016/j.virusres.2004.01.016  1
2004 Bushman FD. Evolutionary teamwork Scientist. 18: 33-34.  1
2003 Bushman FD. Targeting survival: Integration site selection by retroviruses and LTR-Retrotransposons Cell. 115: 135-138. PMID 14567911 DOI: 10.1016/S0092-8674(03)00760-8  1
2003 Kilzer JM, Stracker T, Beitzel B, Meek K, Weitzman M, Bushman FD. Roles of host cell factors in circularization of retroviral dna. Virology. 314: 460-7. PMID 14517098 DOI: 10.1016/S0042-6822(03)00455-0  1
2003 Podtelezhnikov AA, Gao K, Bushman FD, McCammon JA. Modeling HIV-1 integrase complexes based on their hydrodynamic properties. Biopolymers. 68: 110-20. PMID 12579583 DOI: 10.1002/bip.10217  1
2003 Gao K, Gorelick RJ, Johnson DG, Bushman F. Cofactors for human immunodeficiency virus type 1 cDNA integration in vitro. Journal of Virology. 77: 1598-603. PMID 12502875 DOI: 10.1128/JVI.77.2.1598-1603.2003  1
2003 Mittal S, Bushman F, Orgel LE. Thiol-mediated degradation of DNA adsorbed on a colloidal gold surface Journal of Chemical Technology and Biotechnology. 78: 471-473. DOI: 10.1002/jctb.806  1
2002 Rowley DC, Hansen MS, Rhodes D, Sotriffer CA, Ni H, McCammon JA, Bushman FD, Fenical W. Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase. Bioorganic & Medicinal Chemistry. 10: 3619-25. PMID 12213478 DOI: 10.1016/S0968-0896(02)00241-9  1
2002 Schröder ARW, Shinn P, Chen H, Berry C, Ecker JR, Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots Cell. 110: 521-529. PMID 12202041 DOI: 10.1016/S0092-8674(02)00864-4  1
2002 Hu WY, Myers CP, Kilzer JM, Pfaff SL, Bushman FD. Inhibition of retroviral pathogenesis by RNA interference. Current Biology : Cb. 12: 1301-11. PMID 12176358 DOI: 10.1016/S0960-9822(02)00975-2  1
2002 Butler SL, Johnson EP, Bushman FD. Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circles. Journal of Virology. 76: 3739-47. PMID 11907213 DOI: 10.1128/JVI.76.8.3739-3747.2002  1
2002 Bushman FD. Integration site selection by lentiviruses: Biology and possible control Current Topics in Microbiology and Immunology. 261: 165-177. PMID 11892246  1
2002 Ridley CP, Reddy MVR, Rocha G, Bushman FD, Faulkner DJ. Total synthesis and evaluation of lamellarin α 20-Sulfate analogues Bioorganic and Medicinal Chemistry. 10: 3285-3290. DOI: 10.1016/S0968-0896(02)00237-7  1
2001 Johnson EP, Bushman FD. Paired DNA three-way junctions as scaffolds for assembling integrase complexes. Virology. 286: 304-16. PMID 11485398 DOI: 10.1006/viro.2001.0978  1
2001 Gao K, Butler SL, Bushman F. Human immunodeficiency virus type 1 integrase: Arrangement of protein domains in active cDNA complexes Embo Journal. 20: 3565-3576. PMID 11432843 DOI: 10.1093/emboj/20.13.3565  1
2001 Li L, Olvera JM, Yoder KE, Mitchell RS, Butler SL, Lieber M, Martin SL, Bushman FD. Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection. The Embo Journal. 20: 3272-81. PMID 11406603 DOI: 10.1093/emboj/20.12.3272  1
2001 Butler SL, Hansen MST, Bushman FD. A quantitative assay for HIV DNA integration in vivo Nature Medicine. 7: 631-634. PMID 11329067 DOI: 10.1038/87979  1
2001 Molteni V, Greenwald J, Rhodes D, Hwang Y, Kwiatkowski W, Bushman FD, Siegel JS, Choe S. Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain. Acta Crystallographica. Section D, Biological Crystallography. 57: 536-44. PMID 11264582 DOI: 10.1107/S0907444901001652  1
2001 Martin SL, Bushman FD. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon Molecular and Cellular Biology. 21: 467-475. PMID 11134335 DOI: 10.1128/MCB.21.2.467-475.2001  1
2000 Yoder KE, Bushman FD. Repair of gaps in retroviral DNA integration intermediates Journal of Virology. 74: 11191-11200. PMID 11070016 DOI: 10.1128/JVI.74.23.11191-11200.2000  1
2000 Li L, Yoder K, Hansen MS, Olvera J, Miller MD, Bushman FD. Retroviral cDNA integration: stimulation by HMG I family proteins. Journal of Virology. 74: 10965-74. PMID 11069991 DOI: 10.1128/JVI.74.23.10965-10974.2000  1
2000 Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. Developing a dynamic pharmacophore model for HIV-1 integrase. Journal of Medicinal Chemistry. 43: 2100-14. PMID 10841789 DOI: 10.1021/jm990322h  1
2000 Mitchell SS, Rhodes D, Bushman FD, Faulkner DJ. Cyclodidemniserinol trisulfate, a sulfated serinolipid from the Palauan ascidian Didemnum guttatum that inhibits HIV-1 integrase. Organic Letters. 2: 1605-7. PMID 10841490  1
2000 Molteni V, Rhodes D, Rubins K, Hansen M, Bushman FD, Siegel JS. A new class of HIV-1 integrase inhibitors: the 3,3,3', 3'-tetramethyl-1,1'-spirobi(indan)-5,5',6,6'-tetrol family. Journal of Medicinal Chemistry. 43: 2031-9. PMID 10821715 DOI: 10.1021/jm990600c  1
2000 Mitchell SS, Faulkner DJ, Rubins K, Bushman FD. Dolastatin 3 and two novel cyclic peptides from a palauan collection of Lyngbya majuscula. Journal of Natural Products. 63: 279-82. PMID 10691729 DOI: 10.1021/np990353f  1
2000 Yang ZN, Mueser TC, Bushman FD, Hyde CC. Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase Journal of Molecular Biology. 296: 535-548. PMID 10669607 DOI: 10.1006/jmbi.1999.3463  1
1999 Greenwald J, Le V, Butler SL, Bushman FD, Choe S. The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity Biochemistry. 38: 8892-8898. PMID 10413462 DOI: 10.1021/bi9907173  1
1999 Carteau S, Gorelick RJ, Bushman FD. Coupled integration of human immunodeficiency virus type 1 cDNA ends by purifed integrase in vitro: Stimulation by the viral nucleocapsid protein Journal of Virology. 73: 6670-6679. PMID 10400764  1
1999 Hansen MS, Smith GJ, Kafri T, Molteni V, Siegel JS, Bushman FD. Integration complexes derived from HIV vectors for rapid assays in vitro. Nature Biotechnology. 17: 578-82. PMID 10385323 DOI: 10.1038/9886  1
1999 Bushman FD. Host proteins in retroviral cDNA integration Advances in Virus Research. 52: 301-317. PMID 10384239  1
1999 Reddy MV, Rao MR, Rhodes D, Hansen MS, Rubins K, Bushman FD, Venkateswarlu Y, Faulkner DJ. Lamellarin alpha 20-sulfate, an inhibitor of HIV-1 integrase active against HIV-1 virus in cell culture. Journal of Medicinal Chemistry. 42: 1901-7. PMID 10354398 DOI: 10.1021/jm9806650  1
1999 Hwang Y, Rowley D, Rhodes D, Gertsch J, Fenical W, Bushman F. Mechanism of inhibition of a poxvirus topoisomerase by the marine natural product sansalvamide A Molecular Pharmacology. 55: 1049-1053. PMID 10347247 DOI: 10.1124/mol.55.6.1049  1
1998 Hwang Y, Wang B, Bushman FD. Molluscum contagiosum virus topoisomerase: Purification, activities, and response to inhibitors Journal of Virology. 72: 3401-3406. PMID 9525670  1
1998 Li L, Farnet CM, Anderson WF, Bushman FD. Modulation of activity of Moloney murine leukemia virus preintegration complexes by host factors in vitro Journal of Virology. 72: 2125-2131. PMID 9499068  1
1997 Miller MD, Farnet CM, Bushman FD. Human immunodeficiency virus type 1 preintegration complexes: Studies of organization and composition Journal of Virology. 71: 5382-5390. PMID 9188609  1
1997 Hansen MST, Bushman FD. Human immunodeficiency virus type 2 preintegration complexes: Activities in vitro and response to inhibitors Journal of Virology. 71: 3351-3356. PMID 9060709  1
1997 Farnet CM, Bushman FD. HIV-1 cDNA integration: Requirement of HMG I(Y) protein for function of preintegration complexes in vitro Cell. 88: 483-492. PMID 9038339 DOI: 10.1016/S0092-8674(00)81888-7  1
1997 Bushman FD, Miller MD. Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites Journal of Virology. 71: 458-464. PMID 8985371  1
1996 Yeou-Cherng B, Miller MD, Bushman FD, Orgel LE. Target-sequence preferences of HIV-1 integration complexes in vitro Virology. 222: 283-288. PMID 8806511 DOI: 10.1006/viro.1996.0422  1
1996 Farnet CM, Wang B, Lipford JR, Bushman FD. Differential inhibition of HIV-1 preintegration complexes and purified integrase protein by small molecules Proceedings of the National Academy of Sciences of the United States of America. 93: 9742-9747. PMID 8790401 DOI: 10.1073/pnas.93.18.9742  1
1996 Farnet CM, Bushman FD. HIV cDNA integration: molecular biology and inhibitor development Aids (London, England). 10: S3-11.  1
1995 Miller MD, Wang B, Bushman FD. Human immunodeficiency virus type 1 preintegration complexes containing discontinuous plus strands are competent to integrate in vitro Journal of Virology. 69: 3938-3944. PMID 7745750  1
1995 Bor YC, Bushman FD, Orgel LE. In vitro integration of human immunodeficiency virus type 1 cDNA into targets containing protein-induced bends Proceedings of the National Academy of Sciences of the United States of America. 92: 10334-10338. PMID 7479779 DOI: 10.1073/pnas.92.22.10334  1
1993 Bushman FD, Engelman A, Palmer I, Wingfield P, Craigie R. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding Proceedings of the National Academy of Sciences of the United States of America. 90: 3428-3432. PMID 8386373 DOI: 10.1073/pnas.90.8.3428  1
1991 Craigie R, Mizuuchi K, Bushman FD, Engelman A. A rapid in vitro assay for HIV DNA integration. Nucleic Acids Research. 19: 2729-34. PMID 2041748 DOI: 10.1093/nar/19.10.2729  1
1989 Bushman FD, Shang C, Ptashne M. A single glutamic acid residue plays a key role in the transcriptional activation function of lambda repressor. Cell. 58: 1163-71. PMID 2570642 DOI: 10.1016/0092-8674(89)90514-X  1
1988 Bushman FD, Ptashne M. Turning lambda Cro into a transcriptional activator. Cell. 54: 191-7. PMID 2968842 DOI: 10.1016/0092-8674(88)90551-X  1
1986 Bushman FD, Ptashne M. Activation of transcription by the bacteriophage 434 repressor. Proceedings of the National Academy of Sciences of the United States of America. 83: 9353-7. PMID 3467310 DOI: 10.1073/pnas.83.24.9353  1
1985 Bushman FD, Anderson JE, Harrison SC, Ptashne M. Ethylation interference and X-ray crystallography identify similar interactions between 434 repressor and operator Nature. 316: 651-653. PMID 4033762 DOI: 10.1038/316651a0  1
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