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Effect of child abuse and neglect on risk behaviors in inner-city minority female adolescents and young adults.

Diaz A, Shankar V, Nucci-Sack A, Linares LO, Salandy A, Strickler HD, Burk RD, Schlecht NF.

Child Abuse Negl. 2019 Dec 26;101:104347. doi: 10.1016/j.chiabu.2019.104347. [Epub ahead of print]


Altered Gut Microbiota and Host Metabolite Profiles in HIV-infected Women.

Wang Z, Usyk M, Sollecito CC, Qiu Y, Williams-Nguyen J, Hua S, Gradissimo A, Wang T, Xue X, Kurland IJ, Ley K, Landay AL, Anastos K, Knight R, Kaplan RC, Burk RD, Qi Q.

Clin Infect Dis. 2019 Nov 21. pii: ciz1117. doi: 10.1093/cid/ciz1117. [Epub ahead of print]


Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity.

Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD.

Genome Biol. 2019 Nov 1;20(1):219. doi: 10.1186/s13059-019-1831-z.


Risk of Oral Human Papillomavirus Infection Among Sexually Active Female Adolescents Receiving the Quadrivalent Vaccine.

Schlecht NF, Masika M, Diaz A, Nucci-Sack A, Salandy A, Pickering S, Strickler HD, Shankar V, Burk RD.

JAMA Netw Open. 2019 Oct 2;2(10):e1914031. doi: 10.1001/jamanetworkopen.2019.14031.


Epidemiological evidence that common HPV types may be common because of their ability to evade immune surveillance: Results from the Women's Interagency HIV study.

Castle PE, Burk RD, Massad LS, Eltoum IE, Hall CB, Hessol NA, Anastos K, Xie X, Minkoff H, Xue X, D'Souza G, Flowers L, Colie C, Rahangdale L, Fischl MA, Palefsky JM, Strickler HD.

Int J Cancer. 2019 Oct 2. doi: 10.1002/ijc.32693. [Epub ahead of print]


Non-human Primate Papillomaviruses Share Similar Evolutionary Histories and Niche Adaptation as the Human Counterparts.

Chen Z, Long T, Wong PY, Ho WCS, Burk RD, Chan PKS.

Front Microbiol. 2019 Sep 10;10:2093. doi: 10.3389/fmicb.2019.02093. eCollection 2019.


HPV73 a nonvaccine type causes cervical cancer.

Amaro-Filho SM, Gradissimo A, Usyk M, Moreira FCB, de Almeida LM, Moreira MAM, Burk RD.

Int J Cancer. 2020 Feb 1;146(3):731-738. doi: 10.1002/ijc.32315. Epub 2019 Apr 29.


Genetic variants in CYP and GST genes, smoking and risk for head and neck cancers: a gene-environment interaction hospital-based case-control study among Canadian Caucasians.

ThekkePurakkal AS, Nicolau B, Burk RD, Franco EL, Schlecht NF.

Carcinogenesis. 2019 Apr 2. pii: bgz051. doi: 10.1093/carcin/bgz051. [Epub ahead of print]


Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota.

Rosenbaum J, Usyk M, Chen Z, Zolnik CP, Jones HE, Waldron L, Dowd JB, Thorpe LE, Burk RD.

Sci Rep. 2019 Feb 6;9(1):1531. doi: 10.1038/s41598-018-38049-6.


The molecular biology and HPV drug responsiveness of cynomolgus macaque papillomaviruses support their use in the development of a relevant in vivo model for antiviral drug testing.

Tombak EM, Männik A, Burk RD, Le Grand R, Ustav E, Ustav M.

PLoS One. 2019 Jan 25;14(1):e0211235. doi: 10.1371/journal.pone.0211235. eCollection 2019.


An Observational Study of Deep Learning and Automated Evaluation of Cervical Images for Cancer Screening.

Hu L, Bell D, Antani S, Xue Z, Yu K, Horning MP, Gachuhi N, Wilson B, Jaiswal MS, Befano B, Long LR, Herrero R, Einstein MH, Burk RD, Demarco M, Gage JC, Rodriguez AC, Wentzensen N, Schiffman M.

J Natl Cancer Inst. 2019 Sep 1;111(9):923-932. doi: 10.1093/jnci/djy225.


Complete Genome Sequences of Six Novel Macaca mulatta Papillomavirus Types Isolated from Genital Sites of Rhesus Monkeys in Hong Kong SAR, China.

Long T, Wong PY, Ho WCS, Burk RD, Chan PKS, Chen Z.

Microbiol Resour Announc. 2018 Dec 6;7(22). pii: e01414-18. doi: 10.1128/MRA.01414-18. eCollection 2018 Dec.


Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans.

Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD.

PLoS Pathog. 2018 Nov 1;14(11):e1007352. doi: 10.1371/journal.ppat.1007352. eCollection 2018 Nov.


Gut microbiota and plasma metabolites associated with diabetes in women with, or at high risk for, HIV infection.

Moon JY, Zolnik CP, Wang Z, Qiu Y, Usyk M, Wang T, Kizer JR, Landay AL, Kurland IJ, Anastos K, Kaplan RC, Burk RD, Qi Q.

EBioMedicine. 2018 Nov;37:392-400. doi: 10.1016/j.ebiom.2018.10.037. Epub 2018 Oct 23.


Diversity of macaque microbiota compared to the human counterparts.

Chen Z, Yeoh YK, Hui M, Wong PY, Chan MCW, Ip M, Yu J, Burk RD, Chan FKL, Chan PKS.

Sci Rep. 2018 Oct 22;8(1):15573. doi: 10.1038/s41598-018-33950-6.


Methylation of High-Risk Human Papillomavirus Genomes Are Associated with Cervical Precancer in HIV-Positive Women.

Gradissimo A, Lam J, Attonito JD, Palefsky J, Massad LS, Xie X, Eltoum IE, Rahangdale L, Fischl MA, Anastos K, Minkoff H, Xue X, D'Souza G, Flowers LC, Colie C, Shrestha S, Hessol NA, Strickler HD, Burk RD.

Cancer Epidemiol Biomarkers Prev. 2018 Dec;27(12):1407-1415. doi: 10.1158/1055-9965.EPI-17-1051. Epub 2018 Sep 20.


Racial differences in human papilloma virus types amongst United States women with HIV and cervical precancer.

Keller MJ, Burk RD, Massad LS, Eltoum IE, Hessol NA, Anastos K, Xie X, Minkoff H, Xue X, Reimers LL, Kuniholm M, DʼSouza G, Colie C, Aouizerat B, Palefsky JM, Strickler HD.

AIDS. 2018 Nov 28;32(18):2821-2826. doi: 10.1097/QAD.0000000000002005.


Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies.

Wang Z, Zolnik CP, Qiu Y, Usyk M, Wang T, Strickler HD, Isasi CR, Kaplan RC, Kurland IJ, Qi Q, Burk RD.

Front Cell Infect Microbiol. 2018 Aug 28;8:301. doi: 10.3389/fcimb.2018.00301. eCollection 2018.


Oral Alpha, Beta, and Gamma HPV Types and Risk of Incident Esophageal Cancer.

Agalliu I, Chen Z, Wang T, Hayes RB, Freedman ND, Gapstur SM, Burk RD.

Cancer Epidemiol Biomarkers Prev. 2018 Oct;27(10):1168-1175. doi: 10.1158/1055-9965.EPI-18-0287. Epub 2018 Aug 7.


ICTV Virus Taxonomy Profile: Papillomaviridae.

Van Doorslaer K, Chen Z, Bernard HU, Chan PKS, DeSalle R, Dillner J, Forslund O, Haga T, McBride AA, Villa LL, Burk RD, Ictv Report Consortium.

J Gen Virol. 2018 Aug;99(8):989-990. doi: 10.1099/jgv.0.001105. Epub 2018 Jun 21.


Gut Microbial-Related Choline Metabolite Trimethylamine-N-Oxide Is Associated With Progression of Carotid Artery Atherosclerosis in HIV Infection.

Shan Z, Clish CB, Hua S, Scott JM, Hanna DB, Burk RD, Haberlen SA, Shah SJ, Margolick JB, Sears CL, Post WS, Landay AL, Lazar JM, Hodis HN, Anastos K, Kaplan RC, Qi Q.

J Infect Dis. 2018 Sep 22;218(9):1474-1479. doi: 10.1093/infdis/jiy356.


Association of an intact E2 gene with higher HPV viral load, higher viral oncogene expression, and improved clinical outcome in HPV16 positive head and neck squamous cell carcinoma.

Anayannis NV, Schlecht NF, Ben-Dayan M, Smith RV, Belbin TJ, Ow TJ, Blakaj DM, Burk RD, Leonard SM, Woodman CB, Parish JL, Prystowsky MB.

PLoS One. 2018 Feb 16;13(2):e0191581. doi: 10.1371/journal.pone.0191581. eCollection 2018.


The Intersection of HPV Epidemiology, Genomics and Mechanistic Studies of HPV-Mediated Carcinogenesis.

Mirabello L, Clarke MA, Nelson CW, Dean M, Wentzensen N, Yeager M, Cullen M, Boland JF; NCI HPV Workshop, Schiffman M, Burk RD.

Viruses. 2018 Feb 13;10(2). pii: E80. doi: 10.3390/v10020080.


Human Papillomavirus DNA Methylation as a Biomarker for Cervical Precancer: Consistency across 12 Genotypes and Potential Impact on Management of HPV-Positive Women.

Clarke MA, Gradissimo A, Schiffman M, Lam J, Sollecito CC, Fetterman B, Lorey T, Poitras N, Raine-Bennett TR, Castle PE, Wentzensen N, Burk RD.

Clin Cancer Res. 2018 May 1;24(9):2194-2202. doi: 10.1158/1078-0432.CCR-17-3251. Epub 2018 Feb 2.


Plasma Tryptophan-Kynurenine Metabolites Are Altered in Human Immunodeficiency Virus Infection and Associated With Progression of Carotid Artery Atherosclerosis.

Qi Q, Hua S, Clish CB, Scott JM, Hanna DB, Wang T, Haberlen SA, Shah SJ, Glesby MJ, Lazar JM, Burk RD, Hodis HN, Landay AL, Post WS, Anastos K, Kaplan RC.

Clin Infect Dis. 2018 Jul 2;67(2):235-242. doi: 10.1093/cid/ciy053.


T cell receptor repertoire among women who cleared and failed to clear cervical human papillomavirus infection: An exploratory proof-of-principle study.

Lang Kuhs KA, Lin SW, Hua X, Schiffman M, Burk RD, Rodriguez AC, Herrero R, Abnet CC, Freedman ND, Pinto LA, Hamm D, Robins H, Hildesheim A, Shi J, Safaeian M.

PLoS One. 2018 Jan 31;13(1):e0178167. doi: 10.1371/journal.pone.0178167. eCollection 2018.


Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61).

Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Chan PKS, Burk RD.

Virology. 2018 Mar;516:86-101. doi: 10.1016/j.virol.2018.01.002. Epub 2018 Jan 11.


Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer.

Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM, Pei Z.

JAMA Oncol. 2018 Mar 1;4(3):358-365. doi: 10.1001/jamaoncol.2017.4777.


Complete Genome Sequences of Three Novel Saimiri sciureus Papillomavirus Types Isolated from the Cervicovaginal Region of Squirrel Monkeys.

Chen Z, Wood CE, Abee CR, Burk RD.

Genome Announc. 2018 Jan 4;6(1). pii: e01400-17. doi: 10.1128/genomeA.01400-17.


Novel ITS1 Fungal Primers for Characterization of the Mycobiome.

Usyk M, Zolnik CP, Patel H, Levi MH, Burk RD.

mSphere. 2017 Dec 13;2(6). pii: e00488-17. doi: 10.1128/mSphere.00488-17. eCollection 2017 Nov-Dec.


HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis.

Mirabello L, Yeager M, Yu K, Clifford GM, Xiao Y, Zhu B, Cullen M, Boland JF, Wentzensen N, Nelson CW, Raine-Bennett T, Chen Z, Bass S, Song L, Yang Q, Steinberg M, Burdett L, Dean M, Roberson D, Mitchell J, Lorey T, Franceschi S, Castle PE, Walker J, Zuna R, Kreimer AR, Beachler DC, Hildesheim A, Gonzalez P, Porras C, Burk RD, Schiffman M.

Cell. 2017 Sep 7;170(6):1164-1174.e6. doi: 10.1016/j.cell.2017.08.001.


Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants.

Chen Z, Ho WCS, Boon SS, Law PTY, Chan MCW, DeSalle R, Burk RD, Chan PKS.

J Virol. 2017 Oct 13;91(21). pii: e01285-17. doi: 10.1128/JVI.01285-17. Print 2017 Nov 1.


Molecular tests potentially improving HPV screening and genotyping for cervical cancer prevention.

Gradíssimo A, Burk RD.

Expert Rev Mol Diagn. 2017 Apr;17(4):379-391. doi: 10.1080/14737159.2017.1293525. Epub 2017 Feb 20. Review.


Therapeutic Vaccine Against Primate Papillomavirus Infections of the Cervix.

Ragonnaud E, Andersson AC, Mariya S, Pedersen AG, Burk RD, Folgori A, Colloca S, Cortese R, Nicosia A, Pamungkas J, Iskandriati D, Holst PJ.

J Immunother. 2017 Feb/Mar;40(2):51-61. doi: 10.1097/CJI.0000000000000153.


Cervical cancer incidence after screening with HPV, cytology, and visual methods: 18-Year follow-up of the Guanacaste cohort.

Rodríguez AC, Ávila C, Herrero R, Hildesheim A, Sherman ME, Burk RD, Morales J, Alfaro M, Guillén D, Trejos ME, Vargas RM, Torres G, Schiffman M.

Int J Cancer. 2017 Apr 15;140(8):1926-1934. doi: 10.1002/ijc.30614. Epub 2017 Feb 7.


The association of medication use with clearance or persistence of oral HPV infection.

Lam JO, Sugar EA, Cranston RD, Weber KM, Burk RD, Wiley DJ, Reddy S, Margolick JB, Strickler HD, Wentz A, Jacobson L, Coles CL, Bream JH, Rositch AF, Guo Y, Xiao W, Gillison ML, D'Souza G.

Cancer Causes Control. 2016 Dec;27(12):1491-1498. Epub 2016 Nov 1.


Risk of Delayed Human Papillomavirus Vaccination in Inner-City Adolescent Women.

Schlecht NF, Diaz A, Shankar V, Szporn AH, Wu M, Nucci-Sack A, Peake K, Strickler HD, Burk RD.

J Infect Dis. 2016 Dec 15;214(12):1952-1960. Epub 2016 Oct 12.


Distinct Ecological Niche of Anal, Oral, and Cervical Mucosal Microbiomes in Adolescent Women.

Smith BC, Zolnik CP, Usyk M, Chen Z, Kaiser K, Nucci-Sack A, Peake K, Diaz A, Viswanathan S, Strickler HD, Schlecht NF, Burk RD.

Yale J Biol Med. 2016 Sep 30;89(3):277-284. eCollection 2016 Sep.


A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma.

Wijetunga NA, Ben-Dayan M, Tozour J, Burk RD, Schlecht NF, Einstein MH, Greally JM.

Oncotarget. 2016 Sep 20;7(38):62133-62143. doi: 10.18632/oncotarget.11390.


The Cervicovaginal Microbiota and Its Associations With Human Papillomavirus Detection in HIV-Infected and HIV-Uninfected Women.

Reimers LL, Mehta SD, Massad LS, Burk RD, Xie X, Ravel J, Cohen MH, Palefsky JM, Weber KM, Xue X, Anastos K, Minkoff H, Atrio J, D'Souza G, Ye Q, Colie C, Zolnik CP, Spear GT, Strickler HD.

J Infect Dis. 2016 Nov 1;214(9):1361-1369. Epub 2016 Aug 11.


Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia.

Wijetunga NA, Belbin TJ, Burk RD, Whitney K, Abadi M, Greally JM, Einstein MH, Schlecht NF.

Gynecol Oncol. 2016 Sep;142(3):566-73. doi: 10.1016/j.ygyno.2016.07.006. Epub 2016 Jul 9.


β- and γ-Human Papillomavirus Types and Smoking in Head and Neck Cancer-Reply.

Agalliu I, Wang T, Burk RD.

JAMA Oncol. 2016 May 1;2(5):687-8. doi: 10.1001/jamaoncol.2016.0973. No abstract available.


HPV16 Sublineage Associations With Histology-Specific Cancer Risk Using HPV Whole-Genome Sequences in 3200 Women.

Mirabello L, Yeager M, Cullen M, Boland JF, Chen Z, Wentzensen N, Zhang X, Yu K, Yang Q, Mitchell J, Roberson D, Bass S, Xiao Y, Burdett L, Raine-Bennett T, Lorey T, Castle PE, Burk RD, Schiffman M.

J Natl Cancer Inst. 2016 Apr 29;108(9). pii: djw100. doi: 10.1093/jnci/djw100. Print 2016 Sep.


Association of serum cytokines with oral HPV clearance.

Lam JO, Bream JH, Sugar EA, Coles CL, Weber KM, Burk RD, Wiley DJ, Cranston RD, Reddy S, Margolick JB, Strickler HD, Wentz A, Jacobson L, Guo Y, Xiao W, Gillison ML, D'Souza G.

Cytokine. 2016 Jul;83:85-91. doi: 10.1016/j.cyto.2016.04.002. Epub 2016 Apr 8.


Global Genomic Diversity of Human Papillomavirus 11 Based on 433 Isolates and 78 Complete Genome Sequences.

Jelen MM, Chen Z, Kocjan BJ, Hošnjak L, Burt FJ, Chan PKS, Chouhy D, Combrinck CE, Estrade C, Fiander A, Garland SM, Giri AA, González JV, Gröning A, Hibbitts S, Luk TNM, Marinic K, Matsukura T, Neumann A, Oštrbenk A, Picconi MA, Sagadin M, Sahli R, Seedat RY, Seme K, Severini A, Sinchi JL, Smahelova J, Tabrizi SN, Tachezy R, Tohme Faybush S, Uloza V, Uloziene I, Wong YW, Židovec Lepej S, Burk RD, Poljak M.

J Virol. 2016 May 12;90(11):5503-5513. doi: 10.1128/JVI.03149-15. Print 2016 Jun 1.


Knowledge about Human Papillomavirus and Time to Complete Vaccination among Vulnerable Female Youth.

Nagpal J, Linares LO, Weiss J, Schlecht NF, Shankar V, Braun-Courville D, Nucci-Sack A, Strickler HD, Burk RD, Diaz A.

J Pediatr. 2016 Apr;171:122-7. doi: 10.1016/j.jpeds.2015.12.070. Epub 2016 Feb 2.


Sholom Wacholder: In Memoriam (1955-2015).

Schiffman M, Burk RD.

Cancer Epidemiol Biomarkers Prev. 2016 Feb;25(2):229-30. doi: 10.1158/1055-9965.EPI-15-1201. Epub 2016 Jan 21. No abstract available.


Associations of Oral α-, β-, and γ-Human Papillomavirus Types With Risk of Incident Head and Neck Cancer.

Agalliu I, Gapstur S, Chen Z, Wang T, Anderson RL, Teras L, Kreimer AR, Hayes RB, Freedman ND, Burk RD.

JAMA Oncol. 2016 May 1;2(5):599-606. doi: 10.1001/jamaoncol.2015.5504.


Association of High-Risk Human Papillomavirus with Genital Tract Mucosal Immune Factors in HIV-Infected Women.

Buckley N, Huber A, Lo Y, Castle PE, Kemal K, Burk RD, Strickler HD, Einstein MH, Young M, Anastos K, Herold BC.

Am J Reprod Immunol. 2016 Feb;75(2):146-54. doi: 10.1111/aji.12461. Epub 2015 Dec 18.


Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection.

Cullen M, Boland JF, Schiffman M, Zhang X, Wentzensen N, Yang Q, Chen Z, Yu K, Mitchell J, Roberson D, Bass S, Burdette L, Machado M, Ravichandran S, Luke B, Machiela MJ, Andersen M, Osentoski M, Laptewicz M, Wacholder S, Feldman A, Raine-Bennett T, Lorey T, Castle PE, Yeager M, Burk RD, Mirabello L.

Papillomavirus Res. 2015 Dec 1;1:3-11.

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