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Incense Burning is Associated with Human Oral Microbiota Composition.

Vallès Y, Inman CK, Peters BA, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Aljunaibi A, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Vallès H, Zaabi EA, Sherman S, Ali R, Ahn J, Hayes RB.

Sci Rep. 2019 Jul 11;9(1):10039. doi: 10.1038/s41598-019-46353-y.


An ATAC-seq atlas of chromatin accessibility in mouse tissues.

Liu C, Wang M, Wei X, Wu L, Xu J, Dai X, Xia J, Cheng M, Yuan Y, Zhang P, Li J, Feng T, Chen A, Zhang W, Chen F, Shang Z, Zhang X, Peters BA, Liu L.

Sci Data. 2019 May 20;6(1):65. doi: 10.1038/s41597-019-0071-0.


Childhood epilepsy with a small number of seizures may be left untreated: an international prospective study.

Arts WF, Geerts AT, Brouwer OF, van Donselaar CA, Stroink H, Peters BA, Peeters EA, Camfield P, Camfield C.

Epileptic Disord. 2019 Apr 1;21(2):141-153. doi: 10.1684/epd.2019.1040.


Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly.

Wang O, Chin R, Cheng X, Wu MKY, Mao Q, Tang J, Sun Y, Anderson E, Lam HK, Chen D, Zhou Y, Wang L, Fan F, Zou Y, Xie Y, Zhang RY, Drmanac S, Nguyen D, Xu C, Villarosa C, Gablenz S, Barua N, Nguyen S, Tian W, Liu JS, Wang J, Liu X, Qi X, Chen A, Wang H, Dong Y, Zhang W, Alexeev A, Yang H, Wang J, Kristiansen K, Xu X, Drmanac R, Peters BA.

Genome Res. 2019 May;29(5):798-808. doi: 10.1101/gr.245126.118. Epub 2019 Apr 2.


The Microbiome in Lung Cancer Tissue and Recurrence-Free Survival.

Peters BA, Hayes RB, Goparaju C, Reid C, Pass HI, Ahn J.

Cancer Epidemiol Biomarkers Prev. 2019 Apr;28(4):731-740. doi: 10.1158/1055-9965.EPI-18-0966. Epub 2019 Feb 7.


Significant abundance of cis configurations of coding variants in diploid human genomes.

Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T.

Nucleic Acids Res. 2019 Apr 8;47(6):2981-2995. doi: 10.1093/nar/gkz031.


3' Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3'OH ends in DNA or RNA.

Wang L, Xi Y, Zhang W, Wang W, Shen H, Wang X, Zhao X, Alexeev A, Peters BA, Albert A, Xu X, Ren H, Wang O, Kirkconnell K, Perazich H, Clark S, Hurowitz E, Chen A, Xu X, Drmanac R, Jiang Y.

DNA Res. 2019 Feb 1;26(1):45-53. doi: 10.1093/dnares/dsy037.


Association of dietary fibre intake and gut microbiota in adults.

Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB, Ahn J.

Br J Nutr. 2018 Nov;120(9):1014-1022. doi: 10.1017/S0007114518002465.


Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study.

Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB, Ahn J.

Sci Rep. 2018 Jul 27;8(1):11327. doi: 10.1038/s41598-018-29730-x.


A taxonomic signature of obesity in a large study of American adults.

Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB, Ahn J.

Sci Rep. 2018 Jun 27;8(1):9749. doi: 10.1038/s41598-018-28126-1.


Clinical and genetic analysis of a rare syndrome associated with neoteny.

Walker RF, Ciotlos S, Mao Q, Chin R, Drmanac S, Barua N, Agarwal MR, Zhang RY, Li Z, Wu MKY, Sun K, Lee K, Nguyen S, Liu JS, Carnevali P, Drmanac R, Peters BA.

Genet Med. 2018 Apr;20(5):495-502. doi: 10.1038/gim.2017.140. Epub 2017 Sep 21.


Association of Coffee and Tea Intake with the Oral Microbiome: Results from a Large Cross-Sectional Study.

Peters BA, McCullough ML, Purdue MP, Freedman ND, Um CY, Gapstur SM, Hayes RB, Ahn J.

Cancer Epidemiol Biomarkers Prev. 2018 Jul;27(7):814-821. doi: 10.1158/1055-9965.EPI-18-0184. Epub 2018 Apr 27.


Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults.

Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB, Ahn J.

Microbiome. 2018 Apr 24;6(1):59. doi: 10.1186/s40168-018-0448-x.


Comparison of the oral microbiome in mouthwash and whole saliva samples.

Fan X, Peters BA, Min D, Ahn J, Hayes RB.

PLoS One. 2018 Apr 11;13(4):e0194729. doi: 10.1371/journal.pone.0194729. eCollection 2018.


Advanced Whole-Genome Sequencing and Analysis of Fetal Genomes from Amniotic Fluid.

Mao Q, Chin R, Xie W, Deng Y, Zhang W, Xu H, Zhang RY, Shi Q, Peters EE, Gulbahce N, Li Z, Chen F, Drmanac R, Peters BA.

Clin Chem. 2018 Apr;64(4):715-725. doi: 10.1373/clinchem.2017.281220. Epub 2018 Mar 15.


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.


Genomic variants in the FTO gene are associated with sporadic amyotrophic lateral sclerosis in Greek patients.

Mitropoulos K, Merkouri Papadima E, Xiromerisiou G, Balasopoulou A, Charalampidou K, Galani V, Zafeiri KV, Dardiotis E, Ralli S, Deretzi G, John A, Kydonopoulou K, Papadopoulou E, di Pardo A, Akcimen F, Loizedda A, Dobričić V, Novaković I, Kostić VS, Mizzi C, Peters BA, Basak N, Orrù S, Kiskinis E, Cooper DN, Gerou S, Drmanac R, Bartsakoulia M, Tsermpini EE, Hadjigeorgiou GM, Ali BR, Katsila T, Patrinos GP.

Hum Genomics. 2017 Dec 8;11(1):30. doi: 10.1186/s40246-017-0126-2.


Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers.

Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB, Ahn J.

Cancer Res. 2017 Dec 1;77(23):6777-6787. doi: 10.1158/0008-5472.CAN-17-1296.


Pure CTCs, advanced WGS, and precise personalized combination therapies.

Peters BA, Park JW, Drmanac R.

Oncoscience. 2017 Sep 21;4(7-8):75-76. doi: 10.18632/oncoscience.362. eCollection 2017 Jul. No abstract available.


Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer.

Gulbahce N, Magbanua MJM, Chin R, Agarwal MR, Luo X, Liu J, Hayden DM, Mao Q, Ciotlos S, Li Z, Chen Y, Chen X, Li Y, Zhang RY, Lee K, Tearle R, Park E, Drmanac S, Rugo HS, Park JW, Drmanac R, Peters BA.

Cancer Res. 2017 Aug 15;77(16):4530-4541. doi: 10.1158/0008-5472.CAN-17-0688.


The oral fungal mycobiome: characteristics and relation to periodontitis in a pilot study.

Peters BA, Wu J, Hayes RB, Ahn J.

BMC Microbiol. 2017 Jul 12;17(1):157. doi: 10.1186/s12866-017-1064-9.


Erratum to: The gut microbiota in conventional and serrated precursors of colorectal cancer.

Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB, Ahn J.

Microbiome. 2017 Mar 6;5(1):29. doi: 10.1186/s40168-017-0238-x. No abstract available.


Long Fragment Read (LFR) Technology: Cost-Effective, High-Quality Genome-Wide Molecular Haplotyping.

McElwain MA, Zhang RY, Drmanac R, Peters BA.

Methods Mol Biol. 2017;1551:191-205. doi: 10.1007/978-1-4939-6750-6_11.


The gut microbiota in conventional and serrated precursors of colorectal cancer.

Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB, Ahn J.

Microbiome. 2016 Dec 30;4(1):69. doi: 10.1186/s40168-016-0218-6. Erratum in: Microbiome. 2017 Mar 6;5(1):29.


Novel genetic risk variants for pediatric celiac disease.

Balasopoulou A, Stanković B, Panagiotara A, Nikčevic G, Peters BA, John A, Mendrinou E, Stratopoulos A, Legaki AI, Stathakopoulou V, Tsolia A, Govaris N, Govari S, Zagoriti Z, Poulas K, Kanariou M, Constantinidou N, Krini M, Spanou K, Radlovic N, Ali BR, Borg J, Drmanac R, Chrousos G, Pavlovic S, Roma E, Zukic B, Patrinos GP, Katsila T.

Hum Genomics. 2016 Oct 24;10(1):34.


Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study.

Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB, Ahn J.

Gut. 2018 Jan;67(1):120-127. doi: 10.1136/gutjnl-2016-312580. Epub 2016 Oct 14.


The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

Mao Q, Ciotlos S, Zhang RY, Ball MP, Chin R, Carnevali P, Barua N, Nguyen S, Agarwal MR, Clegg T, Connelly A, Vandewege W, Zaranek AW, Estep PW, Church GM, Drmanac R, Peters BA.

Gigascience. 2016 Oct 11;5(1):42.


Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies.

Hellner K, Miranda F, Fotso Chedom D, Herrero-Gonzalez S, Hayden DM, Tearle R, Artibani M, KaramiNejadRanjbar M, Williams R, Gaitskell K, Elorbany S, Xu R, Laios A, Buiga P, Ahmed K, Dhar S, Zhang RY, Campo L, Myers KA, Lozano M, Ruiz-Miró M, Gatius S, Mota A, Moreno-Bueno G, Matias-Guiu X, Benítez J, Witty L, McVean G, Leedham S, Tomlinson I, Drmanac R, Cazier JB, Klein R, Dunne K, Bast RC Jr, Kennedy SH, Hassan B, Lise S, Garcia MJ, Peters BA, Yau C, Sauka-Spengler T, Ahmed AA.

EBioMedicine. 2016 Aug;10:137-49. doi: 10.1016/j.ebiom.2016.06.048. Epub 2016 Jul 2.


Cigarette smoking and the oral microbiome in a large study of American adults.

Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H, Alekseyenko AV, Hayes RB, Ahn J.

ISME J. 2016 Oct;10(10):2435-46. doi: 10.1038/ismej.2016.37. Epub 2016 Mar 25.


Whole genome sequence analysis of BT-474 using complete Genomics' standard and long fragment read technologies.

Ciotlos S, Mao Q, Zhang RY, Li Z, Chin R, Gulbahce N, Liu SJ, Drmanac R, Peters BA.

Gigascience. 2016 Feb 9;5:8. doi: 10.1186/s13742-016-0113-x. eCollection 2016.


Renal function is associated with indicators of arsenic methylation capacity in Bangladeshi adults.

Peters BA, Hall MN, Liu X, Slavkovich V, Ilievski V, Alam S, Siddique AB, Islam T, Graziano JH, Gamble MV.

Environ Res. 2015 Nov;143(Pt A):123-30. doi: 10.1016/j.envres.2015.10.001. Epub 2015 Oct 19.


Low-Dose Creatine Supplementation Lowers Plasma Guanidinoacetate, but Not Plasma Homocysteine, in a Double-Blind, Randomized, Placebo-Controlled Trial.

Peters BA, Hall MN, Liu X, Parvez F, Siddique AB, Shahriar H, Uddin MN, Islam T, Ilievski V, Graziano JH, Gamble MV.

J Nutr. 2015 Oct;145(10):2245-52. doi: 10.3945/jn.115.216739. Epub 2015 Aug 26.


Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach.

Karageorgos I, Mizzi C, Giannopoulou E, Pavlidis C, Peters BA, Zagoriti Z, Stenson PD, Mitropoulos K, Borg J, Kalofonos HP, Drmanac R, Stubbs A, van der Spek P, Cooper DN, Katsila T, Patrinos GP.

Hum Genomics. 2015 Jun 20;9:12. doi: 10.1186/s40246-015-0034-2.


Epigenetic age analysis of children who seem to evade aging.

Walker RF, Liu JS, Peters BA, Ritz BR, Wu T, Ophoff RA, Horvath S.

Aging (Albany NY). 2015 May;7(5):334-9.


Folic Acid and Creatine as Therapeutic Approaches to Lower Blood Arsenic: A Randomized Controlled Trial.

Peters BA, Hall MN, Liu X, Parvez F, Sanchez TR, van Geen A, Mey JL, Siddique AB, Shahriar H, Uddin MN, Islam T, Balac O, Ilievski V, Factor-Litvak P, Graziano JH, Gamble MV.

Environ Health Perspect. 2015 Dec;123(12):1294-301. doi: 10.1289/ehp.1409396. Epub 2015 May 15.


Arsenic exposure, inflammation, and renal function in Bangladeshi adults: effect modification by plasma glutathione redox potential.

Peters BA, Liu X, Hall MN, Ilievski V, Slavkovich V, Siddique AB, Alam S, Islam T, Graziano JH, Gamble MV.

Free Radic Biol Med. 2015 Aug;85:174-82. doi: 10.1016/j.freeradbiomed.2015.04.020. Epub 2015 Apr 24.


Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing.

Peters BA, Kermani BG, Alferov O, Agarwal MR, McElwain MA, Gulbahce N, Hayden DM, Tang YT, Zhang RY, Tearle R, Crain B, Prates R, Berkeley A, Munné S, Drmanac R.

Genome Res. 2015 Mar;25(3):426-34. doi: 10.1101/gr.181255.114. Epub 2015 Feb 11.


Co-barcoded sequence reads from long DNA fragments: a cost-effective solution for "perfect genome" sequencing.

Peters BA, Liu J, Drmanac R.

Front Genet. 2015 Jan 14;5:466. doi: 10.3389/fgene.2014.00466. eCollection 2014.


Involvement of the δ-opioid receptor in exercise-induced cardioprotection.

Miller LE, McGinnis GR, Peters BA, Ballmann CG, Nanayakkara G, Amin R, Quindry JC.

Exp Physiol. 2015 Apr 1;100(4):410-21. doi: 10.1113/expphysiol.2014.083436.


Accurate whole genome sequencing as the ultimate genetic test.

Drmanac R, Peters BA, Church GM, Reid CA, Xu X.

Clin Chem. 2015 Jan;61(1):305-6. doi: 10.1373/clinchem.2014.224907. Epub 2014 Dec 5. No abstract available.


Creatinine, arsenic metabolism, and renal function in an arsenic-exposed population in Bangladesh.

Peters BA, Hall MN, Liu X, Neugut YD, Pilsner JR, Levy D, Ilievski V, Slavkovich V, Islam T, Factor-Litvak P, Graziano JH, Gamble MV.

PLoS One. 2014 Dec 1;9(12):e113760. doi: 10.1371/journal.pone.0113760. eCollection 2014.


Whole-genome sequencing of asian lung cancers: second-hand smoke unlikely to be responsible for higher incidence of lung cancer among Asian never-smokers.

Krishnan VG, Ebert PJ, Ting JC, Lim E, Wong SS, Teo AS, Yue YG, Chua HH, Ma X, Loh GS, Lin Y, Tan JH, Yu K, Zhang S, Reinhard C, Tan DS, Peters BA, Lincoln SE, Ballinger DG, Laramie JM, Nilsen GB, Barber TD, Tan P, Hillmer AM, Ng PC.

Cancer Res. 2014 Nov 1;74(21):6071-81. doi: 10.1158/0008-5472.CAN-13-3195. Epub 2014 Sep 4.


Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism.

Schaaf CP, Gonzalez-Garay ML, Xia F, Potocki L, Gripp KW, Zhang B, Peters BA, McElwain MA, Drmanac R, Beaudet AL, Caskey CT, Yang Y.

Nat Genet. 2013 Nov;45(11):1405-8. doi: 10.1038/ng.2776. Epub 2013 Sep 29.


Oncogenic ERBB3 mutations in human cancers.

Jaiswal BS, Kljavin NM, Stawiski EW, Chan E, Parikh C, Durinck S, Chaudhuri S, Pujara K, Guillory J, Edgar KA, Janakiraman V, Scholz RP, Bowman KK, Lorenzo M, Li H, Wu J, Yuan W, Peters BA, Kan Z, Stinson J, Mak M, Modrusan Z, Eigenbrot C, Firestein R, Stern HM, Rajalingam K, Schaefer G, Merchant MA, Sliwkowski MX, de Sauvage FJ, Seshagiri S.

Cancer Cell. 2013 May 13;23(5):603-17. doi: 10.1016/j.ccr.2013.04.012. Erratum in: Cancer Cell. 2014 Apr 14;25(4):543-4.


Batch effects and pathway analysis: two potential perils in cancer studies involving DNA methylation array analysis.

Harper KN, Peters BA, Gamble MV.

Cancer Epidemiol Biomarkers Prev. 2013 Jun;22(6):1052-60. doi: 10.1158/1055-9965.EPI-13-0114. Epub 2013 Apr 29.


A public resource facilitating clinical use of genomes.

Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM.

Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):11920-7. doi: 10.1073/pnas.1201904109. Epub 2012 Jul 13.


Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells.

Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R.

Nature. 2012 Jul 11;487(7406):190-5. doi: 10.1038/nature11236.


Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples.

Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S, Wu TD.

BMC Med Genomics. 2011 Jan 24;4:11. doi: 10.1186/1755-8794-4-11.


The relationship of pressure ulcers, race, and socioeconomic conditions after spinal cord injury.

Saunders LL, Krause JS, Peters BA, Reed KS.

J Spinal Cord Med. 2010;33(4):387-95.


Diverse somatic mutation patterns and pathway alterations in human cancers.

Kan Z, Jaiswal BS, Stinson J, Janakiraman V, Bhatt D, Stern HM, Yue P, Haverty PM, Bourgon R, Zheng J, Moorhead M, Chaudhuri S, Tomsho LP, Peters BA, Pujara K, Cordes S, Davis DP, Carlton VE, Yuan W, Li L, Wang W, Eigenbrot C, Kaminker JS, Eberhard DA, Waring P, Schuster SC, Modrusan Z, Zhang Z, Stokoe D, de Sauvage FJ, Faham M, Seshagiri S.

Nature. 2010 Aug 12;466(7308):869-73. doi: 10.1038/nature09208. Epub 2010 Jul 28.


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