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BO PENG

TitleSenior Faculty
InstitutionBaylor College of Medicine
DepartmentDepartment of Medicine
DivisionMedicine-Epidemiology & Populat Sci
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    Collapse Biography 
    Collapse education and training
    Rice University, HoustonPh.D06/2006Biostatistics
    University of Houston, HoustonMS06/2001Applied Mathematics
    Collapse awards and honors
    2011 - 2011Richard C. Devereaux Outstanding Young Investigator Award in Lung Cancer Prevention, Prevent Cancer Foundation
    2006 - 2009R25 Postdoctoral Fellowship in Cancer Prevention, National Institutes of Health
    2004 - 2006Predoctoral W.M. Keck Fellowship, W.M. Keck Foundation

    Collapse Overview 
    Collapse overview
    Dr. Peng completed his Ph.D. training in 2006 at Rice University with a Ph.D. in Biostatistics. He also received a Master of Arts in Applied Mathematics at Rice University in 2001. He completed postdoctoral training through an NIH R25 Postdoctoral Fellowship in Cancer Prevention, in Genetic Epidemiology from 2006-2008. Dr. Peng has produced more than 40 publications.

    Dr. Peng’s specialties include genetic simulations, epidemiological association analysis, and bioinformatic and next-generation sequencing data analysis. As an open-source advocate and an experienced software developer, he is the author of multiple large-scale software projects, including simuPOP, Variant Tools, and SoS Polyglot Notebook and Workflow System.

    Collapse Research 
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    R01HG008972     (LEAL, SUZANNE MARGARET)Jun 14, 2016 - Mar 31, 2020
    NIH/NHGRI
    Computational tools for sequence-based large-scale epidemiology studies
    Role: Co-Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Singhmar P, Trinh RTP, Ma J, Huo X, Peng B, Heijnen CJ, Kavelaars A. The fibroblast-derived protein PI16 controls neuropathic pain. Proc Natl Acad Sci U S A. 2020 03 10; 117(10):5463-5471. PMID: 32079726.
      View in: PubMed
    2. Ma J, Trinh RT, Mahant ID, Peng B, Matthias P, Heijnen CJ, Kavelaars A. Cell-specific role of histone deacetylase 6 in chemotherapy-induced mechanical allodynia and loss of intraepidermal nerve fibers. Pain. 2019 12; 160(12):2877-2890. PMID: 31356453.
      View in: PubMed
    3. Du D, Chang CH, Wang Y, Tong P, Chan WK, Chiu Y, Peng B, Tan L, Weinstein JN, Lorenzi PL. Response envelope analysis for quantitative evaluation of drug combinations. Bioinformatics. 2019 10 01; 35(19):3761-3770. PMID: 30851108.
      View in: PubMed
    4. Ruiz-Cordero R, Rao P, Li L, Qi Y, Atherton D, Peng B, Singh RR, Kim TB, Kawakami F, Routbort MJ, Alouch N, Chow CB, Tang X, Lu W, Brimo F, Matin SF, Wood CG, Tannir NM, Wistuba II, Chen K, Wang J, Medeiros LJ, Karam JA, Tamboli P, Sircar K. Hybrid oncocytic/chromophobe renal tumors are molecularly distinct from oncocytoma and chromophobe renal cell carcinoma. Mod Pathol. 2019 11; 32(11):1698-1707. PMID: 31231128.
      View in: PubMed
    5. Wang G, Peng B. Script of Scripts: A pragmatic workflow system for daily computational research. PLoS Comput Biol. 2019 02; 15(2):e1006843. PMID: 30811390.
      View in: PubMed
    6. Du D, Tan L, Wang Y, Peng B, Weinstein JN, Wondisford FE, Su X, Lorenzi PL. ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments. BMC Bioinformatics. 2019 Feb 19; 20(1):89. PMID: 30782135.
      View in: PubMed
    7. Peng B, Leong MC, Chen HS, Rotunno M, Brignole KR, Clarke J, Mechanic LE. Genetic Simulation Resources and the GSR Certification Program. Bioinformatics. 2019 02 15; 35(4):709-710. PMID: 30101297.
      View in: PubMed
    8. Tetzlaff MT, Curry JL, Ning J, Sagiv O, Kandl TL, Peng B, Bell D, Routbort M, Hudgens CW, Ivan D, Kim TB, Chen K, Eterovic AK, Shaw K, Prieto VG, Yemelyanova A, Esmaeli B. Distinct Biological Types of Ocular Adnexal Sebaceous Carcinoma: HPV-Driven and Virus-Negative Tumors Arise through Nonoverlapping Molecular-Genetic Alterations. Clin Cancer Res. 2019 02 15; 25(4):1280-1290. PMID: 30420449.
      View in: PubMed
    9. Peng B, Wang G, Ma J, Leong MC, Wakefield C, Melott J, Chiu Y, Du D, Weinstein JN. SoS Notebook: an interactive multi-language data analysis environment. Bioinformatics. 2018 11 01; 34(21):3768-3770. PMID: 29790910.
      View in: PubMed
    10. Chiu GS, Boukelmoune N, Chiang ACA, Peng B, Rao V, Kingsley C, Liu HL, Kavelaars A, Kesler SR, Heijnen CJ. Nasal administration of mesenchymal stem cells restores cisplatin-induced cognitive impairment and brain damage in mice. Oncotarget. 2018 Oct 30; 9(85):35581-35597. PMID: 30473752.
      View in: PubMed
    11. Keene KS, King T, Hwang ES, Peng B, McGuire KP, Tapia C, Zhang H, Bae S, Nakhlis F, Klauber-Demore N, Meszoely I, Sabel MS, Willey SC, Eterovic AK, Hudis C, Wolff AC, De Los Santos J, Thompson A, Mills GB, Meric-Bernstam F. Molecular determinants of post-mastectomy breast cancer recurrence. NPJ Breast Cancer. 2018; 4:34. PMID: 30345349.
      View in: PubMed
    12. Peng BY, Chiou CS, Dubey NK, Yu SH, Deng YH, Tsai FC, Chiang HS, Shieh YH, Chen WH, Deng WP. Correction: Non-invasive in vivo molecular imaging of intra-articularly transplanted immortalized bone marrow stem cells for osteoarthritis treatment. Oncotarget. 2018 05 18; 9(38):25383. PMID: 29863193.
      View in: PubMed
    13. Peng BY, Chiou CS, Dubey NK, Yu SH, Deng YH, Tsai FC, Chiang HS, Shieh YH, Chen WH, Deng WP. Non-invasive in vivo molecular imaging of intra-articularly transplanted immortalized bone marrow stem cells for osteoarthritis treatment. Oncotarget. 2017 Nov 14; 8(57):97153-97164. PMID: 29228600.
      View in: PubMed
    14. Mitra S, Montgomery JE, Kolar MJ, Li G, Jeong KJ, Peng B, Verdine GL, Mills GB, Moellering RE. Stapled peptide inhibitors of RAB25 target context-specific phenotypes in cancer. Nat Commun. 2017 09 22; 8(1):660. PMID: 28939823.
      View in: PubMed
    15. Wang Z, Kim TB, Peng B, Karam J, Creighton C, Joon A, Kawakami F, Trevisan P, Jonasch E, Chow CW, Canales JR, Tamboli P, Tannir N, Wood C, Monzon F, Baggerly K, Varella-Garcia M, Czerniak B, Wistuba I, Mills G, Shaw K, Chen K, Sircar K. Sarcomatoid Renal Cell Carcinoma Has a Distinct Molecular Pathogenesis, Driver Mutation Profile, and Transcriptional Landscape. Clin Cancer Res. 2017 Nov 01; 23(21):6686-6696. PMID: 28710314.
      View in: PubMed
    16. Moss TJ, Qi Y, Xi L, Peng B, Kim TB, Ezzedine NE, Mosqueda ME, Guo CC, Czerniak BA, Ittmann M, Wheeler DA, Lerner SP, Matin SF. Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma. Eur Urol. 2017 10; 72(4):641-649. PMID: 28601352.
      View in: PubMed
    17. Lu JH, Wei HJ, Peng BY, Chou HH, Chen WH, Liu HY, Deng WP. Adipose-Derived Stem Cells Enhance Cancer Stem Cell Property and Tumor Formation Capacity in Lewis Lung Carcinoma Cells Through an Interleukin-6 Paracrine Circuit. Stem Cells Dev. 2016 12 01; 25(23):1833-1842. PMID: 27596042.
      View in: PubMed
    18. Zhu X, Wang J, Peng B, Shete S. Empirical estimation of sequencing error rates using smoothing splines. BMC Bioinformatics. 2016 Apr 22; 17:177. PMID: 27102907.
      View in: PubMed
    19. Liu X, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs R, Klein RJ, Boerwinkle E. WGSA: an annotation pipeline for human genome sequencing studies. J Med Genet. 2016 Feb; 53(2):111-2. PMID: 26395054.
      View in: PubMed
    20. Miller FW, Chen W, O'Hanlon TP, Cooper RG, Vencovsky J, Rider LG, Danko K, Wedderburn LR, Lundberg IE, Pachman LM, Reed AM, Ytterberg SR, Padyukov L, Selva-O'Callaghan A, Radstake TR, Isenberg DA, Chinoy H, Ollier WE, Scheet P, Peng B, Lee A, Byun J, Lamb JA, Gregersen PK, Amos CI. Genome-wide association study identifies HLA 8.1 ancestral haplotype alleles as major genetic risk factors for myositis phenotypes. Genes Immun. 2015 Oct; 16(7):470-80. PMID: 26291516.
      View in: PubMed
    21. Wei C, Peng B, Han Y, Chen WV, Rother J, Tomlinson GE, Richard Boland C, Chaussabel D, Frazier ML, Amos CI. Erratum to: Mutations of HNRNPA0 and WIF1 predispose members of a large family to multiple cancers. Fam Cancer. 2015 Jun; 14(2):307. PMID: 25820142.
      View in: PubMed
    22. Peng B, Chen HS, Mechanic LE, Racine B, Clarke J, Gillanders E, Feuer EJ. Genetic data simulators and their applications: an overview. Genet Epidemiol. 2015 Jan; 39(1):2-10. PMID: 25504286.
      View in: PubMed
    23. Peng B. Reproducible simulations of realistic samples for next-generation sequencing studies using Variant Simulation Tools. Genet Epidemiol. 2015 Jan; 39(1):45-52. PMID: 25395236.
      View in: PubMed
    24. Chen HS, Hutter CM, Mechanic LE, Amos CI, Bafna V, Hauser ER, Hernandez RD, Li C, Liberles DA, McAllister K, Moore JH, Paltoo DN, Papanicolaou GJ, Peng B, Ritchie MD, Rosenfeld G, Witte JS, Gillanders EM, Feuer EJ. Genetic simulation tools for post-genome wide association studies of complex diseases. Genet Epidemiol. 2015 Jan; 39(1):11-19. PMID: 25371374.
      View in: PubMed
    25. Gorlov IP, Moore JH, Peng B, Jin JL, Gorlova OY, Amos CI. SNP characteristics predict replication success in association studies. Hum Genet. 2014 Dec; 133(12):1477-86. PMID: 25273843.
      View in: PubMed
    26. Wang GT, Peng B, Leal SM. Variant association tools for quality control and analysis of large-scale sequence and genotyping array data. Am J Hum Genet. 2014 May 01; 94(5):770-83. PMID: 24791902.
      View in: PubMed
    27. Wang GT, Li B, Santos-Cortez RP, Peng B, Leal SM. Power analysis and sample size estimation for sequence-based association studies. Bioinformatics. 2014 Aug 15; 30(16):2377-8. PMID: 24778108.
      View in: PubMed
    28. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20; 507(7492):315-22. PMID: 24476821.
      View in: PubMed
    29. Miller FW, Cooper RG, Vencovský J, Rider LG, Danko K, Wedderburn LR, Lundberg IE, Pachman LM, Reed AM, Ytterberg SR, Padyukov L, Selva-O'Callaghan A, Radstake TR, Isenberg DA, Chinoy H, Ollier WE, O'Hanlon TP, Peng B, Lee A, Lamb JA, Chen W, Amos CI, Gregersen PK. Genome-wide association study of dermatomyositis reveals genetic overlap with other autoimmune disorders. Arthritis Rheum. 2013 Dec; 65(12):3239-47. PMID: 23983088.
      View in: PubMed
    30. Dawson JA, Dhurandhar EJ, Vazquez AI, Peng B, Allison DB. Propagation of obesity across generations: the roles of differential realized fertility and assortative mating by body mass index. Hum Hered. 2013; 75(2-4):204-12. PMID: 24081235.
      View in: PubMed
    31. Peng B, Chen HS, Mechanic LE, Racine B, Clarke J, Clarke L, Gillanders E, Feuer EJ. Genetic Simulation Resources: a website for the registration and discovery of genetic data simulators. Bioinformatics. 2013 Apr 15; 29(8):1101-2. PMID: 23435068.
      View in: PubMed
    32. Vasemägi A, Nilsson J, McGinnity P, Cross T, O'Reilly P, Glebe B, Peng B, Berg PR, Primmer CR. Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon. Comp Funct Genomics. 2012; 2012:628204. PMID: 23326209.
      View in: PubMed
    33. Gorlova OY, Ying J, Amos CI, Spitz MR, Peng B, Gorlov IP. Derived SNP alleles are used more frequently than ancestral alleles as risk-associated variants in common human diseases. J Bioinform Comput Biol. 2012 Apr; 10(2):1241008. PMID: 22809343.
      View in: PubMed
    34. San Lucas FA, Wang G, Scheet P, Peng B. Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. Bioinformatics. 2012 Feb 01; 28(3):421-2. PMID: 22138362.
      View in: PubMed
    35. Xu Y, Peng B, Fu Y, Amos CI. Genome-wide algorithm for detecting CNV associations with diseases. BMC Bioinformatics. 2011 Aug 09; 12:331. PMID: 21827692.
      View in: PubMed
    36. Peng B, Liu X. Simulating sequences of the human genome with rare variants. Hum Hered. 2010; 70(4):287-91. PMID: 21212684.
      View in: PubMed
    37. Swartz MD, Peng B, Reyes-Gibby C, Shete S. Using Ascertainment for Targeted Resequencing to Increase Power to Identify Causal Variants. Stat Interface. 2011; 4(3):285-294. PMID: 22468169.
      View in: PubMed
    38. Peng B, Amos CI. Forward-time simulation of realistic samples for genome-wide association studies. BMC Bioinformatics. 2010 Sep 01; 11:442. PMID: 20809983.
      View in: PubMed
    39. Peng B. Simulating gene-environment interactions in complex human diseases. Genome Med. 2010 Mar 23; 2(3):21. PMID: 20346093.
      View in: PubMed
    40. Gu X, Frankowski RF, Rosner GL, Relling M, Peng B, Amos CI. A modified forward multiple regression in high-density genome-wide association studies for complex traits. Genet Epidemiol. 2009 Sep; 33(6):518-25. PMID: 19365845.
      View in: PubMed
    41. Wu CC, Shete S, Chen WV, Peng B, Lee AT, Ma J, Gregersen PK, Amos CI. Detection of disease-associated deletions in case-control studies using SNP genotypes with application to rheumatoid arthritis. Hum Genet. 2009 Aug; 126(2):303-15. PMID: 19415332.
      View in: PubMed
    42. Peng B, Kimmel M. Simulations provide support for the common disease-common variant hypothesis. Genetics. 2007 Feb; 175(2):763-76. PMID: 17151262.
      View in: PubMed
    43. Peng B, Kimmel M. simuPOP: a forward-time population genetics simulation environment. Bioinformatics. 2005 Sep 15; 21(18):3686-7. PMID: 16020469.
      View in: PubMed
    44. Gorlova O, Peng B, Yankelevitz D, Henschke C, Kimmel M. Estimating the growth rates of primary lung tumours from samples with missing measurements. Stat Med. 2005 Apr 15; 24(7):1117-34. PMID: 15568189.
      View in: PubMed
    45. Pusztai L, Gregory BW, Baggerly KA, Peng B, Koomen J, Kuerer HM, Esteva FJ, Symmans WF, Wagner P, Hortobagyi GN, Laronga C, Semmes OJ, Wright GL, Drake RR, Vlahou A. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Cancer. 2004 May 01; 100(9):1814-22. PMID: 15112261.
      View in: PubMed
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