Headshot photo of Benjamin N. Bimber, Ph.D.

Benjamin N. Bimber, Ph.D.

  • Assistant Professor, Oregon National Primate Research Center


Benjamin Bimber, Ph.D. joined OHSU in 2012.  His research focuses on the influence of genetics on infectious disease and the immune response, with an emphasis on using new technologies to drive understanding.  Most of his work is designed to understand how the immune system responds to HIV, a global disease with more than 30 million people actively infected worldwide.  His work has included high-resolution sequencing of HIV, and the study of complex families of immune receptors that associate with protection from HIV infection.  Most recently, Dr. Bimber is focused on understanding non-classical T-cells induced by some candidate HIV vaccines using single-cell sequencing and characterization of T-cell receptor diversity.

As a member of the ONPRC Primate Genetics Program, Dr. Bimber is also involved in efforts to promote genomics research using macaques.  He is a member of a project that is conducting large-scale whole-genome sequencing of the ONPRC macaque colony, ultimately providing data from more than 2000 subjects.  These data, along with clinical histories will be made publically available.  He is very interested in ensuring both the data from this project and infrastructure required to analyze data of this scale are available to a range of scientists, including those who may not be genetics or bioinformatics experts.

Dr. Bimber graduated in 2004 from Kalamazoo College with a B.A. in Biology, and received his Ph.D. in Cellular and Molecular Biology in 2009 from the University of Wisconsin.  Prior to joining research faculty at OHSU, he led efforts to develop a modern research-oriented health record system at both the Wisconsin and Oregon National Primate Research Centers.  This open source system, based on LabKey Server, is now in use at five NIH Primate Centers and continues to expand.

Education and training

    • B.A., 2004, Biology - Kalamazoo College
    • Ph.D., 2009, Cellular and Molecular Biology - University of Wisconsin

Memberships and associations:

  • Institutional Animal Care and Use Committee (IACUC), 2013-2020

Areas of interest

  • Infectious Disease
  • Immunogenetics
  • Next-generation Sequencing / Novel Technologies


Selected publications

  • Boggy GJ, McElfresh GW, Mahyari E, Ventura AB, Hansen SG, Picker LJ, Bimber BN. BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data. Bioinformatics. 2022 May 13;38(10):2791-2801. doi: 10.1093/bioinformatics/btac213. PubMed PMID: 35561167; PubMed Central PMCID: PMC9113275.
  • Chang XL, Reed JS, Webb GM, Wu HL, Le J, Bateman KB, Greene JM, Pessoa C, Waytashek C, Weber WC, Hwang J, Fischer M, Moats C, Shiel O, Bochart RM, Crank H, Siess D, Giobbi T, Torgerson J, Agnor R, Gao L, Dhody K, Lalezari JP, Bandar IS, Carnate AM, Pang AS, Corley MJ, Kelly S, Pourhassan N, Smedley J, Bimber BN. Suppression of human and simian immunodeficiency virus replication with the CCR5-specific...PubMed PMID: 3535829; PubMed Central PMCID: PMC8970399. 
  • Ryu J, Chan W, Wettengel JM, Hanna CB, Burwitz BJ, Hennebold JD, Bimber BN. Rapid, accurate mapping of transgene integration in viable rhesus macaque embryos using enhanced-specificity tagmentation-assisted PCR. Mol Ther Methods Clin Dev. 2022 Mar 10;24:241-254. doi: 10.1016/j.omtm.2022.01.009. eCollection 2022 Mar 10. PubMed PMID: 35211637; PubMed Central PMCID: PMC8829455.
  • Abdulhaqq S, Ventura AB, Reed JS, Bashirova AA, Bateman KB, McDonald E, Wu HL, Greene JM, Schell JB, Morrow D, Wisskirchen K, Martin JN, Deeks SG, Carrington M, Protzer U, Früh K, Hansen SG, Picker LJ, Sacha JB, Bimber BN. Identification and Characterization of Antigen-Specific CD8(+) T Cells Using Surface-Trapped TNF-α and Single-Cell Sequencing. Epub 2021 Nov 22. PubMed PMID: 34810222; PubMed Central PMCID: PMC9124229.
  • Yan MY, Ferguson B, Bimber BN. VariantQC: a visual quality control report for variant evaluation. Bioinformatics. 2019 Dec 15;35(24):5370-5371. doi: 10.1093/bioinformatics/btz560. PubMed PMID: 31309221; PubMed Central PMCID: PMC7963085.
  • Bimber BN, Yan MY, Peterson SM, Ferguson B. mGAP: the macaque genotype and phenotype resource, a framework for accessing and interpreting macaque variant data, and identifying new models of human disease. BMC Genomics. 2019 Mar 6;20(1):176. doi: 10.1186/s12864-019-5559-7. PubMed PMID: 30841849; PubMed Central PMCID: PMC6402181.
  • Bimber BN, Dudley DM, Lauck M, Becker EA, Chin EN, Lank SM, Grunenwald HL, Caruccio NC, Maffitt M, Wilson NA, Reed JS, Sosman JM, Tarosso LF, Sanabani S, Kallas EG, Hughes AL, O'Connor DH. Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J Virol. 2010 Nov;84(22):12087-92. doi: 10.1128/JVI.01378-10. PubMed PMID: 20844037; PubMed Central PMCID: PMC2977871.


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