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Post-Ph.D. - Mammalian Reproduction, OHSU-ONPRC, Division of Genetics. Prof. Don F. Conrad. Ph.D. - Bioinformatics and Computational Biology, OHSU, Department of Medical Informatics and Clinical Epidemiology (DMICE), Division of Bioinformatics and Computational Biology (BCB), Portland, OR. “Robust and reproducible classification of rare cellular subsets/signatures (RCS) in single-cell technologies within a transfer learning framework.” (doi:10.6083/NX9EZJ). Committee members: Shannon K. McWeeney Ph.D., David M. Lewinsohn MD./Ph.D., Michael Mooney Ph.D., Christina Zheng Ph.D., and Evan Lind Ph.D. (2013 – 2018).
M.S. - Biochemistry and Molecular Biology. Oregon Health and Science University (OHSU), Div. Environmental and Biomolecular Systems, Portland, OR. “A six-compartment Physiologically Based Pharmacokinetic (PBPK) Markov-chain Monte Carlo Model to simulate and quantify nicotine metabolism in human populations.” (2006 – 2008).
B.S. - Biology and Chemistry double major. Portland State University (PSU), Portland, OR. (2002 – 2006)
I am a computational biologist focused on multi-disciplinary translational biomedical research with expertise in machine learning, immunology, and male reproductive biology. My day-to-day tasks are mostly researched focused, managing several ongoing projects and the team members involved in them. I oversee writing code, running statistical tests, and translating the biology to meaningful and actionable targets, with the support of the involved PIs. I consult and provide technical training and assistants to various labs and projects. I also mentor and guide prospective or current graduate students both on their work and career development. I am fascinated by how the immune system, throughout life, functions and influences the development, health, and death of an organism. Specifically, leveraging modern technology, computational power, and statistics to bring about new insight and information, as well as testing research hypotheses that were not previously possible. Currently, I am focused on two domains of biomedical research split between the labs of Don F. Conrad Ph.D., and Benjamin Bimber Ph.D., and mainly work with single-cell transcriptomic and spatial-omics data. In the Conrad Lab, broadly, we investigate the genetics of infertility and in the Bimber lab, we are focused on the immune system, often, T cells, in the context of several infectious diseases.
2022 - Current Research Assistant Professor, Mammalian Reproduction, Lab of Donald F. Conrad Ph.D. - Div. Genetics, ONPRC-OHSU.
2018 - 2022 Computational Biologist, Molecular Immunopathology - RA, Lab of Benjamin N. Bimber Ph.D. - Primate Genetics, ONPRC-OHSU.
2018 - 2022 Computational Biologist, Reproductive biology - RA, Lab of Donald F. Conrad Ph.D. - Reproductive Genetics, ONPRC-OHSU.
2016 - 2018 Doctoral Candidate, DMICE-BCB, OHSU. Developed novel machine learning framework for automated classification of rare cells in single-cell RNA-seq data. 2013 - 2016 Doctoral Student, DMICE-BCB, OHSU. Research Involvement: Genome-based Bioinformatics, Assessment of bioinformatics pipelines identifying genomic structural variants across several sequenced Gibbons. Lucia Carbone Ph.D. Computational phenotyping in cancer cell lines, CyTOF-based computational analysis of phenotypic heterogeneity in breast cancer-derived cell in the context of combinatory anti-cancer drug treatments to identify sensitive phenotypic subtypes within several breast cancer cell lines. Paul T. Spellman Ph.D. Computational immunophenotyping, CyTOF-based computational immunophenotypic analysis of a unique population of tuberculosis (TB)-recognizing T-cells known as mucosal associated invariant T (MAIT) cells. David M. Lewinsohn M.D./Ph.D.
2008 - 2012 Sr. Research Associate, Louis Picker M.D., Vaccine & Gene Therapy Institute (VGTI), OHSU. Contribution: Performed experiments, analyzed flow cytometric data, performed statistical tests, and developed reports and presentation martials.
2005 - 2007 Research Associate, Research Associate, Clinical Research Investigative Studies Program (CRISP) and Critical Care Academics Associates Program (CCAAP), OHSU. Contribution: Acquired clinical data from patient charts for ongoing studies and identified candidates for enrollment into qualifying research in the emergency department and the intensive care units.
Liina Nagirnaja, Alexandra M. Lopes, Wu-Lin Charng, Brian Miller, Rytis Stakaitis, Ieva Golubickaite, Alexandra Stendahl, Tianpengcheng Luan, Corinna Friedrich, Eisa Mahyari, […], Kristian Almstrup, Kenneth I Aston, Donald F Conrad “Diverse monogenic subforms of human spermatogenic failure”, Nature Communications, 13, 1, (2022). link
Yoshinori Fukazawa, Jeremy Smedley, Bryan Randall, Eisa Mahyari, Carly Starke, Richard Lum, Manuel Medina, Benjamin Varco-Merth, Kathleen Busman-Sahay, Miranda Fisher, “Mesenteric lymph nodes are sites of increased SIV RNA expression in SIV-infected rhesus macaques on antiretroviral therapy”, Journal of Medical Primatology, 51, 5, 320-320, (2022)
GW McElfresh, Gregory Boggy, Eisa Mahyari, Michael Stutz, Abigail Ventura, Scott Hansen, Louis Picker, Benjamin Bimber, “Single cell transcriptomic profiling of early tuberculosis infection and granuloma formation in rhesus macaque”, Journal of Medical Primatology, 51, 5, 313-314, (2022)
Eisa Mahyari, Abigail Ventura, Eric McDonald, Gregory Boggy, GW McElfresh, Scott Hansen, Louis Picker, Benjamin Bimber, “Rhesus Immunome Reference Atlas (RIRA): A multi-tissue single-cell landscape of immune cells”, Journal of Medical Primatology, 51, 5, 296-296, (2022)
Gregory J Boggy, GW McElfresh, Eisa Mahyari, Abigail B Ventura, Scott G Hansen, Louis J Picker, Benjamin N Bimber “BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data.” Bioinformatics (2022). link
Eisa Mahyari, Jingtao Guo, Ana C. Lima, Daniel P. Lewinsohn, Alexandra M. Stendahl, Katinka A. Vigh-Conrad, Xichen Nie, Liina Nagirnaja, Nicole B. Rockweiler, Douglas T.Carrell, James M.Hotaling, Kenneth I.Aston, Donald F.Conrad “Comparative single-cell analysis of biopsies clarifies pathogenic mechanisms in Klinefelter syndrome.” The American Journal of Human Genetics 108, no. 10 (2021): 1924-1945. link
N Haigwood, M Shapiro, T Cheever, S Pandey, E Mahyari, K Onwuzu, J Reed, H Sidener, J Smedley, L Colgin, A Lewis, A Johnson, B Bimber, J Sacha, A Hessell “Immune perturbation is more profound in newborn than in infant macaques during acute SHIV infection.” Journal of the International AIDS Society (2021). link
Bruce K. Patterson, Harish Seethamraju, Kush Dhody, Michael J. Corley, Kazem Kazempour, Jay Lalezari, Alina PS Pang, Eisa Mahyari et al. “CCR5 inhibition in critical COVID-19 patients decreases inflammatory cytokines, increases CD8 T-cells, and decreases SARS-CoV2 RNA in plasma by day 14.” International Journal of Infectious Diseases 103 (2021): 25-32.Link
Husam Taher, Eisa Mahyari, Craig Kreklywich, Luke S Uebelhoer, Matthew R McArdle, Matilda J Moström, Amruta Bhusari, Michael Nekorchuk, Travis Whitmer, Elizabeth A Scheef, Lesli M Sprehe, Dawn Roberts, Colette M Hughes, Kerianne A Jackson, Andrea N Selseth, Abigail B Ventura, Yujuan Yue, Kimberli A Schmidt, Jason Shao, Paul T Edlefsen, Jeremy Smedley, Richard J Stanton, Michael K Axthelm, Jacob D Estes, Scott G Hansen, Amitinder Kaur, Peter A Barry, Benjamin N Bimber, Louis J Picker, Daniel N Streblow, Klaus Früh, Daniel Malouli. “In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genome.” PLoS pathogens, 2020. Link.
Helen L Wu, Whitney C Weber, Christine Shriver‐Munsch, Tonya Swanson, Mina Northrup, Heidi Price, Kimberly Armantrout, Mitchell Robertson‐LeVay, Jason S Reed, Katherine B Bateman, Eisa Mahyari, Archana Thomas, Stephanie L Junell, Theodore R Hobbs, Lauren D Martin, Rhonda MacAllister, Benjamin N Bimber, Mark K Slifka, Alfred W Legasse, Cassandra Moats, Michael K Axthelm, Jeremy Smedley, Anne D Lewis, Lois Colgin, Gabrielle Meyers, Richard T Maziarz, Benjamin J Burwitz, Jeffrey J Stanton, Jonah B Sacha. “Viral opportunistic infections in Mauritian cynomolgus macaques undergoing allogeneic stem cell transplantation mirror human transplant infectious disease complications.” Xenotransplantation, 2020. Link.
Emily B Wong, Marielle C Gold, Erin W Meermeier, Bongiwe Z Xulu, Sharon Khuzwayo, Zuri A Sullivan, Eisa Mahyari, Zoe Rogers, Hénrik Kløverpris, Prabhat K Sharma, Aneta H Worley, Umesh Lalloo, Prinita Baijnath, Anish Ambaram, Leon Naidoo, Moosa Suleman, Rajhmun Madansein, James E McLaren, Kristin Ladell, Kelly L Miners, David A Price, Samuel M Behar, Morten Nielsen, Victoria O Kasprowicz, Alasdair Leslie, William R Bishai, Thumbi Ndung’u, David M Lewinsohn. “TRAV1-2+ CD8+ T-cells including oligoconal expansions of MAIT cells are enriched in the airways in human tuberculosis.” Nature Communications biology, 2019. NCBI link.
Yoshinori Fukazawa, Haesun Park, Mark J. Cameron, Francois Lefebvre, Richard Lum, Noel Coombes, Eisa Mahyari, Shoko I. Hagen, Jin Young Bae, Marcelo Delos Reyes, Tonya Swanson, Alfred W. Legasse, Andrew Sylwester, Scott G. Hansen, Andrew T. Smith, Petra Stafova, Rebecca Shoemaker, Yuan Li, Kelli Oswald, Michael K. Axthelm, Adrian McDermott, Guido Ferrari, David C. Montefiori, Paul T. Edlefsen, Michael Piatak, Jeffrey D. Lifson, Rafick P. Sékaly, and Louis J. Picker. “Lymph node T cell responses predict the efficacy of live attenuated SIV vaccines.” Nature Medicine, 2012. NCBI link.