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Biomedical Informatics Students

Aaron Evan Boussina

Aaron Broukim

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Behrooz Mamandipoor

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Brian Daniel Johnson

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David Brian Laub

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Grace Yu

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Hyrum Surya Eddington

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    BISB PhD Student

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Jonathan Lam

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    BISB Ph.D. Student

    Research Interests
    Artificial intelligence for disease diagnosis, Data privacy and storage using blockchain

    Education
    B.S. in Neurobiology, University of Washington (2017)

    • Selected Publications
      Bevacqua R, Dai X, Lam JY, Gu X, Friedlander M, Tellez K, et al. CRISPR-based genome editing in primary human pancreatic islet cells. Nature Communications (2021)
    • Bevacqua R, Lam JY, Peiris H, Whitener RL, Kim S, Gu X, Kim SK. SIX2 and SIX3 coordinately regulate functional maturity and fate of human pancreatic cells. Genes and Development (2021)
    • The Tabula Muris Consortium et al. A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature (2020)
    • The Tabula Muris Consortium et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature (2018)
    • Peiris H, Park S, Louis S, Gu X, Lam JY, Asplund O, Ippolito GC, Bottino R, Groop L, Tucker H, Kim SK. Discovering human diabetes-risk gene function with genetics and physiological assays. Nature Communications (2018)
    • Melief EJ, McKinley JW, Lam JY, Whiteley N, Bamford NS, Palmiter RD, Darvas M. (2018) Loss of glutamate signaling from the thalamus to dorsal striatum impairs motor function and slows the execution of learned behaviors. npj Parkinson's Disease (2018)

    Contact
    j7lam@ucsd.edu

Kuan-Hung (Peter) Yeh

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    BISB PhD Student

    Research Interests

    Real-World Evidence (RWE), Survival Analysis, Precision Oncology, Clinical Trials

    Education

    M.S. in Biostatistics, University of California, Los Angeles (UCLA)

    B.S. in Public Health, National Taiwan University (NTU)

     

    Contact 

    k1yeh@ucsd.edu

    Kuan-Hung (Peter) Yeh | LinkedIn

Lauryn Keeler Bruce

  • BISB PhD Student

    BISB PhD Student

    Research Interests
    Women's health, pregnancy, pregnancy complications, wearable devices, longitudinal data, decision support tools, equitable health care

    Education

    B.S. in Chemistry, UC Santa Barbara
    M.S. in Bioinformatics, San Diego State University

    Selected Publications: 
     
    Bruce, Lauryn Keeler, Dalila González, Subhasis Dasgupta, and Benjamin L. Smarr. "Biometrics of complete human pregnancy recorded by a wearable device." Accepted at npj Digital Medicine.
     
    Bruce, Lauryn Keeler, Patrick Kasl, Severine Soltani, Varun K. Viswanath, Wendy Hartogensis, Stephan Dilchert, Frederick M. Hecht ... Ashley E. Mason, and Benjamin L. Smarr. "Variability of temperature measurements recorded by a wearable device by biological sex." Biology of sex Differences 14, no. 1 (2023): 76. https://doi.org/10.1186/s13293-023-00558-z
     
    Keeler Bruce, Lauryn, Paulina Paul, Katherine K. Kim, Jihoon Kim, Theresa HM Keegan, Robert A. Hiatt, Lucila Ohno-Machado, and All of Us Research Program Investigators. "Family and personal history of cancer in the All of Us research program for precision medicine." PLoS One 18, no. 7 (2023): e0288496. https://doi.org/10.1371/journal.pone.0288496
    Kasl, Patrick, Lauryn Keeler Bruce, Wendy Hartogensis, Subhasis Dasgupta, Leena S. Pandya, Stephan Dilchert, Frederick M. Hecht et al... Ashley E. Mason, and Benjamin L. Smarr. "Utilizing Wearable Device Data for Syndromic Surveillance: A Fever Detection Approach." Sensors 24, no. 6 (2024): 1818. https://doi.org/10.3390/s24061818
    Nachmanson, Daniela, Meghana Pagadala, Joseph Steward, Callie Cheung, Lauryn Keeler Bruce, Nicole Q. Lee, Thomas J. O’Keefe et al. "Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes." Journal of Translational Medicine 20, no. 1 (2022): 623. https://doi.org/10.1101/2022.03.31.22273116
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Samuel R. Reynolds

  • BISB PhD Student

    BISB PhD Student

    Research Interests

    Epigenomics, Understanding the tumor microenvironment, Cancer modeling

    Education 

    B.A. in Biological Sciences, Dartmouth College, 2023

    Selected Publications

    Reynolds, S. R., Zhang, Z., Salas, L. A., & Christensen, B. C. (2024). Tumor microenvironment deconvolution identifies cell-type-independent aberrant DNA methylation and gene expression in prostate cancer. Clinical epigenetics16(1), 5. https://doi.org/10.1186/s13148-023-01609-3
    Reynolds, S. R., Salas, L. A., Chen, J. Q., & Christensen, B. C. (2024). Detailed immune profiling in pediatric Crohn's disease using methylation cytometry. Epigenetics19(1), 2289786. https://doi.org/10.1080/15592294.2023.2289786
    Zhang, Z.,  Reynolds, S. R.,  Stolrow, H. G.,  Chen, J.-Q.,  Christensen, B. C., &  Salas, L. A. (2023).  Deciphering the role of immune cell composition in epigenetic age acceleration: Insights from cell-type deconvolution applied to human blood epigenetic clocks. Aging Cell,  00, e14071. https://doi.org/10.1111/acel.14071

    Contact

    LinkedIn

     

Timothy Arthur

  • Biomedical Sciences PhD Student

    Biomedical Sciences PhD Student

    Research Interests 

    Comparative genomics, Microbial ecology, Host-microbe interactions, Microbiome

    Education

    Master of Science, Microbial Biology - Rutgers University, 2014, Bachelor of Science, Biological Sciences - Rowan University, 2012

    Publications

    Jiang X*, Hall AB*, Arthur TD , [4 more authors], Alm EJ, and Xavier RJ. Invertible promoters mediate antibiotic resistance and interhost adaptation. In review, Science.

    Vatanen T, Plichta CR, Somani J, Arthur TD , [13 more authors], Huttenhower C, Knip M, and Xavier RJ. Strain diversity of the human gut microbiome in early life. In review, Nature Microbiology.

    Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD , [16 more authors], Huttenhower C, and Xavier RJ. The human gut microbiome of early onset type 1 diabetes in the TEDDY study. Accepted, Nature, April 2018.

    Yassour M*, Jason E*, Hogstrom L*, Arthur TD, [12 more authors], Lander ES, Huttenhower C, Knip M and Xavier RJ. Strain-level identification of mother-to-child bacterial transmission during the first few months of life. Cell Host and Microbe, 2018. PMID: 30001517

    Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD , [16 more authors], Xavier RJ. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell , 2016. PMID: 27133167

    Arthur TD, Cavera VL, Chikindas ML. On bacteriocin delivery systems and potential applications. Future Microbiology , 2014. PMID: 24571075

    Contact 

    tarthur@ucsd.edu

Timothy Viet Pham

Varshini Sathish

  • BISB PhD Student

    BISB PhD Student

    Research Interests

    Predictive modeling using machine/deep learning, disease management, precision medicine, genomics

    Education 

    B.S. in Bioengineering: Bioinformatics, University of California, San Diego (2023)

    Selected Publications

    Jia H, Simpson S, Sathish V, et al. Development and benchmarking of machine learning models to classify patients suitable for outpatient lower extremity joint arthroplasty. J Clin Anesth. 2023;88:111147. doi:10.1016/j.jclinane.2023.111147
    Simpson S, Zhong W, Mehdipour S, Armaneous M, Sathish V, Walker N, Said ET, Gabriel RA. Classifying high risk patients for persistent opioid use after major spine surgery: A machine learning approach. Anesth Analg 2024 

    Contact

    https://www.linkedin.com/in/varshinisathish/ 

Wilfredo Gabriel Gonzalez-Rivera

  • BISB PhD Student

    BISB PhD Student

    Research Interests 

    Precision Medicine, Genetics, Genomics, Social Science in Genomics

     Research Focus: "I aim to increase recognition of the importance of including underrepresented racial and ethnic groups in genomic research to improve the accuracy and generalizability of precision medicine for all."

    Education 

    B.S. Computer Science - University of Puerto Rico, Mayaguez, 2021
    B.S. Industrial Biotechnology - University of Puerto Rico, Mayaguez, 2021

    Awards

    STARS Graduate Advocate, 2023
    Alfred P. Sloan Scholar Fellowship, 2022
    Competitive Edge Scholar, 2022

    Contact 

    wgonzalezrivera@ucsd.edu
     

Ziqi Xu

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    BISB PhD Student

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