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Biomedical Informatics Students

Aaron Evan Boussina

Adam Officer

  • BISB Ph.D. Student

    BISB Ph.D. Student

    Research Interests

    Tumor immune microenvironment, Mechanisms of breast cancer progression, Triple-negative breast cancer subtyping and treatment

    Education 

    B.S. in Biochemistry, The University of Washington

    Selected Publications

    Gopal, Lu, Man, Baur, Rao, Litichevskiy, Papanastasiou, Creech, DeRuff, Mullahoo, Officer, Egri, Davison, Jaffe, Jaffe, A phosphoproteomic signature in endothelial cells predicts vascular toxicity of tyrosine kinase inhibitors used in CML, Blood Advances, 2018 Jul

    Horwitz, Koch, Porcu, Oki, Moskowitz, Perez, Myskowski, Officer, Jaffe, Allen, Douglas, Stern, Sweeney, Kelly, Kelly, Aster, Foss, Weinstock, Activity of the PI3k-d,g inhibitor Duvelisib in a Phase I Trial and Preclinical Models of T-Cell Lymphoma, Blood, 2017 Nov

    Abelin, Patel, Lu, Feeney, Fagbami, Creech, Hu, Lam, Davison, Pino, Qiao, Kuhn, Officer, Li, Abbatiello, Subramanian, Sidman, Snyder, Carr, Jaffe, Reduced-representation phosphosignatures measured by quantitative targeted MS capture cellular states and enable large-scale comparison of drug-induced phenotypes, Molecular and Cellular Proteomics, 2016 May

Alex Wenzel

  • BISB Ph.D. Student

    BISB Ph.D. Student

    Research Interests

    Cancer genomics, Computational analysis of genome sequencing

    Education 

    B.S. in Computer Science, Northwestern University McCormick School of Engineering and Applied Science

    Publications

    Park, et al. "Genomic Analysis of 220 CTCLs Identifies a Novel Recurrent Gain-of-Function Alteration in RLTPR (p.Q575E)", Blood 2017

    Marcel Flores, Alexander Wenzel, Aleksander Kuzmanovic. "Kick-Ass: Enabling Router-Assisted Congestion Control", ICNP 2016

    Yelamos, et al. "Non-overlapping Clinical and Mutational Patterns in Melanomas from the Female Genital Tract and Atypical Genital Nevi", Journal of Investigative Dermatology (2016)

    Haugh, et al. "Distinct Patterns of Acral Melanoma Based on Site and Relative Sun Exposure", Journal of Investigative Dermatology (2017)

    Marcel Flores, Alexander Wenzel, Aleksander Kuzmanovic. "Oak: User-Targeted HTTP Performance"

    Marcel Flores, Alexander Wenzel, Kevin Chen, Aleksander Kuzmanovic. "Fury Route: Leveraging CDNs to Remotely Measure Network Distance" (under submission)

    Contact 

    atwenzel@eng.ucsd.edu

Alexis Garduno

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    PhD Student

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Anh Pham

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    Ph.D. Student

    Research Interests 

    Text and data mining in medical literature, Knowledge representation and sharing using machine learning and AI, Data management

    Education 

    Bachelor of Sciences (Mathematics/Economics) - UC San Diego, La Jolla, CA

    Projects

    SciCrunch: promote research reproducibility with machine learning tools

    Karen Stocks, Stephen Diggs (Scripps Institution of Oceanography): SeaView (part of EarthCube), data integration across multiple repositories

    Contact 

    anp055@eng.ucsd.edu

Behrooz Mamandipoor

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Briana Chronister

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    UCSD/SDSU Joint Doctoral Program in Public Health, Global Health

    Education
    BS Biological Sciences
    MS Global Health 

    Research Interests
    Environmental health, and more specifically, in identifying social and behavioral factors that increase exposures to toxic chemicals, and assessing their subsequent effects on health

    Contact
    bcortez@health.ucsd.edu

Brian Daniel Johnson

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Christopher Fong

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    UCSD/SDSU Joint Doctoral Program in Clinical Psychology

    Education
    MA in Psychology

    Research Interests
    Examining the neural correlates of treatment in comorbid Posttraumatic Stress Disorder and Alcohol Use Disorders.

    Contact
    c4fong@ucsd.edu

David Brian Laub

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Fatemeh Amrollahi

  • Ph.D. Student

    Ph.D. Student

    Research Interests

    Critical Care Informatics, Machine Learning/Deep Learning, Natural Language Processing, Systems Engineering

    Education 

    M.S. in Computer Science with a Biomedical Informatics Specialization, Emory University, B.Sc in Computer Engineering, Amirkabir University of Technology

Grace Yu

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Hyrum Surya Eddington

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    BISB PhD Student

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Jennifer Nguyen

  • Ph.D. Student

    Ph.D. Student

    Research Interests

    Human Genetics, Epigenomics, Developmental Biology

    Education

    B.S. in Biochemistry, The University of Texas at Dallas - Richardson

    Selected Publications

    D'Antonio-Chronowska A, Donovan M, Benaglio P, Greenwald W, Nguyen J, Fujita K, Hashem S, Matsui H, Soncin F, Parast M, Ward M, Coulet F, Smith E, Adler E, D'Antonio M, Frazer K. Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac Differentiation Trajectories. Cell Stem Cell Reports (2019)

    Martire S, Gogate A, Whitmill A, Tafessu A, Nguyen J, Teng Y, Tastemel M, Banaszynski L. "Phosphorylation of histone H3. 3 at serine 31 promotes p300 activity and enhancer acetylation." Nature genetics (2019)

    Nguyen, J, Jiao J, Smoot K, Watt G, Zhao C, Song X, Stevenson H.L., McCormick J, Fisher-Hoch S, Zhang J, Futreal A, Beretta L. "Toll-like Receptor 4: a Target for Chemoprevention of Hepatocellular Carcinoma in Obesity and Steatohepatitis." Oncotarget (2018)

    Chen L, Long C, Nguyen J, Kumar D, Lee J. "Discovering alkylamide derivatives of bexarotene as new therapeutic agents against triple-negative breast cancer." Bioorganic & Medicinal Chemistry Letters (2017).

    Nguyen J, Chen L, Kumar D, Lee J. "Facile synthesis of autophagonizer and evaluation of its activity to induce autophagic cell death in apoptosis-defective cell line."

    Bioorganic & Medicinal Chemistry Letters (2016)

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

Jonathan Pekar

Kuan-Hung Yeh

  • BISB PhD Student

    BISB PhD Student

    Research Interests

    Clinical Informatics, Genetic Disease Screening, Techniques for combining DNA and RNA-sequencing analyses with electronic medical records to aid in personalized medicine efforts.

    Education

    B.S. in Bioengineering- University of California, San Diego

    Selected Publications

    Pineda G, Lennon KM, Delos santos NP, et al. Tracking of Normal and Malignant Progenitor Cell Cycle Transit in a Defined Niche. Sci Rep. 2016;6:23885.

    Holm F, Hellqvist E, Mason CN, Ali SA, Delos-Santos N, Barrett CL, Chun HJ, Minden MD, Moore RA, Marra MA, Runza V, Frazer KA, Sadarangani A, Jamieson CH. Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal. Proc Natl Acad Sci USA. 2015;112(50):15444-9.

    Contact 

    Nathaniel.P.DelosSantos@jacobs.ucsd.edu

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Lauryn Keeler Bruce

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    BISB PhD Student

Margie Hernandez Mejia

  • Margie Hernandez Mejia, M.A.

    Margie Hernandez Mejia, M.A.

    Education

    M.A. in Clinical Psychology, University of North Carolina Wilmington

    Research Interests

    Neurocognitive and structural brain changes related to healthy adolescent neurodevelopment and substance misuse. Risk factors for adverse neural and behavioral outcomes among ethnic minority youth.

    Contact

    mihernandez065@gmail.com

Molly Wilkinson

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    Joint Ph.D. program in Clinical Psychology

    Education
    BS Behavioral Neurosciences

    Research Interests
    The use of multimodal task-based neuroimaging integration, specifically fMRI and MEG, to study neural activity in adolescents with autism spectrum disorder

    Contact
    mollykwilkinson@gmail.com

Nancy Yuan

  • BISB PhD Student

    BISB PhD Student

    Research Interests

    Deep learning for clinical applications, Predictive analytics, Disease diagnostics

    Education

    Master of Science in Biology, UC San Diego, Bachelor of Science in Biology, University of Texas at Austin

    Projects 

    Characterizing species-independent attraction to biofilms through electrical signaling (Masters Thesis)

    Isolating dehydrating modules from trans-acyltransferase polypeptide synthases (Undergraduate Project)

    Contact 

    f5yuan@eng.ucsd.edu

Nora Satybaldiyeva

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    Joint Ph.D. program in Public Health, Epidemiology

    Education
    BS Biology
    MPH Epidemiology

    Research Interests
    Using epidemiological methods to understand cannabis and tobacco co-use among adolescents

    Contact
    norasati@gmail.com

Timothy Arthur

  • BISB PhD Student

    BISB 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

Varshini Sathish

  • BISB PhD Student

    BISB PhD Student

    Research Interests

    Machine-assisted protein characterization, Disease discovery and characterization using probabilistic models

    Education 

    Bachelor of Arts (Computer Science) Pomona College, Claremont CA, 2017

    Projects 

    Aaron Leconte, Andre Cavalcanti: Adapting Statistical Coupling Analysis (SCA) for protein engineering (undergraduate)

    Contact

    ochapman@eng.ucsd.edu

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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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