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Biomedical Informatics Students

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

  • Joint Ph.D. Program in Public Health, Epidemiology

    Education
    BS Bioengineering
    MPH Epidemiology

    Research Interests
    Genetic and behavioral epidemiology, using advanced statistical learning to address questions in the field of circadian rhythm and aging

    Contact
    agarduno@health.ucsd.edu

Andrea Castro

  • BISB Ph.D. Student

    BISB Ph.D. Student

    Research Interests 

    Artificial intelligence for precision medicine and drug discovery, Immunoinformatics

    Education 

    B.S. Microbiology Immunology and Molecular Genetics - UCLA, 2017

    Projects

    Elevated Neoantigen Levels in Tumors with Somatic Mutations to B2M and HLA (Spring Rotation, Dr. Hannah Carter)

    Nomograms for Patient Drug Response Prediction (Winter Rotation, Dr. Pablo Tamayo)

    Using Deep Learning to Predict ICU Patient Mortality (Fall Rotation, Dr. Jejo Koola)

    Contact

    andreabcastro@ucsd.edu

Anh Pham

  • 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

Briana Chronister

  • 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

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

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)

Jihoon Kim

  • BISB PhD Student

    Selected Publications 
    Jiang X, Osl M, Kim J, Ohno-Machado L (2012) Calibrating predictive model estimates to support personalized medicine, J Am Med Inform Assoc. 2012 Mar 1;19(2):263-74

    Kim HE, Jiang X, Kim J, Ohno-Machado L (2011) Trends in biomedical informatics: most cited topics from recent years, Journal of the American Medical Informatics Association 18 (Suppl 1), i166-i170

    Ohno-Machado L, Bafna V, AA Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, and iDASH Team, iDASH: integrating data for analysis, anonymization, and sharing
    Journal of the American Medical Informatics Association

    Kim J, Grillo JM, Boxwala AA, Jiang XJ, Mandelbaum RB, Patel BA, Mikels D, Vinterbo SA, Ohno-Machado L (2011), Anomaly and Signature Filtering Improve Classifier Performance For Detection Of Suspicious Access To EHRs, American Medical Informatics Association Annual Symposium

    Boxwala A, Kim J,  Grillo JM, Ohno-Machado L (2011) Using statistical and machine learning to help institutions detect suspicious access to electronic health records, JAMIA, 18:498-505

    Kim J, Patel K, Jung H, Kuo WP, Ohno-Machado L (2011) AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm, BMC Bioinformatics, March 17:12-75

    Jiang X, Osl M, Kim J, Ohno-Machado L (2011) Smooth Isotonic Regression: A New Method to Calibrate Predictive Models, American Medical Informatics Association Annual Symposium

    Eckert MA, Lwin TM, Chang AT, Kim J, Danis E, Ohno-Machado L, Yang J (2011) Twist1-induced invadopodia formation promotes tumor metastasis, Cancer Cell, 19(3):372-386.

    Casas E, Kim J, Bendesky A, Ohno-Machado L, Wolfe CJ, Yang J (2011) Snail2 is an essential mediator of Twist1-induced epithelial mesenchymal transition and metastasis, Cancer Res, 71(1):245-254

Jonathan Lam

  • 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

Lauryn Keeler Bruce

  • BISB PhD Student

Molly Wilkinson

  • 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

Nathaniel Delos Santos

  • 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

Nora Satybaldiyeva

  • 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

Owen Chapman

  • 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

Steven Rick

  • CSE PhD Student

    CSE PhD Student

    Research Interests 

    HCl and Computational Ethnography in Healthcare, Autonomous agents as they support clinical decision support and care coordination

    Education

    B.S. Cognitive Science, University of California, San Diego

    Selected Publications 

    N. Weibel, S. Hwang, S. Rick, E. Sayyari, D. Lenzen, and J. Hollan, “Hands that Speak: An Integrated Approach to Studying Complex Human Communicative Body Movements,” in Proceedings of HICSS-49, Hawaii International Conference on System Sciences, Kauai, HI, USA, 2016.

    A. Rule, S. Rick, M. Chiu, P. Rios, S. Ashfaq, A. Calvitti, W. Chan, N. Weibel, and Z. Agha, “Validating free-text order entry for a note-centric EHR,” in Proceedings of AMIA 2015, American Medical Informatics Association, Annual Symposium, San Francisco, USA, 2015.

    S. Rick, A. Calvitti, Z. Agha, N. Weibel. "Eyes on the clinic: Accelerating meaningful interface analysis through unobtrusive eye tracking," in Pervasive Computing Technologies for Healthcare (PervasiveHealth), 2015 9th International Conference, Istanbul, Turkey, 2015.

    S. Rick, A. Calvitti, Z. Agha, N. Weibel. "Eyes on the clinic: Accelerating meaningful interface analysis through unobtrusive eye tracking," in Pervasive Computing Technologies for Healthcare (PervasiveHealth), 2015 9th International Conference, Istanbul, Turkey, 2015.

    Contact

    srick@eng.ucsd.edu

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

Timothy Viet Pham

  • BISB PhD Student