Biomedical Informatics Students

Education:

Research Interests:

Contact: aeboussina@ucsd.edu

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

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

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

Full Name

Research Interests

Education 

Contact

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

Full Name

Research Interests

Education 

Contact

Full Name

Research Interests

Education 

Contact

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

Full Name

Research Interests

Education 

Contact

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

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."

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

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

Ph.D. Student

Research Interests

Phylogenetics, Viral evolution and transmission, Blockchain platforms

Education 

B.A. in Biology, Williams College, M.S. in Bioengineering, UC San Diego

Selected Publications

Machado, et al. "Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus Aureus", Applied and Environmental Microbiology (2019)

Pekar, et al. "Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology", Microbiology Resource Announcements (2018) 

Contact
jepekar@eng.ucsd.edu

BISB PhD Student

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

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

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

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

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

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

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

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

BISB PhD Student

Full Name

Research Interests

Education 

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