Aaron Evan Boussina
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Education:
Research Interests:
Contact: aeboussina@ucsd.edu
Adam Officer
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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
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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
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
Behrooz Mamandipoor
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Full Name
Research Interests
Education
Contact
Briana Chronister
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UCSD/SDSU Joint Doctoral Program in Public Health, Global Health
Education
BS Biological Sciences
MS Global HealthResearch Interests
Environmental health, and more specifically, in identifying social and behavioral factors that increase exposures to toxic chemicals, and assessing their subsequent effects on healthContact
bcortez@health.ucsd.edu
Brian Daniel Johnson
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Full Name
Research Interests
Education
Contact
Carina Samantha Brown
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Full Name
Research Interests
Education
Contact
Christopher Fong
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UCSD/SDSU Joint Doctoral Program in Clinical Psychology
Education
MA in PsychologyResearch 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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Full Name
Research Interests
Education
Contact
Fatemeh Amrollahi
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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
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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
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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):263-74Kim 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 AssociationKim 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
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BISB Ph.D. Student
Research Interests
Artificial intelligence for disease diagnosis, Data privacy and storage using blockchainEducation
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 - Selected Publications
Jonathan Pekar
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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
Lauryn Keeler Bruce
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BISB PhD Student
Margie Hernandez Mejia
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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
Molly Wilkinson
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Joint Ph.D. program in Clinical Psychology
Education
BS Behavioral NeurosciencesResearch Interests
The use of multimodal task-based neuroimaging integration, specifically fMRI and MEG, to study neural activity in adolescents with autism spectrum disorderContact
mollykwilkinson@gmail.com
Nancy Yuan
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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
Nathaniel Delos Santos
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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
Nora Satybaldiyeva
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Joint Ph.D. program in Public Health, Epidemiology
Education
BS Biology
MPH EpidemiologyResearch Interests
Using epidemiological methods to understand cannabis and tobacco co-use among adolescentsContact
norasati@gmail.com
Owen Chapman
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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
Steven Rick
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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
Timothy Arthur
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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
Timothy Viet Pham
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BISB PhD Student
Wilfredo Gabriel Gonzalez-Rivera
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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, 2021Awards
STARS Graduate Advocate, 2023
Alfred P. Sloan Scholar Fellowship, 2022
Competitive Edge Scholar, 2022Contact