Aaron Evan Boussina
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Education:
Research Interests:
Contact: aeboussina@ucsd.edu
Aaron Broukim
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Full Name
Research Interests
Education
Contact
Brian Daniel Johnson
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Full Name
Research Interests
Education
Contact
David Brian Laub
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Full Name
Research Interests
Education
Contact
Grace Yu
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Full Name
Research Interests
Education
Contact
Hyrum Surya Eddington
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BISB PhD Student
Research Interests
Education
Projects
Contact
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
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
Lauryn Keeler Bruce
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BISB PhD Student
Research InterestsWomen's health, pregnancy, pregnancy complications, wearable devices, longitudinal data, decision support tools, equitable health care
Education
B.S. in Chemistry, UC Santa BarbaraM.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-zKeeler 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.0288496Kasl, 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/s24061818Nachmanson, 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/10.1101/2022.03.31.22273116Contact
Samuel R. Reynolds
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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 epigenetics, 16(1), 5. https://doi.org/10.1186/s13148-023-01609-3Reynolds, S. R., Salas, L. A., Chen, J. Q., & Christensen, B. C. (2024). Detailed immune profiling in pediatric Crohn's disease using methylation cytometry. Epigenetics, 19(1), 2289786. https://doi.org/10.1080/15592294.2023.2289786Zhang, 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.14071Contact
Timothy Arthur
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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
Timothy Viet Pham
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Bioinformatics and Systems Biology PhD Student
Contact: tvp005@health.ucsd.edu
Varshini Sathish
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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.2023.111147Simpson 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 2024Contact
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
Ziqi Xu
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BISB PhD Student
Research Interests
Education
Selected Publications
Contact