Benjamin Fefferman
Benjamin Fefferman
bfefferman@g.harvard.edu
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Education
Education
Harvard Graduate School of Arts and Sciences
Department of Biomedical Informatics - Longwood, MA
Ph.D. candidate, Bioinformatics & Integrative Genomics
The University of Chicago
Bachelor of Science, Biological Sciences - Specialization, Cancer Biology, Minor, Data Science
Research Interests
Research Interests
Machine learning, natural language processing, generative AI
Computational genomics, precision oncology
Data engineering, data science
Statistical data analysis
Drug discovery
Experience
Experience
Dana Farber Cancer Institute
Fall 2024 - Spring 2025
Massachusetts General Hospital
Fall 2024
Computer Science & Artificial Intelligence Laboratory
Spring 2023-24
Broad Institute of MIT and Harvard
Fall 2022
The University of Chicago - Department of Chemistry
2018-2022
Publications & Presentations
Publications & Presentations
LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA - Summer 2024
Xiao-Long Cui, Ji Nie, Houxiang Zhu, Krissana Kowitwanich, Alana
V Beadell, Diana C West-Szymanski, Zhou Zhang, Urszula Dougherty, Akushika Kwesi, Zifeng Deng, Yan Li, Danqing Meng, Kevin Roggin, Teresa Barry, Ryan Owyang, Ben Fefferman, Chang Zeng, Lu Gao, Carolyn W T Zhao, Yuri Malina, Jiangbo Wei, Melanie Weigert, Wenjun Kang, Ajay Goel, Brian C-H Chiu, Marc Bissonnette, Wei Zhang, Mengjie Chen, Chuan He
Data Analysis Presentation to NCI Human Cancer Models Initiative - “Proteogenomic Analysis of Sequence, Structure, & Function for Modular MPRA (Massively Parallel Reporter Assay) Design in NGCMs (Next Generation Cancer Models)” - Winter 2023
Data Analysis Presentation to NCI Human Cancer Models Initiative - “Updates on massively parallel reporter assays that model intratumoral heterogeneity using NGCMs” - Spring 2023
Bachelor of Science Thesis (from research during 2019-2022) - "5-
Hydroxymethylcytosine Profiles in Cancer - High-Throughput Epigenetics & Machine Learning Applied Toward Precision Oncology" - Fall 2021 - Spring 2022
Beckman Symposium - Bio-Chem Speaker & Poster Presentation
Summer 2021
Institute for Biophysical Dynamics - Research Meetings
Summer 2019
Skills
Skills
Programming Languages
Python
Unix / Linux / Bash
JAX for parallel programming / multi-GPU simulations
SQL
R
Use of HPC clusters for data analysis
Pythonic workflow management systems (Snakemake)
Certificates
Algorithms: Design and Analysis I, Stanford EdX
R & Statistics - Data Analysis for Life Sciences, Harvard EdX
Languages
Spanish - Awarded Illinois State Seal of Biliteracy (2018)
English
Service & Leadership
Service & Leadership
Peer Mentoring - Bioinformatics & Integrative Genomics, Fall 2024
Graduate student mentor
Phoenix Tutoring - The University of Chicago
Section coordinator
Leading groups and serving as a volunteer tutor, teaching local Chicago students math, science and reading
McLean Center for Medical Ethics Lecture Series - University of Chicago Medical Center
Attendee
Attending lectures by researchers at the University of Chicago and throughout the United States regarding medical ethics, including topics of diversity and inclusion in medicine, providing care with limited resources, and the impact of COVID-19 on the healthcare system
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