Benjamin James
Computational Biology
I recently completed my Ph.D in EECS at MIT CSAIL performing research in computational biology in Manolis Kellis's lab, where my dissertation focused on computational genomics techniques such as single-cell and spatial omics to understand the gene regulatory landscape of human disease. You can find my resume here and my cv here
Previously, I completed my undergraduate studies at the University of Tulsa, where I wrote efficient methods for alignment-free k-mer based methods for sequence homology under Hani Girgis, and where I graduated with Bachelor of Science degrees in Computer Science and Mathematics.
I am an NSF Graduate Research Fellow and a Frederick (1953) and Barbara Cronin Fellow.
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Selected Publications
Xiong*, X., James*, B. T., Boix*, C. A., Park, Y. P., Galani, K., Victor, M. B., Sun, N., Hou, L., Ho, L.-L., Mantero, J., Scannail, A. N., Dileep, V., Dong, W., Mathys, H., Bennett, D. A., Tsai, L.-H., & Kellis, M. (2023). Epigenomic dissection of Alzheimer’s disease pinpoints causal variants and reveals epigenome erosion. Cell, 186(20), 4422–4437.e21. https://doi.org/10.1016/j.cell.2023.08.040
Boix, C. A., James, B. T., Park, Y. P., Meuleman, W., & Kellis, M. (2021). Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature, 590(7845), 300–307. https://doi.org/10.1038/s41586-020-03145-z
James, B. T., Luczak, B. B., & Girgis, H. Z. (2018). MeShClust: an intelligent tool for clustering DNA sequences. Nucleic Acids Research, 46(14), e83. https://doi.org/10.1093/nar/gky315
News Links
- Atlas of the brain’s striatum could guide researchers to new drug treatments
- Decoding the complexity of Alzheimer's disease
- Epigenomic map reveals circuitry of 30,000 human disease regions
- MIT researchers invent new human brain model to enable disease research, drug discovery
- Alzheimer’s erodes brain cells’ control of gene expression, undermining function, cognition
- Study across multiple brain regions discerns Alzheimer’s vulnerability and resilience factors
- A noninvasive treatment for "chemo brain"
- Unlocking the Secrets of Genetic Variants: New Insights from the eGTEx Project