Benjamin James

Boix, C. A., James, B. T., Park, Y. P., Meuleman, W., & Kellis, M. (2025). Author Correction: Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature, 643(8071), E11. https://doi.org/10.1038/s41586-025-09134-4

Liu, Z., Zhang, S., James, B. T., Galani, K., Mangan, R. J., Fass, S. B., Liang, C., Wagle, M. M., Boix, C. A., Tanigawa, Y., Yun, S., Sung, Y., Xiong, X., Sun, N., Hou, L., Wohlwend, M., Qiu, M., Han, X., Xiong, L., … Kellis, M. (2025). Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience. Cell, 188(18), 4980–5002.e29. https://doi.org/10.1016/j.cell.2025.06.031

Mudge, J. M., Carbonell-Sala, S., Diekhans, M., Martinez, J. G., Hunt, T., Jungreis, I., Loveland, J. E., Arnan, C., Barnes, I., Bennett, R., Berry, A., Bignell, A., Cerdán-Vélez, D., Cochran, K., Cortés, L. T., Davidson, C., Donaldson, S., Dursun, C., Fatima, R., … Frankish, A. (2025). GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Research, 53(D1), D966–D975. https://doi.org/10.1093/nar/gkae1078

Stanton, A. E., Bubnys, A., Agbas, E., James, B., Park, D. S., Jiang, A., Pinals, R. L., Liu, L., Truong, N., Loon, A., Staab, C., Cerit, O., Wen, H.-L., Mankus, D., Bisher, M. E., Lytton-Jean, A. K. R., Kellis, M., Blanchard, J. W., Langer, R., & Tsai, L.-H. (2025). Engineered 3D immuno-glial-neurovascular human miBrain model. Proceedings of the National Academy of Sciences, 122(42), e2511596122. https://doi.org/10.1073/pnas.2511596122

Kim, T., James, B. T., Kahn, M. C., Blanco-Duque, C., Abdurrob, F., Islam, M. R., Lavoie, N. S., Kellis, M., & Tsai, L.-H. (2024). Gamma entrainment using audiovisual stimuli alleviates chemobrain pathology and cognitive impairment induced by chemotherapy in mice. Science Translational Medicine, 16(737), eadf4601. https://doi.org/10.1126/scitranslmed.adf4601

Mathys, H., Boix, C. A., Akay, L. A., Xia, Z., Davila-Velderrain, J., Ng, A. P., Jiang, X., Abdelhady, G., Galani, K., Mantero, J., Band, N., James, B. T., Babu, S., Galiana-Melendez, F., Louderback, K., Prokopenko, D., Tanzi, R. E., Bennett, D. A., Tsai, L.-H., & Kellis, M. (2024). Single-cell multiregion dissection of Alzheimer’s disease. Nature, 632(8026), 858–868. https://doi.org/10.1038/s41586-024-07606-7

Frankish, A., Carbonell-Sala, S., Diekhans, M., Jungreis, I., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Arnan, C., Barnes, I., Banerjee, A., Bennett, R., Berry, A., Bignell, A., Boix, C., Calvet, F., Cerdán-Vélez, D., Cunningham, F., Davidson, C., … Flicek, P. (2023). GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research, 51(D1), D942–D949. https://doi.org/10.1093/nar/gkac1071

Hou, L., Xiong, X., Park, Y., Boix, C., James, B., Sun, N., He, L., Patel, A., Zhang, Z., Molinie, B., Van Wittenberghe, N., Steelman, S., Nusbaum, C., Aguet, F., Ardlie, K. G., & Kellis, M. (2023). Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease. Nature Genetics, 55(10), 1665–1676. https://doi.org/10.1038/s41588-023-01509-5

Sun, N., Victor, M. B., Park, Y. P., Xiong, X., Scannail, A. N., Leary, N., Prosper, S., Viswanathan, S., Luna, X., Boix, C. A., James, B. T., Tanigawa, Y., Galani, K., Mathys, H., Jiang, X., Ng, A. P., Bennett, D. A., Tsai, L.-H., & Kellis, M. (2023). Human microglial state dynamics in Alzheimer’s disease progression. Cell, 186(20), 4386–4403.e29. https://doi.org/10.1016/j.cell.2023.08.037

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

Girgis, H. Z., James, B. T., & Luczak, B. B. (2021). Identity: rapid alignment-free prediction of sequence alignment identity scores using self-supervised general linear models. Nar Genomics and Bioinformatics, 3(1), lqab001. https://doi.org/10.1093/nargab/lqab001

Velasco, A. II, James, B. T., Wells, V. D., & Girgis, H. Z. (2020). Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models. Bioinformatics, 36(2), 380–387. https://doi.org/10.1093/bioinformatics/btz551

Luczak, B. B., James, B. T., & Girgis, H. Z. (2019). A survey and evaluations of histogram-based statistics in alignment-free sequence comparison. Briefings in Bioinformatics, 20(4), 1222–1237. https://doi.org/10.1093/bib/bbx161

Zielezinski, A., Girgis, H. Z., Bernard, G., Leimeister, C.-A., Tang, K., Dencker, T., Lau, A. K., Röhling, S., Choi, J. J., Waterman, M. S., Comin, M., Kim, S.-H., Vinga, S., Almeida, J. S., Chan, C. X., James, B. T., Sun, F., Morgenstern, B., & Karlowski, W. M. (2019). Benchmarking of alignment-free sequence comparison methods. Genome Biology, 20(1), 144. https://doi.org/10.1186/s13059-019-1755-7

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

Middelbeek, R. J. W., Yang, J., Nigro, P., James, B., Papadopoulos, D., Simpson, L. K., Park, J., Vamvini, M., Ho, L.-L., Zhang, H., Carbone, N. P., Hirshman, M. F., Kellis, M., & Goodyear, L. J. (2025). Type 2 Diabetes and Obesity Alter Exercise Training-Induced Transcriptional Adaptations to Subcutaneous White Adipose Tissue. bioRxiv. https://doi.org/10.1101/2025.10.11.681273

Gschwind, A. R., Mualim, K. S., Karbalayghareh, A., Sheth, M. U., Dey, K. K., Jagoda, E., Nurtdinov, R. N., Xi, W., Tan, A. S., Jones, H., Ma, X. R., Yao, D., Nasser, J., Avsec, Ž., James, B. T., Shamim, M. S., Durand, N. C., Rao, S. S. P., Mahajan, R., … Engreitz, J. M. (2023). An encyclopedia of enhancer-gene regulatory interactions in the human genome. bioRxiv. https://doi.org/10.1101/2023.11.09.563812

James, B. T., & Girgis, H. Z. (2018). MeShClust2: Application of alignment-free identity scores in clustering long DNA sequences. bioRxiv. https://doi.org/10.1101/451278

James, B. T. (2023). Correlation-based Linking of Epigenomic Regions to Target Genes in Bulk and Single Cell Epigenomic Data [Thesis, Massachusetts Institute of Technology]. https://dspace.mit.edu/handle/1721.1/151538