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Ramana Davuluri is a world leader in Molecular Data Science, with research focus on computational analysis of non-coding genomic regions and isoform-level gene regulation. Davuluri is well-known for his pioneering efforts to use machine learning in biomedical applications – for example, development of gene promoter prediction algorithms, molecular subtyping assays for glioblastoma and ovarian cancers, deep learning algorithm for integrative earning from multi-omics datasets, and informatics pipelines for the analysis of cancer drug target interactions affected by alternative splicing. Recently, Davuluri has developed novel deep learning approaches for understanding the DNA language, and how genetic and epigenetic changes in the non-coding genome alter the DNA linguistics. Working at the interface of artificial intelligence and genomics, Davuluri is one of the first groups to develop genomic large language model, called “DNABERT”. Released in 2021, DNABERT has been widely used in understanding and decoding genomic and epigenomic languages. The DNABERT model can predict allele-specific activity based only on local nucleotide sequence context, and prioritize candidate transcription-factor-binding sites, core-promoters and splice sites that are sensitive to variants at genome-scale. Building on DNABERT’s success, his group is developing informatics methods to calculate genome-wide mutational scores, based on whole genome sequence data, and integrate other biomedical data, such as histology and RNA expression to improve prognosis and cancer outcome prediction.
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Collaborations and top research areas from the last five years
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Developing Novel Deep-Learning Based Methods for Deciphering Non-Coding Gene Regulatory Code
Davuluri, R. (PI) & Dutta, P. (CoPI)
08/5/25 → 06/30/27
Project: Research
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The Spinal Cell Atlas of Opioid-Targeted Inflammasomes in the HIV Pain Model: Mechanisms and Pathogenic Role
Tang, S. J. (PI), Davuluri, R. (CoPI) & Wollmuth, L. (CoPI)
National Institute on Drug Abuse
09/30/24 → 07/31/27
Project: Research
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Molecular signaling in mechanobiology regulation by single-cell analyses using bioinformatics approach
Qin, Y.-X. (PI), Davuluri, R. (CoPI), Wang, J. (CoPI) & Yang, Y. K. (CoPI)
10/1/23 → 09/30/26
Project: Research
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IPA Ramana Davuluri: New Epigenetic Targets in Ovarian Cancer Stem Cells
Davuluri, R. (PI)
10/1/22 → 09/30/23
Project: Research
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IPA Agreement Ramana Davuluri: New Epigenetic Targets in Ovarian Cancer Stem Cells
Davuluri, R. (PI)
10/1/21 → 09/30/22
Project: Research
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TSProm: deep learning framework to predict tissue-specific regulatory logic
Surana, P., Dutta, P., Papineni, N., Sathian, R., Zhou, Z., Liu, H. & Davuluri, R. V., Jun 2026, In: NAR Genomics and Bioinformatics. 8, 2, p. 1-11 11 p.Research output: Contribution to journal › Article › peer-review
Open Access -
A community effort to optimize sequence-based deep learning models of gene regulation
Random Promoter DREAM Challenge Consortium, Aug 2025, In: Nature Biotechnology. 43, 8, p. 1373-1383 11 p.Research output: Contribution to journal › Article › peer-review
Open Access19 Scopus citations -
Augmenting DNABERT Embeddings with Multimodal DNA Features for Improved Regulatory Sequence Interpretation
Papineni, N., Dutta, P., Chao, M. L., Acanto, O., Sathian, R., Surana, P. & Davuluri, R. V., 2025, In: Proceedings of Machine Learning Research. 311Research output: Contribution to journal › Conference article › peer-review
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Designing a time-dependent therapeutic strategy using CDK4/6 inhibitors in an intracranial ATRT model
Martin, B., Guadix, S. W., Sathian, R., Laramee, M., Pandey, A., Ray, I., Wang, A., Davuluri, R., Thomas, C. J., Dahmane, N. & Souweidane, M., Apr 1 2025, In: Neuro-Oncology. 27, 4, p. 1076-1091 16 p.Research output: Contribution to journal › Article › peer-review
Open Access -
DNABERT-S: Pioneering species differentiation with species-aware DNA embeddings
Zhou, Z., Wu, W., Ho, H., Wang, J., Shi, L., Davuluri, R. V., Wang, Z. & Liu, H., Jul 1 2025, In: Bioinformatics. 41, p. i255-i264Research output: Contribution to journal › Article › peer-review
Open Access23 Scopus citations