Genome resource announcement of a Leptodophora sp. fungus isolated from roots of broadleaf plants in Wisconsin, USA
July 23, 2026
Tristan Yang , Amanda Certano , Venkatacha Lakshmanan , Sebastian Bassi , Neeraj Purushotham , Tegan Nock , Abed M. Chaudhury , Animesh Ray. Genome resource announcement of a Leptodophora sp. fungus isolated from roots of broadleaf plants in Wisconsin, USA. Microbiol Resour Announc 14:e00936-24 (2025). https://doi.org/10.1128/mra.00936-24
Fine-tuned protein language model identifies antigen-specific B cell receptors from immune repertoires
October 30, 2025
Karen Paco, Mariana Paco Mendivil, Zihao Zhang, Sanaz Zebardast, Christian Davila, Ryan M. Mooney, Peace Olatoyinbo, Tristan Yang, Sebastian Bassi, Virginia Gonzalez, Eva Chen, Faisal Bin Ashraf, Isabel Condori Roman, Jonathan R. Felix, Rashid M. Alam, Jordan A. Lay, Malkiat S. Johal, Karine G. Le Roch, Ilya Tolstorukov, Jeniffer B. Hernandez, Fernando L. Barroso da Silva, Stefano Lonardi, Matthew H. Sazinsky, and Animesh Ray. Fine-tuned protein language model identifies antigen-specific B cell receptors from immune repertoires. BioRxiv 2025.10.30.685465; doi: https://doi.org/10.1101/2025.10.30.685465
Red Blood Cell-Derived Exosomes as Mediators of Age – Related Neurodegeneration
June 24, 2025
Jonalyn DeCastro, Ami Mehta-Doshi, Chao Liu, Animesh Ray, and Kiana Aran. Red Blood Cell-Derived Exosomes as Mediators of Age- Related Neurodegeneration. Rejuvenation Res. 4:184-194 (2025). https://doi.org/10.1089/rej.2025.0013
Biophysics of SARS-CoV-2 spike protein’s receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights
March 8, 2025
Fernando L. Barroso da Silva, Karen Paco, A. Laaksonen, and Animesh Ray. Biophysics of SARS-CoV-2 spike protein’s receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights. Biophysical Reviews 17: 309-333 (2025). doi: https://doi.org/10.1007/s12551-025-01276-z
A Large Language Model Guides the Affinity Maturation of Antibodies Generated by Combinatorial Optimization Algorithms
December 19, 2024
Faisal Bin Ashraf, Karen Paco, Zihao Zhang, Christian J. Dávila Ojeda, Mariana P. Mendivil, Jordan A. Lay, Tristan Y. Yang, Fernando L. Barroso da Silva, Matthew H. Sazinsky, Animesh Ray, Stefano Lonardi. A Large Language Model Guides the Affinity Maturation of Antibodies Generated by Combinatorial Optimization Algorithms. BioRxiv 2024.12.19.629473; doi: https://doi.org/10.1101/2024.12.19.629473
Systematic transcriptomic analysis of childhood medulloblastoma identifies N6-methyladenosine-dependent lncRNA signatures associated with molecular subtype, immune cell infiltration, and prognosis
August 28, 2024
Joshi, K, Yuan, M, Katsushima, K, Saulnier, O, Ray, A, Amankwah, E, Stapleton, S, Jallo, G, Taylor, MD, Eberhart, CG, Perera, RJ. Systematic transcriptomic analysis of childhood medulloblastoma identifies N6-methyladenosine-dependent lncRNA signatures associated with molecular subtype, immune cell infiltration, and prognosis. Acta Neuropathol Commun 28:138 (2024). https://doi.org/10.1186/s40478-024-01848-2
Identification of Antigen Specific B-cell receptors from single-cell V(D)J sequences using a Large Language Model, ASPred
April 4, 2024
Karen Paco ⋅ Zihao Zhang ⋅ Mariana Paco Mendivil ⋅ Peace Olatoyinbo ⋅ Sanaz Zebardast ⋅ Dhruv Patel ⋅ Isabel Condori ⋅ Jordan Lay ⋅ Karine Le Roch ⋅ Tristan Yang ⋅ Jonathan Felix ⋅ Jeniffer Hernandez ⋅ Matthew Sazinsky ⋅ Ilya Tolstorukov ⋅ Stefano Lonardi ⋅ Animesh Ray. Identification of Antigen Specific B-cell receptors from single-cell V(D)J sequences using a Large Language Model, ASPred. NeurIPS (2024); https://neurips.cc/virtual/2024/107782
miRNA-211 maintains metabolic homeostasis in medulloblastoma through its target gene long-chain acyl-CoA synthetase 4
December 19, 2023
Yuan, M., Mahmud, I., Katsushima, K., Joshi, K., Saulnier, O., Pokhrel, R., Lee, B., Liyanage, W., Kunhiraman, H., Stapleton, S., Gonzalez-Gomez, I., Kannan, R.M., Eisemann, T., Kolanthai, E., Seal, S., Garrett, T.J., Abbasi, S., Bockley, K., Hanes, J., Chapagain, P., Jallo, G., Wechsler-Reya, R.J., Taylor, M.D., Eberhart, C.G., Ray, A. & Perera, R.J. miRNA-211 maintains metabolic homeostasis in medulloblastoma through its target gene long-chain acyl-CoA synthetase 4. Acta Neuropathol Commun 11: 203 (2023). https://doi.org/10.1186/s40478-023-01684-w
The long non-coding RNA SPRIGHTLY and its binding partner PTBP1 regulate exon 5 skipping of SMYD3 transcripts in group 4 medulloblastomas
August 2, 2023
Lee, B., Katsushima, K., Pokhrel, R., Yuan, M., Stapleton, S., Jallo, G., Wechsler-Reya, R.J., Eberhart, C.G., Ray, A., and Perera, R.J. (2022). The long non-coding RNA SPRIGHTLY and its binding partner PTBP1 regulate exon 5 skipping of SMYD3 transcripts in group 4 medulloblastomas. Neuro-Oncology Advances 4, Issue 1 (2022) DOI: 10.1093/noajnl/vdac120
Machine learning in post-genomic biology
January 24, 2022
Ray, A. Machine learning in post-genomic biology. Data Mining Knowledge Discov. e1451 (2022) DOI: https://doi.org/10.1002/widm.1451
The paradoxical behavior of microRNA211 in melanomas and other human cancers
February 8, 2021
Ray, A. Kunhiraman, H, and Perera, R. The paradoxical behavior of microRNA211in melanomas and other human cancers. Front Oncol 10:628367 (2021) DOI: 3389/fonc.2020.628367
MicroRNA-211 modulates the DUSP6-ERK5 signaling axis to promote BRAFV600E-driven melanoma growth in vivo and BRAF/MEK inhibitor resistance
September 1, 2020
Lee, B., Sahoo, A., Mahmud, I., Sawada, J., Marchica, J., Sahoo, S., Layng,F.I.A.L., Finlay, D., Mazar, J., Joshi, P., Komatsu, M., Vuori, K., de Jong, R., Garrett, T., Ray, A., and Perera, R.J. MicroRNA-211 modulates the DUSP6-ERK5 signaling axis to promote BRAFV600E-driven melanoma growth in vivo and BRAF/MEK inhibitor resistance. J. Invest Dermatol 141: 385-394 (2021) https://doi.org/10.1016/j.jid.2020.06.038
Brahmachary’s contributions during the infancy of molecular embryology
September 1, 2020
Ray, A. Fields, Patterns and Information: R. L. Brahmachary’s contributions during the infancy of molecular embryology. J. Dev. Biol. 64: 35-40 (2020) doi: 10.1387/ijdb.190171ar
Supervised machine learning with protein structural and network topological features predicts physical interactors of the human Huntington’s disease protein
January 1, 2019
Lokhande, S., Koo, S. & Ray, A. Supervised machine learning with protein structural and network topological features predicts physical interactors of the human Huntington’s disease protein. In Proceedings of the IEEE International Conference on Computational Science and Computational Intelligence – International Society on Computational Biology (CSCI-ISCB’18) (2019). https://american-cse.org/csci2018/pdfs/CSCI2018-3OvSlHpbnpxVCh7wjFqa17/7ht0x0jlF6ti2iEcwm7ZHe/5D1IyF8caGwh7GwoGnrSse.pdf
The long noncoding RNA SPRIGHTLY acts as an intra-nuclear organizing hub for pre-mRNA molecules
May 3, 2017
Lee, B., Sahoo, A., Marchica1, J., Holzhauser, E., Chen, X., Li, J.-L., Seki, T., Govindarajan, S., Markey, F.B., Batish, M., Lokhande, S.J., Zhang, S., Ray, A. & Perera, R.J. The long noncoding RNA SPRIGHTLY acts as an intra-nuclear organizing hub for pre-mRNA molecules. Science Adv 3: e1602505 May 3 (2017). https://doi.org/10.1126/sciadv.1602505