Alisa Yurovsky

Alisa Yurovsky headshot

Alisa Yurovsky

Assistant Professor
Department of Biomedical Informatics

CS 2313A
Stony Brook University
Stony Brook, NY 11794
Alisa.Yurovsky@stonybrookmedicine.edu

Biography

Dr. Alisa Yurovsky is an Assistant Professor in the Department of Biomedical Informatics at Stony Brook University. She was previously a postdoctoral researcher in the same department under the supervision of Richard Moffitt. She completed her PhD in Computer Science at Stony Brook University under the supervision of Steve Skiena. During her research-focused Master's degree, she worked with Bernard Moret at EPFL. She received her undergraduate degree in Computer Science from Carnegie Mellon University.

Dr. Yurovsky is a computational biologist who works at the intersection of computer science, genetics, and statistics. She is interested in the development of new algorithms and computational methods that aid in the advances of precision medicine, with the potential to address existing racial disparities in health data. Her current research projects include precise compartment deconvolution and weight estimation of mixed tissue samples, analysis of spatial transcriptomics data, methods for small size differential expression studies, and applied machine learning.

Selected Publications

  1. Huang W, Xu M, Hu X, Abousamra S, Ganguly A, Kapse S, Yurovsky A, Prasanna P, Kurc T, Saltz J, Miller ML, Chen C. RankByGene: gene-guided histopathology representation learning through cross-modal ranking consistency. IEEE Trans Med Imaging. 2026 Aug 21. doi: 10.1109/TMI.2026.3725898. Epub ahead of print. PMID: 42627750.
  2. Nelson B, Delgado-Coka L, Marchenko N, Escobar-Hoyos LF, Shroyer KR, Yurovsky A, Ideker T, Balázsi G, MacCarthy T, Powers S. Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer. Mol Oncol. 2026 Jul;20(7):1857-76. doi: 10.1002/1878-0261.70218. PMID: 41766370.
  3. Chinthalapudi S, Mallipattu SK, Yurovsky A, Ma T. A novel approach to zero-shot drug-drug interaction prediction enabled by EHR-augmented knowledge graphs. AMIA Jt Summits Transl Sci Proc. 2026;2026:107-16. PMID: 42317832; PMCID: PMC13274378.
  4. Das A, Gocaj I, Yurovsky A. Systematic review of methods for measuring circulating cell-free DNA in plasma of healthy individuals. Diagnostics (Basel). 2026 Mar 10;16(6):821. doi: 10.3390/diagnostics16060821. PMID: 41897554.
  5. Majumder S, Kapse S, Bhattacharya M, Xu X, Yurovsky A, Prasanna P. PEaRL: pathway-enhanced representation learning for gene and pathway expression prediction from histology. In: Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV); 2026. p. 8052-62. doi: 10.1109/WACV61042.2026.00777.
  6. Ganguly A, Chatterjee D, Huang W, Zhang J, Yurovsky A, Johnson TS, Chen C. MERGE: multi-faceted hierarchical graph-based GNN for gene expression prediction from whole slide histopathology images. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR); 2025. p. 15611-20.
  7. Sha C, Van Brunt T, Kudria J, Schmidt D, Yurovsky A, Bandovic J, Giarrizzo M, Lin J, Tsirka SA, Bialkowska AB, Wollmuth LP, Speer EM, Hsieh H. A graded neonatal mouse model of necrotizing enterocolitis demonstrates that mild enterocolitis is sufficient to activate microglia and increase cerebral cytokine expression. PLoS One. 2025 May 30;20(5):e0323626. doi: 10.1371/journal.pone.0323626. PMID: 40445990.
  8. Hasan M, Kim Silva A, Abousamra S, Tang S, Prasanna P, Saltz J, Gardner KL, Chen C, Yurovsky A. New spatial phenotypes from imaging uncover survival differences for breast cancer patients. In: Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '24); 2024. p. 1-12. doi: 10.1145/3698587.3701333.
  9. Sweeney MD, Torre-Healy LA, Ma VL, Hall MA, Chrastecka L, Yurovsky A, Moffitt RA. FaStaNMF: a fast and stable non-negative matrix factorization for gene expression. IEEE/ACM Trans Comput Biol Bioinform. 2024 Nov;21(6):1633-44. doi: 10.1109/TCBB.2023.3296979. PMID: 37467096.
  10. Sejour R, Leatherwood J, Yurovsky A, Futcher B. Enrichment of rare codons at 5' ends of genes is a spandrel caused by evolutionary sequence turnover and does not improve translation. eLife. 2024 Jul 15;12:RP89656. doi: 10.7554/eLife.89656. PMID: 39008347.
  11. Hegelmeyer NK, Parkin LA, Previti ML, Andrade J, Utama R, Sejour RJ, Gardin J, Muller S, Ketchum S, Yurovsky A, Futcher B, Goodwin S, Ueberheide B, Seeliger JC. Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. mBio. 2023 Oct 31;14(5):e0084123. doi: 10.1128/mbio.00841-23. PMID: 37787543.
  12. Yurovsky A, Gardin J, Futcher B, Skiena S. Statistical methodology for ribosomal frameshift detection. In: Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '22); 2022. p. 1-10. doi: 10.1145/3535508.3545529.
  13. Yurovsky A, Futcher B, Skiena S. Pre-Phaser: precise cell-cycle phase detector for scRNA-seq. In: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19); 2019. p. 376-82. doi: 10.1145/3307339.3342174.
  14. Yurovsky A, Amin MR, Gardin J, Chen Y, Skiena S, Futcher B. Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs. PLoS One. 2018 Aug 23;13(8):e0202768. doi: 10.1371/journal.pone.0202768. PMID: 30138485.
  15. Yurovsky A, Moret BME. FluReF, an automated flu virus reassortment finder based on phylogenetic trees. BMC Genomics. 2011;12 Suppl 2:S3. doi: 10.1186/1471-2164-12-S2-S3. PMID: 21989112.