Curriculum Vitae - October 2026

Also available as PDF

Research Interests

• Algorithms in Computational Biology, statistical analysis of biological data.
• Analysis of single cell and bulk RNA-seq, spatial transcriptomics, genome composition.
• Algorithms for enabling more precise survival, differential expression, and classification analyses for genomics and imaging data.

Education

Ph.D. Computer Science, Stony Brook University, December 2020

Specialization: Computational Biology
Advised by: Steven Skiena
Dissertation: Understanding Mechanisms of Translation and Transcription

M.S. Computer Science, EPFL, December 2010

Specialization: Computational Biology
Advised by: Bernard Moret
Dissertation: A Study of Flu Virus Reassortment

B.S. Computer Science, Carnegie Mellon University, May 2001

Minor: Mathematics

Employment

• 2025– Assistant Professor, tenure track, Stony Brook University, Dept. of Biomedical Informatics, Stony Brook, NY.
• 2025– Assistant Professor, affiliate, Stony Brook University, Dept. of Computer Science, Stony Brook, NY.
• 2023-25 IDEA Fellow, Lecturer, Stony Brook University, Dept. of Biomedical Informatics, Stony Brook, NY.
• 2021-23 Postdoctoral Fellow, Stony Brook University School of Medicine, Dept. of Biomedical Informatics, Stony Brook, NY.
• 2016-20 Research Assistant, Stony Brook University, Dept. of Computer Science, Stony Brook, NY.
• 2015-16 Teaching Assistant, Stony Brook University, Dept. of Computer Science, Stony Brook, NY.
• 2013-15 Data Manager/Statistician, Stony Brook University, Dept. of Microbiology and Immunology, Stony Brook, NY.
• 2011–12 Bioinformatician, University of Geneva Medical School, Functional Population Genomics and Genetics of Complex Traits Lab, Geneva, Switzerland.
• 2004–08 Senior Member of Technical Staff, Cadence Design System, Inc., Pittsburgh, PA.
• 2001–04 Software Engineer, Neolinear, Inc., Pittsburgh, PA.
• 2000–01 Research Programmer, Medical Robotics and Assisted Surgery, Inc., Pittsburgh, PA.
• 1998–99 Summer Research Programmer, Carnegie Mellon University, Language Technologies Institute, Pittsburgh, PA.

Fellowships, Grants, Awards

• 2026 Stony Brook OR&I Seed Grant Integrating EHRs and Knowledge Graphs to Identify Drug-Drug Interactions Affecting Post-AKI Kidney Outcomes, Co-I, $40,000, 10/12/2026-04/12/2028
• 2026 NIH NCI Investigating Targetable Mechanisms of Altered Cell States in Castration-Resistant Prostrate Cancer, Co-I, $3,019,550, 07/01/2026-06/30/2031
• 2025 Startup Funding: early career support from Stony Brook University, PI, $450,000, 09/01/2025-08/31/2028
• 2023 IDEA Fellowship: Full-time, 12-month, non tenure-track faculty position at the lecturer level. Two year support with anticipated transition to tenure-track.
• 2020 NSF/CRA/CCC Computing Innovation Postdoctoral Fellow 2020 (CIFellows 2020): Full financial support for two years of postdoctoral research, with 9 months extension.
• 2017 CEWIT 2017 Best Poster Award: one of three Best Poster Awards based on technical merit, potential impact, clarity, poster aesthetics, and quality of presentation.
• 2016 NSF Graduate Research Fellowship Program (GRFP): Full financial support for three years of graduate study.
• 2015 Computer Science Department Chair Fellowship for first year PhD students.
• 2015 Pieper Merit Award for first year PhD students.
• 2010 Prix Annaheim - Mattille for high quality Master’s Thesis devoted to bringing together life sciences and information technology.
• 2007 Organizational Level Award awarded by Cadence Design Systems, Inc. for work on semiconductor process constraints.

Teaching

• 2022- 5 semesters, developing and teaching BMI540, a graduate course in Statistical Methods in Biomedical Informatics, Stony Brook University School of Medicine, Dept. of Biomedical Informatics.
• 2023- 5 semesters, faculty co-advisor for the Stony Brook VIP Webgen team, a long-term multi-disciplinary project for undergraduate students. Stony Brook’s Vertically Integrated Projects Program is a member of the VIP Consortium.
• 2024- Once per semester lecture on Bioinformatics at the BMI Bootcamp for Stony Brook undergraduate students.
• 2024-25 Excellence in Teaching Program participant, nominated for the 2024-2025 cohort by the CEAS dean, offered through Stony Brook University Office of the Provost.
• 2021-25 Once per year lecture on RNA-seq Informatics for BMI511, a graduate Translational Bioinformatics course, Stony Brook University School of Medicine, Dept. of Biomedical Informatics.
• 2023-23 Developing and teaching BMI530, a graduate course in Software Development in Biomedical Informatics, Stony Brook University School of Medicine, Dept. of Biomedical Informatics.
• 2015-16 Teaching Assistant for undergraduate Algorithms and Software Engineering courses, Stony Brook University, Dept. of Computer Science.

Publications

Jump to Publications Page

Talks and Presentations

Refereed Conference Talks (presenter name is in bold)

• 2026 - Chinthalapudi S, Mallipattu SK, Yurovsky A, Ma, T. A Novel Approach to Zero-Shot Drug-Drug Interaction Prediction Enabled by EHR-Augmented Knowledge Graphs. Presented at Amplify Informatics Conference, May 17–21, 2026, Denver, CO.

• 2025 - 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. Presented at CVPR 2025: June 11-15, Nashville, TN.

• 2025 - Pratik Dutta, Matthew Obusan, Rekha Sathian, Pallavi Surana, Max Chao, Nimisha Papineni, Alisa Yurovsky, Ramana V. Davuluri. Leveraging Genomic Foundation Models to Predict Short Nucleotide Variants That Impact Non-Coding Functional Sites in Cancer Genomes. Presented at GLBIO 2025: May 12-15, Minneapolis, MN.

• 2025 - Aggarwal P, Sochan AJ, Kim R, Kuhia R, Zhao Z, Fiore SM, Chesler D, Egnor M, Yurovsky A, Hsieh H. Pediatric Traumatic Brain Injury: Uncovering Injury Patterns and Their Clinical Consequences. Presented at ACS 2025: Feb 11-13, Las Vegas, Nevada.

• 2025 - Aggarwal P, Kim R, Kuhia R, Zhao Z, Fiore SM, Chesler D, Egnor M, Yurovsky A, Hsieh H. Breaking Up a Bimodal Distribution: Guidelines for Pediatric Traumatic Brain Injury Research. Presented at ACS 2025: Feb 11-13, Las Vegas, Nevada.

• 2024 - 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. Presented at ACM-BCB 2024.

• 2022 - Sweeney MD, Torre-Healy LA, Ma VL, Hall MA, Chrastecka L, Yurovsky A and Moffitt RA. FaStaNMF: a Fast and Stable Non-negative Matrix Factorization for Gene Expression, presented at APBC 2022.

• 2022 - Yurovsky A, Gardin J, Futcher B, Skiena S. Statistical Methodology for Ribosomal Frameshift Detection, presented at ACM-BCB 2022.

• 2019 - Yurovsky A, Futcher B, Skiena S. Pre-Phaser: Precise Cell-Cycle Phase Detector for scRNA-seq, presented at ACM-BCB 2019.

• 2018 - Amin MR, Yurovsky A, Tian Y, Skiena S. DeepAnnotator: Genome Annotation with Deep Learning, presented at ACM-BCB 2018.

• 2010 - Yurovsky A, Moret BME. FluRF, an automated flu virus reassortment finder based on phylogenetic trees, presented at BIBM-2010.

Refereed Conference Poster Presentations (presenter name is in bold)

• 2026 - Pande KP, Yang E, Zhu B, Mallipattu SK, Yurovsky A, Ma T. Dialysis Risk Prediction and Treatment Effect Estimation for AKI patients using Longitudinal Electronic Health Records. Poster accepted for presentation at AMIA 2026 Annual Symposium in Dallas, TX.

• 2026 - 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. Poster presentation at IEEE/CVF Winter Conference on Applications of Computer Vision (WACV) March 2026 in Tucson, Arizona.

• 2024 - Dutta P, Sathian R, Obusan M, Surana P, Chao M, Papineni N, Yurovsky A, Davuluri RV. Prediction of Cancer Somatic Mutations that impact Gene Regulatory Elements by application of DNABERT fine-tuned models on Whole Genome Sequencing Data. Poster presentation at 2024 CSHL Biological Data Science Meeting in Cold Spring Harbor, NY.

• 2024 - Yurovsky A, Moffitt RA. Improving Differential Expression and Survival Analyses with Sample-Specific Compartment Deconvolution (SSCD). Poster Presentation at 2024 ISMB in Montreal, Canada.

• 2023 - Yurovsky A, Moffitt RA. Sample-Specific Compartment Deconvolution. Poster Presentation at 2023 ISMB/ECCB in Lyon, France.

• 2017 - Yurovsky A, Amin MR, Skiena S. Word Embeddings for Genome Annotation with Deep Learning. Poster presentation at the 13th International Conference on Emerging Technologies for a Smarter World (CEWIT2017), November 2017.

• 2010 - Yurovsky A, Moret BME. FluRF. Poster presentation at the 1st European Student Council Symposium workshop at the 9th European Conference on Computational Biology (ECCB-10), September 2010.

Invited Talks and Panel Discussions

• 2026 - Invited speaker, “Pathway-Enhanced Representation Learning for Gene and Pathway Expression Prediction from Histology”, Western North American Region of the International Biometric Society (WNAR) 2026, Pullman, WA, invited by Debolina Chatterjee, June 16, 2026.

• 2025 - Panelist for CSTEP Engineering Panel, Stony Brook, NY, invited by Peter Saenz, April 30, 2025.

• 2024 - Invited speaker, “Improving Differential Expression and Survival analyses”, 2024 Stony Brook Cancer Center GI Symposium, Port Jefferson, NY, invited by Georgios Georgakis, May 31, 2024.

• 2024 - Panelist for CSTEP Engineering Panel, Stony Brook, NY, invited by Daniene Byrne, March 20, 2024.

• 2024 - Panelist for CELT AI Ethics in Teaching and Learning Panel, Stony Brook, NY, invited by Rose Tirotta-Esposito, February 20, 2024.

• 2023 - Panelist for CSTEP Biomedical Engineering Panel, Stony Brook, NY, invited by Daniene Byrne, October 4, 2023.

• 2022 - Invited speaker, “Compartment Deconvolution for Precision Medicine”, Pathology Cancer Center Grand Rounds Seminar, Stony Brook University School of Medicine, Stony Brook, NY, invited by Kenneth R. Shroyer, December 13, 2022.

Professional Service

Conferences and Journals

• 2026-26 - Workshops Chair Co-chair of workshops for 2026 IEEE BIBM.
• 2026-26 - Area Chair for ACM-BCB 2026.
• 2023-26 - Conference Reviewer for AMIA 2026 Annual Symposium, AMIA 2026 Amplify Informatics Conference, ACM-BCB 2023-2025.
• 2019-25 - Journal Reviewer for , Bioinformatics 2019-2026, npj Breast Cancer 2025, BMC Genomics 2024, Computational and Structural Biotechnology 2022 and Scientific Reports 2022 Journals.
• 2022-25 - Session Chair for ACM-BCB 2024-2025, 2022.

University Service

• 2024-24 - Stony Brook University College of Engineering and Applied Sciences, DEI climate survey committee member.

Department Service

• 2025- - Stony Brook University BMI Department Graduate Program committee member.
• 2018-20 - Stony Brook University Computer Science Department, WPhD Vice President.
• 2019-19 - Stony Brook University Computer Science Department, WPhD Acting President.

PhD committees

Chelsea Kirkland (TBD), Nimisha Papineni (A Multimodal Transformer Framework for Cross-Species Interpretation of Non-Coding Regulatory Variants), Max Chao (AI driven Discovery of Functional Impact of Mutations in Regulatory Regions across Translational Species Modalities to Understand the Environmental Impacts of Arsenic and Ultraviolet Radiation in Mouse Skin Tumors: Adapting DeepVRegulome across Species Modalities), Rekha Sathian (Decoding Enhancer Regulatory Language in Human and Mouse Genomes Using Genome Language Model), Pallavi Surana (Unraveling tissue specific gene regulation in normal and cancer tissues using AI)

MS committees

Jack Vaska (Predicting Antimicrobial Resistance Using Microbiome-Pretrained DNABERT2 and DBGWAS-Derived Genomic Features)

Professional Memberships

ISCB member since 2023. ACM and ACM-W member since 2024.

Mentees

Faculty Development and Peer Mentoring

• 2026- Miruna Oprescu, SUNY PRODiG+ Fellow, Stony Brook University, Dept. of Computer Science

Current PhD Students

• 2026- Sejuti Majumder

Undergraduate Research

• 2025-26 Samuel George Thomas: Senior Honors Research Project: Visualizing Health Insurance Coverage in the US.

• 2024-26 Aaron Das: joint work resulted in a journal publication, with the student as a co-first author.

• 2024-26 Ilirjana Gocaj: joint work resulted in a journal publication, with the student as a co-first author.

• 2021-22 Michael D. Sweeney: joint work resulted in coauthored paper with student as the first author. Next position: graduate student research assistant at the University of Michigan.

High School Research

• 2026- Srihith Chennareddy: Simons Summer Research student: joint work resulted in a publication, currently under review.

• 2026- Ronit Sharma: Simons Summer Research student: joint work resulted in a publication, currently under review.

• 2025- Ryan Kim: Simons Summer Research student: joint work resulted in manuscript, currently in preparation. Next postition: undergraduate student at University of Illinois Urbana-Champaign.

• 2025-26 Bryan Zhu: Simons Summer Research student: joint work resulted in a poster presentation at AMIA 2026 Annual Symposium. Next position: undergraduate student at MIT.

• 2024-26 Shriya Jaddu: Simons Summer Research student: joint work resulted in a publication, currently under review. Next position: undergraduate student at Yale University.

• 2024-25 Thomas Li: Simons Summer Research student: joint work resulted in a publication, currently under review. Next position: undergraduate student at MIT.

• 2021-22 Ashley Hsu: joint work resulted in a winning entry for the bioinformatics category at the 2022 International Science and Engineering Fair, while representing New York. Next position: undergraduate student at Duke University.