Curriculum Vitae - March 2023

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Research Interests

• Algorithms in Computational Biology, statistical analysis of biological data.
• Analysis of single cell and bulk RNA-seq, spatial transcriptomics, genome composition.
• Precision Medicine, mixture modeling/deconvolution.

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

Fellowships, Grants, Awards

• 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.

Employment

• 2023– 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.

Teaching

• 2024- - Excellence in Teaching Program participant, nominated for the 2024-2025 cohort by the CEAS dean, offered through Stony Brook University Office of the Provost.
• 2022-24 - Developing and teaching BMI540, a graduate course in Statistical Methods in Biomedical Informatics, Stony Brook University School of Medicine, Dept. of Biomedical Informatics.
• 2023-24 - 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.
• 2021-24 - Yearly lecture on RNA-seq Informatics for BMI511, a graduate Translational Bioinformatics course, Stony Brook University School of Medicine, Dept. of Biomedical Informatics.
• 2024-24 - Lecture on Bioinformatics at the BMI Fall 2024 Bootcamp for Stony Brook undergraduate students.
• 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

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Talks and Presentations

Refereed Conference Talks (presenter name is in bold)

• 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

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

• 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.

Inivted Talks and Panel Discussions

• 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

• 2023-24 - Program Committee Member for ACM-BCB 2024, 2023.
• 2019-24 - Reviewer for BMC Genomics 2024, Computational and Structural Biotechnology 2022 and Scientific Reports 2022 Journals, Bioinformatics 2019.
• 2022-22 - Session Chair for ACM-BCB 2022.

University Service

• 2024-24 - Stony Brook University College of Engineering and Applied Sciences, DEI climate survey committee member.
• 2018-20 - Stony Brook University Computer Science, WPhD Vice President.
• 2019-19 - Stony Brook University Computer Science, WPhD Acting President.

Professional Memberships

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

Mentees

Undergraduate Research

• 2024- Aaron Das

• 2024- Ilirjana Gocaj

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

High School Research

• 2024- Shriya Jaddu: Simons Summer Research student

• 2024- Thomas Li: Simons Summer Research student

• 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.