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

• 2023-24 - Faculty co-advisor for the Stony Brook VIP Webgen team, a long-term multi-disciplinary project for undergraduate and graduate students. Stony Brook’s Vertically Integrated Projects Program is a member of the VIP Consortium.
• 2021-24 - Lectures on RNA-seq Informatics for BMI511, a graduate Translational Bioinformatics course, Stony Brook University School of Medicine, Dept. of Biomedical Informatics.
• 2022-23 - Developing and teaching BMI540, a graduate course in Statistical Methods in Biomedical Informatics, 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

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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

• 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.

Campus Talks and Panel Discussions

• 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 - “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

• 2019-24 - Reviewer for BMC Genomics 2024, Computational and Structural Biotechnology 2022 and Scientific Reports 2022 Journals, Bioinformatics 2019.
• 2023-23 - Program Committee Member for ACM-BCB 2023.
• 2022-22 - Session Chair for ACM-BCB 2022.
• 2018-20 - Stony Brook University Computer Science, WPhD Vice President.
• 2019-19 - Stony Brook University Computer Science, WPhD Acting President.

Professional Memberships

Member of ISCB.

Mentees

MS Research

• 2023– Eliezer Aravera

Undergraduate Research

• 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

• 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.