Publications

You can also find my articles on my Google Scholar Profile.

Pre-prints and Manuscripts Under Review

• [2026] Mehta K, Majumder S, Chennareddy S, Yurovsky A, Prasanna P. An Interpretable Spatial Taxonomy of Breast Immune and Tumor Cell Organization in Large-Scale Spatial Transcriptomics Datasets. Under review at the conference on Digital and Computational Pathology, part of SPIE Medical Imaging.

• [2026] Chennareddy S, Majumder S, Mehta K, Prasanna P, Yurovsky A. Connecting Histologic Tumor–Immune Architecture and Spatial Transcriptomic Pathway Activity in Colorectal Cancer. Under review at a workshop for BIBM 2026.

• [2026] Jaddu S, Li T, Ma T, Yurovsky A. Racial Disparities in Machine-learning Based Acute Kidney Injury Prediction from eGFR Time Series: Characterization and Augmentation Strategies. Under review at a workshop for BIBM 2026.

• [2026] Sharma R, Gupta R, Kurc T, Yurovsky A. Stage IV Breast Cancer Classification From Bulk RNA-seq Using Transcriptomic Foundation Models. Under review at a workshop for BIBM 2026.

• [2026] Pande K, Liu Y, Yang E, Mallipattu S, Yurovsky A, Ma T. Hyperbolic Multimodal EHR Representation for Dialysis Prediction and Dose-Aware Treatment Effect Estimation. Under review at a workshop for BIBM 2026.

• [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. arXiv. 2026, April 28. doi:10.48550/arXiv.2604.24547

• [2026] Dutta P, Obusan M, Sathian R, Surana P, Chao M, Papineni N, Yurovsky A, Davuluri RV. DeepVRegulome: DNABERT-based deep learning framework for predicting functionally disruptive and clinically relevant non-coding regulatory variants. Under review in Bioinformatics Advances.

• [2026] Young AM, Yurovsky A, Peng XL, Yehc JJ, Li D, Rashid NU. Survival-guided matrix factorization identifies reproducible prognostic programs in pancreatic cancer. Under review in PNAS.

• [2025] Yurovsky A, Moffitt RA. Improving Differential Expression and Survival Analyses with Sample Specific Compartment Deconvolution. bioRxiv. 2025, June 7. doi: 10.1101/2025.06.04.657908.

Peer-Reviewed Journal Articles and Conference Proceedings

• [2026] 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 Transactions on Medical Imaging. August 21, 2026. doi: 10.1109/TMI.2026.3725898
• [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. Proceedings or AMIA Summits on Translational Science, 2026. PMID: 42317832 PMCID: PMC13274378
• [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. Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2026, pp. 8052-8062. doi: 10.1109/WACV61042.2026.00777
• [2026] Das A, Gocaj I, Yurovsky A. (2026) Systematic Review of Methods for Measuring Circulating Cell-Free DNA in Plasma of Healthy Individuals. Diagnostics. March 10, 2026. 16(6), 821. doi: 10.3390/diagnostics16060821
• [2026] Nelson B, Delgado-Coka L, Marchenko N, Escobar-Hoyos LF, Shroyer KR, Yurovsky A, Ideker T, Balázsi G, MacCarthy T and Powers S. (2026), Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer. Mol Oncol. https://doi.org/10.1002/1878-0261.70218
• [2025] Sha C, Van Brunt T, Kudria J, Schmidt D, Yurovsky A, Bandovic J, Giarrizzo M, Lin J, Tsirka SA, Bialkowska AB, Wollmuth L, Speer E, Hsieh H. (2024) A graded neonatal mouse model of necrotizing enterocolitis demonstrates that mild enterocolitis is sufficient to activate microglia and increase cerebral cytokine expression. PLoS One. May 30, 2025. doi: 10.1371/journal.pone.0323626
• [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. Proceedings of the Computer Vision and Pattern Recognition Conference (CVPR) 2025. pp. 15611-15620.
• [2024] Hasan M, Kim Silva A, Abousamra S, Tang S, Prasanna P, Saltz J, Gardner KL, Chen C, Yurovsky A. (2024) New Spatial Phenotypes from Imaging Uncover Survival Differences for Breast Cancer Patients. Proceedings of the 2024 ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB). 17:1-12. doi: 10.1145/3698587.370133.
• [2024] Sejour R, Leatherwood J, Yurovsky A, Futcher B. (2024) 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.89656.3
• [2023] 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. PubMed PMID: 37787543.
• [2023] Sweeney MD, Torre-Healy LA, Ma VL, Hall MA, Chrastecka L, Yurovsky A, Moffitt RA. (2023) FaStaNMF: a Fast and Stable Non-negative Matrix Factorization for Gene Expression. IEEE/ACM Trans Comput Biol Bioinform. 2023/07/19; doi: 10.1109/TCBB.2023.3296979. PubMed PMID: 37467096.
• [2022] Yurovsky A, Gardin J, Futcher B, Skiena S. (2022) Statistical Methodology for Ribosomal Frameshift Detection. Proceedings of the 2022 ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB). 12:1-10. doi: 10.1145/3535508.3545529.
• [2019] Yurovsky A, Futcher B, Skiena S. (2019) Pre-Phaser: Precise Cell-Cycle Phase Detector for scRNA-seq. Proceedings of the 2019 ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB). 376-382 doi: 10.1145/3307339.3342174.
• [2018] Yurovsky A, Amin MR, Gardin J, Chen Y, Skiena S, Futcher B. (2018) Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs. PLoS One. 13(8):e0202768. doi: 10.1371/journal.pone.0202768. PubMed PMID: 30138485.
• [2018] Amin MR, Yurovsky A, Chen Y, Skiena S, Futcher B. (2018) Re-annotation of 12,495 prokaryotic 16S rRNA 3’ ends and analysis of Shine-Dalgarno and anti-Shine-Dalgarno sequences. PLoS One 13(8):e0202767. doi: 10.1371/journal.pone.0202767. PubMed PMID: 30138483.
• [2018] Amin MR, Yurovsky A, Tian Y, Skiena S. (2018) DeepAnnotator: Genome Annotation with Deep Learning. Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). 2018;254-259. doi: 10.1145/3233547.3233577.
• [2015] Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki, RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. (2015) Population variation and genetic control of modular chromatin architecture in humans. Cell. 2015;162(5):1039-1050. doi: 10.1016/j.cell.2015.08.001. PubMed PMID: 26300124.
• [2015] Futcher B, Gorbatsevych O, Shen SH, Stauft CB, Song Y, Wang B, Leatherwood J, Gardin J, Yurovsky A, Mueller S, Wimmer E. (2015) Reply to Simmonds et al.: Codon pair and dinucleotide bias have not been functionally distinguished. Proceedings of the National Academy of Sciences. 2015/07/14;112(28):E3635-6. doi: 10.1073/pnas.1507710112. PubMed PMID: 26071446.
• [2015] Shen SH, Stauft CB, Gorbatsevych O, Song Y, Ward CB, Yurovsky A, Mueller S, Futcher B, Wimmer E. (2015) Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference. Proceedings of the National Academy of Sciences. 112(15):4749-4754. doi: 10.1073/pnas.1502864112. PubMed PMID: 25825721.
• [2015] Gutierrez-Arcelus M, Ongen H, Lappalainen T, Montgomery SB, Buil A, Yurovsky A, Bryois J, Padioleau I, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Giger T, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PLoS Genet. 2015 Jan 29;11(1):e1004958. doi: 10.1371/journal.pgen.1004958. PMID: 25634236.
• [2014] - Gardin J, Yeasmin R, Yurovsky A, Cai Y, Skiena S, Futcher B. (2014) Measurement of average decoding rates of the 61 sense codons in vivo. eLife. 2014 Oct 27:3:e03735. doi: 10.7554/eLife.03735. PubMed PMID: 25347064.
• [2014] - Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. (2014) Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics. 2014 Jan 15;30(2):165-71. doi: 10.1093/bioinformatics/btt667. PubMed PMID: 24255646.
• [2013] - Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. (2013) Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013;342(6159):744-7. doi: 10.1126/science.1242463. PubMed PMID: 24136355.
• [2013] - Gutierrez-Arcelus M, Lappalainen T, Montgomery SB, Buil A, Ongen H, Yurovsky A, Bryois J, Giger T, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Padioleau I, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. (2013) Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife. 2013 Jun 4:2:e00523. doi: 10.7554/eLife.00523. PubMed PMID: 23755361.
• [2011] - Yurovsky A, Moret BME. (2011) FluReF, an automated flu virus reassortment finder based on phylogenetic trees. BMC Genomics. 2011;12 Suppl 2(Suppl 2):S3. doi: 10.1186/1471-2164-12-S2-S3. PubMed PMID: 21989112.
• [2010] - Yurovsky A, Moret BME. FluRF, an automated flu virus reassortment finder based on phylogenetic trees. 2010 IEEE International Conference on Bioinformatics & Biomedicine (BIBM-2010)
• [2005] - Yurovsky A, Gopalakrishnan P. A new Cell-Planning based automatic placement technique for optimization of Analog, RF, and mixed-signal circuit layouts. Cadence Technical Conference, May 2005.

US Patents

• [2019] Futcher B, Gardin J, Skiena S, Yurovsky A, Wimmer E, Mueller S. Modified protein encoding sequences having increased rare hexamer content. US Patent App. 15/773,685.
• [2011] Colwell R, Lamant GSC, Yurovsky A, Rosek T. Registry for Electronic Design Automation of Integrated Circuits. Assignee: Cadence Design Systems. Issued on 05/17/2011.
• [2010] Gopalakrishnan P, Yurovsky A. Optimizing Circuit Layouts by Configuring Rooms for Placing Devices Assignee: Cadence Design Systems. Issued on 02/16/2010.