CV
Education
- PhD in Computational & Systems Biology, Washington University School of Medicine, expected 2030.
- Doctoral advisor: Ting Wang, PhD.
- Thesis: Designing a predictive model to estimate epigenetic treatment-induced changes in transposable element expression from pre-treatment genomic and epigenomic data in glioblastoma.
- Precision Medicine Pathway Fellow, Washington University School of Medicine, 2025-2027.
- BS in Computer Science & Engineering, Bangladesh University of Engineering & Technology, 2023.
- Thesis: Modeling single-cell time series for cell trajectories inference.
- Supervisor: M. Sohel Rahman, PhD.
Research interests
My broad research interest lies in understanding cancer epigenetic landscapes, identifying changes induced by epigenetic drugs, and determining possible therapeutic interventions using deep learning-based frameworks.
Work experience
- Graduate Research Assistant, Wang Lab, Department of Genetics, WashU Medicine, Apr 2025-present.
- Developing predictive models capable of estimating epigenetic treatment-induced changes in transposable element expression from pre-treatment genome and epigenome in glioblastoma.
- Studying DNA methylation and hydroxymethylation in natural killer cells in collaboration with Dr. Marco Colonna’s lab.
- Deciphering the role of transposable elements in human brain development in collaboration with Dr. Yin Shen’s lab.
- Investigating the role of prenatal Dio2 surge in shaping the human liver epigenetic landscape and gene expression in collaboration with Dr. Tatiana Fonseca’s lab.
- Pre-doctoral Trainee, Division of Biology & Biomedical Sciences, WashU Medicine, Aug 2024-Mar 2025.
- Wang Lab, Department of Genetics: analyzed DNA sequencing and methylation data to identify potential novel structural variants and methylation sites using the human pangenome reference.
- Mokalled Lab, Department of Developmental Biology: studied Slc13a5a and Kcnj10b in zebrafish neuronal regeneration and gained wet-lab experience in PCR primer design, bacterial transformation, plasmid miniprep, gel electrophoresis and extraction, HiFi DNA assembly, fish injection, and fluorescence microscopy.
- Mitra Lab, Department of Genetics: studied chronic IFN-beta and IFN-gamma signaling in human oral cancer cell lines and prepared Calling Cards and ATAC-seq libraries for sequencing.
- Research Assistant, Department of Computer Science & Engineering, Bangladesh University of Engineering & Technology, Jul 2020-Jul 2024.
- Developed a predictive model for cellular dynamics that incorporates intercellular communication into cell differentiation dynamics.
- Designed a deep learning model for reconstructing gene expression values from biological pathway scores and assessed pathway-level biological processes with Cytoscape.
- Conducted preprocessing, quality control, batch integration benchmarking, and downstream analysis for multiple single-cell RNA-seq datasets.
- Collaborated on COVID-19 public health analytics, Bangladesh forecasting models, geospatial QGIS visualizations, social-media analysis, ICT labor-market analysis, remote sensing for flood detection, and GLDAS groundwater downscaling.
Skills
- Programming and mathematical packages: Matlab, Mathematica, C, C++, Java, Python, R, Bash, SQL.
- Machine learning, deep learning, natural language processing, computer vision, evolutionary and genetic algorithms.
- Genomics and omics analysis: WGS, WGBS, 5hmC-Seal, ChIP-seq, ATAC-seq, Fiber-seq, RNA-seq, CAGE-seq, scRNA-seq, scATAC-seq, and GWAS.
Publications
Jony, S. S. R., et al. (2026). TET2 and TET3 safeguard the epigenetic identity and immune surveillance of group 1 innate lymphoid cells. Manuscript under review.
Jony, S. S. R., et al. (2025). Leveraging complementary attention maps in Vision Transformers for OCT image analysis. IEEE International Conference on Image Processing.
Jony, S. S. R., et al. (2025). A light-weight model to generate NDWI from Sentinel-1. Manuscript under review.
Jony, S. S. R., et al. (2025). GroundHog: Revolutionizing GLDAS groundwater storage downscaling for enhanced recharge estimation in Bangladesh. Manuscript under review.
Jony, S. S. R., et al. (2024). CC-Tempo: A cell-cell communication-aware model of cellular dynamics. Manuscript under review.
Jony, S. S. R., et al. (2022). An exploratory study of online job portal data of the ICT sector in Bangladesh: Analysis, recommendations, and preliminary implications for ICT curriculum reform. Education Sciences, 12(7), 423.
Jony, S. S. R., et al. (2022). An agent-based model for COVID-19 in Bangladesh. Manuscript under review.
Jony, S. S. R., et al. (2022). Linking tweets towards geo-localized policies: COVID-19 perspective. Studies in Health Technology and Informatics, 290, 709-713.
Jony, S. S. R., et al. (2021). The disproportionate impact of COVID-19 among undocumented immigrants and ethnic minorities in the US. International Journal of Environmental Research and Public Health, 18(23), 12708.
Jony, S. S. R., et al. (2021). Analyzing predictors of control measures and psychosocial problems associated with the COVID-19 pandemic: Evidence from eight countries. Behavioral Sciences, 11(8), 106.
Presentations
June 01, 2026
Poster presentation at 90th Cold Spring Harbor Laboratory Symposium on Quantitative Biology: AI in Biology, Cold Spring Harbor, New York
January 01, 2022
Oral presentation at IEEE BD CS Symposium, Bangladesh
January 01, 2021
Oral presentation at MEDINFO 2021, Virtual
Teaching
Honors and awards
- Associate Member, American Association for Cancer Research, 2026-present.
- Winner, IEEE VIP CUP 2023, Kuala Lumpur, Malaysia.
- Certification from Aspire to Innovate (a2i), ICT Division, and Cabinet Division of the Bangladesh Government for developing COVID-19 forecasting models for Bangladesh.
- Nominated by the Department of Computer Science & Engineering at BUET to participate in the 58th Conference of Directors General of Civil Aviation, Asia and Pacific Region.
- University Merit List, Bangladesh University of Engineering & Technology.
Leadership and service
- International Student Committee Member, Student Advisory Committee, Division of Biology & Biomedical Sciences, WashU Medicine, Jan 2025-present.
- Ad-hoc reviewer for Journal of Big Data, BMC Public Health, Nature Scientific Reports, The Journal of Supercomputing, Social Network Analysis and Mining, Frontiers in Psychology, Frontiers in Public Health, and PLOS One.
- Journal clubs: Cancer Informatics Journal Club, Genetics Journal Club, Human Genetics Journal Club.
Selected coursework
- Computer Science & Engineering: data structures and algorithms, theory of computation, database systems, software engineering, compiler, operating systems, artificial intelligence, computer networks, computer security, computer graphics, high performance database systems, simulation and modeling, machine learning, data mining, advanced algorithms, and meta-heuristics.
- Computational Biology: bioinformatics, computational proteomics, advanced bioinformatics algorithms, computational molecular biology, cell biology, genomics, foundations in cancer biology, genetics and genomics of diseases, and neuroimmunology.
- Mathematics: calculus, discrete mathematics, differential equations, vector calculus, numerical methods, complex variables and statistics, linear algebra, Laplace transformation, Fourier analysis, and mathematical analysis for computer science.
