* denotes equal contribution

• Personalized Single-cell Transcriptomics Reveals Molecular Diversity in Alzheimer’s Disease.
  Pramod Bharadwaj Chandrashekar*, Sayali Anil Alatkar*, Noah Cohen Kalafut*, Ting Jin*, Chirag Gupta, Ryan Burzak, Xiang Huang, Shuang Liu, Athan Z. Li, PsychAD Consortium, Kiran Girdhar, Georgios Voloudakis, Gabriel E. Hoffman, Jaroslav Bendl, John F. Fullard, Donghoon Lee, Panos Roussos#, Daifeng Wang#, Nature Communications, 2026 link code
• ARTEMIS integrates autoencoders and schrödinger bridges to predict continuous dynamics of gene expression, cell population and perturbation from time-series single-cell data.
  Sayali Anil Alatkar & Daifeng Wang, Bioinformatics (Proceedings of ISMB/ECCB 2025, acceptance rate 12%) link code
• Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution.
  John F. Fullard, Prashant Nm, Donghoon Lee, Deepika Mathur, Karen Therrien, Aram Hong, Clara Casey, Zhiping Shao, Marcela Alvia, Stathis Argyriou, Tereza Clarence, David Burstein, Sanan Venkatesh, Pavan K. Auluck, Lisa L. Barnes, David A. Bennett, Stefano Marenco, Kiran Girdhar, Vahram Haroutunian, Gabriel E. Hoffman, Georgios Voloudakis, Jaroslav Bendl, Panos Roussos, PsychAD Consortium, Scientific Data, 2025 link
• Dynamic landscapes of gene regulatory networks in early mammalian neurogenesis: Insights into brain evolution and disorder risk.
  Kalpana Hanthanan Arachchilage*, Ryan D. Risgaard*, Jie Sheng, Pubudu Kumarage, Jerome J. Choi, Sayali Alatkar, Chirag Gupta, Xinyu Zhao, Andre M. M. Sousa#, Daifeng Wang#, (under review), 2025 link
• NeuroTD: A Time-Frequency Based Multimodal Learning Approach to Analyze Time Delays in Neural Activities.
  Xiang Huang, Noah Cohen Kalafut, Sayali Alatkar, Athan Z. Li, Qiping Dong, Qiang Chang, Daifeng Wang, (under review), 2024 link code
• CMOT: Cross-Modality Optimal Transport for multimodal inference.
  Sayali Anil Alatkar & Daifeng Wang, Genome Biology, 2023 link code
• DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype–phenotype prediction
  Pramod Bharadwaj Chandrashekar, Sayali Alatkar, Jiebiao Wang, Gabriel E. Hoffman, Chenfeng He, Ting Jin, Saniya Khullar, Jaroslav Bendl, John F. Fullard, Panos Roussos & Daifeng Wang, Genome Medicine, 2023 link code
• Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease
  Chirag Gupta, Jielin Xu, Ting Jin, Saniya Khullar, Xiaoyu Liu, Sayali Alatkar, Feixiong Cheng, Daifeng Wang, PLoS Computational Biology, 2022 link
• CMOT: Cross-Modality Optimal Transport for multi-modal inference [poster]
  Sayali Anil Alatkar & Daifeng Wang, RECOMB, 2022