Publications
For a complete and up-to-date list, see Google Scholar.
Preprints
Pratapa A, Tata PR, Singh R. (2025) Transforming Biological Foundation Model Representations for Out-of-Distribution Data. bioRxiv. (Accepted at RECOMB’26) doi:10.1101/2025.11.20.689462
Pratapa A, Mansouri S, Nikulina N, Matuck B, Schneider MA, Byrd KM, Savai R, Tata PR, Singh R. (2025) SAME: Topology-flexible transforms enable robust integration of multimodal spatial omics. bioRxiv. (Under review) doi:10.1101/2025.07.12.664419
Matuck BF, Huynh KLA, Pereira D, Zhang X, Kunz M, Kumar N, Easter QT, Fernandes A, Ghodke A, Predeus AV, Pratapa A, et al. (2024) The immunoregulatory architecture of the adult oral cavity. bioRxiv. doi:10.1101/2024.12.01.626279
Journal Articles
Huynh KLA, Tyc KM, Matuck BF, Easter QT, Pratapa A, Kumar NV, Pérez P, Kulchar RJ, Pranzatelli TJF, de Souza D, Weaver TM, et al. (2025) Deconvolution of cell types and states in spatial multiomics utilizing TACIT. Nature Communications 16:3747. doi:10.1038/s41467-025-56357-0
Dallos MC, Obradovic AZ, McCann P, Chowdhury N, Pratapa A, Aggen DH, Gaffney C, Autio KA, Virk RK, De Marzo AM, et al. (2024) Androgen deprivation therapy drives a distinct immune phenotype in localized prostate cancer. Clinical Cancer Research 30:5218–5230. doi:10.1158/1078-0432.CCR-24-1052
Quek C*, Pratapa A*, Bai X*, Al-Eryani G, da Silva IP, Mayer A, Bartonicek N, Harvey K, Maher NG, Conway JW, Kasalo RJ, et al. (2024) Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy. Cell Reports 43(7). doi:10.1016/j.celrep.2024.114418
Pratapa A, Doron M, Caicedo JC. (2021) Image-based cell phenotyping with deep learning. Current Opinion in Chemical Biology 65:9–17. doi:10.1016/j.cbpa.2021.04.001
Pratapa A, Jalihal AP, Law JN, Bharadwaj A, Murali TM. (2020) Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data. Nature Methods 17:147–154. doi:10.1038/s41592-019-0690-6
Mason MJ, Schinke C, Eng CLP, Towfic F, Gruber F, Dervan A, White BS, Pratapa A, Guan Y, Chen H, et al. (2020) Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease. Leukemia 34:1866–1874. doi:10.1038/s41375-020-0742-z
Wagner MJ, Pratapa A, Murali TM. (2019) Reconstructing signaling pathways using regular language constrained paths. Bioinformatics 35:i624–i633. doi:10.1093/bioinformatics/btz360
Pratapa A, Adames N, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, Murali TM. (2018) CrossPlan: systematic planning of genetic crosses to validate mathematical models. Bioinformatics 34:2237–2244. doi:10.1093/bioinformatics/bty072
Raman K, Pratapa A, Mohite O, Balachandran S. (2017) Computational prediction of synthetic lethals in genome-scale metabolic models using Fast-SL. Methods in Molecular Biology 1716:315–336. doi:10.1007/978-1-4939-7528-0_14
Pratapa A, Balachandran S, Raman K. (2015) Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks. Bioinformatics 31:3299–3305. doi:10.1093/bioinformatics/btv352
Conference Papers
Pernice WM, Doron M, Quach A, Pratapa A, Kenjeyev S, De Veaux N, Hirano M, Caicedo JC. (2023) Out of distribution generalization via interventional style transfer in single-cell microscopy. IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) 4326–4335. doi:10.1109/CVPR52729.2023.00420
Pratapa A, Jalihal AP, Law JN, Bharadwaj A, Murali TM. (2020) How to build regulatory networks from single-cell gene expression data. ACM-BCB 1–1. doi:10.1145/3388440.3414213
Pratapa A, Jalihal AP, Ravi SS, Murali TM. (2018) Efficient Synthesis of Mutants Using Genetic Crosses. ACM-BCB 53–62. doi:10.1145/3233547.3233556
Thesis
Pratapa A. (2020) Algorithms for regulatory network inference and experiment planning in systems biology. PhD Thesis, Virginia Tech. hdl:10919/93221
* denotes equal contribution