Publications
For a complete and up-to-date list, see Google Scholar.
2026
An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity Matuck BF, Huynh KLA, Pereira D, Easter QT, Zhang X, Kunz M, Kumar N, Pratapa A, et al.
Spatial proteomic analysis in human Alzheimer’s disease brains enables identification of microenvironment-dependent microglial cell states Sanchez-Molina P, Rosmus DD, Brownell D, Meral M, Gohlich C, Pratapa A, et al.
USHER: Guiding Foundation Model Representations through Distribution Shifts Pratapa A, Tata PR, Singh R
TP53-mediated bidirectional lineage plasticity drives alveolar epithelial cell extrusion and tissue remodeling Morowitz J, Whitlow T, Miyashita N, Enkhbayar K, Pratapa A, Singh R, et al.
2025
Deconvolution of cell types and states in spatial multiomics utilizing TACIT Huynh KLA, Tyc KM, Matuck BF, Easter QT, Pratapa A, Kumar NV, et al.
SAME: Topology-flexible transforms enable robust integration of multimodal spatial omics Pratapa A, Mansouri S, Nikulina N, Matuck B, Schneider MA, Byrd KM, et al.
2024
Androgen deprivation therapy drives a distinct immune phenotype in localized prostate cancer Dallos MC, Obradovic AZ, McCann P, Chowdhury N, Pratapa A, Aggen DH, et al.
Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy Quek C*, Pratapa A*, Bai X*, Al-Eryani G, da Silva IP, Mayer A, et al.
The immunoregulatory architecture of the adult oral cavity Matuck BF, Huynh KLA, Pereira D, Zhang X, Kunz M, Kumar N, et al.
7 presentations
- A spatio-temporal approach to mapping the dynamics of cutaneous squamous cell carcinoma progression and immunotherapy response: A journey through TiME Cancer Research
- Comparative spatial analyses of the tumor immune landscape in different mouse models of glioblastoma Cancer Research
- Deciphering spatial microglial diversity in the brain of Alzheimer’s disease patients Alzheimer's & Dementia
- Integrating ultrahigh-plex spatial phenotyping: From discovery to clinical applications Cancer Research
- Integration of high-plex tumor-Immune phenotyping and checkpoint interactions for deeper spatial characterization of human cancer tissues Cancer Research
- Mutational analysis and spatial phenotyping to decipher racial disparities in pancreatic adenocarcinoma Cancer Research
- Ultrahigh-plex spatial phenotyping of head and neck cancer tissue uncovers multiomic signatures of immunotherapy response Cancer Research
2023
Mapping the spatial proteome of head and neck tumors: key immune mediators and metabolic determinants in the tumor microenvironment Jhaveri N, Ben Cheikh B, Nikulina N, Ma N, Klymyshyn D, DeRosa J, Mihani R, Pratapa A, et al.
Out of distribution generalization via interventional style transfer in single-cell microscopy Pernice WM, Doron M, Quach A, Pratapa A, Kenjeyev S, De Veaux N, et al.
Single-cell Spatial Metabolic and Immune Phenotyping of Head and Neck Cancer Tissues Identifies Tissue Signatures of Response and Resistance to Immunotherapy Jhaveri N, Cheikh BB, Nikulina N, Ma N, Klymyshyn D, DeRosa J, Mihani R, Pratapa A, et al.
Single-cell spatial proteomic analysis by multiplexed imaging enables identification of microglial heterogeneity in Alzheimer’s disease human brain Sanchez-Molina P, Pratapa A, Nikulina N, Cheikh B, Singh J, Dhawan A, et al.
12 presentations
- 117 Ultrahigh-plex to high-throughput spatial phenotyping: an integrated pathway from discovery to translational and clinical studies Journal for ImmunoTherapy of Cancer
- 124 Location, location, location: spatial analysis of ultrahigh-plex immunofluorescence panel in head and neck cancer Journal for ImmunoTherapy of Cancer
- 2323P Multi-omic spatial phenotyping of the NSCLC tumour microenvironment for the development of a spatial score associated with immunotherapy resistance Annals of Oncology
- 90 Spatio-temporal monitoring of the tumor microenvironment in cutaneous squamous cell carcinoma Journal for ImmunoTherapy of Cancer
- Distinct spatial and molecular maps in the tumour microenvironment of resistant melanoma patients treated with checkpoint inhibitor immunotherapy Cancer Research
- Identifying a role for macrophages in predicting immunotherapy responses of non-small cell lung cancer (NSCLC) Journal for ImmunoTherapy of Cancer
- Multi-parametric comparison of scRNA-seq with CITE-seq and ultrahigh-plex spatial phenotyping of proteins in FFPE head and neck tumor biopsies: An opportunity to generate uniquely comprehensive multi-omic single cell datasets to investigate the tumor microenvironment Cancer Research
- Single cell, multiomic spatial phenotyping of immunotherapy responses in head and neck cancer Cancer Research
- Single-cell Spatial Phenotyping of Immune and Metabolic Landscapes in Systemic Lupus Erythematosus The Journal of Immunology
- Single-cell spatial proteomics approach to study microglial cell phenotype in health and pathology using CODEX multiplex imaging technology GLIA
- Spatial phenotyping of cytokine signatures reflecting the immunotherapy responses in head and neck cancer The Journal of Immunology
- The potential predictive role of spatial phenotyping in non-small cell lung cancer Cancer Research
2022
7 presentations
- 120 Decoding immunotherapy responses with high-dimensional and high-throughput spatial phenotyping of non-small cell lung cancer (NSCLC) Journal for ImmunoTherapy of Cancer
- 654MO High dimensional immuno-phenotyping of immunotherapy response in head and neck cancer Annals of Oncology
- Deep spatial phenotyping of microglial populations and pathological features in Alzheimer’s disease brains using CODEX Multiplexed Imaging Alzheimer's & Dementia
- Deep ultrahigh-plex spatial phenotyping of human cancer tissues Cancer Research
- DEEP-LEARNING BASED CELLULAR PROFILING TO ENABLE PATIENT-SPECIFIC GENETIC AND PHARMACOLOGICAL PERTURBATION SCREENS IN INHERITED NEUROMUSCULAR DISEASES Journal of the Peripheral Nervous System
- EP16. 04-003 High Dimensional Spatial Profiling of the NSCLC Tumour Microenvironment Journal of Thoracic Oncology
- Spatially resolved single-cell features reveal distinct cellular maps in the tumour microenvironment of melanoma patients with primary and acquired resistance to immunotherapies Histopathology
2021
Image-based cell phenotyping with deep learning Pratapa A, Doron M, Caicedo JC
2020 and older
Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data Pratapa A, Jalihal AP, Law JN, Bharadwaj A, Murali TM
Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease Mason MJ, Schinke C, Eng CLP, Towfic F, Gruber F, Dervan A, White BS, Pratapa A, et al.
How to build regulatory networks from single-cell gene expression data Pratapa A, Jalihal AP, Law JN, Bharadwaj A, Murali TM
Reconstructing signaling pathways using regular language constrained paths Wagner MJ, Pratapa A, Murali TM
CrossPlan: systematic planning of genetic crosses to validate mathematical models Pratapa A, Adames N, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, et al.
Efficient Synthesis of Mutants Using Genetic Crosses Pratapa A, Jalihal AP, Ravi SS, Murali TM
Computational prediction of synthetic lethals in genome-scale metabolic models using fast-SL Raman K, Pratapa A, Mohite O, Balachandran S
Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks Pratapa A, Balachandran S, Raman K
1 presentation
- The hypergraph algorithms package F1000Research (poster) · 2018
- denotes equal contribution