Scholars@Duke
Aditya Pratapa

Aditya Pratapa

Postdoctoral Associate
Cell Biology

Selected Publications

Basic Science and Pathogenesis

Journal Article Alzheimer's & dementia : the journal of the Alzheimer's Association · December 1, 2024 BACKGROUND: Single-cell technologies have revealed significant microglial cell heterogeneity across the human brain in both health and disease. However, the integration of high-plex protein and spatial information in single-cell approaches constitutes a ch ... Full text Cite

Data from Androgen Deprivation Therapy Drives a Distinct Immune Phenotype in Localized Prostate Cancer

Other · November 15, 2024 <div>AbstractPurpose:<p>Androgen deprivation therapy (ADT) remains the backbone of prostate cancer treatment. Beyond the suppression of testosterone and tumor cell growth, emerging evidence suggests that ADT also modulates the immune tu ... Full text Cite

Supplemental Figure S3 from Androgen Deprivation Therapy Drives a Distinct Immune Phenotype in Localized Prostate Cancer

Other · November 15, 2024 <p>Supplemental Figure S3. Top differentially activated GO pathways with ADT.</p> ... Full text Cite

Supplemental Figure S6 from Androgen Deprivation Therapy Drives a Distinct Immune Phenotype in Localized Prostate Cancer

Other · November 15, 2024 <p>Supplemental Figure S6. Spatial proximity between immune cells and tumor cells.</p> ... Full text Cite

Supplemental Figure S2 from Androgen Deprivation Therapy Drives a Distinct Immune Phenotype in Localized Prostate Cancer

Other · November 15, 2024 <p>Supplemental Figure S2. Differential expression of androgen-related genes with or without degarelix.</p> ... Full text Cite

Supplemental Figure S1 from Androgen Deprivation Therapy Drives a Distinct Immune Phenotype in Localized Prostate Cancer

Other · November 15, 2024 <p>Supplemental Figure S1. Sample clustering by RNAseq and top differentially expressed genes by treatment group.</p> ... Full text Cite

Supplemental Figure S4 from Androgen Deprivation Therapy Drives a Distinct Immune Phenotype in Localized Prostate Cancer

Other · November 15, 2024 <p>Supplemental Figure S4. GO Activated Immune Response Genes.</p> ... Full text Cite

Supplemental Figure S5 from Androgen Deprivation Therapy Drives a Distinct Immune Phenotype in Localized Prostate Cancer

Other · November 15, 2024 <p>Supplemental Figure S5. Top differentially expressed genes by expression level and statistical significance.</p> ... Full text Cite

Androgen Deprivation Therapy Drives a Distinct Immune Phenotype in Localized Prostate Cancer.

Journal Article Clinical cancer research : an official journal of the American Association for Cancer Research · November 2024 PurposeAndrogen deprivation therapy (ADT) remains the backbone of prostate cancer treatment. Beyond the suppression of testosterone and tumor cell growth, emerging evidence suggests that ADT also modulates the immune tumor microenvironment. Howeve ... Full text Cite

Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy.

Journal Article Cell reports · July 2024 Heterogeneous resistance to immunotherapy remains a major challenge in cancer treatment, often leading to disease progression and death. Using CITE-seq and matched 40-plex PhenoCycler tissue imaging, we performed longitudinal multimodal single-cell analysi ... Full text Cite

Out of Distribution Generalization via Interventional Style Transfer in Single-Cell Microscopy

Conference IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops · January 1, 2023 Real-world deployment of computer vision systems, including in the discovery processes of biomedical research, requires causal representations that are invariant to contextual nuisances and generalize to new data. Leveraging the internal replicate structur ... Full text Cite

Image-based cell phenotyping with deep learning.

Journal Article Current opinion in chemical biology · December 2021 A cell's phenotype is the culmination of several cellular processes through a complex network of molecular interactions that ultimately result in a unique morphological signature. Visual cell phenotyping is the characterization and quantification of these ... Full text Cite

Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease.

Journal Article Leukemia · July 2020 While the past decade has seen meaningful improvements in clinical outcomes for multiple myeloma patients, a subset of patients does not benefit from current therapeutics for unclear reasons. Many gene expression-based models of risk have been developed, b ... Full text Cite

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data.

Journal Article Nature methods · February 2020 We present a systematic evaluation of state-of-the-art algorithms for inferring gene regulatory networks from single-cell transcriptional data. As the ground truth for assessing accuracy, we use synthetic networks with predictable trajectories, literature- ... Full text Cite

Reconstructing signaling pathways using regular language constrained paths.

Conference Bioinformatics (Oxford, England) · July 2019 MotivationHigh-quality curation of the proteins and interactions in signaling pathways is slow and painstaking. As a result, many experimentally detected interactions are not annotated to any pathways. A natural question that arises is whether or ... Full text Cite

Efficient Synthesis of Mutants Using Genetic Crosses

Conference ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics · August 15, 2018 The genetic cross is a fundamental, flexible, and widely-used experimental technique to create new mutant strains from existing ones. Surprisingly, the problem of how to efficiently compute a sequence of crosses that can make a desired target mutant from a ... Full text Cite

CrossPlan: systematic planning of genetic crosses to validate mathematical models.

Journal Article Bioinformatics (Oxford, England) · July 2018 MotivationMathematical models of cellular processes can systematically predict the phenotypes of novel combinations of multi-gene mutations. Searching for informative predictions and prioritizing them for experimental validation is challenging sin ... Full text Cite

Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models Using Fast-SL.

Journal Article Methods in molecular biology (Clifton, N.J.) · January 2018 In this chapter, we describe Fast-SL, an in silico approach to predict synthetic lethals in genome-scale metabolic models. Synthetic lethals are sets of genes or reactions where only the simultaneous removal of all genes or reactions in the set abolishes g ... Full text Cite

Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks.

Journal Article Bioinformatics (Oxford, England) · October 2015 MotivationSynthetic lethal sets are sets of reactions/genes where only the simultaneous removal of all reactions/genes in the set abolishes growth of an organism. Previous approaches to identify synthetic lethal genes in genome-scale metabolic net ... Full text Cite