Publications & Presentations

* indicates co-first authorship

Preprints & In Preparation

• Spatial analysis of human colorectal cancer identifies anti-tumor immunity hubs at epithelial/stromal interface as site enriched for effector and exhausted T cells
  Chen JH*, Chen H*, Palshikar MG*, Spurrell M, Demaray J, …, Hacohen N, Korsunsky I, Pelka K.
  Under review

• Spatial Reconstruction of Interstitial Lung Disease
  Tran M, Gao C, Palshikar MG, …, Kim E, Wei K, Korsunsky I.
  In preparation

• Powerful and accurate case-control analysis of spatial molecular data with deep learning-defined tissue microniches
  Reshef Y, Sood L, …, Palshikar MG, … Korsunsky I, Raychaudhuri S.
  bioRxiv (2024)

Published

• Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns
  Millard N, Chen JH, Palshikar MG, …, He J, Wei K, Korsunsky I.
  Genome Biol. (2025)

• Synovial tissue atlas in juvenile idiopathic arthritis reveals pathogenic niches associated with disease severity
  Bolton C, Mahony CB, …Palshikar MG, Garnett J, Raychaudhuri S, Frank MM.
  Sci Transl Med. (2025)

• Discrete-state models identify pathway specific B cell states across diseases and infections at single-cell resolution
  Kassis G*, Palshikar MG*, Hilchey SP, Zand MS, Thakar J.
  J Theor Biol. (2024)

• Executable Network Models of Integrated Multiomics Data
  Palshikar MG, Min X, Crystal A, Thakar J.
  J Proteome Res. (2023)

• Executable models of immune signaling pathways in HIV-associated atherosclerosis
  Palshikar MG, Palli R, …, Zand MS, Thakar J.
  npj Syst Biol Appl. (2022)

• Cyclosporine A Modulates LSP1 Protein Levels in Human B Cells to Attenuate B Cell Migration at Low O₂ Levels
  Hilchey SP*, Palshikar MG*, …, Zand MS, Thakar J.
  Life (Basel). (2022)

• WikiNetworks: translating manually created biological pathways for topological analysis
  Palshikar MG, Hilchey SP, Zand MS, Thakar J.
  Bioinformatics. (2022)

• Cyclosporine A Directly Affects Human and Mouse B cell Migration in vitro by Disrupting a HIF1α-Dependent, O₂ Sensing, Molecular Switch
  Hilchey SP, Palshikar MG, …, Elliott MR, Zand MS, Thakar J.
  BMC Immunol. (2020)

• Executable pathway analysis using ensemble discrete-state modeling for large-scale data
  Palli R, Palshikar MG, Thakar J.
  PLoS Comput Biol. (2019)

Conference Presentations

• Abstract 5492: Spatial organization and cellular composition of immunity hubs in human colorectal cancer
  Palshikar MG, Spurrell M, Demaray J, …, Hacohen N, Chen JH, Korsunsky I.
  American Association for Cancer Research (AACR) Annual Meeting (2024)

• WikiNetworks: translating manually created biological pathways for topological analysis
  Palshikar MG.
  Computational Modeling in Biology Network (COMBINE) (2021)

• Executable models of pathways built using single-cell RNAseq data reveal immune signaling dysregulations in people living with HIV and atherosclerosis
  Palshikar MG.
  American Society for Microbiology (ASM) Eastern New York Fall Symposium (2021)

• Executable models of pathways built using single-cell RNAseq data reveal immune cell heterogeneity in people living with HIV and atherosclerosis
  Palshikar MG.
  Conference on Intelligent Systems for Molecular Biology (ISMB) (2020)