Sitemap
A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
portfolio
publications
IFN-γ signaling maintains skin pigmentation homeostasis through regulation of melanosome maturation
Published in Proceedings of the National Academy of Sciences (PNAS), 2014
Co-author. Demonstrates that interferon-γ signaling regulates melanosome maturation and is required for skin pigmentation homeostasis.
Recommended citation: Natarajan, V. T., Ganju, P., Singh, A., Vijayan, V., Kirty, K., Yadav, S., Puntambekar, S., et al., & Gokhale, R. S. (2014). "IFN-γ signaling maintains skin pigmentation homeostasis through regulation of melanosome maturation." Proceedings of the National Academy of Sciences. 111(6), 2301–2306.
Download Paper
Identification of unintuitive features of sumoylation through mathematical modeling
Published in Journal of Biological Chemistry, 2016
First author. Reconstructs the sumoylation network and develops ODE-based mathematical models to uncover non-obvious system-level features of this post-translational modification.
Recommended citation: Puntambekar, S. S., Nyayanit, D., Saxena, P., & Gadgil, C. J. (2016). "Identification of unintuitive features of sumoylation through mathematical modeling." Journal of Biological Chemistry. 291(18), 9458–9468.
Download Paper
Method for identification of sensitive nodes in Boolean models of biological networks
Published in IET Systems Biology, 2018
Co-author. Proposes a method to identify sensitive nodes in Boolean models of biological networks, supporting model-driven hypothesis generation.
Recommended citation: Dnyane, P. A., Puntambekar, S. S., & Gadgil, C. J. (2018). "Method for identification of sensitive nodes in Boolean models of biological networks." IET Systems Biology. 12(1), 1–6.
Download Paper
Evolutionary divergence of novel open reading frames in cichlids speciation
Published in Scientific Reports, 2020
First author. Develops an optimized comparative-transcriptomics pipeline for cichlid fishes and uses evolutionary rate analysis to characterize accelerated regions and novel open reading frames implicated in cichlid speciation.
Recommended citation: Puntambekar, S., Newhouse, R., San-Miguel, J., Chauhan, R., Vernaz, G., et al., & Prabakaran, S. (2020). "Evolutionary divergence of novel open reading frames in cichlids speciation." Scientific Reports. 10(1), 21570.
Download Paper
Pan-cancer analysis of transcripts encoding novel open reading frames (nORFs) and their potential biological functions
Published in NPJ Genomic Medicine, 2021
Co-first author. Pan-cancer analysis of RNA-seq and Ribo-seq data to characterize transcripts encoding novel open reading frames, including survival analysis, structure prediction, mutation mapping, and in-silico drug screening.
Recommended citation: Erady, C.*, Boxall, A.*, Puntambekar, S.*, Jagannathan, N. S.*, Chauhan, R.*, et al., & Prabakaran, S. (2021). "Pan-cancer analysis of transcripts encoding novel open reading frames (nORFs) and their potential biological functions." NPJ Genomic Medicine. 6(1), 4. (* contributed equally)
Download Paper
Recognition of diverse GATA motifs necessitates multimodal GATA3-DNA binding
Published in Biochemical and Biophysical Research Communications, 2026
Co-author. Combines computational and experimental analyses to show that recognition of diverse GATA DNA motifs by the transcription factor GATA3 requires multimodal binding modes, with implications for GATA3 regulatory function in breast cancer.
Recommended citation: Gharui, S., Puntambekar, S., Sarkar, R. R., Narlikar, L., & Sengupta, D. (2026). "Recognition of diverse GATA motifs necessitates multimodal GATA3-DNA binding." Biochemical and Biophysical Research Communications. 817, 153718.
Download Paper
talks
teaching
Boolean Modeling in Biology — Systems Biology course
Postgraduate (M.Sc.) lectures, Department of Bioinformatics, Savitribai Phule Pune University, 2026
Delivered a series of guest lectures on Boolean modeling of biological networks as part of the Systems Biology course for M.Sc. (Second Year) students at Savitribai Phule Pune University (March 2026).