Posts by Collection

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.
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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.
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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.
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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.
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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)
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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.
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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).