Shraddha Puntambekar

Bioinformatics Scientist

Enabling data-driven drug discovery through bioinformatics, multi-omics, and scientific workflows

Publications

Six peer-reviewed publications across multi-omics, cancer biology, comparative genomics, and systems-biology modeling — including first- or co-first author papers in Journal of Biological Chemistry, NPJ Genomic Medicine, Scientific Reports, and Biochemical and Biophysical Research Communications.

You can also find my articles on my Google Scholar profile.

Journal Articles

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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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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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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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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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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