Publications

This work was carried out by Soumitra Pal working with Anand Swaroop (National Eye Institute), Teresa Przytycka (NCBI), Sanguthevar Rajasekaran (University of Connecticut), Srinivas Aluru and Abhiram Ranade (IIT Bombay), and T. S. Jayram (IBM Research India).

Also on Google Scholar, with citation counts.

Soumitra Pal in bold; † co-first author; * corresponding author

Journal articles

2026

  • Soumitra Pal, Jerome Avellaneda, Celena M. Cherian, Puja Biswas, Georg Vogler, Elizabeth J. Rideout, Frank Schnorrer, Teresa M. Przytycka*, Brian Oliver. Cell type specific allometry controls sex-differences in Drosophila organ size. Genetics 233(2): iyag091, 2026. doi:10.1093/genetics/iyag091 Selected as a GENETICS Featured Article.

2025

  • Soumitra Pal*, Brian Oliver, Teresa M. Przytycka*. Cell-Type Specific Variation in X-Chromosome Dosage Compensation in Drosophila. microPublication Biology, 2025. doi:10.17912/micropub.biology.001501
  • Laura Campello†, Matthew Brooks†, Benjamin Fadl, Hyo Sub Choi, Soumitra Pal, Anand Swaroop*. Transcriptional Heterogeneity and Differential Response of Rod Photoreceptor Pathway Uncovered by Single-Cell RNA Sequencing of the Aging Mouse Retina. Aging Cell, e70001, 2025. doi:10.1111/acel.70001
  • M.G. Hirsch, Soumitra Pal, Farid Rashidi Mehrabadi, Salem Malikic, Charli Gruen, Antonella Sassano, Eva Pérez-Guijarro, Glenn Merlino, Cenk Sahinalp, Erin K. Molloy, Chi-Ping Day*, Teresa M. Przytycka*. Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones. Cell Systems 16(1), 2025. doi:10.1016/j.cels.2024.11.013

2024

  • Sharvani Mahadevaraju†*, Soumitra Pal†*, Pradeep Bhaskar, Brennan McDonald, Leif Benner, Luca Denti, Davide Cozzi, Paola Bonizzoni, Teresa M. Przytycka, Brian Oliver*. Diverse somatic Transformer and sex chromosome karyotype pathways regulate gene expression in Drosophila gonad development. eLife, 2024. doi:10.7554/eLife.101641

2023

  • Raghuveer Kavarthapu*, Rajakumar Anbazhagan, Soumitra Pal, Maria L. Dufau*. Single-Cell Transcriptomic Profiling of the Mouse Testicular Germ Cells Reveals Important Role of Phosphorylated GRTH/DDX25 in Round Spermatid Differentiation and Acrosome Biogenesis during Spermiogenesis. International Journal of Molecular Sciences 24(4): 3127, 2023. doi:10.3390/ijms24043127 Main bioinformatician (the journal did not permit co-first authorship among four authors).
  • Amelie Raz†, Gabriela Vida†, Sarah Stern†, Sharvani Mahadevaraju†, Jaclyn Fingerhut†, Jennifer Viveiros†, Soumitra Pal†, Jasmine Grey†, Mara Grace†, Cameron Berry, Hongjie Li, Jasper Janssens, Wouter Saelens, Zhantao Shao, Chun Hu, Yukiko M. Yamashita, Teresa Przytycka, Brian Oliver, Julie A. Brill, Henry Krause, Erika Matunis, Helen White-Cooper, Stephen DiNardo*, Margaret T. Fuller*. Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes. eLife 12: e82201, 2023. doi:10.7554/eLife.82201
  • Soumitra Pal, Brian Oliver, Teresa M. Przytycka. Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus. Journal of Computational Biology 30: 21–40, 2023. doi:10.1089/cmb.2022.0121 Introduces EvoGeneX.

2022

  • Hongjie Li, Jasper Janssens, …, Soumitra Pal, Teresa M. Przytycka, …, Brian Oliver, Norbert Perrimon, Bart Deplancke, Stephen R. Quake, Liqun Luo, Stein Aerts. Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly. Science 375(6584): eabk2432, 2022. doi:10.1126/science.abk2432

2020

  • Soumitra Pal, Tingyang Xu, Tianbao Yang, Sanguthevar Rajasekaran, Jinbo Bi. Hybrid-DCA: A Double Asynchronous Approach for Stochastic Dual Coordinate Ascent. Journal of Parallel and Distributed Computing 143: 47–66, 2020. doi:10.1016/j.jpdc.2020.04.002
  • Soumitra Pal, Teresa M. Przytycka. Bioinformatics pipeline using JUDI: Just Do It! Bioinformatics 36(8): 2572–2574, 2020. doi:10.1093/bioinformatics/btz956

2019

  • Subrata Saha, Jethro Johnson, Soumitra Pal, George M. Weinstock, Sanguthevar Rajasekaran. MSC: a metagenomic sequence classification algorithm. Bioinformatics 35(17): 2932–2940, 2019. doi:10.1093/bioinformatics/bty1071
  • Soumitra Pal, Jan Hoinka, Teresa M. Przytycka. Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro. Nucleic Acids Research 47(13): 6632–6641, 2019. doi:10.1093/nar/gkz540

2017

  • Peng Xiao, Soumitra Pal, Sanguthevar Rajasekaran. Randomised sequential and parallel algorithms for efficient quorum planted motif search. International Journal of Data Mining and Bioinformatics 18(2): 105–124, 2017. doi:10.1504/IJDMB.2017.086457

2016

  • Soumitra Pal, Peng Xiao, Sanguthevar Rajasekaran. Efficient sequential and parallel algorithms for finding edit distance based motifs. BMC Genomics 17: 465, 2016. doi:10.1186/s12864-016-2789-9
  • Abdullah-Al Mamun, Soumitra Pal, Sanguthevar Rajasekaran. KCMBT: a k-mer Counter based on Multiple Burst Trees. Bioinformatics 32(18): 2783–2790, 2016. doi:10.1093/bioinformatics/btw345

2015

  • Soumitra Pal, Srinivas Aluru. In search of perfect reads. BMC Bioinformatics 16(Suppl 17): S7, 2015. doi:10.1186/1471-2105-16-S17-S7
  • Ajit Diwan, Soumitra Pal, Abhiram Ranade. Fragmented coloring of proper interval and split graphs. Discrete Applied Mathematics 193: 110–118, 2015. doi:10.1016/j.dam.2015.04.014

2012

  • Soumitra Pal, Abhiram Ranade. Scheduling light-trails on WDM rings. Journal of Parallel and Distributed Computing 72(10): 1226–1236, 2012. doi:10.1016/j.jpdc.2012.05.010

Conference papers

2016

  • Soumitra Pal, Sudipta Pathak, Sanguthevar Rajasekaran. On Speeding-up Parallel Jacobi Iterations for SVDs. IEEE HPCC 2016, Sydney, pp. 9–16, 2016. doi:10.1109/HPCC-SmartCity-DSS.2016.0013
  • Peng Xiao, Soumitra Pal, Sanguthevar Rajasekaran. qPMS10: A Randomized Algorithm for Efficiently Solving Quorum Planted Motif Search Problem. IEEE BIBM 2016, Shenzhen, pp. 670–675, 2016. doi:10.1109/BIBM.2016.7822598

2015

  • Soumitra Pal, Sanguthevar Rajasekaran. Improved Algorithms for Finding Edit Distance Based Motifs. IEEE BIBM 2015, Washington DC, pp. 537–542, 2015. doi:10.1109/BIBM.2015.7359740
  • Abdullah-Al Mamun, Soumitra Pal, Sanguthevar Rajasekaran. Efficient techniques for k-mer counting. IEEE ICCABS 2015, Miami, FL, 2015. doi:10.1109/ICCABS.2015.7344733

2014

2013

  • Vijay Arya, T. S. Jayram, Soumitra Pal, Shivkumar Kalyanaraman. Inferring Connectivity Model from Meter Measurements in Distribution Networks. ACM International Conference on Future Energy Systems (e-Energy), pp. 173–182, 2013. doi:10.1145/2487166.2487186

2011

  • T. S. Jayram, Soumitra Pal, Vijay Arya. Recovery of a Sparse Integer Solution to an Underdetermined System of Linear Equations. NIPS Workshop on Sparse Representation and Low-rank Approximation, Granada, 2011. arxiv.org/abs/1112.1757

2009

  • Soumitra Pal, Abhiram Ranade. Scheduling Light-trails on WDM Rings. International Conference on Advanced Computing and Communications (ADCOM), 2009. arxiv.org/abs/1112.6254

2004

  • Soumitra Pal, Ish Dham, Tor E. Jeremiassen. Design and Validation Techniques to Implement a Robust Hindsight Feature on ISA Simulators. Global Signal Processing Expo and Conference (GSPx), Santa Clara, 2004.
  • Soumitra Pal, Prem Kumar Vadapalli. A methodology for Saving and Restoring the State of ISA simulators. Global Signal Processing Expo and Conference (GSPx), Santa Clara, 2004.

Preprints / under review

2026

  • Soumitra Pal†*, Noor D. White Carreiro†, Zachary Batz, Leo Goubet-McCall, Caroline Judy, Anand Swaroop*. Evolution of MAF and OTX families during the emergence and stabilization of rod photoreceptors across Metazoans. Research Square, 2026. Under review. doi:10.21203/rs.3.rs-10144266/v1
  • Soumitra Pal*, Ojas Chaudhary, Anand Swaroop*. PINNOU: Physics-Informed Neural Networks for Phylogenetic Ornstein–Uhlenbeck Inference. Extended abstract, EvolCompGen COSI, ISMB 2026, 2026. doi:10.5281/zenodo.22814087 Full manuscript in preparation.