Publications

Google scholar profile and  entry in the DBLP bibliography

Thesis

• PhD: Scheduling Light-trails on WDM Rings: an Application of Component Coloring of Graphs

• MTech: Improving Branch-and-Price Algorithms for Solving One Dimensional Cutting Stock Problem

Preprints

• Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes. AA Raz, GS Vida,  SR Stern, S Mahadevaraju, JM Fingerhut, JM Viveiros,  S Pal, JR Grey, MR Grace, CW Berry, H Li, J Janssens, W Saelens, Z Shao, C Hu, YM Yamashita, TM Przytycka, B Oliver, JA Brill, HM Krause, EL Matunis, H White-Cooper, S DiNardo, MT Fuller. bioRxiv 2021.

Journal Publications

• 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. R Kavarthapu, R Anbazhagan, S Pal, ML Dufau. International Journal of Molecular Sciences, January 2023

• Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus. S Pal, B Oliver, TM Przytycka. Journal of Computational Biology, August 2022

• Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. H Li, J Janssens, MD Waegeneer, SS Kolluru, K Davie, V Gardeux, W Saelens, FPA David, M Brbić, K Spanier, J Leskovec, CN McLaughlin, Q Xie, RC Jones, K Brueckner, J Shim, SG Tattikota, F Schnorrer, K Rust, TG Nystul, Z Carvalho-Santos, C Ribeiro, S Pal, S Mahadevaraju, TM Przytycka, AM Allen, SF Goodwin, CW Berry, MT Fuller, H White-Cooper, EL Matunis, S DiNardo, A Galenza, LE O’Brien, JAT Dow, H Jasper, B Oliver, N Perrimon, B Deplancke, SR Quake, L Luo, S Aerts, Fly Cell Atlas Consortium. Science 2022

• Hybrid-DCA: A Double Asynchronous Approach for Stochastic Dual Coordinate Ascent (arXiv). with Tingyang Xu, Tianbao Yang, Sanguthevar Rajasekaran and Jinbo Bi. Journal of Parallel and Distributed Computing, Volume 143, Pages 47-66, September 2020

• Bioinformatics pipeline using JUDI: Just Do It! (bioRxiv). With Teresa M. Przytycka. Bioinformatics, 27 December 2019

• Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro (bioRxiv). with Jan Hoinka and Teresa M. Przytycka. Nucleic Acids Research, Volume 47, Issue 13, 26 July 2019

• Randomised sequential and parallel algorithms for efficient quorum planted motif search. with Peng Xiao and Sanguthevar Rajasekaran. International Journal of Data Mining and Bioinformatics, Volume 18, Issue 2, 2017

• Efficient sequential and parallel algorithms for finding edit distance based motifs. with Peng Xiao and Sanguthevar Rajasekaran. BMC Genomics, Special Issue, 2016

• KCMBT: A k-mer Counter based on Multiple Burst Trees. with Abdullah-Al Mamun and Sanguthevar Rajasekaran. Bioinformatics, 2016

• In Search of Perfect Reads. with Srinivas Aluru. BMC Bioinformatics Special Issue, 2015

• Fragmented Coloring of Proper Interval and Split Graphs (arXiv). with Ajit A. Diwan, and Abhiram Ranade. Discrete Applied Mathematics, 2015

• Scheduling Light-trails on WDM Rings (arXiv). with Abhiram Ranade. Journal of Parallel and Distributed Computing, Volume 72, Issue 10, October 2012, Pages 1226–1236

Conference Publications

• On Speeding-up Parallel Jacobi Iterations for SVDs (preprint) (slides). with Sudipta Pathak and Sanguthevar Rajasekaran. IEEE International Conferences on High Performance Computing and Communications (HPCC), 2016

• qPMS10: A Randomized Algorithm for Efficiently Solving Quorum Planted Motif Search Problem (preprint). with Peng Xiao and Sanguthevar Rajasekaran. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016

• Improved Algorithms for Finding Edit Distance Based Motifs (bioRxiv) (slides). with Sanguthevar Rajasekaran. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015

• In Search of Perfect Reads (slides). with Srinivas Aluru. IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2014

• Scheduling Light-trails on WDM Rings (slides). with Abhiram Ranade. Seventeenth International Conference on Advanced Computing and Communications (ADCOM), December 2009

• Inferring Connectivity Model from Meter Measurements in Distribution Networks. with Vijay Arya, T. S. Jayram, and Shivkumar Kalyanaraman. Fourth International Conference on Future Energy Systems (eEnergy), 2013

Workshop Publications

• Efficient techniques for k-mer counting (slides). with Abdullah-Al Mamum and Sanguthevar Rajasekaran. CANGS Workshop in International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2015

• Recovery of a Sparse Integer Solution to an Underdetermined System of Linear Equations (slides). with T. S. Jayram and Vijay Arya. NIPS Workshop on Sparse Representation and Low-rank Approximation, December 2011