Published in TCS, 2015
An approximation algorithm and some related proofs for the two player game in facility location problems. Voronoi game is a geometric model of competitive facility location problem played between two players. Read more
Recommended citation: S Bandyapadhyay, A Banik, S Das, H Sarkar - Theoretical Computer Science, 2015 (authors alphabetical order)
Published in RECOMB-Seq, 2015
We present a method for clustering contigs from de novo transcriptome assemblies based upon the relationships exposed by multi-mapping sequencing fragments. Read more
Recommended citation: Accurate, fast and lightweight clustering of de novo transcriptomes using fragment equivalence classes A Srivastava*, H Sarkar*, L Malik, R Patro - arXiv preprint arXiv:1604.03250, 2016
Published in ISMB, 2016
We introduce a novel concept, quasi-mapping, and an efficient algorithm implementing this approach for mapping sequencing reads to a transcriptome. Read more
Recommended citation: RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes A Srivastava, H Sarkar, N Gupta, R Patro - Bioinformatics, 2016
Published in Bioinformatics, 2017
We present Quark, a semi-reference-based compression tool designed for RNA-seq data. Quark makes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. Read more
Recommended citation: Hirak Sarkar, and Rob Patro. Quark enables semi-reference-based compression of RNA-seq data. Bioinformatics 33.21 (2017): 3380-3386.
Published in ISMB, 2018
We present a novel data structure for representing and indexing the compacted colored de Bruijn graph, which allows for efficient pattern matching and retrieval of the reference information associated with each k-mer. Read more
Recommended citation: F Almodaresi*, H Sarkar*, A Srivastava, R Patro - Bioinformatics, 2018
Published in ACM-BCB, 2018
We introduce an algorithm for selectively aligning high-throughput sequencing reads to a transcriptome, with the goal of improving transcript-level quantification in difficult or adversarial scenarios. Read more
Recommended citation: Sarkar, Hirak*, Mohsen Zakeri*, Laraib Malik, Rob Patro Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 2018.
Published in BioXiv, 2018
We investigate the influence of mapping and alignment on the accuracy of transcript quantification in both simulated and experimental data, as well as the effect on subsequent differential expression analysis. Read more
Recommended citation:
Published in ISMB, 2019
We present minnow, a comprehensive sequence-level droplet-based single-cell RNA-sequencing (dscRNA-seq) experiment simulation framework. Read more
Recommended citation: H Sarkar, A Srivastava, R Patro - Bioinformatics, 2019
Published in Arxiv, 2020
In this paper, we explore how can we use social media data and an AI-driven approach to complement traditional surveys and automatically extract attribution factors. Read more
Recommended citation: R Sarkar, H Sarkar, S Mahinder, AR KhudaBukhsh - arXiv preprint arXiv:2001.01697
Published in ISMB, 2020
We introduce a Bayesian framework for information sharing across cells within a sample, or across multiple modalities of data using the same sample, to improve gene quantification estimates for dscRNA-seq data. Read more
Recommended citation: A Srivastava, L Malik, H Sarkar, R Patro - bioRxiv, 2020
Published in ISMB, 2020
We introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Read more
Recommended citation: H Sarkar, A Srivastava, HC Bravo, MI Love, R Patro - bioRxiv, 2020