Chirag Jain
Chirag Jain
Indian Institute of Science
Verified email at - Homepage
Cited by
Cited by
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
C Jain, LM Rodriguez-R, AM Phillippy, KT Konstantinidis, S Aluru
Nature communications 9 (1), 5114, 2018
Critical Assessment of Metagenome Interpretation- a benchmark of metagenomics software
A Sczyrba, P Hofmann, P Belmann, D Koslicki, S Janssen, J Dröge, ...
Nature methods 14 (11), 1063-1071, 2017
A fast approximate algorithm for mapping long reads to large reference databases
C Jain, A Dilthey, S Koren, S Aluru, AM Phillippy
International Conference on Research in Computational Molecular Biology, 2017
A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps
C Jain, S Koren, A Dilthey, A Phillippy, S Aluru
Bioinformatics 34 (17), i748–i756, 2018
The structure, function and evolution of a complete human chromosome 8
GA Logsdon, MR Vollger, PH Hsieh, Y Mao, MA Liskovykh, S Koren, ...
Nature 593 (7857), 101--107, 2021
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
AT Dilthey, C Jain, S Koren, AM Phillippy
Nature communications 10 (1), 1-12, 2019
Weighted minimizer sampling improves long read mapping
C Jain, A Rhie, H Zhang, C Chu, S Koren, A Phillippy
Bioinformatics, i111–i118, 2020
A comprehensive evaluation of long read error correction methods
H Zhang, C Jain, S Aluru
BMC genomics 21 (6), 1-15, 2020
A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications
P Flick, C Jain, T Pan, S Aluru
Proceedings of the International Conference for High Performance Computing …, 2015
Kmerind: A flexible parallel library for k-mer indexing of biological sequences on distributed memory systems
T Pan, P Flick, C Jain, Y Liu, S Aluru
IEEE/ACM transactions on computational biology and bioinformatics 16 (4 …, 2017
An Adaptive Parallel Algorithm for Computing Connected Components
C Jain, P Flick, T Pan, O Green, S Aluru
IEEE Transactions on Parallel and Distributed Systems, 2017
The complete sequence of a human genome
S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ...
bioRxiv, 2021
On the complexity of sequence-to-graph alignment
C Jain*, H Zhang*, Y Gao, S Aluru
Journal of Computational Biology 27 (4), 640-654, 2020
Accelerating sequence alignment to graphs
C Jain, S Misra, H Zhang, A Dilthey, S Aluru
2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS …, 2019
Efficient detection of viral transmissions with next-generation sequencing data
I Rytsareva, DS Campo, Y Zheng, S Sims, SV Thankachan, C Tetik, ...
BMC genomics 18 (4), 1-7, 2017
precisionFDA Truth Challenge V2: Calling variants from short-and long-reads in difficult-to-map regions
ND Olson, J Wagner, J McDaniel, SH Stephens, ST Westreich, ...
Biorxiv, 2020.11. 13.380741, 2021
A long read mapping method for highly repetitive reference sequences
C Jain, A Rhie, N Hansen, S Koren, AM Phillippy
bioRxiv, 2020
Fine-grained GPU parallelization of pairwise local sequence alignment
C Jain, S Kumar
High Performance Computing (HiPC), 2014 21st International Conference on, 1 - 10, 2014
A Self-Correcting Connected Components Algorithm
P Sao, O Green, C Jain, R Vuduc
Proceedings of the ACM Workshop on Fault-Tolerance for HPC at Extreme Scale …, 2016
Validating paired-end read alignments in sequence graphs
C Jain, H Zhang, A Dilthey, S Aluru
19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 143 …, 2019
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