Chirag Jain
Chirag Jain
Indian Institute of Science
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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
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
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
A comprehensive evaluation of long read error correction methods
H Zhang, C Jain, S Aluru
BMC genomics 21 (6), 1-15, 2020
The structure, function, and evolution of a complete human chromosome 8
GA Logsdon, MR Vollger, PH Hsieh, Y Mao, MA Liskovykh, S Koren, ...
bioRxiv, 2020
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
Weighted minimizer sampling improves long read mapping
C Jain, A Rhie, H Zhang, C Chu, S Koren, A Phillippy
Bioinformatics, i111–i118, 2020
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
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
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
A long read mapping method for highly repetitive reference sequences
C Jain, A Rhie, N Hansen, S Koren, AM Phillippy
bioRxiv, 2020
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
Biological and Environmental Research Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Biological and …
A Arkin, DC Bader, R Coffey, K Antypas, D Bard, E Dart, S Dosanjh, ...
US Department of Energy, Washington, DC (United States). Advanced Scientific …, 2016
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