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
The complete sequence of a human genome
S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ...
Science 376 (6588), 44-53, 2022
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
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 (RECOMB), 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
Weighted minimizer sampling improves long read mapping
C Jain, A Rhie, H Zhang, C Chu, S Koren, A Phillippy
Bioinformatics, i111–i118, 2020
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 comprehensive evaluation of long read error correction methods
H Zhang, C Jain, S Aluru
BMC genomics 21 (6), 1-15, 2020
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, ...
Cell Genomics 2 (5), 100129, 2022
Long-read mapping to repetitive reference sequences using Winnowmap2
C Jain, A Rhie, NF Hansen, S Koren, AM Phillippy
Nature Methods, 1-6, 2022
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
A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications
P Flick, C Jain, T Pan, S Aluru
SC'15: Proceedings of the International Conference for High Performance …, 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
Proceedings of the 7th ACM International Conference on Bioinformatics …, 2016
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
Reply to:“Re-evaluating the evidence for a universal genetic boundary among microbial species”
LM Rodriguez-R, C Jain, RE Conrad, S Aluru, KT Konstantinidis
Nature communications 12 (1), 1-7, 2021
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
AM Mc Cartney, K Shafin, M Alonge, AV Bzikadze, G Formenti, ...
Nature Methods, 1-9, 2022
Real-time mapping of nanopore raw signals
H Zhang, H Li, C Jain, H Cheng, KF Au, H Li, S Aluru
Bioinformatics 37 (Supplement_1), i477-i483, 2021
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
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