Publications with Chirag Jain, PhD

Postdoctoral Fellow

see entire profile
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Nature Methods, April 1, 2022
Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, Sović I, Wood JM, Zook JM, Phillippy AM, Rhie A
Long-read mapping to repetitive reference sequences using Winnowmap2
Nature Methods, April 1, 2022
Jain C, Rhie A, Hansen N, Koren S, Phillippy AM
The complete sequence of a human genome
Science, April 1, 2022
Nurk S, Koren S, Rhie A, Rautiainen M … Hansen NF … Jain C … Mc Cartney AM … Walenz BP … Phillippy AM
The structure, function and evolution of a complete human chromosome 8
Nature, April 7, 2021
Logsdon GA … Koren S, Nurk S … Rhie A … Jain C … Phillippy AM, Eichler EE
Weighted minimizer sampling improves long read mapping
Bioinformatics, July 13, 2020
Jain C, Rhie A, Zhang H, Chu C, Koren S, Phillippy A
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Nature Communications, July 11, 2019
Dilthey A, Jain C, Koren S, Phillippy AM
High-throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Nature Communications, November 30, 2018
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S
A fast adaptive algorithm for computing whole-genome homology maps
Bioinformatics, September 1, 2018
Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S
A fast approximate algorithm for mapping long reads to large reference databases
RECOMB 2017, May 3, 2017
Jain C, Dilthey A, Koren S, Aluru S, Phillippy AM