Publications with Chirag Jain, PhD

Postdoctoral Fellow

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
bioRxiv, July 2, 2021
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
The complete sequence of a human genome
bioRxiv, May 27, 2021
Nurk S, Koren S, Rhie A, Rautiainen MJain CMc Cartney AMWalenz BPPhillippy AM
The structure, function and evolution of a complete human chromosome 8
Nature, April 7, 2021
Logsdon GA … Koren S, Nurk SRhie AJain CPhillippy AM, Eichler EE
A long read mapping method for highly repetitive reference sequences
bioRxiv, November 2, 2020
Jain C, Rhie A, Hansen N, Koren S, Phillippy AM
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