Publications

Accelerating whole-genome alignment in the age of complete genome assemblies
G Chandra, M Vasimuddin, S Misra, C Jain. bioRxiv

Integer programming framework for pangenome-based genome inference
G Chandra, M Hossen, S Scholz, A Dilthey, D Gibney, C Jain. RECOMB (accepted)

Telomere-to-telomere assembly by preserving contained reads
S S Kamath, M Bindra, D Pal, C Jain. Genome Research (Long-read special issue)
On the coverage required for diploid genome assembly
D Mahajan, C Jain, N Kashyap. IEEE ISIT
Haplotype-aware sequence alignment to pangenome graphs
G Chandra, D Gibney, C Jain. Genome Research (extended abstract appeared in RECOMB’24)
Co-linear chaining on pangenome graphs
J Rajput, G Chandra, C Jain. Algorithms for Molecular Biology (extended abstract appeared in WABI’23)

A lossless compression pipeline for petabyte-scale whole-genome sequencing data
A Bhat, S M Chadalavada, N Jammula, C Jain, Y Simmhan. IEEE HiPC
Coverage-preserving sparsification of overlap graphs for long-read assembly
C Jain. Bioinformatics
Gap-sensitive colinear chaining algorithms for acyclic pangenome graphs
G Chandra, C Jain. Journal of Computational Biology (extended abstract appeared in RECOMB’23)

Long-read mapping to repetitive reference sequences using Winnowmap2
C Jain, A Rhie, N Hansen, S Koren, A Phillippy. Nature Methods
Accelerating minimap2 for long-read sequencing applications on modern CPUs
S Kalikar, C Jain, V Md, S Misra. Nature Computational Science
Co-linear chaining with overlaps and gap costs
C Jain, D Gibney, SV Thankachan. Journal of Computational Biology (extended abstract appeared in RECOMB’22)
The complete sequence of a human genome
Nurk et al. Science
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Mc Cartney et al. Nature Methods

A variant selection framework for genome graphs
C Jain, N Tavakoli, S Aluru. Bioinformatics (ISMB/ECCB proceedings)
Real-time mapping of nanopore raw signals
H Zhang, H Li, C Jain et al. Bioinformatics (ISMB/ECCB proceedings)
The structure, function, and evolution of a complete human chromosome 8
Logsdon et al. Nature

Weighted minimizer sampling improves long read mapping
C Jain, A Rhie, H Zhang, C Chu, B Walenz, S Koren, A Phillippy. Bioinformatics (ISMB proceedings)
A comprehensive evaluation of long read error correction methods
H Zhang, C Jain, S Aluru. BMC Genomics
On the complexity of sequence to graph alignment
C Jain, ⇔ H Zhang, Yu Gao, S Aluru. Journal of Computational Biology (extended abstract appeared in RECOMB’19)

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
A Dilthey, C Jain, S Koren, A Phillippy. Nature Comm.
Validating paired-end read alignments in sequence graphs
C Jain, H Zhang, A Dilthey, S Aluru. WABI
Accelerating sequence alignment to graphs
C Jain, S Misra, H Zhang, A Dilthey, S Aluru. IEEE IPDPS

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
C Jain, L Rodriguez, A Phillippy, K Konstantinidis, S Aluru. Nature Comm.
A fast adaptive algorithm for computing whole-genome homology maps
C Jain, S Koren, A Dilthey, A Phillippy, S Aluru. Bioinformatics (ECCB proceedings)
A fast approximate algorithm for mapping long reads to large reference databases
C Jain, A Dilthey, S Koren, S Aluru, A Phillippy. Journal of Computational Biology (extended abstract appeared in RECOMB’17)

An adaptive parallel algorithm for computing connected components
C Jain, P Flick, T Pan, O Green, S Aluru. IEEE TPDS (extended abstract appeared in SC’15)
Efficient detection of viral transmissions with next-generation sequencing data
Rytsareva et al. BMC Genomics
Kmerind: A parallel library for k-mer indexing of biological sequences on distributed memory systems
T Pan, P Flick, C Jain, Y Liu, S Aluru. IEEE TCBB (extended abstract appeared in ACM BCB’16)
Critical Assessment of Metagenome Interpretation- a benchmark of metagenomics software
Sczyrba et al. Nature Methods

A self-correcting connected components algorithm
P Sao, O Green, C Jain, R Vuduc. ACM FTXS

Fine-grained GPU parallelization of pairwise local sequence alignment
C Jain, S Kumar. IEEE HiPC