Home Publications


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  • Telomere-to-telomere assembly by preserving contained reads
    S S Kamath, M Bindra, D Pal, C Jain. BioRxiv


  • 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