Home Publications


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  • Accelerating long-read analysis on modern CPUs
    S Kalikar, C Jain, V Md, S Misra. BioRxiv

  • Co-linear chaining with overlaps and gap costs
    C Jain, D Gibney, SV Thankachan. BioRxiv

  • A long read mapping method for highly repetitive reference sequences
    C Jain, A Rhie, N Hansen, S Koren, A Phillippy. BioRxiv


  • A variant selection framework for genome graphs
    C Jain, N Tavakoli, S Aluru. Bioinformatics 2021 (ISMB/ECCB proceedings)

  • Real-time mapping of nanopore raw signals
    H Zhang, H Li, C Jain et al. Bioinformatics 2021 (ISMB/ECCB proceedings)

  • The structure, function, and evolution of a complete human chromosome 8
    Logsdon et al. Nature 2021


  • Weighted minimizer sampling improves long read mapping
    C Jain, A Rhie, H Zhang, C Chu, B Walenz, S Koren, A Phillippy. Bioinformatics 2020 (ISMB proceedings)

  • A comprehensive evaluation of long read error correction methods
    H Zhang, C Jain, S Aluru. BMC Genomics 2020

  • On the complexity of sequence to graph alignment
    C Jain, ⇔ H Zhang, Yu Gao, S Aluru. JCB 2020 (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. 2019

  • Validating paired-end read alignments in sequence graphs
    C Jain, H Zhang, A Dilthey, S Aluru. WABI 2019

  • Accelerating sequence alignment to graphs
    C Jain, S Misra, H Zhang, A Dilthey, S Aluru. IEEE IPDPS 2019


  • High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
    C Jain, L Rodriguez, A Phillippy, K Konstantinidis, S Aluru. Nature Comm. 2018

  • A fast adaptive algorithm for computing whole-genome homology maps
    C Jain, S Koren, A Dilthey, A Phillippy, S Aluru. Bioinformatics 2018 (ECCB proceedings)

  • A fast approximate algorithm for mapping long reads to large reference databases
    C Jain, A Dilthey, S Koren, S Aluru, A Phillippy. JCB 2018 (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 2017 (extended abstract appeared in SC’15)

  • Efficient detection of viral transmissions with next-generation sequencing data
    Rytsareva et al. BMC Genomics 2017

  • 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 2017 (extended abstract appeared in ACM BCB’16)

  • Critical Assessment of Metagenome Interpretation- a benchmark of metagenomics software
    Sczyrba et al. Nature Methods 2017


  • A self-correcting connected components algorithm
    P Sao, O Green, C Jain, R Vuduc. ACM FTXS 2016


  • Fine-grained GPU parallelization of pairwise local sequence alignment
    C Jain, S Kumar. IEEE HiPC 2014