Chirag Jain


PhD Student 
Georgia Insitute of Technology

Email address :  c + lastname at
Office address : 1209, Klaus Advanced Computing Building
                           266 Ferst Dr NW, Atlanta, GA 30332 

I enjoy working on scalable algorithms for data intensive computational problems in genomics. I completed my bachelors in CS major from Indian Institute of Technology Delhi and joined PhD program in fall 2014, currently advised by Srinivas Aluru.    [CV]

Google Scholar (⇔ denotes equal contribution) 
  1. MetaMaps-Strain-level metagenomic assignment and compositional estimation for long reads
    A Dilthey, C Jain, S Koren, A Phillippy. BioRxiv 2018         Github  

  2. A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps
    C Jain, S Koren, A Dilthey, A Phillippy, S Aluru. To appear in Bioinformatics (ECCB Special Issue) 2018        Github

  3. High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries
    C Jain, L Rodriguez, A Phillippy, K Konstantinidis, S Aluru. BioRxiv 2017        Github  Slides
  4. A fast approximate algorithm for mapping long reads to large reference databases.
    C Jain, A Dilthey, S Koren, S Aluru, A Phillippy. RECOMB 2017        Github  Slides

  5. An adaptive parallel algorithm for computing connected components. 
    C Jain, P Flick, T Pan, O Green, S Aluru. IEEE TPDS 2017        Github  Slides

  6. Kmerind: A flexible parallel library for k-mer indexing of biological sequences on distributed memory systems.
    T Pan et. al. ACM BCB 2016, IEEE/ACM TCBB 2017         Github  Slides  

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

  8. A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications.
    P Flick, ⇔ C Jain, ⇔ T Pan, S Aluru. ACM Supercomputing 2015        Github  Slides

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

Selected Awards
  1. Reproducibility Initiative Winner. ACM Supercomputing 2016. Link
  2. Nvidia Conference Best GPU paper award. IEEE HiPC 2014.