Principal Investigator Location Affiliations

Recent Group News

  • In a joint work with R. Chikhi and J. Holub, we've written a survey on data structures to represent k-mer sets.

  • Our new tool SibeliaZ, for doing multiple whole genome alignment, is now released. The paper will be presented a RECOMB-Seq 2019.

  • Paper on de novo clustering of long transcriptomic reads with isONclust is accepted at RECOMB 2019.

  • We have written a new tutorial on how to model biological problems in computer science, using genome assembly as a case study.

Current / Upcoming Courses

  • Algorithms and Data Structures in Bioinformatics, CSE / BMMB 566, Spring 2019.

Recent Software

  • SibeliaZ: whole-genome alignment.
  • isONclust: de novo clustering of long transcript reads into genes
  • IsoCon: deriving finished transcript sequences from Iso-Seq reads.
  • HowDe-SBT: querying long strings in sequencing experiments.
  • VarGeno: SNP genotyping.
  • VarMatch: matching variants in VCF files.

Major Current Funding

  • NSF CAREER award 1453527.
  • NSF award 1439057.
  • NIH (NIGMS) award R01GM130691
  • NIH (NCI) award R01CA237153