Recent Group News

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

  • Our paper on AllSome Sequence Bloom Trees is accepted in RECOMB 2017!

  • Our paper on the compaction of a de Bruijn graph built from reads has been published in ISMB 2016. Read more here.

  • Our TwoPaCo algorithm for building the compacted de Bruijn graph from complete genomes won the best poster award at RECOMB 2016! Read more here.

  • Our paper on the sequencing and assembly of the Gorilla Y Chromosome has been published at Genome Research. You can read more about it in the news.

  • Our paper on safe and complete contig assembly via omnitigs was accepted for publication at RECOMB 2016. Read more here.

Current / Upcoming Courses

  • Data Structures and Algorithms, CMPSC465, Fall 2017.

Recent Software

  • AllSome SBT: querying transcript presence in reads.
  • VarMatch: matching variants in VCF files.
  • BCALM 2 : de Bruijn graph compacation from reads.
  • TwoPaCo : de Bruijn graph construction from complete genomes.
  • KmerGenie : k-mer size selection for genome assembly

Major Current Funding