Algorithms and Computational Biology Lab
Computer Science & Engineering Department
University of California
Riverside, CA 92532

Research interests Combinatorial algorithms. Computational biology. Data-mining. Epigenetics. Metagenomics.
Advisor Dr. Stefano Lonardi






On 08/18/2016, The new classifier CLARK-S is now published in Bioinformatics! The free-access to the PDF manuscript is here. The synthetic datasets and the software are freely available in the public domain here.

On 04/15/2016, our manuscript of BRAT-nova: Fast and accurate mapping of bisulfite-treated reads has been accepted for publication in Bioinformatics. The software is available in the public domain here.

On 10/26/2015, the CLARK project (including its latest development with discriminative spaced k-mers) is being presented during a short talk at the Center for Data Science, New York University. See details of the talk here. See the latest published article online.

On 09/11/2015, the new classifier, CLARK-S is being presented at the 15th International Workshop, WABI 2015. The new mode offers higher sensitivity compared to other modes, while maintaining both high speed and high precision. See the article in the proceedings online.

On 08/07/2015, CLARK used to assign barley BACs to chromosome arms/centromeres.
See results in the article "Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome" published in The Plant Journal.

On 06/15/2015, New version of CLARK accepted as a paper presentation at WABI 2015.
The version includes a new mode of operations (based on discriminative mismatches through different patterns) that increases the overall classification accuracy without a significant loss of speed. It also permits to assign a much higher proportion of reads from real metagenomes compared to other mode (e.g., default) or Kraken.
The WABI conference will take place in Atlanta, GA, on September 10-12, 2015.

On 05/06/2015, Guest post "Accurate metagenomic analysis of a million reads in 20 seconds or less…"
The guest post about CLARK in the Jonathan Eisen's blog, The Tree of Life, is available here.

On 03/25/2015, CLARK paper published and available online
The CLARK article is available here. The project description and source code can be accessed at this page.

On 08/04/2014, CLARK software tool accepted for presentation
Our recent research work about the classification problem of metagenomic and genomic sequences has been accepted for the fifth ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM-BCB 2014) as a poster presentation. We will present "CLARK", an accurate, fast and efficient classification method of DNA sequences.

This conference will take place in Newport beach, CA, on september 20-23, 2014. The method description is available here.