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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

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"The language of nature's book is mathematics and that the way to understand nature is through mathematic."
Galileo Galilei, The Assayer - Il Saggiatore, 1623.


BRAT-nova: Fast and accurate mapping of bisulfite-treated reads
BRAT-nova is a completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-Seq).

On the human genome, BRAT-nova is 2-7 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2-8 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy, and space efficiency.

The software is available in the public domain here.

CLARK, Fast and Accurate Classification of Metagenomic and Genomic Sequences
CLARK is a versatile classifier that can be used in metagenomics or genomics (CLARK webpage).

K-mer based method, CLARK can assign taxonomic labels to a set of 10,000 shorts reads (92 bp in average) at the speed of 32 million of reads per minute, in its fastest single-threaded mode.
The CLARK project has been presented for the first time on september 20-23, 2014 the 5-th ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics ACM-BCB, in Newport beach, CA.