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

Research interests AI. Bioinformatics. Clinical Genomics. Metagenomics. Privacy in Genomics.
Ph.D. Advisor Dr. Stefano Lonardi






On 10/12/2023, new research work about the 2022 mpox virus outbreak published:
The 2022 global outbreak of mpox virus (MPXV) highlighted challenges with PCR detection as divergent strains emerged and atypical presentations limited the applicability of swab sampling. Recommended testing in the United States requires a swab of lesions, which arise late in infection and may be unrecognized. We present MPXV detections using plasma microbial cell-free DNA (mcfDNA) sequencing... To read more, check out the manuscript in the Journal of Infectious Diseases.

On 12/28/2022, new research work about disinfection techniques for medical environments published, in the special issue of Microbiome Analysis Techniques and Discovery, in Genes:
Pathogenic bacteria and viruses in medical environments can lead to treatment complications and hospital-acquired infections. Current disinfection protocols do not address hard-to-access areas or may be beyond line-of-sight treatment, such as with ultraviolet radiation. The COVID-19 pandemic further underscores the demand for reliable and effective disinfection methods to sterilize a wide array of surfaces and to keep up with the supply of personal protective equipment (PPE). We tested the efficacy of Sani Sport ozone devices to treat hospital equipment and surfaces for killing Escherichia coli, Enterococcus faecalis, Bacillus subtilis, and Deinococcus radiodurans by assessing Colony Forming Units (CFUs) after 30 min, 1 h, and 2 h of ozone treatment... To read more, check out the manuscript in Genes.

On 07/29/2021: Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied. To read more, see the manuscript in Frontiers in Microbiology.

On 06/24/2021, the MetaSUB large-scale research work about a global metagenomic map of urban microbiomes and antimicrobial resistance is now published in the Cell Journal! To read more, find the manuscript here.

On 08/11/2019, the MetaSUB study "Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance" gathering 635 authors, provides a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit systems from 58 cities, spanning 3,741 samples and 4,424 taxonomically-defined microorganisms collected for from 2015-2017. To read more, see the biorxiv paper.

On 04/24/2019, the genome of cowpea, is now released in the Plant Journal! Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences.

On 09/18/2018: Pathogenic bacteria in medical environments can lead to treatment complications and hospital acquired infections (HAIs), and current cleaning protocols do not address hard-to-access areas or that may be beyond line-of-sight treatment such as with ultraviolet radiation. In our biorxiv manuscript, we tested the efficacy of Sanisport ozone as a means to treat hospital equipment and surfaces for killing bacteria. We observed a rapid killing of medically-relevant and environmental bacteria (E. coli, E. faecalis, B. subtlis, and D. radiodurans) across four surfaces (blankets, catheter, remotes, and syringes) within 30 minutes, and up to a 99% reduction in viable bacteria at the end of 2-hour treatment cycles. These results show the strong promise of ozone treatment for reducing risk of infection and HAIs.

On 06/28/2017, a comprehensive benchmarking and ensemble approaches for metagenomic classifiers is now available in biorxiv! The results of this study provide positive controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision and sensitivity. Check out the preprint!

On 04/26/2017, a complete reference sequence of barley is now published in Nature! This publication highlights a decade of research and efforts by a international collaboration (in Australia, China, Czech Republic, Denmark, Finland, Germany, Italy, Sweden, UK, and the US). The computational pipeline that enabled the construction of this high-quality reference genome includes the CLARK system. See the UCR press release and the Nature article.

On 01/11/2017, Ph.D. Final Defense before Dr. Lonardi (Chairperson), Dr. Close, Dr. Jiang, Dr. Keogh and Dr. Shinar. See the dissertation webpage for details.

On 10/19/2016, PLoS Computational Biology publishes rasbhari, a new efficient and fast algorithm to generate spaced seeds for database searching, read mapping and alignment-free sequence comparison (see the publication).

On 09/07/2016, The Molecular Ecologist, a leading media in applications of population genetics data in studies of evolution, ecology and diversity, highlights CLARK-S in this blog post!

On 08/31/2016, GenomeWeb, a leading online media that tracks innovations in genomics, genetics and bioinformatics, reviews the recent development in the CLARK series here!

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, An algorithmic extension 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.