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






R   Research Assistant (Designed/implemented efficient algorithms for sequence analysis in metagenomics or epigenetics, such as CLARK, or BRAT-nova)

Lecturer Software Construction CS 100 (upper-division class);

Teaching Assistant (Computer Security CS 165, Introduction to Computer Science CS 10, Introduction to Data Structures and Algorithms CS 14, and Design and Analysis of Algorithms CS 218) ;

Reviewer ( Bioinformatics and BMC Bioinformatics, and for the following conferences: ACM-BCB'16 WABI'16 RECOMB-Seq'16, BIBM'15, ACM-BCB'15, CPM'15, ISMB/ECCB'15, RECOMB'15, RECOMB-CG'14, WABI'14, RECOMB'14, ISMB'14 )
R Software Engineer (Designed and implemented ray-tracing algorithms, and data-mining techniques). 2011 - 2012.
R Research Assistant (Research in computational neuroscience, Designed and Implemented machine learning-based models). 2010.
R IT Analyst (Audited and tested financial software, wroted software specifications). 2008.
R       IT Developer (Implemented stochastic models for evaluating uncertainties in nuclear data measurements). 2007.


  Ph.D. Computer Science,
  University of California, Riverside, CA. Winter 2017.
  Advisor: Dr. Stefano Lonardi.

  Computational biology, Data-mining, Epigenetics, Metagenomics.
  M.S. Computer Science,
  ENSIIE, Evry, France. Fall 2010.

  Computer Science, Applied Mathematics, Project Management.
  Lycee Henri Wallon, Valenciennes, France. Spring 2006.
  Mathematics, Physics.
(*) In France, the CPGE program consists of two to three years of extremely intensive preparatory classes to the national competitive entrance (written and oral) exams of engineering and scientific schools (almost all public). For example, Ecole Polytechique or Ecoles Normales Superieures. In 2006, I have been admitted to ENSIIE (ranked first engineering public school in computer science) and also the Ecole Normale Superieure at Rennes.


  A chromosome conformation capture ordered sequence of the barley genome
Martin Mascher, Heidrun Gundlach, Axel Himmelbach, Sebastian Beier, Sven O. Twardziok, ... & Nils Stein Nature 2017.
  rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
Hahn, L., Leimester, C.-A., Ounit, R., Lonardi, S., Morgenstern, B. PLoS Computational Biology 2016.
  Higher classification sensitivity of short metagenomic reads with CLARK-S
Ounit, R., Lonardi, S. Bioinformatics 2016.
  BRAT-nova: Fast and accurate mapping of bisulfite-treated reads
Harris, E.Y., Ounit, R., Lonardi, S. Bioinformatics, 2016.
  Higher classification accuracy of short metagenomic reads by discriminative k-mers
Ounit, R., Lonardi, S. Proceedings of the 15th International Workshop of Algorithms in Bioinformatics 2015.
  Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome
Munoz-Amatriain, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J. T., Moscou, M. J., ... & Close, T. J. The Plant Journal 2015.
  CLARK: Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
Ounit, R., Wanamaker, S., Close, T. J., Lonardi, S. BMC Genomics 2015, 16:236. Highly accessed.
  CLARK, accurate and efficient classification of DNA sequences
Ounit, R., Close, T. J., Wanamaker, S., Lonardi, S., Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 2014.
  Linking organization and function within an articial-neural-network model of the insect antennal lobe
Ounit, R., Rangan A.V., Preprint. 2011.
  Comparison of error propagation in the FISPACT code with a straightforward Monte Carlo method
Ounit, R., Jacquet, H. P., Dossantos-Uzarralde, P. EFFDOC-1049 JEFF/EFF meeting. 2008.


  The Metagenomic Research Group (Association of Biomolecular Resource Facilities), 2016
  The Metagenomics & Metadesign of Subways & Urban Biomes (MetaSUB), 2016
  International Society of Computational Biology, 2015
  Association for Computing Machinery, 2014


  ACM-BCB Student Travel Award, 2014
  Omicron Delta Kappa (National Leadership Honor Society), 2013
  Dean's Distinguished Fellowship (University of California, Riverside, CA), 2012