Usman Roshan
Assistant Professor, Department of Computer Science, New Jersey Institute of Technology
Ph.D. Computer Science, The University of Texas at Austin, Advisor: Tandy Warnow
Member of CIPRES

Office: GITC 3802
Mailing address: Department of Computer Science, NJIT, GITC 4400, University Heights, Newark, NJ 07102
Phone: 973-596-2872 (office)
Fax: 973-596-5777 (fax)
Best way to reach me: usman@cs.njit.edu

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Research interests: bioinformatics, machine learning, algorithms, experimental performance studies

Publications

Software and benchmarks:

• Genome-wide association studies:
  • Hybrid support vector machine strategy for ranking SNPs in genome-wide association studies
  • Semi-supervised feature extraction for population structure identification using the Laplacian linear discriminant
• Sequence alignment:
  • Identifying distantly related RNAs in genomic sequences
  • eProbalign: web server and source code for probalign multiple sequence alignment program
    Also available at the CIPRES portal
• Large-scale phylogeny reconstruction:
  • Recursive-Iterative-DCM3: divide-and-conquer booster for large-scale phylogeny reconstruction
    Also available at the CIPRES portal
• Gene expression clustering:
  • Diametrical clustering for identifying anti-correlated gene clusters

Teaching

• BNFO 601: Foundations of Bioinformatics I, Fall 09
• BNFO 135: Programming for Bioinformatics I, Fall 09