Usman Roshan
Associate Professor, Department of Computer Science, New Jersey Institute of Technology

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: sequence alignment, evolutionary tree reconstruction, genome-wide association studies, disease risk prediction; Computer science: machine learning, high performance computing

Publications

Software and benchmarks:

• Genome-wide association studies:
  • Ranking causal SNPs and disease associated regions in genome wide association studies by the support vector machine and random forest
• Sequence alignment:
  • PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences
  • 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 602: Foundations of Bioinformatics II, Spring 2012
• BNFO 136: Programming for Bioinformatics II, Spring 2012

Current students

• Srividya Ramakrishnan, MS thesis advisor, (expected 2012)

Previous students

• Andrew Roberts, MS thesis advisor, 2012
• Meera Prasad, MS thesis advisor, 2011, (first position at NYU Langone Medical Center)
• Seif Shahidain, MS thesis advisor, 2011, (first position at NIH)
• Satish Chikkagoudar, PhD advisor, 2010 (first position as postdoc at UPenn, second position as scientist at Pacific Northwest National Lab)
• Tao Wu, PhD committee member, 2010 (first position at Microsoft)
• Suresh Solaimuthu, PhD committee member, 2010 (first position at UBS)
• Paras Garg, MS thesis, 2010 (first position as bioinformatics researcher at Mt Sinai)