Usman Roshan
Associate Professor, Department of Computer Science, New Jersey Institute of Technology
Director of Data Science
MS Data Science degree requirements (current, last updated 05/08/2018)
MS Data Science admission requirements
Director of Bioinformatics
Ph.D. Computer Science, The University of Texas at Austin, Advisor: Tandy Warnow

Office: GITC 4207
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@njit.edu

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Research
Bioinformatics: sequence alignment, evolutionary tree reconstruction, genome-wide association studies, disease risk prediction
Computer science: data science, machine learning, high performance computing (in applications)

Research projects: I'm looking for students with strong programming skills to work on the following projects. These projects involve large datasets, Python and C programming, parallel programming on CPUs and GPUs, and would lead to a Masters or PhD thesis.

• Optimization methods for non-linear non-convex objectives in machine learning
• Representation learning with random weights
• Machine learning methods for sequence alignment
• Machine learning methods for DNA and protein sequence classification
• Cancer and disease risk prediction from whole exome and whole genome sequence data
• Whole genome sequence alignment
• Accuracy of phylogeny reconstruction from simulated whole genomes

Publications

Software and benchmarks

• Machine learning and representation learning
  • Iterated coordinate descent for regularized 0/1 loss (2018)
  • K-means-based feature learning for protein sequence classification (2018)
  • Weighted maximum variance dimensionality reduction (2014)
• Sequence alignment:
  • Anchor selection for pairwise whole genome sequence alignment with the maximum scoring subsequence and GPUs (2018)
  • MaxSSmap: fast and accurate mapping of divergent short reads to genomes (suitable for cross-species mapping and unmapped reads) (2014)
  • PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences (2010)
  • Identifying distantly related RNAs in genomic sequences (2008)
  • eProbalign: web server and source code for Probalign multiple sequence alignment program (2007)
    Also available at the CIPRES portal
• Genomics
  • Chi8: a GPU program for detecting significant interacting SNPs with the chi-square 8-df test (2015)
  • Ranking causal SNPs and disease associated regions in genome wide association studies by the support vector machine and random forest (2011)
• Large-scale phylogeny reconstruction:
  • Recursive-Iterative-DCM3: divide-and-conquer booster for large-scale phylogeny reconstruction (2004)
    Also available at the CIPRES portal
• Gene expression clustering:
  • Diametrical clustering for identifying anti-correlated gene clusters (2003)

Teaching

• CS 698: Current topics in data science, Spring 2018
• BNFO 602: Foundations of Bioinformatics II, Spring 2018

Current students

• Wei Chun Chen, PhD thesis advisor, (expected 2021)
• Yunzhe Xue, PhD thesis advisor, (expected 2021)
• Meiyan Xie, PhD thesis advisor, (expected 2021)
• Abdulrhman Aljouie, PhD thesis advisor, (expected 2018)
• Junilda Spirollari, PhD thesis advisor, (expected 2018)
• Aradhya Chouhan, MS thesis advisor, (expected 2018)

Previous students

• Paul Melman, MS thesis advisor, 2017
• Ling Zhong, PhD thesis advisor, 2017
• Pranitha Andalam, MS thesis advisor, 2016 (first position at Xilinx, Colorado)
• Nandini Ghosh, MS thesis advisor, 2015
• Nihir Patel, MS thesis advisor, 2014 (first position at Mt. Sinai Hospital)
• Wei Wang, PhD committee member 2014, (first position as data scientist in industry)
• Bharati Jhadav, MS thesis advisor, 2014, (first position at Mt. Sinai Hospital)
• Harishitha Damerla, MS project advisor, 2013
• Amiel Meiseles, MS project advisor, 2013
• Srividya Ramakrishnan, MS thesis advisor, 2013 (first position at Cold Spring Harbor Lab)
• Shuo Chen, PhD committee member, 2012
• Andrew Roberts, MS thesis advisor, 2012 (Merck)
• 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 thesis 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 Mount Sinai Hospital)

Some students from the bioinformatics program

• Xiao Ling, MS Bioinformatics 2013 (first position as bioinformatician at Yale University School of Medicine)
• Jharna Miya, MS Bioinformatics 2013 (first position as bioinformatics analyst at Comprehensive Cancer Center, Ohio State University)
• Hajira Naqvi, MS Bioinformatics 2013 (Memorial Sloan Kettering)
• Sagar Changawalla, BS Bioinformatics 2011 (first position at Cornell)
• Aparna Agrawal, MS Bioinformatics 2009 (first position at Roche)
• Wasay Hussain, BS and MS Bioinformatics 2009 (first position as bioinformatics researcher at Cornell)
• Monika Bihan, MS Bioinformatics 2008 (first position as bioinformatics engineer at J. Craig Venture Institute)

Visitors

• Chen Hao, School of Computer Science and Technology, Xi'an University of Posts & Telecommunication (2017-2018)