Papers under preparation
  1. Abdulrhman Aljouie and Usman Roshan, Machine learning based prediction of kidney cancer survival and onset times with somatic and germline mutations from whole exome data
Papers submitted and under revision
  1. Junilda Spirollari and Usman Roshan, The accuracy of phylogeny reconstruction on simulated whole genome sequences from Evolver (Under revision)


  2. Yunzhe Xue and Usman Roshan, Random depthwise signed convolutional neural networks (Submitted)
Book Chapters
  1. U. Roshan, Multiple sequence alignment using Probcons and Probalign, in "Methods in Molecular Biology: Multiple Sequence Alignment Methods", ed. David J. Russell, Humana Press (Springer), 2013, 147-155 (PDF) Springer link to book)

  2. K. M. Kjer, U. Roshan, and J. J. Gillespie, Structural and evolutionary considerations for multiple sequence alignment of RNA, and the challenges for algorithms that ignore them, in "Perspectives on Biological Sequence Alignment: Where, How, and Why It Matters", ed. Michael Rosenberg, University of California Press, USA, 2009, 105-151 (PDF)

  3. D. Bader, U. Roshan, and A. Stamatakis, Computational grand challenges in assembling the Tree of Life: problems and solutions, in "Advances in Computers, Computational Biology and Bioinformatics", ed. Marvin Zelkowitz and Chau-wen Tseng, Elsevier, 2006, 128-178 (PDF)

  4. U. Roshan, B. M. E. Moret, T. L. Williams, T. Warnow, Performance of supertree methods on various dataset decompositions in "Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life", ed. O.R.P. Bininda Emonds, Springer, 2004, 301-329 (PDF)
Publications (peer-reviewed)
  1. Abdulrhman Aljouie, Ling Zhong, and Usman Roshan, Anchor selection for pairwise whole genome sequence alignment with the maximum scoring subsequence and GPUs, accepted to International Conference on Intelligent Biology and Medicine (ICIBM) 2018 (local link to paper)

  2. Abdulrhman Aljouie, Nihir Patel, and Usman Roshan, Cross-validation and cross-study validation of kidney cancer with machine learning and whole exome sequences from the National Cancer Institute, accepted to IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) 2018 (local link to paper)

  3. Paul Melman and Usman Roshan, A k-means based feature learning method for protein sequence classification, accepted to ISCA International Conference on Bioinformatics and Computational Biology (BICOB) 2018 (local link to paper)

  4. Abdulrhman Aljouie, Nihir Patel, and Usman Roshan, Cross-validation and cross-study validation of chronic lymphocytic leukemia with exome sequences and machine learning, International Journal of Data Mining and Bioinformatics, 2016 (PDF, local link to paper)

  5. Nihir Patel, Abdulrhman Aljouie, Bharati Jhadav, and Usman Roshan, Cross-validation and cross-study validation of chronic lymphocytic leukemia with exome sequences and machine learning, Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015 (PDF, local link to paper)

  6. Abdulrhman Aljouie and Usman Roshan, Prediction of continous phenotypes in mouse, fly, and rice genome wide association studies with support vector regression SNPs and ridge regression classifier, Proceedings of the 14th IEEE International Conference on Machine Learning and Applications (ICMLA), 2015 (PDF, local link to paper)

  7. Abdulrhman Aljoiue, Mohammedreza Esfandiari, Srividya Ramakrishnan, and Usman Roshan, Chi8: a GPU program for detecting significant interacting SNPs with the chi-square 8-df test, BMC Research Notes, 8:436, 2015 (PDF) (Source code)

  8. Turki Turki and Usman Roshan, MaxSSmap: A GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence, BMC Genomics, 15(1)1:969, 2014 (PDF) (Source code)

  9. Turki Turki, Muhammad Amimul Ihsan, Nouf Turki, Jie Zhang, Usman Roshan, and Zhi Wei, Top-k parameterized boost, Proceedings of the Second International Conference on Mining Intelligence and Knowledge Exploration, University College Cork, Ireland, 2014 (Springer link) (PDF)

  10. Turki Turki and Usman Roshan, Weighted maximum variance dimensionality reduction, Proceedings of the 6th Mexican Conference on Pattern Recognition, Cancun, Mexico, 2014 (Springer link) (PDF) (Source code)

  11. U. Roshan (corresponding author), S. Chikkagoudar, Z. Wei, K. Wang, and H. Hakonarson, Ranking causal SNPs and disease associated regions in genome wide association studies by the support vector machine and random forest, Nucleic Acids Research, 2011 (PDF)

  12. S. Chikkagoudar , D. R. Livesay, and U. Roshan (corresponding author) PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences, Nucleic Acids Research, 2010 (PDF) (webserver)

  13. U. Roshan (corresponding author), S. Chikkagoudar, and D. R. Livesay, Searching for RNA homologs within large genomic sequences using partition function posterior probabilities, BMC Bioinformatics, 9:61, 2008 (PDF)

  14. D. R. Livesay, P. D. Kidd, S. Eskandari, and U. Roshan, Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family BMC Bioinformatics, 8:397, 2007 (PDF)

  15. S. Chikkagoudar, U. Roshan (corresponding author) and D. R. Livesay, eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities, Nucleic Acids Research, Vol 35, 2007, W675-W677 PDF (webserver)

  16. U. Roshan (corresponding author) and D. R. Livesay, Probalign: multiple sequence alignment using partition function posterior probabilities, Bioinformatics, 22(22), 2006, 2715-21 (PDF)

  17. C. Coarfa, Y. Dotsenko, J. Mellor-Crummey, L. Nakhleh, and U. Roshan, PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction, International Journal on Bioinformatics Research and Applications, 2(4), 2006, 407-419 (PDF)

  18. U. Roshan, D. R. Livesay, and S. Chikkagoudar, Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees, Proceedings of The IEEE 6th Symposium on Bioinformatics and Bioengineering (BIBE06) Washington D.C., USA, 2006 (PDF)

  19. Z. Du, F. Lin, and U. Roshan, Reconstruction of large phylogenetic trees: a parallel approach, Computational Biology and Chemistry, 29(4), 2005, 273-280 (PDF)

  20. U. Roshan, D. R. Livesay, D. La, Improved phylogenetic motif detection using parsimony, Proceedings of The IEEE 5th Symposium on Bioinformatics and Bioengineering (BIBE05) Minneapolis, Minnesota, USA, 2005 (PDF)

  21. Z. Du, A. Stamatakis, F. Lin, U. Roshan, L. Nakhleh, Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood, Proceedings of The 2005 International Conference on High Performance Computing and Communications (HPCC05) 2005, Naples, Italy, 2005 (PDF)

  22. C. Coarfa, Y. Dotsenko, J. Mellor-Crummey, L. Nakhleh, and U. Roshan, PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction, Proceedings of The First IEEE Workshop on High Performance Computing in Medicine and Biology (HiPCoMB 2005), Fukuoka, Japan, 2005 (PDF)

  23. U. Roshan, B. M. E. Moret, T. L. Williams, T. Warnow, Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees, Proceedings of the IEEE Computational Systems Bioinformatics (CSB04) Stanford (CA), USA, 2004 (PDF)

  24. I. S. Dhillon, E. M. Marcotte, U. Roshan (corresponding author), Diametrical Clustering for identifying anti- correlated gene clusters, Bioinformatics, 19, 2003, 1612-1619 (PDF)

  25. B. M. E. Moret, U. Roshan, T. Warnow, "Sequence length requirements for phylogenetic methods", Proc. 2nd Int'l Workshop on Algorithms in Bioinformatics (WABI02) Rome, Italy, 2002 Lecture Notes in Computer Science 2452, 343-356, Springer Verlag, Roderic Guido and Dan Gusfield, eds (PDF)

  26. L. Nakhleh, U. Roshan, L. Vawter, and T. Warnow, "Estimating the deviation from a molecular clock", Proc. 2nd Int'l Workshop on Algorithms in Bioinformatics (WABI02) Rome, Italy, 2002 Lecture Notes in Computer Science 2452, 287-299, Springer Verlag, R. Guido and D. Gusfield, eds (PDF)

  27. L. Nakhleh, B. M. E. Moret, U. Roshan, K. St. John, J. Sun, T. Warnow, "The accuracy of fast phylogenetic methods for large datasets", Proc. 7th Pacific Symposium on BioComputing (PSB02) Kauai, USA, 2002, World Scientific Pub, 211-222 (PDF)

  28. L. Nakhleh, U. Roshan (corresponding author), K. St. John, J. Sun, T. Warnow, Designing fast converging phylogenetic methods", Bioinformatics, 17, 2001, S190-S198 (PDF)

  29. L. Nakhleh, U. Roshan, K. St. John, J. Sun, T. Warnow, "The performance of phylogenetic methods on trees of bounded diameter", Proc. 1st Workshop on Algorithms in Bioinformatics (WABI01) Aarhus, Denmark, 2001, Lecture Notes in Computer Science 2149, 189-203, Springer Verlag, Olivier Gascuel and B. M. E. Moret, eds (PDF)

  30. L. Nakhleh, U. Roshan (corresponding author), K. St. John, J. Sun, T. Warnow, Designing fast converging phylogenetic methods", Proceedings of The 9th Int'l Conference on Intelligent Systems on Molecular Biology (ISMB01) Copenhagen, Denmark, 2001 (PDF)

Tutorials
  1. D. Bader, A. Stamatakis, and U. Roshan, Computational challenges in assembling the Tree of Life, peer reviewed tutorial presented at Supercomputing 2005 (SC05), Seattle, WA, USA