PUBLICATIONS

  1. U. Roshan, S. Chikkagoudar, Z. Wei, K. Wang, and H. Hakonarson, Improved ranking of disease associated regions in genome wide association studies by a discriminative multivariate strategy (Submitted)

  2. U. Roshan, Semi-supervised feature extraction for population structure identification using the Laplacian linear discriminant (Under revision)

  3. U. Roshan, 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)

  4. 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", book chapter in Perspectives on Biological Sequence Alignment: Where, How, and Why It Matters, University of California Press, 2007, In Press (PDF)

  5. 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)

  6. S. Chikkagoudar, U. Roshan and D. R. Livesay, eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities, Nucleic Acids Research, 2007 PDF (webserver)

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

  8. 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)

  9. 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 (IJBRA), 2006 (PDF)

  10. D. Bader, U. Roshan, A. Stamatakis, Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions, Advances in Computers, 2006, Chau-Wen Tzeng, editor. (PDF)

  11. 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)

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

  13. 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)

  14. 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)

  15. 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)

  16. U. Roshan, B. M. E. Moret, T. L. Williams, T. Warnow, "Performance of supertree methods on various dataset decompositions", O. R. P. Bininda-Emonds, editor, Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life ,volume 3 of Computational Biology, pages 301-328, Kluwer Academics, 2004 (Dress A. series editor). (PDF)

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

  18. 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)

  19. 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)

  20. 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)

  21. L. Nakhleh, U. Roshan, K. St. John, J. Sun, T. Warnow, Designing fast converging phylogenetic methods", 9th Int'l Conference on Intelligent Systems on Molecular Biology (ISMB01) Copenhagen, Denmark, 2001, Bioinformatics 17, S190-S198, (PDF)

  22. 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)

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