Publications

2012

Edited Books & Proceedings:


L. Bleris and I.I. Mandoiu and R. Schwartz and J. Wang (Eds.), Proc. 8th International Symposium on Bioinformatics Research and Applications, Springer-Verlag Lecture Notes in Bioinformatics vol. 7292, 2012, publisher url, bibtex

S. Istrail and I.I. Mandoiu and M. Pop and S. Rajasekaran and J. Spouge (Eds.), Proc. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences, IEEE , 2012, publisher url, bibtex

Journal Articles:


F. Duan and S. Simeone and R. Wu and J. Grady and I.I. Mandoiu and P.K. Srivastava, Area under the curve as a tool to measure kinetics of tumor growth in experimental animals, Journal of Immunological Methods 382, pp. 224-228, 2012, publisher url, bibtex

N. Mancuso and B. Tork and P. Skums and L. Ganova-Raeva and I.I. Mandoiu and A. Zelikovsky, Reconstructing viral quasispecies from NGS amplicon reads, In Silico Biology 11, pp. 237-249, 2012, publisher url, bibtex

S. Mangul and A. Caciula and O. Glebova and I.I. Mandoiu and A. Zelikovsky, Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations, In Silico Biology 11, pp. 251-261, 2012, publisher url, bibtex

J. Duitama and P.K. Srivastava and I.I. Mandoiu, Towards Accurate Detection and Genotyping of Expressed Variants from Whole Transcriptome Sequencing Data, BMC Genomics 13(Suppl 2):S6, 2012, pdf preprint, publisher url, bibtex

Conference Articles:


J. Lindsay and H. Salooti and A. Zelikovsky and I.I. Mandoiu, Scalable Genome Scaffolding using Integer Linear Programming, Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 377-383, 2012, pdf preprint, publisher url, ppt, bibtex

S. Mangul and A. Caciula and S. Al Seesi and D. Brinza and A. Rouf Banday and R. Kanadia and I.I. Mandoiu and A. Zelikovsky, An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads, Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 369-376, 2012, pdf preprint, publisher url, ppt, bibtex

M. Hamdalla and D. Grant and I.I. Mandoiu and D. Hill and S. Rajasekaran and R. Ammar, The Use of Graph Matching Algorithms to Identify Biochemical Substructures in Synthetic Chemical Compounds: Application to Metabolomics, Proc. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences, pp. 1-6, 2012, pdf preprint, publisher url, ppt, bibtex

M.S. Thesis:


P. Ghimire, Detection of Genomic Inversion from Single End Reads, University of Connecticut, Storrs, CT, Dec., 2012, pdf preprint, bibtex