Publications

2011

Edited Books & Proceedings:


B. Chen, ..., I.I. Mandoiu, et al. (Eds.), 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops Proceedings , IEEE , 2011, publisher url, bibtex

I.I. Mandoiu and S. Miyano and T. Przytycka and S. Rajasekaran (Eds.), Proc. 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, IEEE , 2011, publisher url, bibtex

Book Chapters:


B. DasGupta and M.-Y. Kao and I.I. Mandoiu, Algorithmic Issues in DNA Barcoding Problems, In M. Elloumi and A. Zomaya, Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley, pp. 129-142, 2011, pdf preprint, publisher url, bibtex

Journal Articles:


B. Pasaniuc and R. Garfinkel and I.I. Mandoiu and A. Zelikovsky, Optimal Testing of Digital Microfluidic Biochips, INFORMS Journal on Computing 23, pp. 518-529, 2011, pdf preprint, publisher url, bibtex

M.B. Renfree, A.T. Papenfuss, J.E. Deakin, J. Lindsay, ..., I.I. Mandoiu, et al., Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development, Genome Biology 12:R81, 2011, publisher url, bibtex

I. Astrovskaya and B. Tork and S. Mangul and K. Westbrooks and I.I. Mandoiu and P. Balfe and A. Zelikovsky, Inferring Viral Quasispecies Spectra from 454 Pyrosequencing Reads, BMC Bioinformatics 12(Suppl 6):S1, 2011, pdf preprint, publisher url, bibtex

M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky, Estimation of alternative splicing isoform frequencies from RNA-Seq data, Algorithms for Molecular Biology 6:9, 2011, pdf preprint, publisher url, bibtex

C. Lee and I.I. Mandoiu and C.E. Nelson, Inferring Ethnicity from Mitochondrial DNA Sequence, BMC Proceedings 5(Suppl 2):S11, 2011, pdf preprint, publisher url, bibtex

J. Duitama and J. Kennedy and S. Dinakar and Y. Hernandez and Y. Wu and I.I. Mandoiu, Linkage Disequilibrium Based Genotype Calling from Low-Coverage Shotgun Sequencing Reads, BMC Bioinformatics 12(Suppl 1):S53, 2011, pdf preprint, publisher url, bibtex

Conference Articles:


S. Mangul and A. Caciula and I.I. Mandoiu and A. Zelikovsky, RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes, Proc. 1st Workshop on Computational Advances in Molecular Epidemiology, pp. 118-123, 2011, publisher url, ppt, bibtex

N. Mancuso and B. Tork and I.I. Mandoiu and P. Skums and A. Zelikovsky, Viral Quasispecies Reconstruction from Amplicon 454 Pyrosequencing Reads, Proc. 1st Workshop on Computational Advances in Molecular Epidemiology, pp. 94-101, 2011, publisher url, ppt, bibtex

S. Mangul and I. Astrovskaya and M. Nicolae and B. Tork and I.I. Mandoiu and A. Zelikovsky, Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data, Proc. 11th Workshop on Algorithms in Bioinformatics, pp. 213-224, 2011, pdf preprint, publisher url, bibtex

M. Nicolae and I.I. Mandoiu, Accurate Estimation of Gene Expression Levels from DGE Sequencing Data, Proc. 7th International Symposium on Bioinformatics Research and Applications , pp. 392-403, 2011, pdf preprint, publisher url, ppt, bibtex

J. Duitama and P.K. Srivastava and I.I. Mandoiu, Towards Accurate Detection and Genotyping of Expressed Variants from Whole Transcriptome Sequencing Data, Proc. 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, pp. 87-92, 2011, pdf preprint, publisher url, ppt, bibtex

M.S. Thesis:


M. Nicolae, Accurate Estimation of Isoform and Gene Expression Levels from Next Generation Sequencing Data, University of Connecticut, Storrs, CT, September, 2011, pdf preprint, bibtex