IIS-0546457

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

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

I.I. Mandoiu and G. Narasimhan and Y.-Q. Zhang (Eds.), Proc. 5th International Symposium on Bioinformatics Research and Applications, Springer-Verlag Lecture Notes in Bioinformatics vol. 5542, 2009, publisher url, bibtex

I.I. Mandoiu and A.Z. Zelikovsky (Eds.), Bioinformatics Algorithms: Techniques and Applications, John Wiley & Sons , 2008, publisher url, bibtex

I.I. Mandoiu and R. Sunderraman and A. Zelikovsky (Eds.), Proc. 4th International Symposium on Bioinformatics Research and Applications, Springer-Verlag Lecture Notes in Bioinformatics vol. 4983, 2008, publisher url, bibtex

X. Hu and I.I. Mandoiu and Z. Obradovic and J. Xia (Eds.), Proc. 2007 IEEE International Conference on Bioinformatics and Biomedicine, IEEE Computer Society Press , 2007, publisher url, bibtex

I.I. Mandoiu and A.Z. Zelikovsky (Eds.), Proc. 3rd International Symposium on Bioinformatics Research and Applications, Springer-Verlag Lecture Notes in Bioinformatics vol. 4463, 2007, 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

K.M. Konwar and I.I. Mandoiu and A. Russell and A. Shvartsman, Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints, In I.I. Mandoiu and A.Z. Zelikovsky, Bioinformatics Algorithms: Techniques and Applications, Wiley, pp. 241-258, 2008, pdf preprint, publisher url, bibtex

I.I. Mandoiu and A. Olshevsky and A.Z. Zelikovsky, QoS Multimedia Multicast Routing, In T.E. Gonzalez, Approximation Algorithms and Metaheuristics, Chapman & Hall/CRC, 2007, pdf preprint, publisher url, bibtex

C. Albrecht and A.B. Kahng and I.I. Mandoiu and A.Z. Zelikovsky, Multicommodity Flow Algorithms for Buffered Global Routing, In T.E. Gonzalez, Approximation Algorithms and Metaheuristics, Chapman & Hall/CRC, 2007, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and A.Z. Zelikovsky, Practical Approximations of Steiner Trees in Uniform Orientation Metrics, In T.E. Gonzalez, Approximation Algorithms and Metaheuristics, Chapman & Hall/CRC, 2007, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and S. Reda and X. Xu and A.Z. Zelikovsky, Computer-Aided Optimization of DNA Array Design and Manufacturing, In K. Chakrabarty and J. Zeng, Design Automation Methods and Tools for Microfluidics-Based Biochips, Springer Verlag, pp. 235-269, 2006, pdf preprint, publisher url, bibtex

Journal Articles:

Y. Huang and M. Khan and I.I. Mandoiu, Neuraminidase subtyping of Avian influenza viruses with PrimerHunter-designed primers and quadruplicate primer pools, PLOS ONE Volume 8, Issue 11, e81842, 2013, 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

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

J. Duitama and D.M. Kumar and E. Hemphill and M. Khan and I.I. Mandoiu and C.E. Nelson, PrimerHunter: A Primer Design Tool for PCR-Based Virus Subtype Identification, Nucleic Acids Research 37, pp. 2483-2492, 2009, pdf preprint, publisher url, bibtex

J. Jun and I.I. Mandoiu and C.E. Nelson, Identification of mammalian orthologs using local synteny, BMC Genomics 10:630, 2009, pdf preprint, publisher url, bibtex

J. Jun and P. Ryvkin and E. Hemphill and I.I. Mandoiu and C.E. Nelson, The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution, Journal of Computational Biology 16, pp. 1429-1444, 2009, publisher url, bibtex

K. Apichonbancha and B. Dasgupta and J. Jun and I.I. Mandoiu and E. Mendonca , A Review of the Primer Approximation Multiplex PCR (PAMP) Technique for Detecting Large Scale Cancer Genomic Lesions, Current Bioinformatics 4, pp. 1-7, 2009, publisher url, bibtex

J. Kennedy and I.I. Mandoiu and B. Pasaniuc, Genotype Error Detection using Hidden Markov Models of Haplotype Diversity, Journal of Computational Biology 15, pp. 1155-1171, 2008, pdf preprint, publisher url, bibtex

A. Gusev and I.I. Mandoiu and B. Pasaniuc, Highly Scalable Genotype Phasing by Entropy Minimization, IEEE/ACM Trans. on Computational Biology and Bioinformatics 5, pp. 252-261, 2008, pdf preprint, publisher url, bibtex

S. Balla and S. Rajasekaran and I.I. Mandoiu, Efficient Algorithms for Degenerate Primer Search, International Journal of Foundations of Computer Science 18, pp. 899-910, 2007, publisher url, bibtex

I.I. Mandoiu and C. Prajescu, High-Throughput SNP Genotyping by SBE/SBH, IEEE Trans. on Nanobioscience 6, pp. 28-35, 2007, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and X. Xu and A. Zelikovsky, Enhanced Design Flow and Optimizations for Multi-Project Wafers, IEEE Trans. on CAD 26, pp. 301-311, 2007, pdf preprint, publisher url, bibtex

I.I. Mandoiu and D. Trinca, Exact and Approximation Algorithms for DNA Tag Set Design, Journal of Computational Biology 13, pp. 732-744, 2006, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and S. Reda and X. Xu and A. Zelikovsky, Computer-Aided Optimization of DNA Array Design and Manufacturing, IEEE Trans. on CAD 25, pp. 305-320, 2006, pdf preprint, publisher url, bibtex

Conference Articles:

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

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

J. Duitama and T. Huebsch and G. McEwen and E. Suk and M.R. Hoehe, ReFHap: A Reliable and Fast Algorithm for Single Individual Haplotyping, BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, pp. 160-169, 2010, 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, Proc. 10th Workshop on Algorithms in Bioinformatics, pp. 202-214, 2010, pdf preprint, publisher url, ppt, bibtex

B. Pasaniuc and J. Kennedy and I.I. Mandoiu, Imputation-based local ancestry inference in admixed populations, Proc. 5th International Symposium on Bioinformatics Research and Applications/2nd Workshop on Computational Issues in Genetic Epidemiology, pp. 221-233, 2009, pdf preprint, publisher url, ppt, bibtex

S. Balla and S. Rajasekaran and I.I. Mandoiu, Faster Greedy Algorithms for Multiple Degenerate Primer Selection, Proc. 8th IEEE International Conference on Bioinformatics and Bioengineering, pp. 1-4, 2008, publisher url, bibtex

J. Jun and P. Ryvkin and E. Hemphill and I.I. Mandoiu and C.E. Nelson, Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events During Mammalian Evolution, Proc. 6th Annual RECOMB Satellite Workshop on Comparative Genomics, pp. 40-54, 2008, pdf preprint, publisher url, bibtex

B. Dasgupta and J. Jun and I.I. Mandoiu, Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP, Proc. 6th Asia-Pacific Bioinformatics Conference, pp. 353-362, 2008, pdf preprint, publisher url, bibtex

J. Kennedy and I.I. Mandoiu and B. Pasaniuc, Genotype Error Detection using Hidden Markov Models of Haplotype Diversity, Proc. 7th Workshop on Algorithms in Bioinformatics, pp. 73-84, 2007, pdf preprint, publisher url, ppt, bibtex

B. Pasaniuc and I.I. Mandoiu, Highly Scalable Genotype Phasing by Entropy Minimization, Proc. 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 3482-3486, 2006, pdf preprint, publisher url, ppt, bibtex

I.I. Mandoiu and C. Prajescu, High-Throughput SNP Genotyping by SBE/SBH, Proc. 6th International Conference on Computational Science, Part II, pp. 742-749, 2006, pdf preprint, publisher url, bibtex

M.T. Hajiaghayi and K. Jain and L.C. Lau and I.I. Mandoiu and A.C. Russell and V.V. Vazirani, The minimum multicolored subgraph problem in haplotyping and PCR primer set selection, Proc. 6th International Conference on Computational Science, Part II, pp. 758-766, 2006, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and X. Xu and A. Zelikovsky, Multi-project reticle design and wafer dicing under uncertain demand, Proc. 22nd European Mask and Lithography Conference, pp. 45-54, 2006, pdf preprint, publisher url, ppt, bibtex

Technical Reports:

J. Kennedy and I.I. Mandoiu and B. Pasaniuc, GEDI: Scalable Algorithms for Genotype Error Detection and Imputation, Cornell University arXiv e-print, 0911.1765, 2009, url, bibtex

Ph.D. Theses:

J. Duitama, Bioinformatics Methods for Diagnosis and Treatment of Human Diseases, University of Connecticut, Storrs, CT, Dec., 2010, pdf preprint, ppt, bibtex

J. Jun, Reconstruction and Analysis of Gene Family Evolution in Mammals, University of Connecticut, Storrs, CT, May, 2010, pdf preprint, url, bibtex

J. Kennedy, Efficient Algorithms for SNP Genotype Data Analysis using Hidden Markov Models of Haplotype Diversity, University of Connecticut, Storrs, CT, Dec., 2009, pdf preprint, ppt, bibtex

B. Pasaniuc, Scalable Algorithms for Analysis of Genomic Diversity Data, University of Connecticut, Storrs, CT, May, 2008, pdf preprint, url, ppt, bibtex

M.S. Theses:

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