Publications

IsoEM

Book Chapters:


O. Glebova and Y. Temate-Tiagueu and A. Caciula and S. Al Seesi and A. Artyomenko and S. Mangul and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, Transcriptome Quantification and Differential Expression from NGS Data, In I.I. Mandoiu and A. Zelikovsky, Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, pp. 301-327, 2016, publisher url, bibtex

S. Al Seesi and S. Mangul and A. Caciula and A. Zelikovsky and I.I. Mandoiu, Transcriptome reconstruction and quantification from RNA sequencing data, In Maria Poptsova, Genome Analysis: Current Procedures and Applications, Caister Academic Press, pp. 39-60, 2014, publisher url, bibtex

Journal Articles:


I. Mandric and Y.T. Tiagueu and T. Shcheglova and S. Al Seesi and A. Zelikovsky and I.I. Mandoiu, Fast Bootstrapping-Based Estimation of Confidence Intervals of Expression Levels and Differential Expression from RNA-Seq Data, Bioinformatics to appear, 2017, pdf preprint, publisher url, bibtex

D.K.P. Karunakaran and S. Al Seesi and A.R. Banday and M. Baumgartner and A. Olthof and C. Lemoine and I.I. Mandoiu and R.N. Kanadia, Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development , BMC Genomics 17(Suppl 5):495, pp. 477-492, 2016, publisher url, bibtex

M Mathew and KI Bean and YT Tiagueu and A Caciula and I.I. Mandoiu and A Zelikovsky and NB Lopanik, Influence of symbiont-produced bioactive natural product on holobiont fitness in the marine bryozoan, Bugula neritina via protein kinase C (PKC), Marine Biology 163:44, 2016, publisher url, bibtex

M. Baumgartner and C. Lemoine and S. Al Seesi and D.K.P. Karunakaran and N. Sturrock and A. Rouf Banday and A.M. Kilcollins and I.I. Mandoiu and R.N. Kanadia, Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons, Developmental Neurobiology 75, pp. 895-907, 2015, publisher url, bibtex

A. Rouf Banday and M. Baumgartner and S. Al Seesi and D.K.P. Karunakaran and A. Venkatesh and S. Congdon and C. Lemoine and A.M. Kilcollins and I.I. Mandoiu and C. Punzo and R.N. Kanadia, Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons, Cell Cycle 13(16), pp. 2526-2541, 2014, publisher url, bibtex

S. Al Seesi and Y.T. Tiagueu and A. Zelikovsky and I.I. Mandoiu, Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates, BMC Genomics 15(Suppl 8):S2 , 2014, pdf preprint, publisher url, bibtex

S. Mangul and S. Al Seesi and A. Caciula and D. Brinza and I.I. Mandoiu and A. Zelikovsky, Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq Data, BMC Genomics 15(Suppl 5):S7, 2014, 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

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

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

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