AFRI

Edited Books & Proceedings:

I.I. Mandoiu and A.Z. Zelikovsky (Eds.), Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons , 2016, 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

Book Chapters:

P. Skums and A. Artyomenko and O. Glebova and S. Ramachandran and D.S. Campo and Z. Dimitrova and I.I. Mandoiu and A. Zelikovsky and Y. Khudyakov, Pooling Strategy for Massive Viral Sequencing, In I.I. Mandoiu and A. Zelikovsky, Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, pp. 57-83, 2016, publisher url, bibtex

E. Nenastyeva and B. Tork and A. Artyomenko and N. Mancuso and M.I. Khan and R. O'Neill and I.I. Mandoiu and A. Zelikovsky, Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data, In I.I. Mandoiu and A. Zelikovsky, Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, pp. 383-400, 2016, publisher url, bibtex

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

I. Mandric and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, Scaffolding Algorithms, In I.I. Mandoiu and A. Zelikovsky, Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, pp. 105-131, 2016, publisher url, bibtex

S. Al Seesi and F. Duan and I.I. Mandoiu and P.K. Srivastava and A. Kueck, Genomics-guided immunotherapy of human epithelial ovarian cancer, In Annabelle Rodriguez-Oquendo, Translational Cardiometabolic Genomic Medicine, Academic Press, pp. 237-250, 2015, 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

I. Astrovskaya and N. Mancuso and B. Tork and S. Mangul and A. Artyomenko and P. Skums and L. Ganova-Raeva and I.I. Mandoiu and A. Zelikovsky, Inferring Viral Quasispecies Spectra from Shotgun and Amplicon Next-Generation Sequencing Reads, In Maria Poptsova, Genome Analysis: Current Procedures and Applications, Caister Academic Press, pp. 231-262, 2014, publisher url, bibtex

Journal Articles:

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

M. Hamdalla and S. Rajasekaran and D. Grant and I.I. Mandoiu, Metabolic pathway predictions for metabolomics: a molecular structure matching approach, Journal of Chemical Information and Modeling 55, pp. 709-718, 2015, pdf preprint, publisher url, bibtex

P. Skums and A. Artyomenko and O. Glebova and S. Ramachandran and I.I. Mandoiu and D.S. Campo and Z. Dimitrova and A. Zelikovsky and Y. Khudyakov, Computational Framework for Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling, Bioinformatics 31, pp. 682-690, 2015, pdf preprint, 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

F. Duan and J. Duitama and S. Al Seesi and C. Ayres and S. Corcelli and A. Pawashe and T. Blanchard and D. McMahon and J. Sidney and A. Sette and B. Baker and I.I. Mandoiu and P.K. Srivastava, Genomic and bioinformatic profiling of mutational neo-epitopes reveals new rules to predict anti-cancer immunogenicity, Journal of Experimental Medicine 211, pp. 2231-2248, 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

E. Hemphill and J. Lindsay and C. Lee and I.I. Mandoiu and C.E. Nelson, Feature selection and classifier performance on diverse biological datasets, BMC Bioinformatics 15(Suppl 13):S4, 2014, pdf preprint, publisher url, bibtex

J. Lindsay and H. Salooti and I.I. Mandoiu and A. Zelikovsky, ILP-based maximum likelihood genome scaffolding, BMC Bioinformatics 15(Suppl 9):S9, 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

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

L. Menikarachchi and D. Hill and M. Hamdalla and I.I. Mandoiu and D. Grant, In silico enzymatic synthesis of a 400,000 compound biochemical database for non-targeted metabolomics, Journal of Chemical Information and Modeling 53, pp. 2483-2492, 2013, publisher url, bibtex

P. Skums and N. Mancuso and A. Artyomenko and B. Tork and I.I. Mandoiu and Y. Khudyakov and A. Zelikovsky, Reconstruction of Viral Population Structure from Next-Generation Sequencing Data Using Multicommodity Flows, BMC Bioinformatics 14(Suppl 9):S2, 2013, pdf preprint, publisher url, bibtex

M. Hamdalla and I.I. Mandoiu and D. Hill and S. Rajasekaran and D. Grant, BioSM: A metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space, Journal of Chemical Information and Modeling 53, pp. 601-612, 2013, 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

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

Conference Articles:

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, Flexible Approach for Novel Transcript Reconstruction from RNA-Seq Data using Maximum Likelihood Integer Programming, Proc. 5th International Conference on Bioinformatics and Computational Biology, pp. 25-34, 2013, pdf preprint, publisher url, bibtex

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

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

Ph.D. Theses:

J. Lindsay, Scalable Optimization Algorithms for High-throughput Genomic Data, University of Connecticut, Storrs, CT, May, 2015, pdf preprint, url, 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