Publications

2014

Book Chapters:


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:


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 scaff olding, 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