Publications

S. Al Seesi

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 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

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

S. Al Seesi and A. Das Mohapatra and A. Pawashe and I.I. Mandoiu and F. Duan, Finding neoepitopes in mouse models of personalized cancer immunotherapy, Frontiers in Biology 11, pp. 366-375, 2016, publisher url, bibtex

Y. Temate-Tiagueu and S. Al Seesi and M. Mathew and I. Mandric and A. Rodriguez and K. Bean and Q. Cheng and O. Glebova and I.I. Mandoiu and N.B. Lopanik and A. Zelikovsky, Inferring metabolic pathway activity levels from RNA-Seq data, BMC Genomics 17(Suppl 5):542, pp. 493-503, 2016, 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. 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

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

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

N.K. Jue and M.B. Murphy and S.D. Kasowitz and S.M. Qureshi and C.J. Obergfell and S. Al Seesi and R.J. Foley and R.J. O'Neill and M.J. O'Neill, Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach, BMC Genomics (to appear) , 2013, pdf preprint, bibtex

S. Rajasekaran and S. Al Seesi and R.A. Ammar, Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots, IEEE/ACM Trans. Comput. Biology Bioinform. 7, pp. 619-627, 2010, 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

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

S. Al Seesi and S. Rajasekaran and R.A. Ammar, RNA Pseudoknot Folding through Inference and Identification Using TAGRNA, Proc. 1st International Conference on Bioinformatics and Computational Biology, pp. 90-101, 2009, publisher url, bibtex

S. Rajasekaran and S. Al Seesi and R.A. Ammar, Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots, Proc. 5th International Symposium on Bioinformatics Research and Applications, pp. 135-147, 2009, publisher url, bibtex

S. Al Seesi and S. Rajasekaran and R.A. Ammar, Pseudoknot Identification through Learning TAGRNA, Proc. 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, pp. 132-143, 2008, publisher url, bibtex