Abstracts and Unpublished Presentations

Lifetech12

I.I. Mandoiu, Challenges and Opportunities in Single Cell Transcriptomics, Keynote talk at 12th International Symposium on Bioinformatics Research and Applications, Minsk, Belarus, June 5-8, 2016, ppt, url

I.I. Mandoiu, Computational Methods for Analysis of Single Cell RNA-Seq Data, JAX-GM course on "Big Genomic Data Skills Training for Professors", May 23-27, 2016, ppt, url

I.I. Mandoiu, Cancer Vaccine Design, CICATS Science Cafe, Oct. 9, 2015, ppt, url

S. Al Seesi, Computational methods for genomics-guided immunotherapy, CICATS Science Cafe, Oct. 9, 2015, ppt, url

I.I. Mandoiu, Computational methods for genomics-guided immunotherapy, Invited talk at 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, Miami, FL, October 15-17, 2015, ppt, url

I.I. Mandoiu, Computational Methods for Analysis of Single Cell RNA-Seq Data, CSHL course on Advanced Techniques in Molecular Neuroscience, June 30 -July 16, 2015, ppt, url

S. Al Seesi and I.I. Mandoiu, Computational methods for genomics-guided immunotherapy, Mini-tutorial at 11th International Symposium on Bioinformatics Research and Applications, Norfolk, VA, June 7-10, 2015, ppt, url

D.K.P. Karunakaran and S. Al Seesi and A. Rouf Banday and M. Baumgartner and A. Olthof and C. Lemoine and I.I. Mandoiu and Rahul Kanadia, Network-based bioinformatics analysis of spatio-temporal RNAseq data reveals transcriptional programs underpinning normal and aberrant retinal development, 11th International Symposium on Bioinformatics Research and Applications, Norfolk, VA, June 7-10, 2015, abstract, url

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, Poster at ImmunoGenomics Symposium at The Jackson Laboratory for Genomic Medicine, Nov 12-14, 2014, ppt, abstract, url

A. Caciula and O. Glebova and A. Artyomenko and S. Mangul and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, Simulated Regression Algorithm for Transcriptome Quantification, 10th International Symposium on Bioinformatics Research and Applications, June 28-30, 2014, abstract, url

A. Caciula and O. Glebova and A. Artyomenko and S. Mangul and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, Deterministic Regression Algorithm for Transcriptome Frequency Estimation, Proc. 4th IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 2-4, 2014, abstract, url

I.I. Mandoiu, Scalable Algorithms for Next-Generation Sequencing Data Analysis, JAX-UCONN/BECAT/UCHC Workshop on Bioinformatics and Computational Biology, Sept. 4, 2013, ppt, url

S. Al Seesi and Y.T. Tiagueu and A. Zelikovsky and I.I. Mandoiu, Accurate differential gene expression analysis for RNA-Seq data without replicates, 9th International Symposium on Bioinformatics Research and Applications, May 20-22, 2013, ppt, abstract, url

J. Lindsay and C.E. Nelson and I.I. Mandoiu, Gene expression deconvolution using single cells, 63rd Annual Meeting of the American Society of Human Genetics, Oct 22-26, 2013, url

J. Lindsay and C.E. Nelson and I.I. Mandoiu, Towards Whole Transcriptome Deconvolution Using Single-cell Data, Proc. 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 12-14, 2013, ppt, abstract, url

G. Ilie and A. Zelikovsky and I.I. Mandoiu, Reference Assisted Nucleic Acid Sequence Reconstruction from Mass Spectrometry Data, Proc. 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 12-14, 2013, ppt, abstract, url

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, Proc. 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 12-14, 2013, ppt, abstract, url

A. Artyomenko and N. Mancuso and I.I. Mandoiu and P. Skums and A. Zelikovsky, kGEM: An EM-based Algorithm for Correction of Amplicon Reads from Viral Quasispecies, Proc. 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 12-14, 2013, ppt, abstract, url

N. Mancuso and A. Artyomenko and P. Skums and I.I. Mandoiu and A. Zelikovsky, Estimation of Viral Population Structure from Amplicon-Based Reads, Proc. 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 12-14, 2013, ppt, abstract, url

A. Caciula and A. Zelikovsky and S. Mangul and J. Lindsay and I.I. Mandoiu, Monte-Carlo Regression Algorithm for Isoform Frequency Estimation from RNA-Seq Data, Proc. 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 12-14, 2013, ppt, abstract, url

P. Skums and O. Glebova and A. Zelikovsky and I.I. Mandoiu and Y. Khudyakov, Optimizing pooling strategies for the massive next-generation sequencing of viral samples, Proc. 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 12-14, 2013, ppt, abstract, url

G. Ilie and A. Zelikovsky and I.I. Mandoiu, Reference Assisted Nucleic Acid Sequence Reconstruction from Mass Spectrometry Data, 9th International Symposium on Bioinformatics Research and Applications, May 20-22, 2013, ppt, abstract, url

A. Caciula and S. Mangul and I.I. Mandoiu and A. Zelikovsky, Transcriptome Reconstruction from Single RNA-Seq Reads Using Expectation Maximization Algorithm with Expected Deviation Minimization Enhancement, 9th International Symposium on Bioinformatics Research and Applications, May 20-22, 2013, ppt, abstract, url

J. Lindsay and C. Jakuba and C.E. Nelson and I.I. Mandoiu, Gene Expression Deconvolution with Single-cell Data, 9th International Symposium on Bioinformatics Research and Applications, May 20-22, 2013, ppt, abstract, url

B. Tork and A. Zelikovsky and I.I. Mandoiu and R.J. O'Neill and M. Khan and E. Nenastyeva and A. Artyomenko and N. Mancuso, Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data, 9th International Symposium on Bioinformatics Research and Applications, May 20-22, 2013, ppt, abstract, url

A. Artyomenko and N. Mancuso and P. Skums and I.I. Mandoiu and A. Zelikovsky, kGEM: An Expectation Maximization Error Correction Algorithm for Next Generation Sequencing of Amplicon-based Data, 9th International Symposium on Bioinformatics Research and Applications, May 20-22, 2013, ppt, abstract, url

E. Nenastyeva and Y. Ionov and I.I. Mandoiu and A. Zelikovsky, Using Random Peptide Phage Display Libraries for early Breast cancer detection, 9th International Symposium on Bioinformatics Research and Applications, May 20-22, 2013, ppt, abstract, url

E. Hemphill and J. Lindsay and C. Lee and C.E. Nelson and I.I. Mandoiu, Biomarker and Classifier Selection in Diverse Genetic Datasets, 9th International Symposium on Bioinformatics Research and Applications, May 20-22, 2013, ppt, abstract, url

I.I. Mandoiu, Reconstruction of Haplotype Spectra from NGS Data, IPDPS Workshop on Future Computing Platforms to Accelerate Next-Gen Sequencing Applications, May 19, 2013, ppt, url

I.I. Mandoiu, Bioinformatics Tools for Viral Quasispecies Reconstruction from Next-Generation Sequencing Data and Vaccine Optimization , USDA NIFA Agriculture and Food Research Initiative - Animal Breeding, Genetics and Genomics Project Director Meeting, Jan. 11, 2013, ppt