2012

I.I. Mandoiu and R.J. O'Neill and M. Khan and A. Zelikovsky and B. Tork and N. Mancuso, Bioinformatics methods for reconstruction of infectious bronchitis virus quasispecies from next generation sequencing data, 11th International Conference on Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases, New Orleans, LA, Oct. 30 – Nov. 2, 2012, ppt, url

I.I. Mandoiu, Towards Personalized Genomics-Guided Cancer Immunotherapy, UConn/JAX Genomics Symposium, Sept 6-7, 2012, ppt, url

N. Mancuso and B. Tork and P. Skums and I.I. Mandoiu and A. Zelikovsky, Multi-Commodity Flow Methods for Quasispecies Spectrum Reconstruction Given Amplicon Reads, 8th International Symposium on Bioinformatics Research and Applications, May 21-23, 2012, abstract, url

S. Mangul and A. Caciula and N. Mancuso and O. Glebova and I.I. Mandoiu and A. Zelikovsky, An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads, Poster at 8th International Symposium on Bioinformatics Research and Applications, May 21-23, 2012, abstract, url

J. Lindsay and H. Salooti and A. Zelikovsky and I.I. Mandoiu, Scaffolding Large Genomes using Integer Linear Programming, 8th International Symposium on Bioinformatics Research and Applications, May 21-23, 2012, ppt, abstract, url

S. Al Seesi and I.I. Mandoiu, Inference of allele specific expression levels from RNA-Seq data, Poster at 8th International Symposium on Bioinformatics Research and Applications, May 21-23, 2012, ppt, abstract, url

S. Mangul and A. Caciula and N. Mancuso and I.I. Mandoiu and A. Zelikovsky, An Integer Programming Approach to Novel Transcript Reconstruction from Paired‐End RNA‐Seq Reads, Poster at 16th Annual International Conference on Research in Computational Molecular Biology, April 21-24, 2012, ppt, abstract, url

S. Al Seesi and I.I. Mandoiu, Inference of allele specific expression levels from RNA-Seq data, Proc. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences, Feb. 23-25, 2012, ppt, abstract, url

S. Mangul and A. Caciula and I.I. Mandoiu and A. Zelikovsky, Novel Transcript Reconstruction from Paired-End RNA-Seq Reads Using Fragment Length Distribution, Proc. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences, Feb. 23-25, 2012, abstract, url

N. Mancuso and B. Tork and P. Skums and L. Ganova-Raeva and I.I. Mandoiu and A. Zelikovsky, A Maximum Likelihood Method For Quasispecies Spectrum Assembly, Proc. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences, Feb. 23-25, 2012, ppt, abstract, url

R.J. O'Neill and I.I. Mandoiu and M. Khan and C. Obergfell and H. Wang and A. Bligh and B. Tork and N. Mancuso and A. Zelikovsky, Bioinformatics Methods For Reconstruction Of Infectious Bronchitis Virus Quasispecies From Next Generation Sequencing Data, Proc. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences, Feb. 23-25, 2012, abstract, url

J. Lindsay and I.I. Mandoiu and H. Salooti and A. Zelikovsky, Accurate Scaffolding of Large Genomes using Integer Programming and Non-Serial Dynamic Programming, Poster at 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences, Feb. 23-25, 2012, ppt, abstract, url

I.I. Mandoiu, Inferring Viral Quasispecies Spectra from NGS Reads, Invited talk, Brown University Center for Computational Molecular Biology, Feb. 1, 2012, ppt, url

I.I. Mandoiu and M. Khan and R.J. O’Neill and A. Zelikovsky and C. Obergfell and H. Wang and A. Bligh and B. Tork and N. Mancuso, Bioinformatics Tools for Viral Quasispecies Reconstruction from Next-Generation Sequencing Data and Vaccine Optimization , Poster at the USDA NIFA Animal Genetics, Genomics and Breeding Program Annual Investigator Meeting, Jan. 13, 2012, ppt