Abstracts and Unpublished Presentations

IIS-0546457

I. Astrovskaya and B. Tork and S. Mangul and K. Westbrooks and I.I. Mandoiu and P. Balfe and A. Zelikovsky, VISPA: Viral Spectrum Assembling Method, Poster at 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, Feb. 3-5, 2011, abstract, url

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, Poster at 8th Georgia Tech-Emory International Conference on Bioinformatics, November 10-12, 2011, ppt

I.I. Mandoiu and S. Al Seesi, Bioinformatics Pipelines for RNA-Seq Data Analysis, Tutorial at 5th IEEE International Conference on Bioinformatics and Biomedicine, Atlanta GA, Nov. 12-15, 2011, ppt, url

I.I. Mandoiu, Reconstruction of infectious bronchitis virus quasispecies from 454 pyrosequencing reads, Invited talk, 1st Workshop on Computational Advances in Molecular Epidemiology, Nov. 13, 2011, ppt, url

S. Mangul and I. Astrovskaya and B. Tork and I.I. Mandoiu and A. Zelikovsky, Viral Quasispecies Reconstruction Based on Unassembled Frequency Estimation, 7th International Symposium on Bioinformatics Research and Applications, Changsha, China, May 27-29, 2011, ppt, abstract, url

I.I. Mandoiu and A. Zelikovsky, Computational Advances for Next Generation Sequencing, Training course in conjunction with 1st SelectBiosciences Next-Gen Sequencing Congress, Boston, MA , April 28, 2011, ppt, url

M. Nicolae and I.I. Mandoiu, Accurate Estimation of Gene Expression Levels from DGE Sequencing Data, Invited talk, 1st Annual RECOMB Satellite Workshop on Massively Parallel Sequencing, March 26-27, 2011, ppt, url

I.I. Mandoiu, Next-Generation Sequencing: Challenges and Opportunities, Invited talk, UCONN Department of Physiology and Neurobiology, March 16, 2011, ppt, url

I.I. Mandoiu, Bioinformatics Tools for Personalized Cancer Immunotherapy, Invited talk, UCONN Working Group on Multiscale Computational Science and Engineering , Feb. 25, 2011, ppt

M. Nicolae and I.I. Mandoiu, Empirical Comparison of Protocols for Sequencing-Based Gene and Isoform Expression Profiling, Poster at 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, Feb. 3-5, 2011, ppt, abstract, url

J. Lindsay and J. Zhang and T. Farnham and E. Bullwinkel and H. Salooti and I.I. Mandoiu and Y. Wu and A. Zelikovsky and R.J. O'Neill, Scaffolding Draft Genomes Using Paired Sequencing Data, Poster at 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, Feb. 3-5, 2011, ppt, abstract, url

J. Duitama and T. Huebsch and G. McEwen and S. Schulz and E. Suk and M.R. Hoehe, Bioinformatics Pipeline for Fosmid Based Molecular Haplotype Sequencing, INFORMS Annual Meeting, Austin, TX, Nov. 7-10, 2010, ppt, url

M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky, Estimation of Alternative Splicing Isoform Frequencies From RNA-Seq Data, INFORMS Annual Meeting, Austin, TX, Nov. 7-10, 2010, ppt, url

I.I. Mandoiu, Estimation of alternative splicing isoform frequencies from RNA-Seq data, Invited talk, Max Planck Institute for Molecular Genetics, July 19, 2010, ppt, url

M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky, Estimation of alternative splicing isoform frequencies from RNA-Seq data, Dagstuhl seminar on Structure Discovery in Biology: Motifs, Networks & Phylogenies, June 6-11, 2010, ppt, abstract, url

C. Lee and I.I. Mandoiu and C.E. Nelson, Inferring Ethnicity from Mitochondrial DNA Sequence, 6th International Symposium on Bioinformatics Research and Applications , May 23-26, 2010, ppt, abstract, url

M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky, Estimation of alternative splicing isoform frequencies from RNA-Seq data, 6th International Symposium on Bioinformatics Research and Applications , May 23-26, 2010, ppt, abstract, url

J. Lindsay and J. Zhang and I.I. Mandoiu and Y. Wu and M. Renfree and A. Pask and T. Heider and C. Obergfell and R.J. O'Neill, Novel multi-platform next generation assembly methods for mammalian genomes, Poster at 6th International Symposium on Bioinformatics Research and Applications , May 23-26, 2010, ppt, abstract, url

Y. Huang and M. Khan and I.I. Mandoiu, Development of Real Time RT-PCR Assays for Neuraminidase Subtyping of Avian Influenza Virus, Poster at 6th International Symposium on Bioinformatics Research and Applications , May 23-26, 2010, ppt, abstract, url

J. Lindsay and D.M. Carone and E. Murchison and A. Pask and G.J. Hannon and I.I. Mandoiu and R.J. O'Neill, Unique small RNA signatures uncovered in the tammar wallaby genome, 6th International Symposium on Bioinformatics Research and Applications , May 23-26, 2010, ppt, abstract, url

K. Westbrooks and I. Astrovskaya and D.S. Campo Rendon and Y. Khudyakov and P. Berman and I.I. Mandoiu and A. Zelikovsky, HCV Quasispecies Assembly using Network Flows, Poster, 5th International Symposium on Bioinformatics Research and Applications, Ft. Lauderdale, FL, May 13-16, 2009, url

J. Duitama, Bioinformatics Methods for Diagnosis and Treatment of Human Diseases, Ph.D. Dissertation Proposal, Dec. 2, 2009, ppt

J. Duitama and I.I. Mandoiu and P.K. Srivastava, Bioinformatics pipeline for detection of immunogenic cancer mutations by high throughput mRNA sequencing, Talk at 9th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Oct 27-30, 2009, ppt, abstract, url

S. Dinakar and J. Duitama and Y. Hernandez and J. Kennedy and I.I. Mandoiu and Y. Wu, Linkage Disequilibrium Based Single Individual Genotyping from Low-Coverage Short Sequencing Reads, Poster at 13th Annual International Conference on Research in Computational Molecular Biology, Tucson, AZ, May 17-21, 2009, ppt, url

J. Duitama and I.I. Mandoiu and P.K. Srivastava, Bioinformatics pipeline for detection of immunogenic cancer mutations by high throughput mRNA sequencing, Poster, 5th International Symposium on Bioinformatics Research and Applications, Ft. Lauderdale, FL, May 13-16, 2009, ppt, abstract, url

I.I. Mandoiu, Imputation-based local ancestry inference in admixed populations, DIMACS Workshop on Algorithmics in Human Population-Genomics, DIMACS Center, Rutgers University, Apr. 27-29, 2009, ppt, url

I.I. Mandoiu, Genotype and Haplotype Reconstruction from Low-Coverage Short Sequencing Reads, Proc. 1st International Conference on Bioinformatics and Computational Biology, New Orleans, LA, Apr. 8-10, 2009, ppt, abstract, url

S. Dinakar, J. Duitama, Y. Hernandez, J. Kennedy, I.I. Mandoiu, and Y. Wu, Algorithms for Genotype and Haplotype Inference from Low-Coverage Short Sequencing Reads, 11th INFORMS Computing Society Conference, Charleston, SC, Jan. 11-13, 2009, ppt, url

J. Duitama and D.M. Kumar and E. Hemphill and S. Babapoor and I.I. Mandoiu and C.E. Nelson and M. Khan , DNA Barcoding: Preliminary Studies with Avian Influenza Virus, Poster, 2008 AAAP/AVMA Annual Meeting, New Orleans, LA, July 19-23, 2008, ppt, url

I.I. Mandoiu, LD-Based Genotype and Haplotype Inference from Low-Coverage Short Sequencing Reads, Invited talk, UCLA bioinformatics seminar series, Nov. 3, 2008, ppt, url

I.I. Mandoiu, Linkage Disequilibrium Based SNP Genotype Calling from Short Sequencing Reads, Invited talk, SoE-UCHC Bioengineering Research Forum, UCONN Health Center, Farmington, CT, Oct. 29, 2008, ppt, url

I.I. Mandoiu, Hidden Markov Models of Haplotype Diversity and Applications in Genetic Epidemiology, INFORMS Annual Meeting, Oct. 12-15, 2008, ppt, url

S. Dinakar and J. Duitama and Y. Hernandez and J. Kennedy and I.I. Mandoiu and Y. Wu, Linkage Disequilibrium Based Single Individual Genotyping from Low-Coverage Short Sequencing Reads, Poster at 2008 Personal Genomes Meeting, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA, Oct 9-12, 2008, ppt, url

S. Dinakar and Y. Hernandez and J. Kennedy and I.I. Mandoiu and Y. Wu, Linkage Disequilibrium Based Single Individual Genotyping from Low-Coverage Short Sequencing Reads, Poster at 2008 Meeting on Genomics of Common Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA, USA, September 6-9, 2008, ppt, url

J. Kennedy, Linkage Disequilibrium Based Single Individual Genotyping from Low-Coverage Short Sequencing Reads, DIMACS Workshop on Computational Issues in Genetic Epidemiology, DIMACS Center, Rutgers University, August 21 - 22, 2008, ppt, url

J. Kennedy and I.I. Mandoiu and B. Pasaniuc, Genotype Error Detection and Imputation using Hidden Markov Models of Haplotype Diversity, Poster, 4th International Symposium on Bioinformatics Research and Applications, Atlanta, GA, May 6-9, 2008, ppt, abstract, url

J. Duitama and M. Khan and I.I. Mandoiu and D.M. Kumar and C.E. Nelson, PrimerHunter: A Primer Selection Tool for Avian Influenza Subtype Identification, Poster, 4th International Symposium on Bioinformatics Research and Applications, Atlanta, GA, May 6-9, 2008, ppt, abstract, url

I.I. Mandoiu, Computational Challenges in Whole-Genome Association Studies, SoE-UCHC Bioengineering Research Forum, University of Connecticut, Storrs, CT, April 22, 2008, ppt, url

I.I. Mandoiu, Rational DNA sequence design for molecular nanotechnology, SoE Nanotechnology Research Forum, University of Connecticut, Storrs, CT, March 5, 2008, ppt, url

J. Kennedy, Genotype Error Detection using Hidden Markov Models of Haplotype Diversity, 3rd RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, Los Angeles, CA, Jan. 27-28, 2007, ppt, url

R. Garfinkel and I.I. Mandoiu and B. Pasaniuc and A. Zelikovsky, Optimal Testing of Digital Microfluidic Biochips: A Multiple Traveling Salesman Problem, INFORMS Annual Meeting, Seattle, WA, Nov. 4-7, 2007, ppt, url

I.I. Mandoiu, Algorithms for Biochip Design and Optimization, Adjacency Lecture, Cadence Research Laboratories, Berkeley, CA, Nov. 1, 2007, ppt, url

A. Gusev and S. Kentros and J. Lindsay and I.I. Mandoiu and B. Pasaniuc, A Comparison of Algorithms for Species Identification Based on DNA Barcodes, Invited talk, 2nd International Barcode of Life Conference, Academia Sinica, Taipei, Taiwan, Sept. 17-21, 2007, ppt, url

B. Dasgupta and J. Jun and I.I. Mandoiu, Primer selection methods for detection of genomic inversions and deletions via PAMP, 1st RECOMB Satellite Workshop on Computational Cancer Biology, San Diego, CA, Sept. 18-20, 2007, ppt, url

B. Pasaniuc, Model-based species identification using DNA barcodes, Invited talk, 39th Symposium on the Interface: Computing Science and Statistics, Philadelphia, PA, May 23-26, 2007, ppt, url

I.I. Mandoiu, Scalable Algorithms for Genotype and Haplotype Analysis, Tutorial, 3rd International Symposium on Bioinformatics Research and Applications, Atlanta, GA, May 7-10, 2007, ppt, url

I.I. Mandoiu, Genotype Error Detection using Hidden Markov Models of Haplotype Diversity, Invited talk, 21st New England Statistics Symposium, Storrs, CT, April 21, 2007, ppt, url

I.I. Mandoiu, Algorithms for SNP Data Collection and Analysis, Invited colloquium, Department of Computer Science, University of Rhode Island, Nov. 10, 2006, ppt, url

I.I. Mandoiu, Design and Optimization of Universal DNA Arrays, Invited talk, Affymetrix, Inc., Santa Clara, CA, July 26, 2006, ppt, url

B. Pasaniuc, Boosting Assignment Accuracy by Combining Distance- and Character-Based Classifiers, The DNA Barcode Data Analysis Initiative (DBDAI): Developing Tools for a New Generation of Biodiversity Data, Paris, France, July 6-8, 2006, ppt, url

I.I. Mandoiu, Combinatorial algorithms for maximum likelihood tag SNP selection and haplotype inference, Invited talk, 3rd International Workshop on Applied Probability, May 15-18, 2006, ppt, url

I.I. Mandoiu, Design and Optimization of Universal DNA Arrays, Invited talk, DATE Workshop on Emerging CAD Challenges for Biochip Design, Munich, Germany, March 10, 2006, ppt, url