IIS-0546457

D.K. Wells, K. Dang, ..., E. Sherafat, ...,I.I. Mandoiu, ..., S. Al Seesi,..., and N.A.Defranoux, Strategies to improve the sensitivity and ranking ability of neoantigen prediction methods: Report on the results of the Tumor nEoantigen SeLection Alliance (TESLA), Advances in Cancer Immunotherapy, Virtual Keystone Symposium, Aug 18, 2020, url

D.K. Wells, K. Dang, ..., E. Sherafat, ...,I.I. Mandoiu, ..., S. Al Seesi,..., and N.A.Defranoux, Strategies to improve the sensitivity and ranking ability of neoantigen prediction methods: Report on the results of the Tumor nEoantigen SeLection Alliance (TESLA), Poster at AACR Annual Meeting 2020, June 22-24, 2020, url

M. Moussa and I.I. Mandoiu, SC1: interactive web-based single cell RNA-seq analysis , Tutorial at 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Sept. 21, 2020, url

S. Dhar and I.I Mandoiu and M.S. Bansal, Inferring the International COVID-19 Transmission Network using TNet, 9th Workshop on Computational Advances in Molecular Epidemiology, Sept. 21, 2020, ppt, url

J.T. Nevin and M.M. Moussa and W.L. Corwin and I.I. Mandoiu and P.K. Srivastava, Sympathetic nervous tone influences the development and function of natural killer cells, IMMUNOLOGY 2020, Honolulu, HI, May 8-12, 2020, url

M.M. George and C.A. Brennick and M.M. Moussa and A.T. Hagymasi and S. Al Seesi and T.V. Shcheglova and R.P. Englander and G.L.J Keller and J.L. Balsbaugh and B.M. Baker and I.I. Mandoiu and P.K. Srivastava, Unbiased analysis of all possible neoepitopes of MC38-FABF tumor reveals a new universe of cancer neoepitopes with unexpected properties, IMMUNOLOGY 2020, Honolulu, HI, May 8-12, 2020, url

M. Moussa and I.I. Mandoiu, Extensions to the SC1 pipeline for web-based single cell RNA-seq analysis, 9th International Conference on Computational Advances in Bio and Medical Sciences, Miami, Florida, Nov. 15-17, 2019, ppt, url

I. Mandric and I.I. Mandoiu and A. Zelikovsky and P. Skums, Genotype imputation from single cell sequencing data by integrating phylogenetic priors, 9th International Conference on Computational Advances in Bio and Medical Sciences, Miami, Florida, Nov. 15-17, 2019, url

I.I. Mandoiu, Single Cell RNA-Seq Data Analysis, ANSC Seminar, Sept. 27, 2019, ppt, url

E. Sherafat and J. Force and I.I Mandoiu, Positive-Unlabeled Learning for Cancer Neoepitope Identification, 8th Workshop on Computational Advances in Molecular Epidemiology, Niagara Falls, NY, Sept. 7, 2019, ppt, url

S. Dhar and C. Zhang and I.I Mandoiu and M.S. Bansal, TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity, 8th Workshop on Computational Advances in Molecular Epidemiology, Niagara Falls, NY, Sept. 7, 2019, url

F. Alqahtani, Algorithms for Circular Organelle Genome Assembly, Ph.D. Proposal, July 23, 2019, ppt

E. Sherafat and I.I. Mandoiu, PU-Caller: Sensitive somatic variant calling using positive-unlabeled learning, 15th International Symposium on Bioinformatics Research and Applications, Barcelona, Spain, June 3-6, 2019, ppt, url

M. Moussa and I.I. Mandoiu, SC1: A Web-based Single Cell RNA-Seq Analysis Pipeline, 33rd New England Statistics Symposium, Hartford, CT, May 15-17, 2019, ppt, url

M. Moussa and I.I. Mandoiu, SC1: A Web-based Single Cell RNA-Seq Analysis Pipeline, Poster at 5th Annual Single Cell Analysis USA Congress, Boston, MA, May 14-15, 2019, ppt, url

H. Ebrahimi-Nik and T. Shcheglova and J. Michaux and H. Pak and E. Sherafat and S. Al Seesi and I.I. Mandoiu and M. Bassani-Sternberg and P.K. Srivastava, Mass spectroscopy-defined neoepitopes are a rich source of tumor rejection-mediating neoepitopes in a mouse sarcoma, IMMUNOLOGY 2019, San Diego CA, May 9–13, 2019, url

E. Sherafat and I.I. Mandoiu, PU-Caller: Sensitive Somatic Variant Calling Using Positive-Unlabeled Learning, Poster at 23rd Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington, DC, May 5-8, 2019, ppt, url

S. Sledzieski and C. Zhang and I.I. Mandoiu and M. Bansal, TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference, Poster at 23rd Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington, DC, May 5-8, 2019, url

A. Zelikovsky and I. Mandric and P. Skums and I.I. Mandoiu and B. Pasaniuc and P.K. Srivastava, Imputation of single cell cancer genotypes, Poster at the 2019 AACR Annual Meeting, Atlanta, GA, March 29 - Apr 3, 2019, url

J.E. Duan and Z. Jiang and F. Alqahtani and I.I. Mandoiu and H. Dong and X. Zheng and S.L. Marjani and J. Chen and X.C. Tian, Whole-genome bisulfite sequencing of bovine gametes and in vivo-produced pre-implantation embryos, Proceedings of the Annual Conference of the International Embryo Technology Society, New Orleans, Louisiana, Jan. 20-23, 2019, url

F. Alqahtani, Statistical Mitogenome Assembly with Repeats, 2018 International Workshop on String Algorithms in Bioinformatics (StringBio), Orlando, FL, Oct. 25-27, 2018, ppt, url

I.I. Mandoiu, Computational Methods for Analysis of Single Cell RNA-Seq Data, CCAM Seminar Series, Oct. 25, 2018, ppt, url

M. Moussa, Computational cell cycle analysis of single cell RNA-Seq data, 8th International Conference on Computational Advances in Bio and Medical Sciences, Las Vegas, NV, Oct. 18‐20, 2018, ppt, url

M. Moussa and I.I. Mandoiu, SC1: A web-based single cell RNA-seq analysis pipeline, 8th International Conference on Computational Advances in Bio and Medical Sciences, Las Vegas, NV, Oct. 18‐20, 2018, ppt, url

S. Sledzieski and C. Zhang and I.I. Mandoiu and M.S. Bansal, TreeFix-VP: Phylogenetic Error-Correction for Viral Transmission Network Inference, 8th International Conference on Computational Advances in Bio and Medical Sciences, Las Vegas, NV, Oct. 18‐20, 2018, url

F. Alqahtani and I.I. Mandoiu, Statistical Mitogenome Assembly with Repeats, 8th International Conference on Computational Advances in Bio and Medical Sciences, Las Vegas, NV, Oct. 18‐20, 2018, ppt, url

I.I. Mandoiu, Challenges in Single Cell Sequencing Data Analysis, Lorentz Center workshop on "Single Cell Data Science: Making Sense of Data from Billions of Single Cells", Jun. 4-8, 2018, ppt

M. Moussa, Computational Methods for the Analysis of Single Cell RNA-Seq Data, Ph.D. Proposal, May 18, 2018, ppt

H. Ebrahimi-Nik and W.L. Corwin and I.I. Mandoiu and P.K. Srivastava, Characterization of a Single Nucleotide Variant of Ccdc85c as a Tumor Rejection-Mediating Neoepitope of Meth A Fibrosarcoma, IMMUNOLOGY 2018, Austin, TX, May 4-8, 2018, url

C.A. Brennick and M.M. George and A.T. Hagymasi and T.V. Shcheglova and S. Al Seesi and I.I. Mandoiu and P.K. Srivastava, Unbiased testing of several hundred tumor-specific single nucleotide variants of a tumor for protective immunogenicity and CD8+ response reveals surprises, IMMUNOLOGY 2018, Austin, TX, May 4-8, 2018, url

S.H. Karandikar and T.V. Shcheglova and A.T. Hagymasi and C.A. Brennick and I.I. Mandoiu and P.K. Srivastava, Unbiased testing of all single nucleotide variants specific to a tumor for anti-tumor CD8+ T cell immune response, IMMUNOLOGY 2018, Austin, TX, May 4-8, 2018, url

M. Moussa, Imputation Methods for single cell RNA-Seq data, CSE Bioinformatics Seminar, March 1, 2018, ppt

I.I. Mandoiu, Computational methods for genomics-guided cancer immunotherapy, UCONN Medical Deans Seminar Series "Interdisciplinary Conversations on Innovations in Informatics", Jan. 25, 2018, ppt

M.S. Bansal, Phylogenetic Inference of Viral Transmission Networks, 6th Workshop on Computational Advances in Molecular Epidemiology, Boston, MA, Aug 20, 2017

M. Moussa, Clustering Single Cell RNA-Seq Data using TF-IDF based Methods, CSE Bioinformatics Seminar, Nov. 15, 2017, ppt

S. Quader and A. Russell and I.I. Mandoiu, Realizing Minimum Spanning Trees from Random Embeddings, 27th Annual Fall Workshop on Computational Geometry, Stony Brook, NY, Nov. 3–4, 2017, abstract, url

T. Daddio and I.I. Mandoiu, Identifying alpha-beta T cell clones via pooling and b-matching, 7th International Conference on Computational Advances in Bio and Medical Sciences, Orlando, FL, October 19-21, 2017, ppt, url

S. Al Seesi, GeNeo: Bioinformatics toolbox for Genomics guidedNeo-epitope prediction, 7th International Conference on Computational Advances in Bio and Medical Sciences, Orlando, FL, October 19-21, 2017, ppt, url

J. Force and I.I. Mandoiu, Prediction of MHC-I epitopes from LC-MS/MS data, 6th Workshop on Computational Advances in Molecular Epidemiology, Boston, MA, Aug. 20, 2017, ppt, url

T. Daddio and I.I. Mandoiu, Identifying alpha-beta T cell clones via pooling and b-matching, 6th Workshop on Computational Advances in Molecular Epidemiology, Boston, MA, Aug. 20, 2017, ppt, url

X. Li and C. Chu and J. Pei and I.I. Mandoiu and Y. Wu, CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection, 13th International Symposium on Bioinformatics Research and Applications, Honolulu, Hawaii, May 29 - June 1, 2017, abstract, url

M. Moussa and I.I. Mandoiu, Clustering scRNA-Seq Data using TF-IDF, 13th International Symposium on Bioinformatics Research and Applications, Honolulu, Hawaii, May 29 - June 1, 2017, ppt, abstract, url

I.I. Mandoiu, Computational Methods for Analysis of Single Cell RNA-Seq Data, JAX-GM course on "Big Genomic Data Skills Training for Graduate Professors", May 14-19, 2017, ppt, url

H. Ebrahimi-Nik and W.L. Corwin and S.M. Floyd and P. Tavousi and I.I. Mandoiu and P.K. Srivastava, Tumor Control Index: a novel tool to assess and compare tumor growth in experimental animals, IMMUNOLOGY 2017, Washington, DC, May 12-16, 2017, url

X. Li and C. Chu and J. Pei and I.I. Mandoiu and Y. Wu, CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection, Poster at 21st Annual International Conference on Research in Computational Molecular Biology, Hong Kong, May 3-7, 2017, abstract, url

M.S. Bansal, Phylogenetic uncertainty and transmission network inference: Lessons from phylogenetic reconciliation, 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, Atlanta, GA, Oct 13-15, 2016, url

T. Daddio, Pairing T cell receptor α and β sequences using combinatorial pooling and min-cost flows, Poster at 4th annual Fall Frontiers in Undergraduate Research, Oct 26, 2016, ppt, url

T. Daddio and I.I. Mandoiu, Pairing T-cell receptor sequences using pooling and min-cost flows, 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, Atlanta, GA, Oct 13-15, 2016, ppt, url

T. Daddio, Pairing T cell receptor α and β sequences using combinatorial pooling and min-cost flows, Holster Scholar Fall Presentations, Sept 30, 2016, ppt, url

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

F. Alqahtani and I.I. Mandoiu, De Novo Assembly of Mitochondrial Genomes from Low Coverage Whole-Genome Sequencing Reads, 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

E. Nenastyeva and A. Zelikovsky and Y. Ionov and I.I. Mandoiu , Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire, 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, Miami, FL, October 15-17, 2015, 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

E. Sherafat and I.I. Mandoiu, Application of clustering to identify different cell types from single-cell transcriptomes, Poster at 11th International Symposium on Bioinformatics Research and Applications, Norfolk, VA, June 7-10, 2015, ppt, url

A. Al-Okaily and I.I. Mandoiu, Hierarchical Genome Assembly, Poster at 11th International Symposium on Bioinformatics Research and Applications, Norfolk, VA, June 7-10, 2015, ppt, url

M. Bemis and D. Chen and Z. Dicesare and N. Kruczek and R. Morillo and J. Lindsay and M. Lydon and I.I. Mandoiu, Cloud-Based Transcriptome Quantification from RNASequencing Reads, Poster at 11th International Symposium on Bioinformatics Research and Applications, Norfolk, VA, June 7-10, 2015, ppt, url

Y.B. Temate-Tiagueu and M. Mathew and I. Mandric and Q. Cheng and O. Glebova and N.B. Lopanik and I.I. Mandoiu and A. Zelikovsky, Metabolic pathway activity estimation from RNA-Seq data, 11th International Symposium on Bioinformatics Research and Applications, Norfolk, VA, June 7-10, 2015, ppt, abstract, url

E. Nenastyeva and Y. Ionov and I.I. Mandoiu and A. Zelikovsky, Identification of Cancer- Specific Motifs in Mimotope Profiles of Serum Antibody Repertoire, Poster at 11th International Symposium on Bioinformatics Research and Applications, Norfolk, VA, June 7-10, 2015, ppt, abstract, 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

I. Mandric and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, SILP3: Maximum Likelihood Approach to Scaffolding, Proc. 4th IEEE International Conference on Computational Advances in Bio and Medical Sciences, June 2-4, 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, Scalable Algorithms for Next-Generation Sequencing Data Analysis, Booth Engineering Center for Advanced Technology Workshop on HPC, May 16, 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

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

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

R.J. O'Neill and J. Lindsay and D. Carone and T. Heider and S. Al Seesi and I.I. Mandoiu and A. Pask, The Utility of Next Generation Sequencing for Genome Scale Studies, Proc. 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

I.I. Mandoiu and C. Prajescu, High-Throughput SNP Genotyping by SBE/SBH, Poster, 2nd SECABC Fall Workshop on Biocomputing, Atlanta, GA, Oct. 27, 2005, ppt

I.I. Mandoiu and B. Pasaniuc, Trio Phasing by Entropy Minimization, Poster, 2nd SECABC Fall Workshop on Biocomputing, Atlanta, GA, Oct. 27, 2005, ppt

I.I. Mandoiu, Design and Optimization of Universal DNA Arrays, Invited talk, 2nd SECABC Fall Workshop on Biocomputing, Atlanta, GA, Oct. 27, 2005, ppt

J. Jun and I.I. Mandoiu, Optimal Tag SNP Selection for Haplotype Reconstruction, Poster, 13th Annual International Conference on Intelligent Systems for Molecular Biology, Detroit, MI, June 25-29, 2005, ppt, url

I.I. Mandoiu and B. Pasaniuc, Haplotype Inference by Entropy Minimization, Poster, 9th Annual International Conference on Research in Computational Molecular Biology, Boston, MA, May 14-18, 2005, ppt, url

N. Hundewale and I.I. Mandoiu and C. Prajescu and A. Zelikovsky, Integrated Design Flow for Universal DNA Tag Arrays, Poster, 9th Annual International Conference on Research in Computational Molecular Biology, Boston, MA, May 14-18, 2005, ppt, url

I.I. Mandoiu, Algorithms for universal DNA tag array design and optimization, Invited colloquium, Department of Computer Science Colloquium, Kent State University, Feb. 25, 2005, ppt, url

K.M. Konwar and I.I. Mandoiu and A.C. Russell and A.A. Shvartsman, Optimization Methods for Reliable Genomic-Based Pathogen Detection Systems, Poster, 2nd International Conference on Advanced Technologies for Homeland Security, Storrs, CT, Aug. 12-13, 2004, ppt, url

I.I. Mandoiu, Minimum PCR Primer Set Selection with Amplification Length and Uniqueness Constraints, Invited talk, 2nd Georgia State Biotech Symposium, Atlanta, GA, May 25, 2004, ppt

I.I. Mandoiu, Non-tree routing for reliability and yield improvement, Invited talk, Fujitsu Laboratories, Kawasaki, Japan, Jan. 20, 2003, ppt, url

A.B. Kahng and I.I. Mandoiu and S. Muddu, The Self-Avoiding Traveling Salesman Problem: A Formulation for Reduction of Resist Heating Effects in Mask Production, Poster, Gigascale Silicon Research Center (GSRC) Annual Review, New Orleans, LA, June, 2002, ppt

A.B. Kahng and B. Liu and I.I. Mandoiu, Potential BEOL Yield Gains from Non-Tree Route Augmentation, Poster, Gigascale Silicon Research Center (GSRC) Annual Review, New Orleans, LA, June, 2002, ppt

A.B. Kahng and I.I. Mandoiu and P. Pevzner and S. Reda and A. Zelikovsky, Border Length Minimization in DNA Array Design, Poster, Applying Bioinformatics, from Genes to Systems: The University System of Georgia Research Symposium, Atlanta, GA, Oct. 3-4, 2002, ppt

A.B. Kahng and B. Liu and I.I. Mandoiu, Minimum-Buffered Routing of Non-Critical Nets for Slew Rate and Reliability Control, Poster, Gigascale Silicon Research Center (GSRC) Annual Review, Santa Clara, CA, Sept., 2001, ppt

C. Albrecht and A.B. Kahng and I.I. Mandoiu and A.Z. Zelikovsky, Floorplan Evaluation with Timing-Driven Global Wireplanning, Pin Assignment, and Buffer/Wire Sizing, Poster, Gigascale Silicon Research Center (GSRC) Annual Review, Santa Clara, CA, Sept., 2001, ppt

I.I. Mandoiu and A.Z. Zelikovsky, Practical Approximation Algorithms for Zero-Skew Trees, 17th International Symposium on Mathematical Programming, Atlanta, GA, Aug., 2000, ppt