PPT-Next-Generation Sequencing: Challenges and Opportunities

Ion Mandoiu Computer Science and Engineering Department University of Connecticut Outline Background on highthroughput sequencing Identification of tumorspecific epitopes Estimation of gene and . Next-generation shotgun sequencing approaches require sequencing every base in a sample several times for two reasons: Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . Phil Bradley. http://www.philb.com. Personal Experiences of Web 2.0. Who am I?. ‘Freelance librarian’ AKA Internet Consultant. Trainer. Writer. Speaker. ‘One man band’. I need…. To keep up to date with news. in Human Disease Genetics & Genomics. Manolis Kellis. MIT Computer Science & Artificial Intelligence Laboratory. Broad Institute of MIT and Harvard. Big data Opportunities & Challenges . in human disease genetics & genomics. Next Generation Sequencer Applications. DeNovo Sequencing. Resequencing, Comparative Genomics. Global SNP Analysis. Gene Expression Analysis. Methylation Studies. ChIP . Sequencing-transcription factors, histones, polymerases. Assembly, and Alignment Methods . Andy Nagar. Agenda. Background. Next Generation Sequencing. Sequence Assembly. Sequence Alignment. Traditional Alignment Algorithms. Next Generation Alignment Algorithms. Craig A. . Praul. Co- Director . Genomics Core Facility. Huck Institutes of the Life Sciences. Penn State University. A very short history of DNA sequencing. I started from the conviction that, if different DNA species exhibited . Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . Analysis 2015. - RNA-sequencing . Jonas Andreas . Sibbesen. & Lasse Maretty. Bioinformatics Centre, University of Copenhagen . Bioinformatics Centre. Next Generation Sequencing Analysis 2015 - RNA-seq. :. Challenges and Opportunities in the era of Precision Medicine. Dr. Paul . Keown, . 2016. Statement of Conflict & Collaboration. Therapeutics collaborations. Novartis, Roche, . Astellas. , Shire. Chen . Bichao. TJ . Treangen. , SL . Salzberg. . Nature Reviews Genetics, 2011. 5.. Scope. Introduction of Repetitive DNA. 1.. 2.. 3. .. 4.. Mapping Assembly. De novo Assembly. RNA-. Seq. Conclusions. Cynthia N Perry, PhD. Assistant Academic Dean of Admissions. Assistant Professor, Molecular Medicine. Department of Medical Education. Foster School of Medicine. https://. youtu.be. /KiQgrK3tge8. Genomics and Healthcare. Subtitle: Part 1: Dark Matter and BSM Involving Neutrinos. What is this white paper for?. Document the work we have done here. Establish the benchmark on. Where we are with the two themed BSM areas?. Alexandre . Gillet-. Markowska. Alexandre.gillet-markowska@upmc.fr. Gilles Fischer Team – . Biology. of . Genomes. . UMR7238. Laboratory . of Computational and Quantitative Biology. Université Pierre et Marie-Curie, Paris.