RNA-Seq 2013 Brochure
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RNA-Seq 2013 Brochure

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Applying Innovative RNA-Seq Technology to Support Research & Drug Discovery

Applying Innovative RNA-Seq Technology to Support Research & Drug Discovery
Informatics & Statistical Analysis of RNA-Seq Data
Transcriptomics: Microarray vs RNA-Seq

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RNA-Seq 2013 Brochure RNA-Seq 2013 Brochure Document Transcript

  • w p no u e ok av 0 Bo d s $50 an to Advanced Approaches for Gathering, Interpreting & Applying Next Generation Transcriptome Data 18th – 20th June 2013 Boston, MA 22 expert speakers including Benefits of attending • Discover how to adopt the most innovative applications of RNA-Seq to improve your research efforts and integrate it into existing pipelines from accessing a plethora of expert case studies • Meet the experts and embrace solid collaboration opportunities to progress the application of RNA-Seq towards drug discovery and development • Break the data bottleneck by applying the most appropriate bioinformatics tools and develop a unified, integrated approach for analysis and interpretation of huge data sets • Learn how to operate RNA-Seq projects efficiently and cost-effectively through a lesson of best practice from industry leaders already adopting the technology • Cost-effectively manage the transition from microarray to RNA-Seq and ensure the smooth integration of technology into existing protocol for optimal transcriptome profiling Workshops: 18th June 2013 A) Structural Re-Annotation Using RNA-Seq of Newly or Poorly Annotated Genomes Maarten Leerkes, Genome Analysis Specialist, NIH B) Genome-Based and Genome-Free Transcript Reconstruction and Analysis Using RNA-Seq Data Brian Haas, Manager of Genome Annotation, Outreach Bioinformatics & Analysis, Broad Institute Cole Trapnell, Postdoctoral Research Fellow, Broad Institute C) Computational Quality Control Methods for RNA-Seq Stuart Brown, Associate Professor, Department of Cell Biology, NYU School of Medicine Expertise Partners Lead Sponsor Exhibitor Thomas Wu Senior Scientist, Bioinformatics & Computational Biology Genentech Brian Haas Manager of Genome Annotation, Outreach, Bioinformatics, and Analysis Broad Institute Edward Oakeley Senior Group Head, Next Generation Sequencing Novartis Mark Gerstein Professor Yale University Rick Stevens Senior Scientist, Head of Next Generation Sequencing Platform Merck Maarten Leerkes Genome Analysis Specialist NIH Sherry Cao Associate Director, Scientific Computing Genzyme Paul Kayne Senior Principal Scientist, Head of Genomic Technologies Bristol Myers-Squibb Colin Dewey Associate Professor University of Wisconsin-Madison Ganesh Sathe Manager, DNA Sequencing GSK Tel: +1 (212) 357 5898 Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com
  • RNA-Seq 2013 Boston, MA 18th – 20th June 2013 Benefits of attending Optimize the practical application of RNA-Seq technology to discover the full complexity of the RNA universe. Accelerate your RNA sequencing capabilities through unparalleled exposure to an exploding field. Bring your lab closer to comprehensively annotating and accurately quantifying the active genome for maximum results. RNA-Seq 2013 gives you access to cutting edge data, presentations and experiences available nowhere else. Led by scientists heading up the most advanced and pioneering transcriptomics programs around, you’ll leave the meeting with a crystal clear idea of how to advance all RNA-Seq projects in your lab. If you are looking to cost-effectively manage the transition from microarray to RNA-Seq and ensure smooth integration of technologies, RNA-Seq 2013 is the must attend meeting this year. You will hear pioneering case studies from experts using the latest tools and the most innovative applications of RNA-Seq to enhance research and drug discovery programs. Leave with an understanding of the complex landscape and dynamics of the transcriptome at an unprecedented level of accuracy and sensitivity. Meet face to face with your peers from genome institutes, universities and pharma to form solid collaborations and leverage the latest advances in technology and experimental design. You’ll meet the people who can help you to progress the application of RNA-Seq quickly and cost-effectively towards drug discovery and development Hear what previous Hanson Wade attendees have to say “The event brought together some of the brightest minds and industry leaders in genomics for a series of illuminating seminars and beneficial meetings. We look forward to working with Hanson Wade in the near future.” Bina Technologies “It was a great conference. Very carefully chosen content and very informative. It is the right balance between industry and academia. I enjoyed all presentations and discussion panels” Millennium What will you find at the meeting…? • Discover how you can apply the tools as Broad Institute, Stanford University and the University of North Carolina reveal how research is impacting emerging technologies and RNA-Seq applications in drug discovery • Learn how to digest huge data sets and extract meaningful information for optimized research efforts through informatics approaches outlined by Genentech, Genzyme and Yale University • Explore the industry perspective as Novartis, Dendreon and Sanofi show you how the latest innovations in NGS are being applied to RNA-seq as a replacement for microarrays for transcriptomics “One of the best NGS workshop tutorials I have seen. Hanson Wade did a great job at bringing the leaders that laid out the workflow of RNA and DNA NGS along with the advantages and challenges.” Viracor-IBT Laboratories • Make sense of the data and learn how it can be applied to streamline drug discovery, through case studies of the tactics and methods used by Merck, NIH, AstraZeneca and GSK • Efforts to apply high-throughput RNA-Seq technology and data integration techniques for optimized biomarker discovery and target validation are outlined by AVEO Pharma and Sanofi No matter what stage you’re at in applying the technology, RNA-Seq 2013 is the perfect platform to meet the pioneers and discover how to achieve your goals in research and targeted drug discovery. Who should attend? “The organized networking opportunities were the best I have experienced in a professional meeting…as a result of the meeting we currently are involved in active negotiations with three companies we met there and are in questionanswering stage with others. Almost too much interest for us to handle!!”” • Pharma and biotech companies looking to better understand how to overcome current barriers in the methodology and application of RNA-Seq • Universities and genome research institutions keen to see how their pioneering research is being translated into drug discovery and looking for collaborations and funding opportunities • Technology companies and software providers who can showcase their latest solutions, embrace this unrivalled opportunity to educate the market to their capabilities and make a claim for leadership in the RNA sequencing space. Washington University “The meeting was well organized and packed with information…diversity and depth of speakers was very well planned.” Search for RNA-Seq Forum to join the online community Tel: +1 (212) 357 5898 Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com Expression Analysis
  • RNA-Seq 2013 Keynote Session Boston, MA Panel Session 18th – 20th June 2013 Networking Session 19th June 2013 Day 1 Breaking the Bottleneck: Informatics & Statistical Analysis of RNA-Seq Data 08.00 Registration & Breakfast 08.50 Chairman’s Opening Remarks Paul Kayne, Senior Principal Scientist & Head of Genomic Technologies, Bristol-Myers Squibb 09.00 Past, Present & Future Best Practices for Transcriptome Analysis • NA-Seq: Challenges, applications and advances – where R do you need to be? • Developing novel tools for transcriptome analysis to optimally utilize RNA-Seq data Mark Gerstein, Professor, Biomedical Informatics, Yale University Applying Innovative RNA-Seq Technology to Support Research & Drug Discovery 09.30 Transcript Sequence Assessment Leading to More Impactful Interpretation of Results Sponsored by • Estimating quantification/titration • Transcriptome disambiguation • Tophat/RSEM/express comparisons • Intergenomics • Evaluating ‘correctness’ in quantitation Vic Weigman, Senior Bioinformatics Scientist, Expression Analysis 10.00 Speed Networking 11.00 Morning Refreshments 11.30 A Comparison of Strand-Specific RNA-Seq Techniques • eveloping a comprehensive computational pipeline to D compare library quality metrics from any RNA-seq method • Selecting optimal sequencing methods based on strand specificity, transcript coverage, ribosomal RNA contamination content and evenness of coverage Rick Stevens, Senior Scientist & Head of Next Generation Sequencing Platform, Merck 12.00 Introducing Lexogen’s SENSE and SQUARE Technologies: Enabling Complete Transcriptome Sequencing • ENSE: Ultra strand specific RNA-Seq Sponsored by S • SQUARE: Uncovering the complexity of the transcriptome: • Results and Consequences for biomarker discovery Alexander Seitz, CEO, Lexogen 12.30 INDUSTRY CASE STUDY: Applications of RNA-Seq within Research & Development at GSK • discussion of various RNA-Seq applications and A associated experimental technical difficulties • RNA-Seq for cancer target identification using very small amount of starting material • Sequencing blood samples for biomarker identification • RNA-Seq for cell line validation Ganesh Sathe, Manager, DNA Sequencing, GSK 14.30 Aligning RNA-Seq Data to Explore the Causes of Schitzophrenia • enomic alignment: Overcoming the major analysis G bottleneck • Attempts to identify risk genes for schizophrenia by integrating gene expression and pathway analyses with genome-wide association • Discussing the technical challenge of using RNA-Seq to map allele-specific expression: examples from efforts to understand genomic imprinting and schizophrenia Tomas Babak, Senior Staff Scientist, Stanford University 15.00 Panel Session: Lost in Transcription… • iscussing the suitability of using RNA-Seq to determine D transcriptional landscape • What is best practice for the interaction between teams, departments and also outsourced providers? • Where do we go from here? Graham Brock, Principal Scientist, Biogen Idec Brian Dougherty, Translational Genomics Lead, AstraZeneca Joel Parker, Director, Bioinformatics, University of North Carolina Mark Gerstein, Professor, Biomedical Informatics, Yale 15.30 Afternoon Refreshments & Networking 16.00 Statistical Modelling in Non-Coding RNA Mediated Regulatory Networks • bioinformatics strategy to construct the microRNAA mediated regulatory network using genome-wide binding patterns of transcription factors • New findings on long noncoding RNA in determining alcohol dependence in rat brains, using RNA-seq derived transcriptome mapping data Yunlong Liu, Associate Professor, Department of Medical & Molecular Genetics, Indiana University School of Medicine 16.30 Using RNA-Seq to Characterize Explant Models to Support Research and Drug Discovery • study of direct sequencing of human tumors growing on A mice • Explant model characterization by expression, mutations, alternative splicing, and fusions from RNA-seq • Comparison of mutations detected by RNA-seq and exome in paired samples Zhongwu Lai, Senior Scientist, Cancer Informatics, AstraZeneca 17.00 Chairman’s Closing Remarks 13.00 Networking Lunch Tel: +1 (212) 357 5898 14.00 Trinity de novo RNA-Seq Assembly for Analysis of Model and Non-Model Organisms • n overview of Trinity de novo assembly A • Learning from a comparison of Trinity used with model and non-model organisms • Beyond Trinity assembly... what are your next steps? Brian Haas, Manager of Genome Annotation, Outreach, Bioinformatics & Analysis, Broad Institute Affymetrix Welcome Drinks Reception Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com
  • RNA-Seq 2013 Keynote Session Boston, MA Panel Session 18th – 20th June 2013 Networking Session 20th June 2013 Day 2 08.15 Registration & Breakfast 12.30 Networking Lunch 08.50 Chairman’s Opening Remarks Paul Kayne, Senior Principal Scientist, Bristol-Myers Squibb Biological Inference: What Does all this Data Mean? 09.00 Optimal Detection of Gene Fusions and Application to Large RNA-Seq Datasets • n overview of the Genentech Genomic Short-Read A Nucleotide Alignment Program software package • An introduction to GSTRUCT: a pipeline for assembling alignment results to gene structures and predicting isoforms and gene fusion events • An insight into the GSTRUCT program and its role in discovering R-spondin gene fusions in colon adenocarcinomas • Analyzing other large datasets to identify other novel gene fusions Thomas Wu, Senior Scientist, Bioinformatics & Computational Biology, Genentech 09.30 Accurate de novo Assembly of RNA-Seq Data without the Need for a Reference Genome • ethods for running the analysis of huge RNA-Seq data M without a reference on a normal PC in the lab • Designing RNA-Seq experiments to maximize discovery of novel transcripts Sherry Cao, Associate Director, Scientific Computing, Genzyme Sponsored by 10.00 Talk by Affymetrix 10.30 Morning Refreshments & Networking 11.00 Inference of Alternative Splicing from RNA-Seq Data with Probabilistic Splice Graphs • An overview of probabilistic splice graphs (PSGs) to alleviate statistical and computational difficulties in analyzing RNASeq data for genes with large numbers of isoforms • A demonstration of the advantages of our approach for using PSGs with RNA-Seq data over alternatives Colin Dewey, Associate Professor, University of Wisconsin-Madison 11.30 AVEO’s Pathway-Based Biomarker Discovery Approach Using Microarray Data from Next-Generation Mouse Models • n introduction to the pathway-based microarray analysis A bioinformatics tools used by AVEO Pharmaceuticals • The use of this tool to identify differentially expressed pathways/modules based on microarray profiles of efficacy tested mice, and validating the biomarker in the Phase 2 study Bin Feng, Director, Bioinformatics, AVEO Pharma 12.30 Using Extensive RNA-Seq Analyses to Reveal Novel Approaches for Gene Model Construction and Alternative Splicing Detection in the Fungal Pathogen Cryptococcus Neoformans • sing RNA-seq to do global screening of potential U Cryptococcus neoformans hypoxia-related transcription factors via gene regulatory network comparison • Replication, randomization and blocking principles in the statistical design and analysis of RNA-seq data Maarten Leerkes, Genome Analysis Specialist, NIH Tel: +1 (212) 357 5898 13.30 Optimizing the National Cyberinfrastructure for Lower Bioinformatic Costs: Making the Most of Resources for Publicly Funded Research • n overview of the NCGAS server-on-demand resources on A a low cost fee-for-cycles basis • The Extreme Science and Engineering Discovery Environment: Demonstrating a need for truly large-scale resources Rich LeDuc, Manager, National Center for Genome Analysis Support, Indiana University 14.00 Analysis Methods for High-Throughput RNA Sequencing Assays • An outline of the algorithms Cufflinks uses for assembly and quantification to show data from a time-course RNA-Seq analysis muscle differentiation • A summary of current efforts to clone and validate novel long, noncoding RNA genes discovered by Cufflinks Cole Trapnell, Postdoctoral Research Fellow, Broad Institute Transcriptomics: RNA-Seq vs. Microarray 14.30 RNA-seq: “But what about all my microarray data?” • ays of transforming sequencing data into microarray data W so that it is as comparable as possible to arrays • Realizing the promise of sequencing: Alternative splicing, exon switching and transcript isoform expression Edward Oakeley, Senior Group Head, Next Generation Sequencing, Novartis 15.00 Afternoon Refreshments & Networking 15.30 Comparison of RNA-Seq and Microarray Profiling of FFPEPreserved Tissues for Biomarker Studies • discussion of noise models for both Affymetrix arrays and A RNA-Seq technology and how they compare in prediction of differentially expressed genes. • An overview of RNA-Seq accuracy for prediction of relative abundance of specific splice variants in a biomarkeroriented context Joachim Theilhaber, Lead Research Investigator, Sanofi 16.00 Panel Discussion: So what’s it to Be - Microarray or RNA-Seq? • summary of the pros and cons: The performance benefits A comparison of RNA-Seq and microarray • Overcoming the biases in RNA-Seq • Is the future the end of the microarray? Edward Oakeley, Senior Group Head, Next Generation Sequencing, Novartis Joachim Theilhaber, Lead Research Investigator, Sanofi Rich LeDuc, Manager, National Center for Genome Analysis Support, Indiana University Maarten Leerkes, Genome Analysis Specialist, NIH Representative from Affymetrix 16.30 Chairman’s Closing Remarks Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com
  • RNA-Seq 2013 Boston, MA 18th – 20th June 2013 Workshop A: Structural Re-Annotation Using RNA-Seq of Newly or Poorly Annotated Genomes Most genome projects produce multiple gene sets because of the variety of gene prediction programs. Each has strengths and weaknesses, and so the multiplicity of gene sets offers users a more comprehensive collection of genes to use than is available from a single program. On the other hand, the availability of multiple gene sets is also a cause for uncertainty among users as regards to which set they should use. This workshop will provide the most up-to-date, hands-on experience on how to incorporate gene models into a single reference-set from multiple sources. Comprehensive transcriptome analysis significantly enhances the current genome annotation of microbes that cause infectious diseases. RNA-Seq has the potential to generate a high-resolution map of the transcriptomes of microbes that cause infectious diseases. In this session we will discuss how RNA-Seq based genome re-annotation serves as a necessary framework for a comprehensive understanding of the molecular mechanisms of pathogenesis for a wide range of important pathogenic microbes of infectious diseases. Several concepts, tools and workflows will be discussed to this end. You will leave this workshop with: • Detailed understanding of how you can use annotation pipelines and interpret their results Date: 18th June 2013 Time: 9.00 – 12.00 Workshop leaders Maarten Leerkes Genome Analysis Specialist NIH Maarten’s expertise is both in genomics and next generation sequencing analyses as well as statistical approaches as applied to functional data analysis and design of experiments. He has worked extensively on identifying molecular signatures for disease prognosis and treatment prediction in patient sub-populations. In addition, he has knowledge of product development, including study design for product validation in clinical settings. His post-doctoral and research experiences span academia as well as biotech settings. His areas of research interest include the use of bioinformatics to interpret sequencing data and to find patterns that can be extrapolated into diagnostic tools for improving treatment options for patients. • Knowledge of concepts and experience that you can apply in the lab with heuristic and ad hoc decision rules to combine standalone gene predictors with additional information such as RNA-Seq and protein homology Workshop B: Genome-Based and Genome-Free Transcript Reconstruction and Analysis Using RNA-Seq Data This workshop will describe how to leverage RNA-Seq data for transcript analysis for genome-based and genome-free studies, leveraging either the Tuxedo or Trinity software suites, respectively. High throughput transcriptome sequencing using Next-gen technologies is enabling unprecedented progress towards unraveling the genetic complexity and transcriptional regulation for both model and non-model organisms. Leveraging RNA-Seq data requires a specialized set of software tools, and analysis paradigms heavily depend on whether or not a reference genome sequence is available. For genome-based studies, the Tuxedo software suite (TopHat2, Cufflinks, and CummeRbund) enable comprehensive studies of transcript structure, expression, and enable rigorous analyses of differential expression coupled with visualizations. Similarly, in the absence of a reference genome, the Trinity software coupled with companion utilities enables de novo (genomefree) transcript reconstruction, and subsequently yields insights into gene content and transcriptional regulation. Dr. Cole Trapnell and Brian Haas will describe and demonstrate the application of Tuxedo and Trinity software tools in workflows to analyze RNA-Seq data for model and non-model organisms. Leave the workshop with: • An understanding of how Tuxedo and Trinity can be applied towards leveraging RNA-Seq in your own transcriptome studies. • Hands-on experience in applying these software tools to next-gen transcriptome data. Tel: +1 (212) 357 5898 Date: 18th June 2013 Time: 1.00 – 4.00 Workshop leaders Brian Haas Manager of Genome Annotation, Bioinformatics & Analysis; Postdoctoral Research Fellow Broad Institute Brian has been based at the Broad Institute since 2007. His main areas of focus include gene discover and genome annotation, and he was part of a collective effort to write the Trinity software for RNA-Seq de novo assembly. Cole Trapnell Manager of Genome Annotation, Bioinformatics & Analysis; Postdoctoral Research Fellow Broad Institute As a postdoc in John Rinn’s lab, Cole is using the tools he’s developed to identify and characterize long, noncoding RNAs that are involved in cell differentiation. He is broadly interested in transcriptional and posttranscriptional regulation in differentiation and development. Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com
  • RNA-Seq 2013 Boston, MA 18th – 20th June 2013 Workshop C: Computational Quality Control Methods for RNA-Seq This workshop will discuss novel biomedical applications of next generation DNA sequencing technology, with an emphasis on bioinformatics methods. Dr. Brown will discuss computational methods for a variety of RNA-Seq applications: • Whole genome, Exome, and amplicon targeted sequencing approaches • Sequence variant discovery in cancer (somatic mutations in tumors) • GWAS studies of large populations for discovery of novel mutations that drive disease • RNA-sequencing for gene expression, quantification of small RNAs, and alternative splicing • ChIP-seq to study DNA-protein interactions and Epigenetics Leave this workshop with: Date: 18th June 2013 Time: 4.30 – 7.30 Workshop leader Stuart Brown Associate Professor, Department of Cell Biology NYU School of Medicine Dr. Brown joined the faculty of New York University School of Medicine in 1997, where he taught Bioinformatics and provided support to projects including EST sequencing and microarrays related to immunology, infectious disease, and cancer. He began working with Next Generation DNA Sequencing Informatics when NYU created a sequencing core facility in 2009. • An understanding of the interplay between automation and custom hands-on methods for RNA-Seq data analysis • An understanding of the impact of sequencing accuracy and depth of coverage on different experimental applications of RNA-Seq • Tips for the design of a NGS core facility, its interaction with bioinformatics, and an integrated best practice approach to the use of sequencing for biomedical research Search for RNA-Seq Forum to join the online community Media Partners Testimonials “Hanson Wade continued their excellent organization skills, and the focus towards making innovative fields and technologies more and more visible” Baylor College of Medicine “All talks were divergent and complimented each other well. Venue great, organizers brilliant and friendly” “I have attended six conferences on bioinformatics this year but I was most impressed with yours…I came away with a much better understanding of the IT related problem facing the scientists and our society in data analysis. This was truly an excellent meeting. The speakers knew their stuff and generally communicated it with passion and clarity” GSK Tel: +1 (212) 357 5898 Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com American Laboratory
  • RNA-Seq 2013 Boston, MA 18th – 20th June 2013 Speakers Brian Dougherty Translational Genomics Lead AstraZeneca Zhongwu Lai Senior Scientist, Cancer Informatics AstraZeneca Brian’s responsibilities at AZ include coordinating the delivery of genetic / genomic technologies, including NextGen sequencing, across the Oncology Translational Science and Oncology iMed with the goal of developing DNAbased biomarkers, patient selection strategies, and identifying geneticsbased cancer targets. Cole Trapnell Postdoctoral Research Fellow Broad Institute Zhongwu has provided informatics solutions to both AstraZeneca’s early and late stage discovery projects. Recently, he’s been leading his informatics team to establish NGS capability in oncology to support both preclinical and translational research. Graham Brock Principal Scientist Biogen Idec As a postdoc in John Rinn’s lab, Cole is using the tools he’s developed to identify and characterize long, noncoding RNAs that are involved in cell differentiation. He is broadly interested in transcriptional and post-transcriptional regulation in differentiation and development. Graham is Head of the Transcript Profiling Lab for the Department of Translational Medicine at Biogen Idec. His lab’s focus is on investigation of disease associated expression of mRNA and ncRNA and potential applications as biomarkers. Vic Weigman Senior Bioinformatics Scientist Expression Analysis Thomas Wu Senior Scientist, Bioinformatics & Computational Biology Genentech Thomas’ group is focused on analyzing data from large-scale biological assays and developing new methods for their analysis. Work in the past has emphasized microarrays, and they have developed a comprehensive infrastructure at Genentech for both laboratory management and scientific analysis of microarray data. Vic has been leading the development of analysis tools and pipelines for nextgeneration sequencing applications for over 3 years. He plans to develop sequencing-based diagnostics for uses ranging from detection of cancer and diseases to public health uses. Alexander Seitz CEO Lexogen Yunlong Liu Associate Professor, Department of Medical & Molecular Genetics Indiana University School of Medicine Yunlong received his Ph.D. from Purdue University, and conducted postdoctoral training in Edenberg’s lab at Indiana University School of Medicine. His research interests span over genomics, bioinformatics, and systems biology, with emphasis on biomedical applications. Maarten Leerkes Genome Analysis Specialist NIH Maarten currently manages large scale application of proteogenomic mapping to human genome annotation for the ENCODE project, which has potential for significantly enhancing knowledge about where protein coding genes are, and what alternative splice forms they take. Tel: +1 (212) 357 5898 Alexander founded Lexogen in 2007, an ambitious biotech start-up with unique proprietary expression profiling technologies that enable detailed profiling of the complete transcriptome as well as individual full length RNAs of interest. Edward Oakeley Senior Group Head, Next Generation Sequencing Novartis Since 2009, Edward has been heading the next generation sequencing group in Biomarker Development at the Novartis Institutes for Biomedical Research in Basel, and with interest and extensive experience in bioinformatics and functional genomics. Bin Feug Director, Bioinformatics AVEO Bin heads up the bioinformatics department at Aveo Pharmaceuticals. His work focuses on developing a pathway-based microarray analysis bioinformatic tools to enable the translation of results across platforms and/or organisms. Brian Haas Manager of Genome Annotation, Outreach, Bioinformatics, and Analysis Broad Institute Brian has been based at the Broad Institute since 2007. His main areas of focus include gene discover and genome annotation, and he was part of a collective effort to write the Trinity software for RNA-Seq de novo assembly. Paul Kayne Senior Principal Scientist, Head of Genomics Technologies Bristol Myers-Squibb As Head of Genomic Technologies at Bristol-Myers Squibb, Paul oversees a number of genome scale technologies. His group collaborates throughout R&D for research on all stages of drug development, from target identification through life cycle management of marketed compounds. Debraj GuhaThakurta Group Leader, Computationl & Systems Biology Dendreon As Group Leader of Computational Biology at Dendreon, Debraj’ main focus is on the application of bioinformatics and genomic technologies towards target and Dx biomarker discovery. The group is also working on disease risk and patient segmentation for therapies in clinical development. Sherry Cao Associate Director, Scientific Computing Genzyme Sherry has worked at Genzyme for the past 13 years as Associate Director of Scientific Computing. Her main area of focus is in bioinformatics and translational informatics. Ganesh Sathe Manager, DNA Sequencing GSK Ganesh joined GSK in 1982 and was instrumental in forming various technology groups including DNA synthesis, mouse-genotyping, DNA/ protein sequencing, microarray, gene synthesis etc. In addition to various technologies, he also worked in the area of 7-transmembrane receptors. Richard LeDuc Manager, National Center for Genome Analysis Support Indiana University Richard currently manages the National Center for Genome Analysis Support at Indiana University, which is an NSF funded resource designed to supply bioinformatic support and computational infrastructure to genomics projects requiring large RAM computational resources – specifically de novo sequence assembly. Rick Stevens Senior Scientist, Head of Next Generation Sequencing Platform Merck Rick spent most of his professional career developing protocols and biomarkers associated with recombinant protein expression and purification. Two years ago he became the head of the core next-generation sequencing facility at Merck in Boston. Joachim Theilhaber Lead Research Investigator Sanofi Joachim has a statistics background and software-implementation skills, combined with biological domain and data analysis experience. His focus is in translational medicine, with concentration on neuroscience. He was chief architect of Gecko, one of the first centralized gene expression data analysis platforms. Tomas Babak Senior Staff Scientist Stanford University Tomas is Senior Staff Scientist and Computational Biologist at Stanford University. His current research interests include assessing advantages of monitoring allele-specific expression with RNA-Seq, in particular deciphering the causes of schizophrenia and genomic imprinting. Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com
  • RNA-Seq 2013 Boston, MA 18th – 20th June 2013 Speakers Continued Colin Dewey Associate Professor University of WisconsinMadison Colin has focused his research on the development of algorithms for comparing multiple whole genome sequences. He has participated in the international sequencing projects for the mouse, rat, and chicken genomes and was a member of the ENCODE Consortium. Mark Gerstein Professor Yale University Mark is Professor of Biomedical Informatics, Molecular Biophysics & Biochemistry and Computer Sciences. His lab aims to understand the structure, function, and evolution of proteins through analyzing populations of them in databases and in whole-genome experiments. “The speaker array and order was perfect and allowed me to take the maximal amount of knowledge back to the lab” Novartis Sponsor RNA-Seq 2013 RNA-Seq 2013 focuses exclusively on the methods and applications of RNA sequencing. Putting you in front of pharma, research institutes and academics looking to invest, RNA-Seq 2013 will provide a fantastic opportunity to present your portfolio to a uniquely targeted audience. It is an unrivalled opportunity to educate the market to your capabilities and make a claim for the market share for leadership in the RNA sequencing space. Lead Sponsor Expertise Partners Lexogen is an Austrian biotech start-up located at the Campus Vienna Biocenter. It was founded in 2007 and currently employs 27 scientists and staff. The company’s mission is already reflected in its name: Lexogen literally means “word of gene”. We are focused on the development of unique technologies enabling complete transcriptome sequencing. Lexogen‘s SENSE mRNA-Seq library preparation kit is a fast, all-in-one protocol which generates rRNA free libraries with exceptional strand-specificity from low amounts of total RNA. Lexogen‘s SQUARE technology subdivides the transcriptome and enables the detection and quantification of unique splice variants as well as exact start- and end-sites, allowing the complete profiling of all transcript isoforms present in an RNA sample. RNA-Seq is a new transcript discovery tool, however, like all new technologies, it presents significant experimental and analysis challenges. Affymetrix(r) microarrays are an indispensible complement to RNA-Seq to help get the most out of your samples in an efficient and cost effective manner. Use arrays upstream of RNA-seq to select samples for further analysis by sequencing or downstream to simultaneously validate thousands of ‘hits’. The new Human Transcriptome Array v2 offers the most detailed analysis of the transcriptome on a microarray, providing information similar to RNA-Seq -an ideal validation or sample pre-selection tool. With accurate analysis of rare transcripts, splice variants and regulatory elements, this array can also be a more prudent alternative to RNA-Seq. www.affymetrix.com/downtoascience Exhibitor Illumina is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare. Tel: +1 (212) 357 5898 Maverix provides life sciences researchers direct interaction with a secure, cloud-based platform to manage, explore, and visualize genomic data generated via high throughput sequencing. Integrating best-in-class open-source software, scientists are empowered to ask new questions; build collaborative “communities of discovery” to share data, methods, and results; and integrate their data in context with the latest public and private biomic information for viral, bacterial, vertebrate, and plant genomes. The Maverix Analytic Platform is also optimized to discover previously unknown roles of small RNA in every aspect of cell regulation. Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com
  • RNA-Seq 2013 Boston, MA 18th – 20th June 2013 Priority Code: SPK Event Prices Register Online: www.rna-seqsummit.com Mail: Hanson Wade 304 Park Avenue South 11th Floor New York, NY 10010 Email: register@hansonwade.com • 10% discount – 3 delegates • 15% discount – 4 delegates • 20% discount – 5 or more delegates Please note that discounts are only valid when three or more delegates from one company book and pay at the same time. Standard Price* $3698 (SAVE $500) $3798 (SAVE $400) $3898 (SAVE $300) Conference +2 workshops Team Discounts Register before Register before Friday 29th March* Friday 10th May* $3197 (SAVE $400) $3297 (SAVE $300) $3597 Conference +1 workshop $2698 (SAVE $300) $2798 (SAVE $200) $2998 Conference only Fax: +1 212 537 5898 Package Conference +3 workshops Tel: +1 212 537 5898 $2199 (SAVE $200) $2299 (SAVE $100) $2399 Venue and Accommodation Venue Sheraton Boston Hotel 39 Dalton Street, Boston, MA 02199, United States Accommodation Overnight accommodation is not included in the registration fee, however accommodation options will be sent out with your confirmation email upon registering. Half day workshop $599 Please select your choice of workshop: Workshop A Workshop B Workshop C There is a 40% discount available for not-for-profit institutions. For more information please email: register@hansonwade.com *All discount offers (including team discounts) require payment at the time of registration to receive any discount. ‘Early Bird’ discounts require payment at time of registration and on or before the cut-off date to receive any discount. All discount offers cannot be combined with any other offer. The conference fee includes lunch, refreshments and course documentation. The fee does not include travel or hotel accommodation. Delegate Details Title: Forename: Surname: Job Title: Company/Organization: Email: Direct Manager: Address: Country: Direct Telephone: Direct Fax: Mobile: Switchboard: Postcode: Signature: Date: Payment Details Number of delegates: Amount: $ Conference Documentation: Card No: Credit Card: Visa Amex / Valid from: Mastercard Expiry Date: / Cardholders name: Signature: Date: Card billing address: TERMS & CONDITIONS Changes to Conference & Agenda: Hanson Wade reserves the right to postpone or cancel an event, to change the location or alter the advertised speakers. Hanson Wade is not responsible for any loss or damage or costs incurred as a result of substitution, alteration, postponement or cancellation of an event for any reason and including causes beyond its control including without limitation, acts of God, natural disasters, sabotage, accident, trade or industrial disputes, terrorism or hostilities. Data Protection: The personal information shown and/or provided by you will be held in a database. It may be used to keep you up to date with developments in your industry. Sometimes your details may be obtained or made available to third parties for marketing purposes. If you do not wish your details to be used for this purpose, please write to: Database Manager, Hanson Wade, Charter House, 13-15 Carteret Street, London SW1H 9DJ Hanson Wade Limited. Registered in England & Wales. Company No: 6752216 Tel: +1 (212) 357 5898 Fax: +1 (212) 357 5898 Email: info@hansonwade.com www.rna-seqsummit.com Code: 3366 Full payment is due on registration. Cancellation and Substitution Policy: Cancellations must be received in writing. If the cancellation is received more than 14 days before the conference attendees will receive a full credit to a future conference. Cancellations received 14 days or less (including the fourteenth day) prior to the conference will be liable for the full fee. A substitution from the same organization can be made at any time.