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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Bo d s $50
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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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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
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speakers. Hanson Wade is not responsible for any loss or damage or costs
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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.