24-26 April 2018

San Francisco, USA

 

Speakers

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Michael Stadnisky
CEO
FlowJo, LLC

Michael Stadnisky, Ph.D. is the CEO of FlowJo, LLC, which provides the leading analysis platform for single cell flow cytometry analysis.  He led the company in its transformation into a leading life science informatics company, bringing a single cell sequencing and gene expression analysis platform to scientists in under 9 months in partnership with Illumina and Bio-Rad and developing a next-generation cloud collaboration system.  He is an author of 7 provisional patents, was a finalist for the 2014 International Society for the Advancement of Cytometry President’s Award, and has received numerous early career awards from American Association of Immunologists, Federation of Clinical Immunology Societies, and the National Institutes of Health.  He has been invited to present his work at the intersection of science, design, and engineering at leading pharmaceutical and biotechnology companies and international conferences.  Mike played division 1 rugby, competed in division 1 track in graduate school, and is a an ultra-marathoner and long distance swimmer.

Day One

Wednesday, April 26, 2017

12.00 | The Command Line is Compromise: A New Paradigm for Single Cell RNA-Seq Analysis

Chris Bunker, Ph.D.
VP of Business Development
Advanced Cell Diagnostics

Chris is the Vice President of Business Development at Advanced Cell Diagnostics (ACD) in Newark, CA. He did his doctoral research in the laboratory of Dr. Robert E. Kingston at Harvard University, investigating oncogene molecular biology and biochemistry.  He continued cancer research with a Leukemia Society of America postdoctoral fellowship at UCSF Dr. Bunker, and then joined Genome Therapeutics Corporation (GTC) as a senior scientist in cancer functional genomics. Dr. Bunker also has an M.B.A from Boston University. He work in business development for ten years at Cell Signaling Technology (CST) and joined Advanced Cell Diagnostics in 2010.

Day Two

Thursday, April 27, 2017

10.30 | Transcriptomes in Context: Validation of RNAseq Discoveries with Tissue-based Cell-specific Expression Analysis by RNAscope ISH

Maria Campo
Field Applications Manager - NGS
Roche

Maria Campo is the Field Applications Manager for NGS at Roche/ Kapa Biosystems.  She has received her B.S. degree in Biology from University of Massachusetts Amherst as well as her M.S. in Molecular and Cellular Biology.  She has been apart of the sequencing arena for the past 8 years in areas of  HLA diagnostics, as well as Oncology diagnostics. She has experience with array of sequencing platforms and has also been apart of the development team for sequencing using Ion Torrent for Transplant diagnostics.  She continues to provide support and technical expertise for users of KAPA and Nimblegen products for all the US.

Day One

Wednesday, April 26, 2017

15.00 | KAPA RNA HyperPrep: Improved Performance with Degraded Inputs & Tumor Profiling Applications

Maroof Adil
Postdoctoral Scholar, Schaffer Lab
University of California at Berkeley

Day Two

Thursday, April 27, 2017

12.00 | Using Single-Cell RNA-Seq to Understand Population Heterogeneity in hPSC Cultures

Dr. Jean-Noel Billaud
Senior Principal Scientist
QIAGEN

Jean-Noel Billaud, Ph.D. is Principal Scientist at Qiagen Bioinformatics. He joined Ingenuity Systems (now QIAGEN) in 2008 as staff scientist for in silico research program in oncology and infectious diseases. Jean-Noel Billaud holds a Ph.D. in Blood Cell Biology from Paris VII, and has done his post-doctoral work at the Scripps Research Institute (San Diego, CA).

Workshop A

Date: April 25, 2017 | Time: 9.00am – 12.00pm

09.00 | Understanding Innate Resistance to Anti-PD-1 Therapy in Melanoma Through Transcriptomics

Anna Salzberg
Senior Bioinformatician
Penn State University

Senior Bioinformatician in the Penn State College of Medicine's Genomic Sciences Core. Anna Salzberg has had over 10 years experience working in industry as a principal software engineer. More recently she became very enthusiastic about bioinformatics and biology and during the last 12 years she worked as a bioinformatician first at Pfizer and then at the Penn State College of Medicine. At Penn State she provides general bioinformatics services for the Genomic Sciences Core, including RNA-Seq analysis, with clients from Penn State and external institutions including research institutes in Europe and Japan. In addition, she has ongoing collaborations with various principal investigators in the areas of oncology, immunology, neuroscience, and other biomedical disciplines.

Day Two

Thursday, April 27, 2017

15.45 | Effects of Duplicated Mapped Read PCR Artefacts on RNA-seq Differential Expression Analysis Based on qRNA-seq

Dr. Samuel Rulli
Global Product Manager
QIAGEN

Samuel Rulli received his PhD in 2002 from Tulane University and did post-doctoral research at Johns Hopkins University and the National Cancer Institute in Frederick, MD. Trained as a molecular biologist, Dr. Rulli has worked on different assay detection technologies for gene expression and nucleic acid analysis. Currently he is a global product manager at QIAGEN specializing in RNAseq applications and technologies.

Workshop A

Date: April 25, 2017 | Time: 9.00am – 12.00pm

09.00 | Understanding Innate Resistance to Anti-PD-1 Therapy in Melanoma Through Transcriptomics

Jianchao (JC) Yao
Associate Principal Scientist, Computational Genomics & Genetics
Merck & Co

Day One

Wednesday, April 26, 2017

14.00 | How Merck has been Leveraging Omicsoft in Supporting Clinical and Discovery Translational Research

Yi Xing
Professor, Microbiology, Immunology, & Molecular Genetics
UCLA

Dr. Yi Xing is a Professor in the Department of Microbiology, Immunology, and Molecular Genetics at UCLA, and the Director of UCLA’s Bioinformatics Interdepartmental Ph.D. Program. He received his Ph.D. training in Bioinformatics with Dr. Christopher Lee at UCLA (2001-2006), and his postdoctoral training with Drs. Wing Hung Wong and Matthew Scott at the Stanford University (2006-2007). Dr. Xing has an extensive publication record in bioinformatics, genomics, and RNA biology. He received prestigious young investigator research awards from the Sloan Foundation and the March of Dimes Foundation, and his research is supported by the NIH and other nonprofit organizations. He serves as a regular member of the NIH Genomics, Computational Biology, and Technology (GCAT) grant review panel

Day One

Wednesday, April 26, 2017

17.00 | Round Tables

16.30 | Elucidating Transcriptome Complexity & Alternative Isoform Variation Using Massive RNA-Seq Data

Douglas Wilson
Associate Principal Scientist
Merck & Co.

Douglas Wilson holds a Bachelor of Science degree in biology from James Madison University and a Doctorate of Philosophy degree in medical sciences from Brown University. His postdoctoral training was completed at Schering-Plough Biopharma/Merck & Co. where he studied human macrophage differentiation and function. Currently, he is a member of the Translational Pathology group in the Department of Profiling and Expression at Merck Research Laboratories in Palo Alto, CA. Douglas Wilson manages the Flow Cytometry and Cell Sorting core lab and contributes to the profiling of Immuno-Oncology targets and to biomarker discovery efforts using fresh clinical samples. His interests include tumor immunology, profiling lymphocytes and myeloid cells, biomarker discovery, and high-dimensional flow cytometric data analysis.

Day One

Wednesday, April 26, 2017

11.30 | RNA-Seq Profiling of Low Numbers of Tumor-Resident Human Immune Cells

Bin Tian
Professor of Microbiology, Biochemistry & Molecular Genetics
Rutgers Cancer Institute of New Jersey

Dr. Bin Tian is currently a Professor and Director of Genome Informatics Center at Rutgers University – New Jersey Medical School. Dr. Tian obtained his Ph.D. degree in Molecular Biology from Rutgers University. After postdoctoral work in Genomic Technologies and Bioinformatics at Johnson and Johnson, he joined Rutgers University as a faculty member. Dr. Tian’s lab studies RNA Biology in development and differentiation, cancer and neurological diseases using genomic approaches. They have reported widespread occurrences of alternative polyadenylation and its dynamic nature in diverse biological systems. The Tian lab has also developed various genomic tools, including methods to specially sequence the 3’ end region of transcripts.

Day One

Wednesday, April 26, 2017

14.30 | Using 3’ Sequencing to Understand Human Diseases

09.45 | Panel Discussion: Specialized RNA Sequencing Methods with Applications to RNA Life Cycles & Drug Development

Chris Mason
Associate Professor
Weill Cornell Medicine

Dr. Christopher Mason completed his dual B.S. in Genetics and Biochemistry (2001) from University of Wisconsin-Madison, his Ph.D. in Genetics (2006) from Yale University, and then completed dual post-doctoral training in clinical genetics (2009) at Yale Medical School, and a joint post-doctoral Fellow of Genomics, Ethics, and Law at Yale Law School (2009). He is currently an Associate Professor at Weill Cornell Medicine, with appointments at the Tri-Institutional Program on Computational Biology and Medicine between Cornell, Memorial Sloan-Kettering Cancer Center and Rockefeller University, the Sandra and Edward Meyer Cancer Center, and the Feil Family Brain and Mind Research Institute. The Mason laboratory develops and deploys new biochemical and computational methods in functional genomics to elucidate the genetic basis of human disease and human physiology. We create and explore novel techniques in next-generation sequencing and algorithms for: tumor evolution, genome evolution, DNA and RNA modifications, and genome/epigenome engineering. We also work closely with NIST/FDA to build international standards for these methods, to ensure clinical-quality genome measurements/editing. We also work with NASA to build integrated molecular portraits of genomes, epigenomes, transcriptomes, and metagenomes for astronauts, which help establish the molecular foundations and genetic defenses for enabling long-term human space travel.

Day Two

Thursday, April 27, 2017

09.30 | RNA-Sequencing for Earth, the Space Station, & Beyond

Chung-Chau Hon
Research Scientist
RIKEN Center for Life Science Technologies

Dr Chung-Chau Hon is a research scientist at the Division of Genomic Technologies of RIKEN in Yokohama. Dr Hon is currently one of the key members of the FANTOM consortium, which is an international research consortium established in RIKEN over a decade ago, aims to functionally annotate mammalian genomes in large scale, with a focus on transcriptomics.  Prior to joining RIKEN, Dr Hon was trained at the Pasteur Institute in Paris and the University of Hong Kong, specializing in transcriptomics of eukaryotic pathogens and phylogenetics of viruses. Since joining RIKEN in 2014, he has been focusing on large-scale integration of high-throughput sequencing datasets for building a better transcriptomic atlas of the human genome. His research advances the understanding of the origins of non-coding RNAs in mammalian genomes and provides compelling evidences for their potential functionalities. Currently, Dr Hon is focusing on the up-coming edition of the FANTOM consortium, which aims to experimentally characterize the functions of non-coding RNAs in the human genome.

Day One

Wednesday, April 26, 2017

08.30 | A 5’Complete Transcriptomic Atlas & its Applications in Studies of Long Non-Coding RNA

Garry Nolan
Rachford and Carlota Harris Professor
Stanford University

Dr. Nolan is the Rachford and Carlota A. Harris Professor in the Department of Microbiology and Immunology at Stanford University School of Medicine. He trained with Leonard Herzenberg (for his Ph.D.) and Nobelist Dr. David Baltimore (for postdoctoral work for the first cloning/characterization of NF-κB p65/ RelA and the development of rapid retroviral production systems). He has published over 180 research articles and is the holder of 17 US patents, and has been honored as one of the top 25 inventors at Stanford University. Dr. Nolan is the first recipient of the Teal Innovator Award (2012) from the Department of Defense, the first recipient of an FDA BAAA for “Bio-agent protection” grant and received the award for “Outstanding Research Achievement in 2011” from the Nature Publishing Group for his development of CyTOF applications in the immune system. His areas of research include hematopoiesis, cancer and leukemia, autoimmunity and inflammation, and computational approaches for network and systems immunology. Dr. Nolan’s most recent efforts are focused on a single cell analysis advance using a mass spectrometry-flow cytometry hybrid device, the so- call “CyTOF”. The approach uses an advanced ion plasma source to determine the levels of tagged reagents bound to cells—enabling a vast increase in the number of parameters that can be measured per cell. .

Day One

Wednesday, April 26, 2017

17.00 | Round Tables

Day Two

Thursday, April 27, 2017

14.00 | Panel Discussion: Successfully Implementing RNA-Seq into the Clinic

11.30 | Single Cell Deep Profiling of Cancer & Immunity

Jin Jen
Co-Director, Genome Analysis Core Medical Genome Facility
Mayo Clinic

Dr. Jen is the co-Director of the Genome Analysis Core of the Medical Genome Facility at Mayo Clinic where she is also a consultant and associate professor in the Department of Laboratory Medicine and Pathology. Dr. Jen is an expert in genetic analyses of solid tumors and in gene expression profiling in a variety of biospecimens. She has been responsible for the development and implementation of whole transcriptome based technologies at the Mayo Clinic. Her research focuses on using the next generation sequencing and single cell based analysis to understand cancer initiation and progression and to help develop molecular markers for cancer diagnosis and treatment stratification. Dr. Jen has authored more than 120 peer reviewed publications and is an inventor to five patents. She is an Associate Editor for Clinical Cancer Research and has served on study sessions for NIH and the American Cancer Society. Dr. Jen is a recipient of grants from the National Cancer Institute, National Foundation for Cancer Research, and the Mayo Clinic – University of Minnesota Partnership.

Day Two

Thursday, April 27, 2017

14.00 | Panel Discussion: Successfully Implementing RNA-Seq into the Clinic

13.30 | Clinical Case Study: Single Cell RNA-Seq to Dissect Tumor Heterogeneity in Multiple Myeloma

Joost Groot
Scientist Computational Biology
Biogen

A computational biology hybrid scientist working across areas of bioinformatics, biomanufacturing, metabolic engineering and systems biology.

Day Two

Thursday, April 27, 2017

15.15 | Next-Generation Sequencing & Omics Technologies for Biotherapeutic Manufacturing Engineering & Systems Biology

Paul Diehl
COO
Cellecta

Day One

Wednesday, April 26, 2017

09.30 | Sensitive & Comprehensive Genome-Wide Expression Profiling Directly from Total RNA

Paul Kayne
Director, Genomics
Bristol-Myers Squibb Co

Paul currently heads the Genomics Technologies group at Bristol-Myers Squibb and is involved in the identification, evaluation, and deployment of new gene expression technologies. Previously, he was based at GSK where he developed microarrays for high throughput expression profiling.  

Day One

Wednesday, April 26, 2017

17.00 | Round Tables

09.45 | Panel Discussion: Specialized RNA Sequencing Methods with Applications to RNA Life Cycles & Drug Development

08.20 | Chairman’s Opening Remarks: An Overview of the RNA-Seq Field & Looking Towards the Next Generation of RNA Technologies

Paul Rejto
Executive Director & Head of Translational Research
Pfizer Inc.

As Executive Director and Head of Translational Research at Pfizer’s Oncology Research Unit, Dr. Rejto leads a team of more than thirty scientists whose mission is to develop the right drugs for the right targets and right patients. The Translational Research group seeks to advance a diverse portfolio of differentiated and targeted cancer therapies based on a comprehensive understanding of the underlying biological mechanisms and the patient populations most likely to benefit. Dr. Rejto earned his Ph.D. in Chemistry from Stanford, and completed a postdoc at UC Berkeley prior to joining Pfizer.  

Day One

Wednesday, April 26, 2017

12.30 | Deconvoluting RNA-Sequencing Profiles into Cellular Subtypes for Oncology

Rob Currie
Chief Technology Officer
UCSC Genomics Institute

Rob Currie has over 25 years of experience as a senior executive at Silicon Valley early stage technology companies including Universal Audio, Dash Navigation/Blackberry, Strangeberry/TiVo, Marimba/BMC and Digidesign/Avid in fields including distributed systems management, signal processing and geospatial navigation. Rob received a BS in EECS from UC Berkeley and an MBA from University of Chicago Booth.  

Day One

Wednesday, April 26, 2017

17.00 | Round Tables

Day Two

Thursday, April 27, 2017

14.00 | Panel Discussion: Successfully Implementing RNA-Seq into the Clinic

Robert Kuhn
Associate Director
UC Santa Cruz Genome Browser

Robert Kuhn received his PhD at the University of California,  Santa Barbara in Biochemistry and Molecular Biology, where he  studied the centromeres of yeast. Following a postdoctoral at  UC Berkeley/USDA Plant Gene Expression Center, he taught  biochemistry, molecular biology and genetics at UC Santa Cruz.  He joined the UCSC Genome Browser project in 2003, where he is   now  Associate Director.  The Genome Browser is a widely used  visualization tool giving access to the genomes of human and   more than one hundred other animals.  Dr. Kuhn's responsibilities   include enabling researchers through teaching the Genome Browser   in workshops and seminars and  learning from them how to improve   the Browser, including identification and integration of useful   new datasets

Workshop D

Date: April 25, 2017 | Time: 1.30 – 4.30pm

13.30 | An Advanced Users Guide to the UCSC Genome Browser

Shanrong Zhao
Director, Computational Biology and Bioinformatics
Pfizer Inc.

Shanrong is Director, Computational Biology and Bioinformatics at Pfizer Inc. More than 20 years of experience in bioinformatics, statistics, genetics with a demonstrated track of records in scientific initiative, innovation, and leadership. A recognized pioneer in the field of RNA-seq and cloud computing. Enthusiastic about using NGS technology, computational approaches and informatics systems to drive drug discovery and biological research.

Day One

Wednesday, April 26, 2017

09.45 | Panel Discussion: Specialized RNA Sequencing Methods with Applications to RNA Life Cycles & Drug Development

09.00 | A Head-to-Head Comparison Between Total vs. mRNA-Sequencing

Thomas Wu
Principal Scientist, Bioinformatics & Computational Biology
Genentech

I obtained my undergraduate education at Stanford, medical training at Harvard Medical School, and doctoral studies in computer science at MIT.  I have worked at Genentech for 17 years, where I have developed computer algorithms and programs for processing high-throughput sequencing data.  My programs include GMAP and GSNAP, which have been found in comparison tests to be among the most accurate for genomic alignment, especially for RNA-Seq data.  I have been developing additional tools to facilitate the analysis of sequencing data.  My colleagues and I have applied next-generation sequencing analysis to discover new biological phenomena, such as the role of R-spondin gene fusions in colon cancer.

Day Two

Thursday, April 27, 2017

09.00 | Designing NGS Alignment & Analysis Software for Modern Computer Processors

Xiang (Sean) Yao
Principal Scientist, Computational Biology
Janssen Pharmaceuticals of Johnson and Johnson

Xiang (Sean) Yao, Ph.D., is a principal scientist in Computational Biology at the Janssen Pharmaceutical Companies of Johnson & Johnson.  He received a M.S. degree in Computer Engineering and a Ph.D. degree in Molecular Biology from the University of Southern California. He worked in Janssen’s Drug Discovery, R&D IT and Discovery Sciences organizations, on a wide range of informatics solutions and analytics supporting to drug discovery projects in therapeutic areas such as metabolics, neuroscience, immunology and regenerative medicine.  He currently leads efforts to build company-wide NGS and Omics infrastructure on data management, computing and integration, and to provide analytics support to drug discovery teams on its La Jolla campus.  

Day Two

Thursday, April 27, 2017

10.00 | Integration & Mining of RNA-Seq Data for Drug Discovery Research

Yoseph Barash
Assistant Professor
Perelman School of Medicine University of Pennsylvania

Yoseph Barash is a computational biologist who works on predictive models to understand RNA biogenesis, its regulation, and its role in human disease. His lab develops machine learning algorithms that integrate genomic and genetic data, followed by wet lab experimental verifications. Yoseph did his Ph.D. in machine learning under Prof. Nir Friedman at the Hebrew University, and his postdoctoral work with Prof. Ben Blencowe and Prof. Brendan Frey at the University of Toronto, focusing on alternative splicing of genes. His dry and wet lab work involves three main themes that pose computational, engineering, and experimental challenges: Deriving new mechanistic insights into RNA biogenesis; Applying the predictive algorithms for RNA processing the lab develops to the study of human disease and phenotypic diversity; Developing software tools that allow the greater scientific community to employ the lab’s algorithms.  

Workshop C

Date: April 25, 2017 | Time: 1.30 – 4.30pm

13.30 | Detection, quantification, and visualization of splicing variations from RNA-Seq data

Day One

Wednesday, April 26, 2017

16.00 | Integrating Big Data for RNA Processing - From Computational Modeling, Through the Wet Lab, to Patients