24-26 April 2018

San Francisco, USA

Download Event Guide

Speakers

Expand/Collapse

Satish Pillai
Associate Investigator, Blood Systems Research Institute, Associate Professor
UCSF Dept. of Lab Medicine

Day One

Wednesday, April 25, 2018

14.25 | Identifying Host Determinants of HIV Latency Using Single-Cell RNA-Seq

Brian Lee
Manager, QA team
UCSC Genome Browser

Brian Lee received a Masters in Molecular Biology at the University of California, Santa Barbara and dual degrees in Gerontology and Biology at the University of Southern California.  With a decade of biotechnology experience varying from product development, sales, and science writing Brian joined the UCSC Genome Browser project in 2012 and is now the manager of the QA team

Day One

Wednesday, April 25, 2018

12.10 | Display of RNA-seq data in the UCSC Genome Browser

Christopher Vollmers
Assistant Professor, Biomolecular Engineering
UCSC

Jun Yin
Scientist, Computational Biology
Amgen

Dr. Jun Yin is the Bioinformatics Project Lead on Cardiovascular and Metabolic Diseases therapeutic target discovery platform. He led and participated in several drug target discovery, optimization and late development projects, including Bispecific T-cell Engager (BiTE), IMLYGIC for cancer therapies, and multiple projects for cardiovascular and metabolic diseases. Prior to joining Amgen, Dr. Yin received Postdoctoral training in Yale University on genomics and epigenomics, and Ph.D. in Bioinformatics and Systems Biology in University College Dublin, Ireland. He has published several research articles in the top scientific journals, including Science, Cell and PNAS

Day Two

Thursday, April 26, 2018

11.50 | A Comprehensive RNA-Seq Computational Pipeline for Investigation of Gene Differential Expression and Alternative Splicing for Target Discovery and Validation

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 One

Wednesday, April 25, 2018

13.55 | Transcriptome-Guided Genomic Alignment

Bin Tian
Professor & Director of Genome Informatics
Rutgers New Jersey Medical School

Dr. Bin Tian received his Ph.D. degree in Molecular Biology from Rutgers University. After postdoctoral research in Bioinformatics and Genomic Technologies at Johnson & Johnson Pharmaceutical Research & Development, he established his research group at Rutgers University New Jersey Medical School. He is now a Professor and Director of Genome Informatics at Rutgers New Jersey Medical School. His research centers on RNA biology and post-transcriptional gene regulation. His lab was among the first to reveal the widespread and dynamic nature of alternative polyadenylation, and has developed several sequencing methods to study the 3’ end of RNA. They are now studying the mechanisms and consequences of alternative polyadenylation in several systems, including cancer and neurological diseases. Dr. Tian is on several editorial boards and review panels, and is an authority on alternative polyadenylation. He has published over 100 research articles, as well as scientific reviews and books.

Day One

Wednesday, April 25, 2018

10.10 | RNA Sequencing From the 3’ end: Methods and Implications

Tae Lee
Scientist
GSK

Tae Lee is a quantitative biologist with interests in applying computational and experimental approaches to drug discovery. He has a wide range of experiences in electrical engineering, synthetic biology, and regenerative medicine. His work at GlaxoSmithKline is focused on leveraging single cell transcriptomics/genomics technologies for target discovery/validation and for disease understanding in complex biological systems.

Day Two

Thursday, April 26, 2018

12.20 | Leveraging Single Cell RNA-Seq in Target Validation and Disease Understanding

Jin Jen
Co-Director, Genome Analysis Core
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 One

Wednesday, April 25, 2018

09.10 | RNA-Seq as a CLIA Test for Gene Fusion Identification and Beyond

Paul Kayne
Director, Genomics
BMS

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 Two

Thursday, April 26, 2018

09.10 | Integrated Analysis of Colorectal Carcinoma by Co-Extraction of RNA, DNA and Protein From FFPE Tumor Samples

Aparna Bhaduri
Scientist
University of California, San Francisco

Dr. Aparna Bhaduri grew up in Wisconsin before attending Rice University for her undergraduate studies. She did her doctoral studies at Stanford University studying cancer biology. She transitioned to developmental neuroscience for her postdoctoral work to pursue a lifelong curiosity of how brain development and disease are interwined. She is currently using single-cell approaches to characterize how various brain regions emerge during development. 

Day Two

Thursday, April 26, 2018

13.50 | Using Single-Cell RNA Sequencing to Understand Brain Development

Timothy Mercer
Principal
Garvan Institute of Medical Research

Dr Tim Mercer completed his PhD at the at the University of Queensland with Prof John Mattick, where he undertook early research into noncoding RNAs making notable contributions to the recognition of long noncoding RNAs as a new class of genes. Dr Mercer continues research at the Garvan Institute, with interests in genome and RNA biology (noncoding RNAs, gene organization, expression and splicing), and bioinformatic and sequencing innovations. He has also undertaken research at the Broad Institute (Boston), Max Planck (Dresden) and Centre for Genome Regulation (Barcelona).

Day Two

Thursday, April 26, 2018

10.10 | Diagnosis of Fusion Genes in Cancer using Targeted RNA Sequencing

Piotr Mieczkowski
Research Associate Professor, Director of High Throughput Sequencing Facility
UNC

Piotr Mieczkowski has completed his PhD at the Institute of Biochemistry and Biophysics Polish Academy of Sciences and postdoctoral studies at the University of North Carolina at Chapel Hill and Duke University. He is the Director of the High Throughput Sequencing Facility at UNC.   He has published more than 120 papers in reputed journals. His work is focused around new applications for next generation sequencing technology, genome stability and mutagenesis.  

Day One

Wednesday, April 25, 2018

11.40 | Detection of Virial Transcripts or Genomes Using RNA-Seq

Rob Currie
CTO
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.  

Eric Klee
Associate Professor
Mayo Clinic

Eric W. Klee, Ph.D., is a senior associate consultant II-research in the Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, with joint appointments in the Department of Medical Genetics and in the Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology. He serves as director of the Bioinformatics Core, Department of Laboratory Medicine and Pathology, and associate director of Bioinformatics, Mayo Clinic Center for Individualized Medicine. Dr. Klee holds the academic rank of assistant professor of biomedical informatics, Mayo Clinic College of Medicine. He joined the staff of Mayo Clinic in 2005.

Day Two

Thursday, April 26, 2018

09.40 | RNAseq in Blood for Diagnostic Odyssey Patients

Joost Groot
Computational Biology Scientist
Biogen

With a background in genetic/metabolic engineering and systems biology (metabolic flux analysis), my interests evolved towards applying and developing computational biology approaches to improve drug discovery and drug (bioprocess) manufacturing. My current work combines customized designs and analyses with Next-Generation Sequencing and other omics technologies to facilitate translation of these large datasets.  

Day Two

Thursday, April 26, 2018

11.20 | Translating Next-Generation Sequencing and Omics Technologies for Drug Discovery and Manufacturing Development

Robert Kuhn
Associate Director
Genome Browser UCSC

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, helping bring the fruits of the Human (and other) Genome Project(s) to scientists worldwide

Workshop B

April 24, 2018

13.00pm | RNA-Seq data in the UCSC Genome Browser - New Display Modes

Alex Chenchik
President
Cellecta

   

Day One

Wednesday, April 25, 2018

12.40 | Targeted Single-Cell RNA Expression Profiling for Biomarker Discovery

Jean-Noel Billaud
Senior Principal Scientist
QIAGEN

Before joining QIAGEN Bioinformatics, Dr. Billaud joined Ingenuity Systems 2008 as staff scientist for in silico research programs in oncology and infectious diseases. Jean-Noël 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) studying the impact of Feline Immunodeficiency Virus and Borna Disease Virus on brain cells. He pursued his career at the Vaccine Research Institute of San Diego where he co-developed a universal vaccine platform using the core antigen of Hepatitis B Virus in order to target infectious (viral and parasitic) diseases as well as metabolic diseases and cancer.    

Workshop A

April 24, 2018

09.00am | Exploring Single-Cell Transcriptomes Using Bioinformatics Solutions from QIAGEN

Nirav M. Amin
Bioinformatics Scientist
QIAGEN

Nirav is a Bioinformatics Scientist at QIAGEN. He obtained his PhD in Genetics and Development from Cornell University (Ithaca, NY), and conducted post-doctoral work in cardiac development at the University of North Carolina at Chapel Hill (Chapel Hill, NC). Nirav joined OmicSoft (now a QIAGEN company) in 2017, specializing in customer support and development.

Workshop A

April 24, 2018

09.00am | Exploring Single-Cell Transcriptomes Using Bioinformatics Solutions from QIAGEN