Keynotes

XIAOLE SHIRLEY LIU, PhD

Professor, Biostatistics, Harvard T.H. Chan School Of Public Health

Co-director, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute

X. Shirley Liu is a computational biologist with expertise in cancer epigenetics. Her research focus is by integrating data from ChIP-seq, RIP-seq, DNase-seq, MNase-seq, RNA-seq, and other high throughput genomics data to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance. Her laboratory developed a number of widely used algorithms for transcription factor motif finding, ChIP-chip/seq and DNase-seq data analysis. In epigenetics, she and colleagues generated the first high throughput nucleosome map in the human genome and were the first to use the dynamics of nucleosome and DNase hypersensitivity to predict driving transcription factors and their genome-wide binding in a biological process. In cancer biology, she and colleagues identified the function of estrogen receptor, androgen receptor, and FoxA1 in breast and prostate cancers, found the direct targets of NOTCH1 in T-LL, and reported the switch of EZH2 from a transcriptional repressor as part of the PRC2 to a transcriptional co-activator in hormone independent prostate cancers.

(Source: Dana Farber Cancer Institute)

SOHRAB SHAH, PhD

Chief of Computational Oncology

Memorial Sloan Kettering Cancer Center

Sohrab Shah is the Chief of Computational Oncology in the Department of Epidemiology and Biostatistics. Dr. Shah received a PhD in computer science from the University of British Columbia in 2008 and developed his research program in computational biology at BC Cancer Agency and the University of British Columbia starting in 2010. His research focuses on developing and using computational methods to understand cancer evolution and treatment response. This encompasses advanced machine learning and Bayesian statistical methods to analyze and interpret large-scale datasets in cancer research. At MSK, Dr. Shah is building new and innovative capacity in computational methods across the spectrum of data-intensive research activity. This includes multimodal data integration such as genomics and imaging, high-resolution single-cell genomics, and transcriptomics. His translational focus lies in breast cancer and ovarian cancer, in which he has pioneered discovery of prognostic mutational signatures and large-scale studies of mutational landscapes and evolution of these cancers. Dr. Shah is a former Canada Research Chair, is a Komen Scholar, and holds the Nicholls-Biondi Endowed Chair in Computational Oncology at MSK.

(Source: Memorial Sloan Kettering Cancer Center)

Presenters

PETER KHARCHENKO, PhD

Gilbert S. Omenn, MD '65, PhD Associate Professor of Biomedical Informatics 

Harvard Medical School

Peter Kharchenko received a PhD in biophysics at Harvard University, studying gene regulation and metabolic networks under the advisement of George Church. He then completed a four-year postdoctoral fellowship in computational biology and genomics in the laboratory of Peter Park. He is currently studying the epigenetic mechanisms that regulate the growth and maintenance of normal tissues as well as the disruptions of the epigenetic state that contribute to a variety of disorders.

(Source: Harvard Medical School)

BENEDICT PATEN, PhD

Director; Assistant Professor

Computational Genomics Laboratory (CGL)

University of California, Santa Cruz

Dr. Paten is the director of the Computational Genomics Laboratory, and an associate director of the UC Santa Cruz Genomics Institute. He has a PhD from Cambridge University and the European Molecular Biology Laboratory. His group is contributing to answering some big questions, for example, how we as a species became human, and how genomes relate to states of health and disease.

(Source: UC Santa Cruz Genomics Institute)

ITAI YANAI, PhD

Director, Institute for Computational Medicine

Professor, Department of Biochemistry and Molecular Pharmacology

NYU Grossman School of Medicine

Itai Yanai joined the faculty at New York University’s School of Medicine in May 2016 as a professor in the Department of Biochemistry and Molecular Pharmacology.  He serves as the inaugural director of the Institute for Computational Medicine (ICM), whose goal is to harness computational approaches for fundamental and medically-relevant discoveries. Through the development of novel tools, the nurturing of young investigators, and translational applications, ICM aims to create a culture that promotes scientific advancements. Dr. Yanai’s research focuses on the interface of gene expression, development, and evolution. Using his training as an experimental embryologist, a molecular biologist, and a computational biologist, his interest is exploring how developmental pathways evolve at the molecular level... More recently, his lab is applying single-cell RNA-Seq to the study of tumorigenesis and bacterial infection. Dr. Yanai has also recently co-authored a popular science book, entitled “The Society of Genes”, along with Dr. Martin Lercher from Heinrich-Heine University in Düsseldorf.

(Source: Abridged from Yanai Lab at NYU School of Medicine)

GOLNAZ VAHEDI, PhD

Assistant Professor of Genetics, 

Member of Institute for Immunology

University of Pennsylvania Perlman School of Medicine

The Vahedi laboratory is multidisciplinary, integrating computational and experimental approaches to develop a single to collective cell understanding of gene regulation in immune cells in health and disease. We exploit the epigenomics mapping of immune cells to understand the biological circuits that underlie immune responses and uncover the molecular basis of major inherited diseases mediated by these cells… We blend epigenomics, human genetics, immunology, and computational biology to pursue a new understanding of human immunology. We generate genome-wide maps of chromatin in relevant immune cells mostly T cells. We are interested in regulators of T cell development and also T cell engagement in autoimmune disorders such as psoriasis and type 1 diabetes. We use population-based assays with strong signal-to-noise ratios. As a result of our computational expertise, we also harvest the vast troves of big data that immunologists and other researchers are pouring into public repositories. Our data integrations rely on available computational pipelines. Furthermore, we develop novel computational techniques to fully understand the complexity of multidimensional epigenomics datasets in T cells.

(Source: Abridged from Penn Epigenetics Institute)

YUN LI, PhD

Associate Professor

Department of Biostatistics

Department of Genetics

Gillings School of Global Public Health

Yun Li is an associate professor in the Department of Genetics, Department of Biostatistics, and an adjunct assistant professor in the Department of Computer Science. She earned her doctoral degree in biostatistics in 2009 from the University of Michigan. Her research focuses on the development of statistical methods and computational tools, as well as their applications to the genetic dissection of complex diseases. She has developed methods for genotype imputation, meta-analysis, and region-based association analysis of rare variants in both genetically homogeneous populations and in admixed populations. She has worked on genome-wide scans for genetic variants underlying several metabolic, auto-immune and cardiovascular diseases and related quantitative traits. 

(Source: Abridged from University of North Carolina Gillings School of Global Public Health)

SAMANTHA MORRIS, PhD

Principal Investigator

Department of Genetics

Department of Developmental Biology

Washington University in St. Louis.

Dr. Samantha Morris, Ph.D., is an Assistant Professor of Genetics and Developmental Biology at Washington University in St. Louis, and Allen Distinguished Investigator. Dr. Morris trained as a Developmental Biologist at the University of Cambridge. In Magdalena Zernicka-Goetz’s group, she investigated mechanisms of cell fate decision-making in the earliest stages of development. She then joined the laboratory of George Daley at Harvard Medical School, where she focused on the analysis of gene regulatory networks to dissect and engineer cell identity. In 2015, she established her independent research group. In 2017, Dr. Morris was named a Vallee Foundation Scholar. In 2019, she was awarded the St. Louis Academy of Science Innovation Award and was named an Allen Distinguished Investigator. She sits on the Board of Directors of the Society for Developmental Biology, serves on the editorial boards of Development, Cell Systems, and Developmental Cell, and is an Associate Editor at Development.

(Source: The Morris Lab, Washington University in St. Louis)