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2013 Speaker Biographies


Yaniv Erlich:

Dr. Erlich earned his Ph.D. from the Watson School of logical Sciences at Cold Spring Harbor Laboratory in 2010 and has received the Harold M. Weintraub Award, the IEEE/ACM-CS HPC Award, Goldberg-Lindsay Fellowship and Wolf Foundation Scholarship for Excellence in Exact Sciences. His research interests lie in computational human genetics and he was selected to be part of the 2010 Tomorrow's PIs team by Genome Technology.


Sherman Weissman:

Dr. Weissman has long contributed to studies of the molecular biology of higher cells, focusing on the globin and MHC loci. Early accomplishments include identification of sequences for transcription termination and initiation for E. coli RNA polymerase and the sequencing of the SV40 virus. His lab has worked extensively on cDNA technology and has been developing methods for genome-scale analysis of individual and small numbers of cells. Widely experienced in genomic technology, Dr. Weissman has co-directed the Yale Center for Genomics and Proteomics, worked to develop technical approaches that can be applied to large-scale analysis, and participated in the NIHGR ENCODE project since its inception.


David Galas:

Before joining Pacific Northwest Diabetes Research Institute, Dr. Galas was Professor and Senior Vice President at the Institute for Systems Biology, Chancellor and Norris Professor of Applied Life Science at the Keck Graduate Institute and Professor and Chairman of Molecular Biology at the University of Southern California. Involved in translating science into diagnostics and therapeutics in several biotechnology companies, he researches human genetics of complex diseases and the development and application of new technologies and computational methods. He has served on the NRC Board on Life Science, among other groups, and is a lifetime Associate of the National Academy of Sciences.


Jeffery Schloss:

Dr. Schloss, in addition to his role at NIH, manages a grants program to develop technologies with which to sequence human genomes for $1,000 and coordinates the Centers of Excellence in Genomic Science program. He helped formulate and then led or served on interdisciplinary initiatives, including the NIH Bioengineering Consortium (BECON), the Trans-NIH Nano Task Force and the U.S. interagency National Nanotechnology Initiative.

 


Betsy Barnes:

Dr. Barnes is an Associate Professor in the Department of Biochemistry and Molecular Biology at the New Jersey Medical School-University Hospital Cancer Center. Her laboratory specializes in understanding the mechanisms by which interferon regulatory factors (IRFs) contribute to autoimmune diseases and cancer. In recent years, her laboratory has specifically focused on one of the newer family members, IRF5. Her lab has shown that IRF5 is a critical regulator of type I IFN gene expression, Toll-like receptor signaling, DNA damage signaling and death receptor signaling. Upon the identification of IRF5 as a susceptibility gene for systemic lupus erythematosus in 2005, her lab became particularly interested in characterizing IRF5 expression and biological function in mouse and human models of SLE. Since the IRF5 risk loci has now been associated with susceptibility to numerous autoimmune diseases, her lab is focused on determining the more "global" function of IRF5 in the immune system.


Mats Ljungman:

I have a long-standing interest in carcinogenesis, DNA damage responses, and regulation of transcription. My thesis work, performed at Stockholm University (mentor Gunnar Ahnström), was focused on assessing the role of the chromatin structure in the induction and repair of DNA damage induced by ionizing radiation. During my postdoctoral studies at Stanford University (mentor Philip Hanawalt), I studied mechanisms of DNA repair and the role of DNA torsional tension in regulating gene expression in cells. After joining the Department of Radiation Oncology at the University of Michigan, my lab has focused on elucidating the mechanisms by which cells sense DNA damage and induce p53 and apoptosis. My lab is currently studying the mechanism of transcriptional and post-transcriptional regulation of gene expression in cancer cells and in cells exposed to various stresses. We have developed techniques to assess nascent RNA synthesis and stability in cells as well as splicing kinetics, elongation rates, and the mapping of transcription start sites and enhancers.


Anastasios Vourekas:

I am fascinated by the numerous functionalities and the essential roles that the ever-growing inventory of RNA molecules assumes in biological systems. Inside the cell, RNA is bound to proteins that control its function and fate. During my Ph.D. program (University of Patras, Greece), I studied the biochemical properties of enzymatic RNA-protein complexes. As a Postdoctoral Researcher in the lab of Zissimos Mourelatos at the University of Pennsylvania, I took upon developing methodology and investigating at the transcriptome level the in vivo RNA targets of proteins with critical regulatory functions in animal development.


Philippe Lefrancois:

Dr. Philippe Lefrancois received his Ph.D. from Yale University in 2012 under the direction of Dr. Michael Snyder and Dr. Shirleen Roeder. He is currently a postdoctoral associate at McGill University and a medical student at the University of Montreal. His research interests include application of high-throughput sequencing-based technologies and bioinformatics for characterizing mitotic and meiotic proteins.


Hojoong Kwak:

Hojoong Kwak graduated from the medical school at Seoul National University in Korea with the degree of Doctor of Medicine in the year 2002. Instead of practicing clinical medicine, he pursued further study in biomedical sciences. He started graduate study at Cornell University with Dr. John T. Lis in 2008, and has been developing the application of the next-generation sequencing technologies to dissect various aspects of transcriptional mechanisms.


Nicholas Ambulos:

I have directed the University of Maryland School of Medicine's Genomics Core Facility for 20 years. More recently, I developed the Translational Genomics Laboratory, a CLIA-compliant genomics resource that provides support to clinical care and enables School of Medicine faculty to conduct prospective clinical trials that contain elements of Personalized Medicine. In addition, I also provide oversight to all of the core resources as the executive director of the School of Medicine core facilities.


Kevin Shianna:

Kevin V. Shianna, Ph.D., joined the New York Genome Center in July 2012 as Senior Vice President, Sequencing Operations. He is responsible for developing the NYGC's production and clinical sequencing labs along with overseeing technology evaluation/development. Before joining the NYGC, he was an Assistant Professor at the Duke University School of Medicine and Director of Operations for the Duke Center for Human Genome Variation along with the Founding Director for the Duke Genomic Analysis Facility.


Lisa White:

I have directed the University of Maryland School of Medicine's Genomics Core Facility for 20 years. More recently, I developed the Translational Genomics Laboratory, a CLIA-compliant genomics resource that provides support to clinical care and enables School of Medicine faculty to conduct prospective clinical trials that contain elements of Personalized Medicine. In addition, I also provide oversight to all of the core resources as the executive director of the School of Medicine core facilities.


Joseph Boland:

Mr. Joseph Boland has been working at the Cancer Genomics Research Laboratory at the National Cancer Institute for the past five years. During that time, Mr. Boland was tasked with the creation and operation of the Development and Sequencing Operations Laboratory. This laboratory division was responsible for the introduction of next-generation sequencing technologies into the Cancer Genomics Research Laboratory services. Since December of 2011, Mr. Boland has assumed the role of Director of Research & Development. His laboratory's primary mission is the identification and evaluation of new sample extraction, genotyping and sequencing technologies for high-throughput genomics. In addition, once a technology is identified for possible inclusion into the Laboratories service offerings, the R&D performs rigorous validation testing before transfer to the main production group within the Cancer Genomics Research Laboratory. Previously, Mr. Boland was employed for 14 years at GeneLogic, where he served in various roles in R&D, Production and Quality Control. Joe received a bachelor's degree in Biology from The Catholic University of America in Washington, D.C. and a master's degree in Bioscience Management, George Mason University in Fairfax, Virginia.


Georg Gerber:

Georg K. Gerber, M.D., Ph.D., MPH is an Instructor in Pathology at Harvard Medical School (HMS), Co-Director of the Center for Clinical and Translational Metagenomics at Brigham and Women's Hospital (BWH), and Pathologist at the Center for Advanced Molecular Diagnostics at BWH. His research involves creating novel computational models and high-throughput experimental systems to understand the role of the microbiota in human diseases, and applying these findings to develop new diagnostic tests and therapeutic interventions to improve patient care. His training includes a Residency in Clinical Pathology at BWH, M.D. from HMS, Ph.D. and Master's in Computer Science from MIT, and Master's in Infectious Diseases and B.A. in Pure Mathematics from UC Berkeley. Prior to returning to graduate school, he founded several companies focused on developing and applying 3D graphics technologies to create feature film, IMAX®, online, and location-based entertainment products starring actors such as Denzel Washington, Russell Crowe, and Danny DeVito.


Aleksandar Milosavljevic:

Aleksandar Milosavljevic, Ph.D., is a Professor of Molecular and Human Genetics at Baylor College of Medicine. Dr. Milosavljevic's laboratory is developing flexible and scalable informatics systems for integration of data and tools and web-based collaborative environments for applications of massively parallel sequencing.


Christian Hoffmann:

Chris Hoffmann is a senior Ph.D. student in Dr. Frederic Bushman's lab. His main interests are the relationships that microorganisms have with each other, as well as how they relate with the environment they are in.


Emma Allen-Vercoe:

Dr. Allen-Vercoe has a B.Sc. (Hons) in Biochemistry from the University of London, and a Ph.D. in Molecular Microbiology obtained through the Open University as part of an industrial partnership with the Centre for Applied Microbiological Research, now part of the Health Protection Agency, U.K. After postdoctoral training in Cell Biology at the University of Calgary, Dr. Allen-Vercoe moved to the University of Guelph and set up her laboratory to study the microbial ecology of the human gut and the relationship between gut ecosystem imbalance and disease. A key component of her laboratory is "RoboGut," an in vitro model of the distal gut that enables the study of entire microbial ecosystems and their responses to various perturbations.


Corinne Maurice:

Dr. Maurice is a postdoc in Dr. Peter Turnbaugh's lab at Harvard University. The lab is generally interested in determining how the human gut microbiota influences drug metabolism and nutrition. More specifically, Dr. Maurice has been developing approaches to analyze complex microbial communities collected from the human gut at single-cell resolution. These techniques allow them to determine the baseline physiology, activity, and gene content of gut microbes, and how these factors are shaped by clinically relevant perturbations, i.e., exposure to host-targeted drugs and antibiotics.


Jessica Richman:

Jessica Richman is CEO of uBiome, a citizen science startup that sequences the human microbiome. She attended Stanford University, where she earned degrees in Economics and Science, Technology & Society (interdisciplinary engineering, emphasis in computer science). Jessica arrived at Oxford University as a Clarendon Scholar and completed an M.Sc. at the Oxford Internet Institute. Currently a Green Templeton D.Phil. Scholar, her academic interests include network analytics, innovation, and collective intelligence.


John Novembre:

John Novembre is a population geneticist who has specialized in computational methods development and large-scale data analysis. Major areas of emphasis in his research have been using genetic variation to study population structure, recombination, and recent adaptation. Much of his work focuses on the study of human genetic variation, in order to understand what it can reveal about human history and disease.


Shibu Yooseph:

Shibu Yooseph is Associate Professor in the Informatics Department at the J. Craig Venter Institute (JCVI) and also leads JCVI's Metagenomics Informatics Group. He has led the informatic analysis on several large-scale metagenomic projects at JCVI, including the Sorcerer II Global Ocean Sampling Project and human microbiome projects. Dr. Yooseph obtained his Ph.D. in Computer and Information Science from the University of Pennsylvania in 1997. He did his post-doctoral training at the Center for Discrete Mathematics and Theoretical Computer Science (Rutgers University) and then was a research associate at the University of Southern California. Prior to joining JCVI in 2003, he was a Computer Scientist at Celera Genomics where he contributed to the human and mouse genome sequencing projects.


Todd Treangen:

Dr. Todd J. Treangen is currently a Senior Bioinformatics Scientist at the National Biodefense Analysis and Countermeasures Center in Frederick, Maryland. His current work focuses on rapid nucleic acid diagnostics and microbial forensics using next-generation sequencing. Before joining NBACC, he spent time as a postdoctoral research scientist at the McKusick–Nathans Institute of Genetic Medicine at Johns Hopkins University, the Center for Bioinformatics and Computational Biology (CBCB) at the University of Maryland, and the Microbial Genome Evolution lab at the Pasteur Institute in Paris, France.


Toby Bloom:

Prior to joining the New York Genome Center as Deputy Scientific Director of Informatics, Toby Bloom led informatics at the Broad Institute’s Genome Sequencing Platform for 10 years, driving the vision and strategy for the massive scale-up in next-generation sequencing data. She directed the design and implementation of the data management, LIMS and pipeline architectures that are now handling data rates of terabytes per day. She was previously Chief Technology Officer at Clinsoft Corporation and an Executive Director at Phase Forward. Dr. Bloom received her Ph.D. in Computer Science from the Massachusetts Institute of Technology. 


Stuart Brown:

Stuart M. Brown is Associate Professor in the Cell Biology Department and a senior faculty member in the Center for Health Informatics and Bioinformatics at NYU School of Medicine, where he serves as Operations Director for the Bioinformatics consulting group and leader of the Sequence Informatics group. He has taught graduate courses in Bioinformatics at NYU for 12 years and he is the author of textbooks on bioinformatics and medical genomics. He received his Ph.D. in molecular biology from Cornell University.

Ernest Fraenkel:

Dr. Fraenkel received his Ph.D. in Biology from MIT after graduating summa cum laude from Harvard College with an A.B. in Chemistry and Physics. His laboratory at MIT focuses on developing new methods to integrate genomic, proteomic, and metabolic data in order to discover disease mechanisms.

Craig Pohl:

Craig Pohl is the Co-Director of Bioinformatics at the Genome Institute at Washington University, where he oversees the LIMS and systems IT groups. HIs primary focus is to provide high-performance computing and data management to facilitate large-scale genomic experiments.

Christina Schweikert:

Dr. Christina Schweikert is a Clare Boothe Luce Assistant Professor of Computer Science in the Division of Computer Science, Mathematics and Science at St. John's University. She obtained her Ph.D. degree in Computer Science from the City University of New York, Graduate Center, and has previously taught at Fordham University, State University of New York, and City University of New York. Dr. Schweikert's research interests include bioinformatics and medical and healthcare informatics.

Ting Gong:

I earned my Ph. D. from Virginia Polytechnic Institute and State University, with the major in Electrical and Computer Engineering in 2009, and then I conducted my postdoc training in Novartis from 2009-2012 for biomarker identification. Now I am an Assistant Professor, Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas.

Andrey Shabalin:

Andrey Shabalin, Postdoctoral Research Associate at the Center for Biomarker Research and Personalized Medicine at Virginia Commonwealth University, earned his Ph.D. at the University of North Carolina in 2010. His research focuses on statistical modeling in genetic and genomics. His current work centers on development of new statistical and computational tools for analysis of genomic and other large high-dimensional data. His work up to date addresses a variety of problems, including, but not limited to: recovery of low-rank structures in high-dimensional data, biclustering, combining gene expression data across multiple studies, fast expression quantitative trait loci (eQTL) analysis, and applications of change-point detection methods.

Jan Vijg:

Jan Vijg is Professor and Chairman of the Department of Genetics at the Albert Einstein College of Medicine in New York. He received his Ph.D. at the University of Leiden, The Netherlands, in 1987 and was previously Scientific Director and Founder of Ingeny B.V., a Dutch biotechnology company, an Associate Professor of Medicine at Harvard Medical School in Boston (1993-1999), a Professor of Physiology at the University of Texas Health Science Center in San Antonio, Texas (1999-2005) and a Professor at the Buck Institute for Research on Aging, Novato, California (2006-2008). With his research team he was the first to develop transgenic mouse models for studying mutagenesis in vivo (in 1989) and used these models in studying the possible relationship between damage to the genome and aging. He has published more than 200 scientific articles and is the inventor or co-inventor on eight patents.

Christine Vogel:

Christine Vogel is an assistant professor at the Center for Genomics and Systems Biology, New York University, New York. Her laboratory investigates protein expression regulation in response to environmental stresses. Prior to joining NYU, Dr. Vogel worked at the University of Texas at Austin (research associate) and the University of Cambridge, U.K. (Ph.D.). She was a fellow of the Human Frontier Science Program and the Boehringer Ingelheim Fonds.

Alec Chapman:

Alec received his undergraduate degree in physics from Princeton University. After working on modeling large-scale datasets for two years, he entered the biophysics graduate program at Harvard, where he is currently a member of the lab of Sunney Xie. His interests include developing and using single-cell sequencing techniques to study how gene expression and cell fate decisions are regulated.

Ester Falconer:

Ester Falconer is currently a Research Fellow in the laboratory of Dr. Peter Lansdorp at the Terry Fox Laboratory of the British Columbia Cancer Agency in Vancouver. Since 2008, her focus has been the role of sister chromatid segregation in cell fate decisions in asymmetrically dividing cells. Dr. Falconer recently developed a novel single-cell sequencing technique (Strand-seq) with promising applications for genomic instability and tumor evolution studies, as well as refining and assembling reference genomes.

Xinghua Pan:

Dr. Xinghua Pan has been a research faculty member in the Department of Genetics, Yale University School of Medicine since 2004. As the head of a research group on Single-Cell Genomics, he closely works with Dr. Sherman Weissman and focuses on the development of novel technologies for genome-wide functional genomics of single cells, including high-throughput sequencing of full-length mRNA transcriptome, of CpG methylome, and other aspects of single-cell analysis. These technologies have been applied to projects on ESC, iPSC, hMSC, hematopoietic stem cells, cancer, and neurons. He is a co-founder of stem cell company ImStem Biotechnology, Inc. and the Editor-in-Chief of the journal Single- Cell Biology. From 2000 to 2004, he served as a Research Scientist and Enzymatic Leader at Molecular Staging, Inc., and contributed to the birth of the whole-genome-amplification (WGA) kit REPLIg with Dr. Roger Lasken. Prior to this, he got postdoctoral training at Yale and developed an approach for global scanning of DNA mutations. He served as a Research Associate in the Cancer Institute of Chinese Academy of Medical Sciences and a junior faculty member in the Second Military Medical University in Shanghai, China, after obtaining his Ph.D. degree in Fudan University Institute of Genetics, Shanghai, and M.D. in South Medical University, Guangzhou, China.

Fan Bai:

Dr. Fan Bai is Assistant Professor of Biophysics at the Biodynamic Optical Imaging Center, Peking University. He received his Bachelor of Science in 2003 (from Physics Department, Peking University) and Doctor of Philosophy in 2008 (from Physics Department, University of Oxford). After three years of postdoctoral training at the University of Oxford and Osaka University, he returned to China in 2011 to lead a research group. His current work deploys single-cell genomic methods and single-molecule imaging technologies to study mechanisms of cancer metastasis and chemotherapy drug resistance.

Gabe Rudy:

Gabe is a 10-year veteran at Golden Helix and spends his days collaborating with a diverse set of scientists and building solutions to enable their research. He earned his Master’s in Computer Science from the University of Utah before setting his sights on the fast-changing field of genomics and bioinformatics. Gabe has been involved in developing various algorithms from copy number segmentation to runs of homozygosity and rare variant association testing. Gabe blogs about the genomics field from the perspective of someone building solutions and curating genomic annotations and public databases. His series “A Hitchhiker’s Guide to Next Generation Sequencing” has become quite popular as a starter guide for those entering the field.

 Jennifer E. Phillips-Cremins:   

Jennifer E. Phillips-Cremins obtained a B.S. in Chemical Engineering with highest distinction from Clarkson University. She received her Ph.D. in Biomedical Engineering from Georgia Institute of Technology while supported by a National Science Foundation Graduate Research Fellowship. During her postdoc, she was funded by an NIH National Research Service Award to lead an interdisciplinary collaboration between the laboratories of Dr. Job Dekker at UMASS Medical School and Dr. Victor Corces at Emory University. Dr. Phillips-Cremins will join the faculty at the University of Pennsylvania January 2014 as an Assistant Professor in the Department of Bioengineering. 

Yijun Ruan:  

Dr. Yijun Ruan is a genome biologist. He is currently a full professor at the Jackson Laboratory (JAX) for Genomic Medicine, and also the scientific director for JAX Genomic Sciences responsible for the development and integration of genomics programs across its Bar Harbor, Farmington and Sacramento campuses. Prior to joining JAX, Dr. Ruan was one of the funding members of the Genome Institute of Singapore, and served as a Senior Group Leader and Associate Director for the institute in Singapore from 2002 to 2012. He had played pivotal roles in establishing Singapore’s genomics capability and the award-winning genomics programs. Dr. Ruan’s primary research interest is to elucidate the structures, functions and interplays of genomic elements in the genomes of the human and model organism, with a focus on uncovering the complex mechanisms of gene transcription regulation. His strategies include the  development of innovative genome interrogation and sequencing technologies to address questions pertinent to human diseases. To this end, his group concentrates on cancer genomics, stem cells biology and in characterizing the metagenome of the microbial populations involved in human biology. Dr. Ruan and his group pioneered the paired-end-tag sequencing strategy and participated in the ENCODE technology development, with which they developed high-throughput DNA sequencing and mapping methodologies, including the RNA-PET/Seq, ChIP-PET/Seq, DNA-PET and ChIA-PET analysis. He and his group is recently focusing on applying ChIA-PET and related methodologies to understand the three-dimensional higher-order structures of chromosomal folding and their conformational impact to nuclear processes such as gene transcription regulation and DNA replication. They have demonstrated that genomic elements such as promoters and enhancers are extensively intertwined with one another to form functional transcriptional foci in the nuclei for specific and coordinated transcription regulation. 

Chia-Lin Wei: 

Dr. Wei joined the DOE Joint Genome Institute in 2010, where she actively engages the development and application of cutting-edge sequencing-based genomic technologies to explore genome function and biology. Prior to that, she was at the Genome Institute of Singapore (GIS), joining in 2002. She was responsible for establishing the genome technology platform and genome biology program there. 

Stacey Broomall:  

Ms. Broomall received her bachelor’s degree in Biological Sciences from the University of Delaware in 1999 and her master’s degree in Biotechnology from Johns Hopkins University in 2009. She is employed by the Edgewood Chemical Biological Center in Edgewood, MD and currently supports the BioSensors Branch by functioning as the Laboratory Manager and a PI for the ECBC Genomic Sciences Group. Her duties include researching and evaluating emerging sequencing technologies, producing internal operating procedures based on research as well as directing daily laboratory operations. She also assists in the STEM (Science, Technology, Engineering and Math) initiative at ECBC by traveling to local schools and performing strawberry DNA extractions to spark scientific interest in children.

Alexander Seitz:  

Alexander Seitz founded Lexogen in 2007, an ambitious biotech startup with unique proprietary expression profiling technologies that enable detailed profiling of the complete transcriptome as well as individual full-length RNAs of interest.

Michael Vishnevetsky:  

Michael Vishnevetsky has joined WaferGen to focus company efforts on launching SmartChip TE target enrichment system. Michael earned a B.Sc. in Genetics from Agricultural University of Leningrad, holds a Ph.D. in Molecular Biology from the Hebrew University of Jerusalem and has completed his posdoctorate at California Institute of Technology. Prior to joining WaferGen, Michael has held positions with PerkinElmer, Life Technologies and NuGEN Technologies.

John-David Herlihy:  

John-David Herlihy is a Product Manager with Covaris, Inc., leading the development of new applications and expanding the use of the company’s patented Adaptive Focused Acoustics technology in pre-analytical sample preparation. He received a Ph.D. in Molecular Biology from the University of Florida, College of Medicine. Prior to joining Covaris, Dr. Herlihy held commercial positions at Cell Signaling Technology in Europe and the U.S. and expanded the adoption of the company’s PTMScan Proteomics platform for biomarker discovery.



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