Breakfast and Registration

Join us for breakfast, and get your symposium badges. Early birds get a free copy of the book Follow Your Gut: The Enormous Impact of Tiny Microbes by Rob Knight. We have ordered a limited number of copies, so come early to get your copy.

Opening remarks

Ami Bhatt, Assistant Professor of Medicine, Stanford University

In perpetual awe of how 'simple' microbial organisms can perturb complex, multicellular eukaryotic organisms, Ami Bhatt has chosen to dedicate her research program to inspecting, characterizing and dissecting the microbe-human interface. 

Award Ceremony

Elisabeth Bik, Research Associate, Stanford University

Elisabeth Bik is a Research Associate at the Department of Medicine, Division Infectious Diseases, at Stanford University School of Medicine. She received her PhD at Utrecht University in The Netherlands and worked at the Dutch National Institute for Health and the St. Antonius Hospital in Nieuwegein. In 2001, she moved to the San Francisco Bay Area to join the laboratory of David Relman at Stanford. In the past 14 years she worked on the characterization of the human microbiome in thousands of oral, gastric, and intestinal samples. She currently works on the microbiota analysis of marine mammals and children with inflammatory bowel diseases. 

Prof Ami Bhatt will honor Elies Bik for Microbiome Digest - Bik's pick.

Keynote

Rob Knight, Professor of Pediatrics, UC San Diego

Rob Knight is a pioneer in studying human microbes, the community of tiny single-cell organisms living inside our bodies that have a huge — and largely unexplored — role in our health. “The three pounds of microbes that you carry around with you might be more important than every single gene you carry around in your genome,” he says.

Elhanan Borenstein, Associate Professor, Dept. of Genome Sciences, University of Washington  

The Borenstein lab is broadly interested in the integration of systems biology approaches, in-silico modeling, and computational metagenomics to address fundamental questions in microbial ecology and in human microbiome research. 

Serafim Batzoglou, Professor of Computer Science, Stanford University

Serafim's research focuses on computational genomics: developing algorithms, machine learning methods, and systems for the analysis of large scale genomic data. 

Benjamin Callahan, Research Associate, Department of Statistics, Stanford University

Dr. Callahan studies the evolutionary and ecological dynamics of large microbial populations. He is currently interested in more precisely quantifying host-associated microbial communities through better bioinformatics tools, as well as understanding how adaptive evolution shapes the ecological properties of microbial communities and their relationship with the host.

Justin Sonnenburg, Associate Professor of Microbiology and Immunology, Stanford University

Dr Sonnenburg us interested in the basic principles that govern interactions within the intestinal microbiota and between the microbiota and the host. To pursue these aims, the lab colonizes germ-free (gnotobiotic) mice with simplified, model microbial communities, apply systems approaches (e.g. functional genomics), and use genetic tools for the host and microbes to gain mechanistic insight into emergent properties of the host-microbial super-organism.

David Relman, Professor of Microbiology and Immunology, Stanford University

Dr. Relman’s research focus is the human indigenous microbiota, and the identification of previously-unrecognized microbial agents of disease. He has advised the U.S. Government on emerging infectious diseases, human-microbe interactions, and future biological threats. 

Susan Holmes, Professor of Statistics, Stanford University

Dr. Holmes is interested in integrating the information provided by phylogenetic trees, community interaction graphs and metabolic networks with sequencing data and clinical covariates. Applications include interactions between the immune system and cancer, resilience in the human microbiome after antibiotic use and drug resistance in HIV.

Ami Bhatt, Assistant Professor of Medicine, Stanford University

The goal of Dr. Bhatt's research program is to understand the interplay between human genetics and the microbial environment in patients with hematological malignancies (leukemia and lymphoma).

George Weinstock, Professor and Director of Microbial Genetics, The Jackson Laboratory

Dr. Weinstock's laboratory leverages advanced metagenomics technologies to investigate human and other microbiomes, and their clinical impact. George is also a leader of infectious disease research - from the tracking of outbreaks to a detailed mechanistic understanding of infectious disease at the individual level and on a wider public health scale. 

Description

Where is Microbiome Research Headed?  How do we generate firm foundations and enable rapid translation? This panel will broadly discuss the potential synergy and tension between different approaches that span from basic to translational/clinical, how to best organize the field to accelerate insight and translation, and how bioinformatics and big data fit into the future of the field in this context.

Ramesh Nair, PhD, Bioinformatics Manager, Stanford Center for Genomics and Personalized Medicine

As Bioinformatics Manager at Stanford Center for Genomics and Personalized Medicine (SCGPM), Ramesh is the bioinformatician in residence for the California Institute for Regenerative Medicine (CIRM) initiated Stem Cell Center of Excellence (CESCG). He is responsible for diverse bioinformatics needs for the Center Initiated Projects and its extensive collaboration network. He brings a diverse engineering and extensive scientific background to solve some of the biggest technical challenges in biotechnology.

Elhanan Borenstein, Associate Professor, Dept. of Genome Sciences, University of Washington  

The Borenstein lab is broadly interested in the integration of systems biology approaches, in-silico modeling, and computational metagenomics to address fundamental questions in microbial ecology and in human microbiome research.

George Weinstock, Professor and Director of Microbial Genetics, The Jackson Laboratory

Dr. Weinstock's laboratory leverages advanced metagenomics technologies to investigate human and other microbiomes, and their clinical impact. George is also a leader of infectious disease research - from the tracking of outbreaks to a detailed mechanistic understanding of infectious disease at the individual level and on a wider public health scale. 

Michael Snyder, Professor & Chair of Genetics, Stanford University

Mike Snyder is a leader in the field of functional genomics and proteomics. His laboratory study was the first to perform a large-scale functional genomics project, and currently carries out a variety of projects in the areas of genomics and proteomics. These include the large-scale analysis of proteins using protein microarrays and the global mapping of the binding sites of chromosomal proteins.

Nick Greenfield, Founder, One Codex

Nick Greenfield is the founder and CEO of One Codex, a Y Combinator-backed microbial genomics startup based in San Francisco. At One Codex, Nick leads the development of the company's data and search infrastructure, and oversees the company's efforts in application areas including infectious disease diagnostics, microbiome R&D, and public health. Prior to One Codex, Nick worked as a software engineer and data scientist on a variety of fraud prevention and scientific computing problems. Nick began his career at the Monitor Group, where he was a manager in the company's geostrategy practice focused on quantitative and qualitative modeling of technology and global economic trends. Nick holds a B.A. in International Relations and a M.A. in Environmental Studies from Brown University.

Lunch break

Gluten free and vegetarian options included.

Bill Bolosky, Principal Researcher, Microsoft Research

Bill Bolosky is a principal researcher in Microsoft Research’s Distributed Systems group, with interests in storage systems, distributed systems, operating systems, and with a little genomics thrown in for spice. He has worked on a number of projects while at Microsoft, ranging from the Tiger Video Server (in the early ‘90s when that was hard), to the Farsite serverless file system, to the SIS deduplicating file store that shipped in Windows long before deduplicating storage became a hot research topic.

Elhanan Borenstein, Associate Professor, Dept. of Genome Sciences, University of Washington  

The Borenstein lab is broadly interested in the integration of systems biology approaches, in-silico modeling, and computational metagenomics to address fundamental questions in microbial ecology and in human microbiome research.

Nikos Kyrpides, Prokaryote Super Program Head, DOE Joint Genome Institute

Dr. Kyrpides joined the DOE Joint Genome Institute in 2004 and became the Metagenomics Program head in 2010 and leads the combined Microbial Genomes and Metagenomes Program since 2011. Prior to joining the DOE Joint Genome Institute, Dr. Kyrpides led the development of the genome analysis and Bioinformatics core at Integrated Genomics Inc. in Chicago, IL. He did his postdoctoral studies with Carl Woese at the University of Illinois at Urbana-Champaign and with Ross Overbeek at the Argonne National Laboratory.

Tomer Altman, Sr. Bioinformaticist, Whole Biome

Dr. Tomer Altman is the Senior Bioinformaticist at Whole Biome, Inc, a microbiome therapeutics company. He has over a decade of experience working in the biotechnology industry prior to obtaining his PhD in Biomedical Informatics from Stanford University. While there as a Fellow of the NIH Biotechnology Training Grant, he conducted research on data mining and modeling of the human microbiome under the direction of Dr. David L. Dill in Computer Science, and Dr. David A. Relman in Immunology and Microbiology. He is interested in functional annotation, metabolic networks, computational modeling and simulation, and machine learning applied to furthering understanding of the human microbiome.

Sharon Greenblum, Postdoctoral Research Fellow, Stanford University

Sharon Greenblum is a Postdoctoral Fellow in Dmitri Petrov's Lab at Stanford. Sharon comes from an engineering, systems biology, and bioinformatics background, and is interested in using computational tools to understand host-microbiome co-evolution. She completed her PhD in Genome Sciences at the University of Washington with Elhanan Borenstein, where she worked on analysis techniques to illuminate community-level functional variation across human gut metagenome samples.  Her work focused on detecting the properties of microbiome-wide metabolic models that differ between hosts, and uncovering the functions associated with host-specific differences in microbial strain composition. Now at Stanford, she has begun to integrate studies of adaptive processes on the host side, investigating the dynamics of rapid seasonal adaptation in Drosophila populations.

Coffee Break

Nikos Kyrpides, Prokaryote Super Program Head, DOE Joint Genome Institute

Dr. Kyrpides joined the DOE Joint Genome Institute in 2004 and became the Metagenomics Program head in 2010 and leads the combined Microbial Genomes and Metagenomes Program since 2011. Prior to joining the DOE Joint Genome Institute, Dr. Kyrpides led the development of the genome analysis and Bioinformatics core at Integrated Genomics Inc. in Chicago, IL. He did his postdoctoral studies with Carl Woese at the University of Illinois at Urbana-Champaign and with Ross Overbeek at the Argonne National Laboratory.

Joshua Elias, Assistant Professor of Chemical and Systems Biology, Stanford University

Prod Elias seeks to develop and apply methods for large scale proteome characterization to solve fundamental problems in cell biology and disease. The lab focuses on developing new methods in protein fractionation, instrumentation, and data analysis and then applies them to studying important biomedical paradigms, including cancer, aging, and stem cell biology.

Kerwyn Huang, Associate Professor of Bioengineering, Stanford University

Prof Huang's laboratory employs diverse interdisciplinary methods of inquiry to understand the relationships among cell shape detection, determination, and maintenance in bacteria. The group uses a combination of analytical, computational, and experimental approaches to probe physical mechanisms of shape-related self-organization in protein networks, membranes, and the cell wall.

Bill Bolosky, Principal Researcher, Microsoft Research

Bill Bolosky is a principal researcher in Microsoft Research’s Distributed Systems group, with interests in storage systems, distributed systems, operating systems, and with a little genomics thrown in for spice. He has worked on a number of projects while at Microsoft, ranging from the Tiger Video Server (in the early ‘90s when that was hard), to the Farsite serverless file system, to the SIS deduplicating file store that shipped in Windows long before deduplicating storage became a hot research topic.

Description

The Bacteria and Archaea are the most genetically diverse kingdoms of life.  Techniques from Sequencing to software’s for exploring that diversity are just starting to be available and we are starting to understand just the tip of the iceberg. Scientist are working really hard in Taxonomically classifying all these organisms to the species level but differences in their biology and variable rates of recombination makes it much more challenging than anything we have ever encountered. This panel should be able to shed the light on why species exists in symbiosis within its environments, and why we need to be able to define these species for practical applications in industry, agriculture, and medicine.

Clotilde Teiling-Perbost, Senior Product Marketing Manager in Microbiology, Illumina

Before joining Illumina  as a Marketing Manager in 2012 Clotilde worked for 454 Sequencing and then Roche Diagnostics in several capacities from 2003 to 2012. Most recently she serves as a Marketing Manager specialized in Microbiology located at the Illumina Head Quarter in San Diego. Beginning as an Research scientist for Affymetrix, she spent many years in product development, it is only in the last 7 years that she has moved in a Marketing role and developed a special interest in microbiome and metagenomics as the field is changing and revolutionizing microbiology, sanitation and food production and evolution.

Devaki Bhaya, Principal Investigator, Carnegie Institution for Science

Research in Bhaya lab is driven by an interest in understanding how photosynthetic microorganisms perceive and evolve in response to environmental stressors, such as light, nutrients and viral attack.

Ami Bhatt, Assistant Professor of Medicine, Stanford University

The goal of Dr. Bhatt's research program is to understand the interplay between human genetics and the microbial environment in patients with hematological malignancies (leukemia and lymphoma).

Susan Holmes, Professor of Statistics, Stanford University

Dr. Holmes is interested in integrating the information provided by phylogenetic trees, community interaction graphs and metabolic networks with sequencing data and clinical covariates. Applications include interactions between the immune system and cancer, resilience in the human microbiome after antibiotic use and drug resistance in HIV.

Rituparna Mukhopadhyay, Research Scientist, California Department of Public Health 

Rituparna Mukhopadhyay is a Research Scientist at the Microbial Diseases Laboratory, California Department of Public Health.  The Microbial Diseases lab uses multiple sequencing platforms to investigate public health related outbreaks.  Her interest includes studying the evolution of virulence and drug resistant genes in bacterial population.  Rituparna received her Ph.D. in Molecular Genetics from Uppsala University, Sweden.  She has used microarrays, sequencing, and computational tools to investigate the interplay of genetic and epigenetic factors in normal human development and disease progression.  She did her postdoctoral research at Lawrence Berkeley National Laboratory and Albert Einstein College of Medicine.  She has also worked at Stanford on a project to build a big data analytical platform to leverage genomics information.

Julie Parsonnet, Professor of Infectious Diseases, and Health Research & Policy, Stanford University

Dr. Parsonnet laboratory's primary research interest is investigating the role of infectious agents in chronic diseases. Much of this work has revolved around Helicobacter pylori infection as a cause of adenocarcinomas and lymphomas of the stomach. Other chronic disease-infection links that the lab has been investigating include the roles of infectious agents in atherosclerosis, and in cancers of the gastrointestinal tract. Additionally the lab is working with other groups inside and outside Stanford to develop teaching tools for clinical investigation and for use in public health in developing countries.

Poster Session

Participants: 

1. Oren Kolodny (Stanford), Holobiome evolution: A computational model of microbiome assembly dynamics and community-level evolutionary change
2. Daniel Sprockett (Stanford), Microbiome Maturation in Tsimané Infants
3. Kris Sankaran (Stanford), Interactive Visualization of Microbial Dynamics
4. Paul Billing-Ross (Stanford), A cloud-based sequencing pipeline: bringing people and analyses to the data
5. Charlie Xia (Stanford), Integrated Metagenomic Data Analysis Identifies The Loss Of Oral Microbiota Diversity Is Strongly Associated With Periodontitis
6. Julia Fukuyama (Stanford), Graph-based testing for microbiome data
7. Maude David (Stanford), The Autism Microbiome Project: A crowdsourced study to assess the impact of the gut microbiome in Autism Spectrum Disorder
8. Lan Nguyen (Stanford), Comparison of popular differential abundance methods for analyzing microbiome data
9. Isaac Liao (Stanford), Loom Workflow Engine: collaboration through portable, shareable data analysis

Closing remarks

Ramesh Nair, PhD, Bioinformatics Manager, Stanford Center for Genomics and Personalized Medicine

As Bioinformatics Manager at Stanford Center for Genomics and Personalized Medicine (SCGPM), Ramesh is the bioinformatician in residence for the California Institute for Regenerative Medicine (CIRM) initiated Stem Cell Center of Excellence (CESCG). He is responsible for diverse bioinformatics needs for the Center Initiated Projects and its extensive collaboration network. He brings a diverse engineering and extensive scientific background to solve some of the biggest technical challenges in biotechnology.