Summer 2021 g2p2pop Workshop
Accessing High-Throughput Genomic Approaches
Broad Institute in Cambridge, Massachusetts
This 2.5 day workshop will feature talks from experts who are using genomics to address questions in physiology, ecology, and evolution, a tour of the Broad sequencing facilities, lightning talks by workshop participants, and a series of breakout sessions. We hope you will be able to join us!
The 2021 g2p2pop workshop will introduce participants to
- Next-generation sequencing technologies.
- Software packages for genomic data analysis.
- Methods for inferring microevolutionary processes and mapping of organismal phenotypes to genomic locations.
- Genomics-based study designs that can address questions across biological scales.
Our Summer 2021 workshop will be held at the Broad Institute of MIT and Harvard in Cambridge, Massachusetts. The Broad Institute is a world leader in sequencing, bioinformatics, and other genomics technologies. Through a focus on integrative, multidisciplinary collaborations, Broad researchers are producing key insights into evolutionary processes and the biological basis of organismal phenotypes.
At the g2p2pop workshop, experts from Broad and nearby academic centers will discuss their work, highlighting the power of genomic data and analyses to address questions at biological scales ranging from individual to population. Speakers will describe key considerations in choosing among various next-generation sequencing options. Participants will learn about genomics- and modeling-based based approaches to study microevolutionary processes through both presentations by invited speakers and active discussions of their own research. There will be particular attention to strategies for mapping phenotypes to specific genomic locations, identifying evidence of positive and purifying selection, and understanding how genetic drift interfaces with biogeography to shape an evolutionary landscape.
“Modeling Mechanism of Phenotypic Plasticity and Epigenetics,” Summer 2022, Las Vegas, NV Accordion Closed
Specific workshop goals:
- Primer on phenotypic plasticity.
- Primer on mechanisms of gene regulation.
- Technologies to study gene regulation in vitro and in silico.
- Consider biotic and abiotic environmental signals that impact genomic regulation and phenotypic plasticity.
- Address timescale: phenotypic plasticity and genomic regulation in the contexts of short-term disturbance versus long-term change.
The University of Nevada Las Vegas is home to excellent biogeography resources, a supercomputing institute, next generation sequencing capability, and the Nevada Institute of Personalized Medicine. The aims of this workshop will be to discuss mechanisms by which the environment can affect phenotypic plasticity as well as an organism’s genome and gene expression over a range of timescales, and how these changes have the potential to propagate through generations.
Participants will be exposed to discovery-driven and hypothesis-based techniques for investigating gene regulatory mechanisms. We will also focus discussion on what phenotypic plasticity can reveal about the limits and responses available to individuals, and what individual features will be necessary to factor into integrative models of whole population processes.
“Synthesizing g2p2pop,” Summer 2023, Brazil Accordion Closed
Specific workshop goals:
- Synthesize concepts, ideas and practices developed over the course of the RCN.
- Plan for continued collaborations and funding opportunities in the interdisciplinary realm of genomes to phenomes to populations in a changing world.
Biologists currently and into the future must deal with complex datasets that vary in spatial and temporal scales. Understanding biological function from genomes to populations and predicting resiliencies and vulnerabilities to climate change will entail integrating knowledge across systems and using mathematical approaches. The final workshop will serve to synthesize and evaluate the concepts, ideas and practices that were developed over the years of RCN activities. Participants will finalize curriculum modules that were developed and tested in the CCSD such that they are ready to distribute as a package. A team will be selected to write a synthesis paper for publication that highlights the findings of the RCN and provides future directions for continued research. Participants will brainstorm and document a plan for continued and new collaborative opportunities in the arena of understanding genomes to phenomes to populations research.
PAST WORKSHOP: “Navigating Climate Change,” September 19-21, 2018, Flagstaff, AZ Accordion Closed
View videos of our featured speakers’ presentations here!
Day 1 of the workshop will include lectures from Featured Speakers such as Dr. Scott Goetz, Dr. Andrew Richardson, Dr. Tom Whitham, Dr. Stephen Jackson, and more! Panel discussions, question and answer sessions, and networking make this a great event for faculty, postdoctoral scholars, undergrad and grad students, and those interested in climate change.
Specific workshop goals:
- Identify climate change resources that biologists and modelers can access.
- Synthesize predictions for abiotic drivers in global climate change models.
- Identify predictions for abiotic drivers in specific regions in climate change models.
- Discuss how abiotic drivers impact different levels in the genome-population hierarchy.
- Generate strategies, priorities and substantive goals for RCN research exchanges.
The first workshop will be foundational and will function to educate RCN members in what to expect of the abiotic drivers under various climate change scenarios and by region. It is evident that the results of climate change induced by anthropogenic greenhouse gases is far more complicated than an increase in average global temperature. Often, climate change manifests in ways that were not initially intuitive. For example, under current climate change, much of the planet is experiencing an advancement of spring-like conditions, whereas the Arctic is experiencing a delayed spring due to increased precipitation that comes in the form of late spring snowfall events. Similarly, winters in the Northern Hemisphere mid-latitudes have, since the late 1980’s, grown more severe due to ‘Arctic amplification’ despite a strong trend in global climate warming over the same time-period. And globally, increased atmospheric CO2, precipitation (regionally), and changes in land cover (e.g., retreat of icefields and glaciers) have resulted in ‘global greening.’ Thus, understanding the vulnerability and resilience of species requires knowledge of environmental drivers and processes and dynamics across space and time; many biologists and modelers lack this foundational knowledge of climate change.
PAST WORKSHOP: “Modeling from Genomes to Phenomes to Populations,” July 17-19, 2019, Minneapolis, MN Accordion Closed
Location: Bruininks Hall, University of Minnesota, Minneapolis, MN
Specific workshop goals:
- Mechanistic modeling of biological systems – from theory to prediction.
- Getting acquainted with existing approaches to model biological systems – model types and complexities.
- Translating biological challenges into models – learning how to speak the same language.
- Generate/discuss goals for research exchanges.
The aims of the modeling workshop will be to familiarize participants with the field of biological modeling for basic and applied research. Mathematical modeling has been a major part of ecology where it propelled the development of theory on population and community dynamics. With the increase in computing power and speed, simulation modeling has become an important tool in biology. Modeling for management and decision-making benefits immensely from following the rules of good modeling practice and the modeling cycle. Participants in this workshop will become familiar with simple and more complex approaches to model biological systems, from genomes to populations. As they are built for specific purposes, model complexities can vary immensely, and part of the workshop will be dedicated to understanding how to balance the need for simplicity with required detail for system-specific models. This workshop will also address the rules of good modeling practice and focus on documenting each step of the modeling cycle to further increase information flow and transparency of the modeling process. Participants in this workshop will have the opportunity to directly interact with experts in modeling biological systems at different scales. This will allow for focused discussions on available data sets, questions, hypotheses, and potential modeling efforts.
We are happy to introduce three confirmed keynote speakers at the workshop:
Valery Forbes, Dean of College of Biological Sciences, University of Minnesota
Keynote Title: “Extrapolating across levels of biological organization and how mechanistic models can help”
Prof. Forbes’ research focuses on understanding how responses to environmental stress links across levels of biological organization – from molecular to ecosystem level. Her group is developing and applying ecological modeling approaches to look at stressor impacts on terrestrial plants, aquatic invertebrates, and fish.
For more information: https://cbs.umn.edu/forbes-lab/
Jonathan Karr, Assistant professor in Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai
Keynote Title: “Systemizing and scaling whole-cell computational models of individual cells”
Prof. Karr’s research in computational systems biology focuses on developing “whole-cell” dynamical models that predict the phenotype of individual cells from their genotype by representing all of the biochemical activity inside cells. To enable comprehensive whole-cell models, his group is also developing the computational methods and software tools needed to build, simulate, and apply whole-cell models to medicine and bioengineering.
For more information: https://www.karrlab.org/
John DeLong, Associate professor in Ecology, Evolution, and Behavior, University of Nebraska-Lincoln
Keynote Title: “Climate change and scaling up across levels with evolution”
Prof. DeLong’s research focuses on ecological and evolutionary energetics, specifically on the role of energy use and how it facilitates evolution and ecological processes. Active areas of research include integrating classic ecological modeling approaches with macroecology, evolution of body size, and the role of metabolic energy use on the evolution of human life histories.
For more information: http://johnpauldelong.weebly.com/
Specific networking activities and outcomes
Most future transformative discoveries will require synergies across scientific disciplines. Thus, the overarching goal of our RCN is to facilitate, refine and diversify scientific discourse among empirical biologists and modelers with expertise that spans from genomes to populations. We anticipate that the RCN will create the pivotal linkages among the multiple disciplines of biology and mathematics such that collaborations will form naturally and result in bidirectional interplay between theory and experimentation to develop unified mechanistic models of genomes to phenomes to populations.
- Workshops: Five workshops (one per year) will be organized to facilitate face-to-face discussion and education among the RCN participants. The workshops will be topical but the participant list will comprise modelers and biologists across levels of biological organization. Common activities at each workshop, irrespective of the topic, include:
- Education. Each workshop will begin with ½ day of interactive lecture by 2-3 ‘experts’ within the topic area. This will ensure scientific grounding of the diverse group of participants as well as a standardization of use of terminology.
- Discussion of modeling approaches, limitations and opportunities within and across levels of biological organization.
- Communication of new techniques and approaches to generation of biological data and modeling.
- Cross-fertilization of ideas across taxa and levels of biological organization.
- Plan for new collaborations and funding opportunities in the interdisciplinary realm of genomes to phenomes to populations in a changing world.