Reverse Ecology:
Computational Integration of Genomes, Organisms, and Environments

IGERT faculty







Faculty

Linda Amaral-Zettler
Assoc. Research Scientist
Josephine Bay Paul Center
From the single-cell as a microcosm to complex microbial consortia that inhabit extreme environments on our planet, my research probes how microbial community structure is shaped by environmental factors and how such relationships might allow us to predict or perhaps influence change in the natural environment. This research spans the fields of microbial ecology, molecular ecology, molecular evolution, cell-physiology, phylogenetics, comparative molecular biology and biogeography. My research investigates the relationships between microbes and the mechanisms that determine their diversity, distribution, survival and impact on local and global processes.
Zoe Cardon, coPI
Senior Scientist
Ecosystems Center
MBL
We have three major, long-term projects active in the lab currently. Each links plants, soils, and microbes. Overall, we are driven to understand how biogeochemical cycles have dramatically affected, and been dramatically affected by, evolutionary changes in the anatomy and physiology of organisms on Earth, and by the ecological interplay of those organisms above- and below-ground in complex mutualisms, symbioses and food webs.
Hugh Ducklow
Senior Scientist
Director, Ecosystems Center
PI Antarctic LTER
MBL
I am a biological oceanographer and have been studying the dynamics of plankton foodwebs in estuaries, the coastal ocean and the open sea since 1980. My students and I have worked principally on microbial foodwebs and the role of heterotrophic bacteria in the marine carbon cycle. I have participated in oceanographic cruises in Chesapeake Bay, the western North Atlantic Ocean, the Bermuda and Hawaii Time Series stations, the Black Sea, the Arabian Sea, the Ross Sea, the Southern Ocean, the Equatorial Pacific and the Great Barrier Reef. Much of the work was done in the decade-long Joint Global Ocean Flux Study (JGOFS), which I led in the late 1990s. Currently I lead the Palmer Antarctica Long Term Ecological Research Project on the west Antarctic Peninsula, where we’re investigating the responses of the marine ecosystem to rapid climate warming. Although our research is primarily experimental and observational, we utilize mathematical models and collaborate with modelers to gain deeper understanding and derive maximum benefit from the data we collect. As part of our research on microbial processes we participated in the MIRADA Project. We deployed a new time-series sediment trap to measure carbon flux during the Amundsen Sea Polynya International Research Expedition (ASPIRE) starting in December 2010. Our lab performs all the nutrient and chlorophyll analyses for the Coalition for Buzzards Bay Baywatchers Program.
Casey Dunn
Assist. Prof.
Ecology & Evolutionary Biology; Molecular and Cellular Biology
Brown
The Dunn Lab investigates how evolution has produced a diversity of life. We primarily focus on form (i.e. morphology), and are interested in learning about both the actual history of life on Earth and general properties of evolution that have contributed to these historical patterns. The type of questions the Dunn Lab asks require field (mostly marine), laboratory, and computational work.
Erika Edwards, co-PI
Assist Prof.
Ecology and Evolutionary Biology
Brown
My lab is interested in all aspects of plant evolution and function, though we do gravitate toward plants living in arid environments.
Anne Giblin
Senior Scientist
Ecosystems Center, PI Plum Island LTER, co-I Arctic LTER
MBL
Julie Huber
Assist. Scientist
Josephine Bay Paul Center
MBL
Research Activities: Deep sea hydrothermal vents; Microbial diversity and oceanography; Astrobiology
Sorin Istrail, coPI
Professor
Director, Center for Computational Molecular Biology (CCMB)
Brown
Professor Sorin Istrail’s research focuses on computational molecular biology, medical informatics, statistical physics and complex systems, combinatorial algorithms, and computational complexity. The main projects in his Brown Lab are:
  • Genomic Regulatory Networks -- focusing on sea urchin developmental gene regulatory networks, building a high-resolution transcriptome map of the embryo, inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation
  • Computational Models of SNPs and Haplotypes -- dealing with HapMap-based analysis tools design for SNP selection, haplotype phasing, and genome-wide disease associations
  • Medical Bioinformatics -- with focus on comparative immunopeptidomics of humans and their pathogens, genetic determinants of sudden cardiac death and human-rabbit comparative genomics, computational support for pathology diagnosis of cancer
  • Building a programming language for genomics
  • Designing protein folding algorithms
  • Continuing John von Neumann's research program towards developing a new computational and information theory for biological systems
Chip Lawrence
Professor
Applied Math, CCMB, Molecular and Cellular Biology
Brown
Heather Leslie
Assist. Prof
Ecology & Evolutionary Biology, Environmental Studies
Brown
Prof. Leslie is interested in the ecological and social processes that link people and marine ecosystems, and how to more effectively integrate science into marine policy and management. Her research areas include coastal ecology, the design and evaluation of marine conservation and management strategies, and human-environment interactions.
David Rand, PI
Professor
Ecology & Evolutionary Biology; Molecular and Cellular Biology
Brown
Professor David Rand is interested in how natural selection acts on genes and genomes. One major focus of his research is how the mitochondrial genome and its interactions with the nuclear genome influence animal performance, evolutionary fitness, and aging. A second major interest is how thermal selection influences the genetic composition of populations. The goals of this work are to identify the genetic interactions that allow organisms to adapt to environmental heterogeneity.
Ben Raphael
Assist. Prof.
Computer Science, CCMB, Molecular and Cellular Biology
Brown
My research is at the interface between computer science, mathematics, and biology. I focus on developing and applying computational and mathematical methods to biological questions. Specific areas of interest are:
  • Cancer genomics, including algorithmic approaches to analyzing genomic alterations in cancer and reconstructing tumor genomes.
  • Comparative genomics, particularly analysis of genome rearrangements in evolution.
  • Biological sequence analysis, including problems in multiple sequence alignment, DNA motif finding, and human genetics.
Ed Rastetter
Senior Scientist
Ecosystems Center,co-I Arctic LTER
MBL
My research focuses on how ecosystems are regulated through the interactions among carbon, nutrient, energy, and water cycles and how this regulation maintains the life-support system of the Earth. The gatekeepers that undertake this regulation are the plants, animals, and microorganisms that make up ecosystems. These organisms themselves require carbon, nutrient, energy, and water from their environment in tightly constrained proportions and have evolved ways to balance their resource acquisition to meet their own metabolic needs. With many billions of organisms acting in concert, all acquiring carbon, nutrient, energy, and water from the environment in about the same proportions, the cycles of these resources become inextricably linked to one another. This tight linkage means that ecosystem responses to perturbations in one of the resource cycles are constrained by the dynamics of the other resource cycles and that perturbations will propagate from one resource cycle to all the others. I simulate these tightly coupled resource cycles using computer models and examine how ecosystems will respond to increasing carbon dioxide concentrations in the atmosphere, changes in rainfall patterns, increases in man-made fertilizer use, and global warming. My work both relies upon data collected from observational and experimental studies in the field and provides the theoretical foundation for new field studies to help unravel the mechanisms underlying the global life-support system.
Jeremy Rich
Assist. Prof.
Ecology & Evolutionary Biology, Center for Environmental Studies
Brown
Dr. Rich's research examines microbial communities and biogeochemical processes in aquatic environments, and specifically the microbial factors that influence nitrogen availability. His current position is Assistant Professor, Research in the Department of Ecology and Evolutionary Biology and the Center for Environmental Studies at Brown University. His research group focuses on microbial ecology and environmental microbiology, with current projects investigating anaerobic ammonium oxidation (anammox) and denitrification in estuarine and marine ecosystems. He teaches a course in Microbial Diversity and the Environment. Dr. Rich received his Ph.D. at Oregon State University in 2003 and postdoctoral work at Princeton University before coming to Brown. Dr. Rich grew up in Wisconsin, graduating from UW-Madison in 1996.
Dov Sax
Assist. Prof
Ecology & Evolutionary Biology
Brown
My interest in species invasions was sparked as an undergraduate at UC Berkeley, where I investigated the impacts of a non-native tree, Eucalyptus globulus, on native biodiversity. As a Ph.D. student with Jim Brown at the University of New Mexico, I examined the impacts of species invasions on plant diversity at local and global scales. As a postdoc at UC Santa Barbara, I explored how biodiversity has changed on oceanic islands around the world as a consequence of species invasions. I also helped to co-found the International Biogeography Society and edited two books, one on biogeography and the other on invasions. At Brown I am excited to continue my work on species invasions. I have also begun an investigation of the usefulness of several newly proposed conservation strategies that aim to reduce the number of species extinctions caused by global warming and rapid climate change.
Sheri Simmons
Assit. Scientist
Josephine Bay Paul Center
MBL
Sheri got her Ph.D. in Biological Oceanography down the road at the Woods Hole Oceanographic Institution in the MIT-WHOI Joint Programstudying marine magnetotactic bacteria with Katrina Edwards. She moved to UC Berkeley for a postdoctoral position with Jill Banfield studying microbes that grow in much less pleasant environments, but which are a fascinating model system for the use of "omic" methods to understand microbial ecology and evolution. She started up a new lab at the Bay Paul Center in December 2009 and is now focusing on using new microbial model systems to understand the interaction between microbial ecology and evolution. Sheri also has an appointment in the Department of Ecology and Evolutionary Biology at Brown University and can accept graduate students through the MBL-Brown Joint Program.
Mitchell Sogin, coPI
Senior Scientist
Director, Josephine Bay Paul Center
MBL
Research Activities: Molecular evolution of protists; Microbial diversity in extreme environments; Microbial oceanography.
Ivan Valiela
Senior Scientist
Ecosystems Center, co-I SIP LTER
MBL
Research areas: Function, structure and controls on coastal ecosystems, land-sea couplings, impacts of urbanization and deforestation on coastal ecosystems, management of coastal environments, international environmental policy
Joseph Vallino
Assist. Scientist
Ecosystems Center, co-I PIE LTER
MBL
My research emphasis concerns whole ecosystem chemistry associated with biological structure synthesis and energy utilization that underlies the development of living systems. Since the majority of metabolic diversity lies almost entirely within microorganisms, my investigations currently target microbial systems, which have the added benefit of fast characteristic timescales that can be studied in the laboratory. The question I am most concerned with is what governs the expression of metabolic function (such as photosynthesis, methanogenesis, nitrogen fixation, etc.) that is orchestrated by the entire microbial consortium? Are the rates of ecosystem metabolic reactions governed by just happenstance depending on which organisms are present, or is the overall chemistry of the system determined by fundamental principles? Current theories in non-equilibrium thermodynamics support the conjecture that systems organize to maximize entropy production (MEP). I am currently exploring whether MEP can be used to describe microbial biogeochemistry, using laboratory microcosms as experimental systems.
Dan Weinreich
Assist. Prof.
Ecology & Evolutionary Biology; Molecular and Cellular Biology
Brown
Professor Weinreich received his bachelor's degree in computer science from the University of Michigan in 1983. Computer science has a long tradition of interest in the algorithmics of Darwin's paradigm and this provides the formal framework for Weinreich's research. After nine years as a software engineer, he began his graduate studies in evolutionary and population genetics at Harvard University. He received his PhD in 1998 and did postdoctoral work at Brown University (1998-2000), the University of California (2000-2001) and at Harvard University (2001-2006). Professor Weinreich is interested in how genetic novelty fuels evolution by natural selection. Using tools from computer science and mathematics he models the evolutionary consequences of various patterns of interaction within the genome. This motivates complementary experimental work using techniques of molecular biology and microbiology to measure patterns of interaction within genes and genomes of bacteria and bacteriophage. This experimental work in turn drives novel theory.
David Mark Welch
Assoc. Scientist
Josephine Bay Paul Center
MBL
Research in the Mark Welch lab spans the mechanisms that govern the evolution of metazoans to the role of rare and unknown microbes in patterns of microbial diversity. We use molecular biology, population genetics, comparative genomics, and phylogenetics to explore the consequences of the long-term absence of meiosis on genome structure and the ecological and evolutionary dynamics of sex loss; to identify genes and biochemical processes involved in longevity and senescence; and to understand the role of the microbial rare biosphere in shaping ecosystem dynamics.