I am a theoretical biologist with a wide variety of interests, but my primary focus is the evolution and spread of infectious diseases, with a particular interest in human health. Diseases that the lab works on include HIV, syphilis, canine rabies, and Ebola. We use theoretical, statistical and computational approaches to understanding disease data, with a particular focus on methods that combine dynamical mechanism with statistical inference.

https://mac-theobio.github.io/dushoff.html

I am a theoretical biologist with a wide variety of interests, but my primary focus is the evolution and spread of infectious diseases, with a particular interest in human health. Diseases that the lab works on include HIV, syphilis, canine rabies, and Ebola. We use theoretical, statistical and computational approaches to understanding disease data, with a particular focus on methods that combine dynamical mechanism with statistical inference.

https://mac-theobio.github.io/dushoff.html

At one level, evolution is remarkably simple, with just a few concepts (mutation, recombination, random drift and natural selection) that underlie the overall process. Yet this description obscures many issues that make evolution a fascinating area for study. Evolution typically involves many genes and often revolves around interactions between individuals and their environments. Moreover, genes interact with one another and with the environment in a nonlinear fashion, resulting in complex phenotypes and evolutionary dynamics. My work aims to describe and analyze such interactions with experimental and quantitative rigor. Specifically work in my lab aims to address the fundamental question about the mechanistic basis of observed phenotypic variation. That is, how genetic (and environmental) variation modulate developmental processes and ultimately influence phenotypic outcomes. My research employs genetic and genomic approaches to address these issues, largely using Drosophila (fruit flies) as a model system. Most labs that work with Drosophila study either individual mutations of large effect (such as those that completely knock out a particular function) or subtle quantitative variation (rarely identifying specific genes). We employ both of these empirical approaches in conjunction with our genomic analyses to help relate our understanding from developmental genetics with the natural variation observed in populations.

At one level, evolution is remarkably simple, with just a few concepts (mutation, recombination, random drift and natural selection) that underlie the overall process. Yet this description obscures many issues that make evolution a fascinating area for study. Evolution typically involves many genes and often revolves around interactions between individuals and their environments. Moreover, genes interact with one another and with the environment in a nonlinear fashion, resulting in complex phenotypes and evolutionary dynamics. My work aims to describe and analyze such interactions with experimental and quantitative rigor. Specifically work in my lab aims to address the fundamental question about the mechanistic basis of observed phenotypic variation. That is, how genetic (and environmental) variation modulate developmental processes and ultimately influence phenotypic outcomes. My research employs genetic and genomic approaches to address these issues, largely using Drosophila (fruit flies) as a model system. Most labs that work with Drosophila study either individual mutations of large effect (such as those that completely knock out a particular function) or subtle quantitative variation (rarely identifying specific genes). We employ both of these empirical approaches in conjunction with our genomic analyses to help relate our understanding from developmental genetics with the natural variation observed in populations.

Development in multicellular bacteria; Regulation by small RNAs; Antibiotic production The goal of our research is to understand development and regulation in multicellular bacteria, using Streptomyces coelicolor as our model system. The streptomycetes are extremely important to the pharmaceutical industry as they make a large number of secondary metabolites having a profound medical benefit, including anti-cancer agents, immunosuppressants, and the majority of clinically useful antibiotics. They are also unusual in that they have a complex, multicellular life cycle and are capable of differentiating into distinct tissue types. Intriguingly, this differentiation process coincides with the production of secondary metabolites. One aspect of our research is focused on understanding the components necessary for differentiation, and centres on a novel family of proteins, termed the chaplins, that are essential for the transition from one differentiated state to another. We are also interested in the regulatory networks that control differentiation, metabolism, and environmental adaptation in S. coelicolor, and are focussing on a newly emerging, and universally important, class of regulators known as the small RNAs.

Development in multicellular bacteria; Regulation by small RNAs; Antibiotic production The goal of our research is to understand development and regulation in multicellular bacteria, using Streptomyces coelicolor as our model system. The streptomycetes are extremely important to the pharmaceutical industry as they make a large number of secondary metabolites having a profound medical benefit, including anti-cancer agents, immunosuppressants, and the majority of clinically useful antibiotics. They are also unusual in that they have a complex, multicellular life cycle and are capable of differentiating into distinct tissue types. Intriguingly, this differentiation process coincides with the production of secondary metabolites. One aspect of our research is focused on understanding the components necessary for differentiation, and centres on a novel family of proteins, termed the chaplins, that are essential for the transition from one differentiated state to another. We are also interested in the regulatory networks that control differentiation, metabolism, and environmental adaptation in S. coelicolor, and are focussing on a newly emerging, and universally important, class of regulators known as the small RNAs.

Evolutionary Genetics, Genomics, and Sex Chromosomes The Evans lab studies how natural selection, recombination, and demography influence genome evolution. One of the major themes of our work is to study speciation and gene duplication in African clawed frogs. This work aims to further understanding of the extent and mechanisms of biological diversification in this group, and to explore interesting genomic phenomena such as the evolution of sex chromosomes and transposable elements. Another focus of our efforts relates to the role of social systems on genome evolution. This work involves simulations of genome evolution under various social systems, and analysis of molecular polymorphisms from sex chromosomes, autosomal DNA, and mitochondrial DNA of cercopithecine monkeys.

Evolutionary Genetics, Genomics, and Sex Chromosomes The Evans lab studies how natural selection, recombination, and demography influence genome evolution. One of the major themes of our work is to study speciation and gene duplication in African clawed frogs. This work aims to further understanding of the extent and mechanisms of biological diversification in this group, and to explore interesting genomic phenomena such as the evolution of sex chromosomes and transposable elements. Another focus of our efforts relates to the role of social systems on genome evolution. This work involves simulations of genome evolution under various social systems, and analysis of molecular polymorphisms from sex chromosomes, autosomal DNA, and mitochondrial DNA of cercopithecine monkeys.

Our research in microbiology is focused on the soil bacterium Sinorhizobium meliloti that forms N2-fixing root nodules on leguminous plants. The genome of S. meliloti consists of a typical chromosome (3.6 Mb) and pSymA (1.35 Mb) and pSymB (1.68 Mb) replicons. We study genes and processes involved in the interaction of the bacteria with the plant and more generally process that are important for survival in a soil environment. A major current project is to define and manipulate the minimal genes that are necessary and sufficient for nodule formation and N2-fixation. In a key step to achieving a minimal symbiotic genome, we constructed a S. meliloti strain lacking 45% of its genome. In other work, we are studying genes and uptake systems that are regulated in response to phosphate limitation, and in a separate project a locus that confers resistance to bacterial viruses.

Our research in microbiology is focused on the soil bacterium Sinorhizobium meliloti that forms N2-fixing root nodules on leguminous plants. The genome of S. meliloti consists of a typical chromosome (3.6 Mb) and pSymA (1.35 Mb) and pSymB (1.68 Mb) replicons. We study genes and processes involved in the interaction of the bacteria with the plant and more generally process that are important for survival in a soil environment. A major current project is to define and manipulate the minimal genes that are necessary and sufficient for nodule formation and N2-fixation. In a key step to achieving a minimal symbiotic genome, we constructed a S. meliloti strain lacking 45% of its genome. In other work, we are studying genes and uptake systems that are regulated in response to phosphate limitation, and in a separate project a locus that confers resistance to bacterial viruses.

My group at McMaster University is interested in the area of molecular evolution, bioinformatics, and sequence analysis. Our research attempts to understand how the processes of evolution act to cause the changes observed between molecules, between genes and between genomes. The recent advances in molecular genetics are providing a storm of new data on DNA sequences, on gene structure and higher order genomic structure. However, the implications of these new data are not always clear. This area of scientific inquiry is inter-disciplinary between biology, computer science and mathematics. We make use of computer based analysis, statistical analysis and mathematical models to answer broad questions about the molecular biology of all organisms.

My group at McMaster University is interested in the area of molecular evolution, bioinformatics, and sequence analysis. Our research attempts to understand how the processes of evolution act to cause the changes observed between molecules, between genes and between genomes. The recent advances in molecular genetics are providing a storm of new data on DNA sequences, on gene structure and higher order genomic structure. However, the implications of these new data are not always clear. This area of scientific inquiry is inter-disciplinary between biology, computer science and mathematics. We make use of computer based analysis, statistical analysis and mathematical models to answer broad questions about the molecular biology of all organisms.

We study gene regulation and physiological adaptation in E. coli and other bacteria to better understand how bacteria cause disease and persist in the environment. We also have many collaborative projects with biochemists, engineers, industry and government agencies to develop new tools for monitoring water quality and understanding waste treatment processes from a microbiological perspective. We are using new DNA sequencing technology and bioinformatics analysis tools to track microorganisms, characterize composition of complex microbial communities and conduct comprehensive studies of gene expression.

We study gene regulation and physiological adaptation in E. coli and other bacteria to better understand how bacteria cause disease and persist in the environment. We also have many collaborative projects with biochemists, engineers, industry and government agencies to develop new tools for monitoring water quality and understanding waste treatment processes from a microbiological perspective. We are using new DNA sequencing technology and bioinformatics analysis tools to track microorganisms, characterize composition of complex microbial communities and conduct comprehensive studies of gene expression.

Astro-, Computational, Developmental, and Evolutionary biology (with smattering from Ecology and Physiology); Viruses to elephants, including human menopause and especially gastropods, echinoids, and water bears (oh my).

Astro-, Computational, Developmental, and Evolutionary biology (with smattering from Ecology and Physiology); Viruses to elephants, including human menopause and especially gastropods, echinoids, and water bears (oh my).

We study an extremophyte, Eutrema salsugineum, a plant closely related to Arabidopsis thaliana but one far more tolerant of extremes in temperature, water deficits, soil salinity, and nutrient deficiencies. We use comparative genomics, physiology, and biochemical approaches to identify traits that allow E. salsugineum to thrive under extreme environmental conditions. Our approach involves comparing plants collected in the challenging field conditions of its native habitat in the Yukon, Canada, with plants subjected to controlled stress treatments in growth cabinets. Identifying stress tolerance traits will enable us to improve our crop species and help us stabilize yields that are already adversely impacted by climate change.

We study an extremophyte, Eutrema salsugineum, a plant closely related to Arabidopsis thaliana but one far more tolerant of extremes in temperature, water deficits, soil salinity, and nutrient deficiencies. We use comparative genomics, physiology, and biochemical approaches to identify traits that allow E. salsugineum to thrive under extreme environmental conditions. Our approach involves comparing plants collected in the challenging field conditions of its native habitat in the Yukon, Canada, with plants subjected to controlled stress treatments in growth cabinets. Identifying stress tolerance traits will enable us to improve our crop species and help us stabilize yields that are already adversely impacted by climate change.