Research
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Research in our lab is broad but focuses around using a systems approach to studying evolution of the genome in different organisms. We study how life is organized, structured, and changes and how we can use theory, computational models and bioinformatic analyses to understand it.
I am an evolutionary biologist and much of my work investigates the influence of sex on genetic and genomic evolution. Students in the lab pursue their own research interests including field, wet lab and computational projects. |
Current Projects
Genome evolution in nematode worms
Nematode worms descended from a dioecious ancestor (with separate males and females) and multiple species in this group have evolved androdioecy (populations with males and self-fertile hermaphrodites). Some species are trioecious with females, males and self-fertile hermaphrodites in the population. In the genus Oscheius we think that the worms evolved androdioecy and some species secondarily re-evolved dioecy. We know that in Caenorhabditis androdioecious species have the smallest genomes. Why does losing sex shrink your genome? In order to answer this question we are assembling genome sequences for dioecious and androdioecious species and studying the differences between them.
Nematodes in the class Chromadorea display diverse mating systems with multiple transitions between dioecy, androdioecy and trioecy.
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The genomic architecture of inbreeding in nematode worms
Dioecious nematodes can be turned into sperm-producing females with just two mutations but in most species these populations would quickly collapse due to severe inbreeding depression. Which genes cause inbreeding depression and how did androdioecious species get past this inbreeding threshold? Graduate student Paula Adams is investigating this with whole genome sequencing data in C. remanei.
Network evolution
One of the central goals of biology is to understand how changes at a genetic level translate into phenotypic differences. Regulatory interactions, molecular networks, and system dynamics determine this relationship and understanding gene networks is a major focus of our research.
Studying genetic networks
We use a combination of empirical data and mathematical modeling to study the design principles that underlay the structure and function of genetic networks. For example, we know that theoretical networks can show a wide variance in system-level properties including robustness to mutation and ability to adapt to new environments. Currently mathematical techniques are used to infer networks from empirical data. How do the system-level properties of the underlying network affect our ability to infer its structure from data? We are simulating genetic networks and using established inference methods to address this question.
Studying genetic networks
We use a combination of empirical data and mathematical modeling to study the design principles that underlay the structure and function of genetic networks. For example, we know that theoretical networks can show a wide variance in system-level properties including robustness to mutation and ability to adapt to new environments. Currently mathematical techniques are used to infer networks from empirical data. How do the system-level properties of the underlying network affect our ability to infer its structure from data? We are simulating genetic networks and using established inference methods to address this question.
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Evolution of acetylene metabolism
Acetylene in the environment today is primarily from anthropogenic sources but on Earth it was abundant during the pre-Cambrian era. Some microbes can transform acetylene for energy in oxygen-free environments; is it possible that acetylene could have formed the basis of a primordial food web? Acetylene is currently found in higher concentrations in space including on Titan and Enceladus, the moons of Saturn; could acetylene support extraterrestrial life? In collaboration with the Akob lab at the United States Geological Survey graduate student John Sutton is using comparative genomics to study the genomic basis of acetylene metabolism.
Methods development
Machine learning for computational genomics
The one common factor in genomic studies is a flood of data. We are developing machine learning methods for pattern recognition in these massive datasets. Our current focus is on developing methods to robustly identify contamination in de novo genome assemblies.
The one common factor in genomic studies is a flood of data. We are developing machine learning methods for pattern recognition in these massive datasets. Our current focus is on developing methods to robustly identify contamination in de novo genome assemblies.
Finding horizontally transferred sequences
Horizontal or lateral gene transfer occurs when genetic material moves between unrelated organisms. We are interested in the influence of mating system on horizontal gene transfer and developing methods to identify these sequences in eukaryotic genomes.
Horizontal or lateral gene transfer occurs when genetic material moves between unrelated organisms. We are interested in the influence of mating system on horizontal gene transfer and developing methods to identify these sequences in eukaryotic genomes.
Undirected interests
We don't currently have projects going in these areas, but we love to talk about these ideas!
- The role of technology in scientific innovation
- Mathematical models as biological technology
- Measurement theory: What do we measure, why, and how should we do it? How do we describe evolutionary quantities like phenotypes, morphology, selection, and inheritance in a portable and dimensionless way?
- Measuring complex networks: Currently, everything we can measure about a network has little biological or evolutionary significance and everything we think is significant can't actually be measured. How can we develop meaningful network measures?
- What can we learn from other fields: Have people addressed these questions in other disciplines, or used methods that we can also use?
- How do we teach evolution, computing, bioinformatics, and biology to students- what is the role of an instructor and mentor?
