Research
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Research in the lab focuses around concepts and computation. We study how life is organized, structured, and changes and how we can use theory, computational models and bioinformatics 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
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.
Mapping the molecular networks underlying stress response
In collaboration with the Phillips lab at the University of Oregon we are mapping and manipulating stress response pathways in nematode worms.
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.
Mapping the molecular networks underlying stress response
In collaboration with the Phillips lab at the University of Oregon we are mapping and manipulating stress response pathways in nematode worms.
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.
The Caenorhabdtis stress response pathway.
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Sex in evolution
Sexual reproduction increases genetic variation through recombination, and that single difference results in a broad array of consequences at genetic and phenotypic levels. The division into two separate sexes results in different reproductive modes, mating systems, patterns of sexual dimorphism and sexual selection. Evolutionary theory predicts that populations and genomes should evolve differently depending on reproductive strategy, but until recently we could not generate the data necessary to test these fundamental theoretical predictions. Advances in sequencing technology and computing power mean that it is now possible to answer these questions. We currently focus on the consequences that sex has for genetic and genomic evolution.
Reproductive mode and genomic evolution in Caenorhabditis
Nematode worms in the genus Caenorhabditis descended from an outcrossing ancestor (with separate males and females). Three species independently evolved self-fertile hermaphroditism and these species also have the smallest genomes. We are investigating the differences in genome size and structure, and addressing the genetic and genomic differences caused by self-fertility.
Reproductive mode and genomic evolution in Caenorhabditis
Nematode worms in the genus Caenorhabditis descended from an outcrossing ancestor (with separate males and females). Three species independently evolved self-fertile hermaphroditism and these species also have the smallest genomes. We are investigating the differences in genome size and structure, and addressing the genetic and genomic differences caused by self-fertility.
Despite > 40 million years of evolution the X chromosome shows a remarkable conservation of gene order between C. briggsae, C. elegans, and C. remanei.
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A neural network can learn to associate input with output by altering the weights connecting layers.
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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 reproductive mode 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 reproductive mode on horizontal gene transfer and developing methods to identify these sequences in eukaryotic genomes.
Collaborative work
Microbial biofuel production
In collaboration with the Liu lab at the University of Alabama we are using comparative genomics and computational modeling to engineer microbes for biofuel production.
In collaboration with the Liu lab at the University of Alabama we are using comparative genomics and computational modeling to engineer microbes for biofuel production.
Microbial metabolism in space
In collaboration with the Akob lab at the United States Geological Survey we are using comparative genomics to study microbial metabolism in oxygen-free environments.
In collaboration with the Akob lab at the United States Geological Survey we are using comparative genomics to study microbial metabolism in oxygen-free environments.
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?
