about
My name is Brant Faircloth, and I'm an assistant researcher (aka asst. research scientist outside of the UC) within the Dept. of Ecology and Evolutionary Biology at UCLA. My research focuses on developing and expanding genome-scale techniques to non-model organisms and efficiently distributing the depth of sequencing reads to answer questions, between individuals within populations, of ecological or evolutionary significance. Of particular interest to me are questions involving the genotypes that influence phenotypes under strong selection - those genetic factors affecting individual survival and reproduction. Generally speaking, I work at the nexus of field and molecular biology, parallel and distributed computational analyses, bioinformatics, genetics (few genes), and genomics (many/all genes).
Within the department, I work with Patty Gowaty, Steve Hubbell, and Michael Alfaro. My work with Patty involves investigating environmental, social, and random effects on multiple mating in eastern bluebirds (Sialia sialis) and Drosophila sp. (D. melanogaster, D. pseudoobscura and D. hydei, and my work with Steve uses molecular tools (pcr, metagenomics, and second-generation DNA sequencing) to help understand the diversity and distribution of tree species in tropical forests. My work with Mike uses genomic tools to resolve the phylogeny of fishes.
Outside UCLA, my collaborators include Travis Glenn, Robb Brumfield, Greg Gilbert, Megan Saunders, John McCormack, Bill Palmer, and John Carroll.
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academic interests
- development of genome-scale, molecular techniques
- non-model organism genomics
- mating systems and mating behavior
- immunogenetics and mate choice
- social behavior
- computer programming
- field biology
- radio-telemetry
current vita
blog
Here are some recent blog posts. See the archive for older posts.
- 05 Nov 2011 » Python multiprocessing - multiple producers, single consumer
- 02 Jul 2011 » (Relatively) Easily get coverage for velvet assemblies
- 09 Apr 2011 » beast in the cloud
- 11 Feb 2011 » 454 assembly on ec2
- 29 Jan 2011 » Getting taxonomy information from NCBI
Software projects
I'm interested in the use of computational techniques to solve problems in ecology, evolution, and genomics - from the mundane to the complex. Here are several software projects I have started or to which I contribute. You can find the source code for most of these projects (and several others) at brantfaircloth@github.
- msatcommander: msatcommander is a GUI program to locate microsatellite repeats and automatically design tagged PCR primers. msatcommander is suited to data-sets both large (thousand of DNA reads) and small (tens of DNA reads), is relatively fast, and replaces the time consuming step of hand-designing microsatellite PCR primers. Source code for msatcommander is available on github.
- gmconvert: gmconvert is a small program that converts output files from Applied Biosystems Genemapper output format (row-by-row) to more useful CSV (column-by-column).
- primer3: primer3 is a program for designing PCR primers from DNA sequence.
- demuxipy: demuxipy is a program for the parsing, error-correcting, and tracking DNA reads identified using molecular sequence tags. linker-py differs from other such programs in its use of fuzzy-string matching and multiprocessing.
- edittag: edittag is a program for the design and application of sequence tags to sequencing adapters and PCR primers.
Several other software packages are available at github.
lab protocols
I'm also interested in techniques development, as any number of advances in biology can be directly traced to the development of new techniques to address the problem at hand. I also work with a number of researchers at other universities on developing molecular methods and protocols to carry out those methods.
We maintain a number of protocols and other useful information at baddna@github. From time to time, you can also find methods/protcols in which I'm currently interested listed below.