I like coffee.
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1067 Evans Hall
Department of Mathematics
University of California, Berkeley
Berkeley, CA 94720-3840
(510) 642-2149
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Research
I'm a postdoc in the groups of Lior Pachter and Mike Eisen.
I am broadly interested in using ideas from machine learning to analyze biological sequence data.
Recently I've worked on the alignment problem, which is central to comparative genomics
and has nice connections to posets
and probabilistic models.
I also study the evolution of the anterior-posterior patterning network in Drosophila with comparative ChIP-Seq data.
I did my Ph.D. work on the structural evolution of non-coding RNAs in the group of Ian Holmes.
Software
FSA: Multiple alignment of proteins, RNA and DNA.
Stemloc-AMA: Multiple alignment of RNA using structural information.
Indiegram: Reconstruction of ancestral RNA structures.
Publications
Submitted:
Published:
- Bradley RK, Holmes I (2009) Evolutionary triplet models of structured RNA. PLoS Computational Biology. 5(8):e1000483.
- Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009) Fast Statistical Alignment. PLoS Computational Biology. 5:e1000392.
- Varadarajan A, Bradley RK, Holmes I (2008) Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biology. 9:R147.
- Bradley RK, Pachter L, Holmes I (2008) Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics. 24:2677-2683.
- Clark AG, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218.
- Bradley RK, Holmes I (2007) Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics 23:3258-3262.
- Klosterman PS, Uzilov AV, Bendana YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I (2006)
XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics. 7:428.
And from my days in theoretical physics:
Miscellaneous
Computer stuff
About me