Robert K. Bradley

Here's my contact info:

• Email: rbradley@no.spam.berkeley.edu (remove the 'no.spam.')
• Lab: 381 Stanley Hall, UC Berkeley, CA
• Lab phone: (510) 666 - 2791

I'm affiliated with the Biophysics Graduate Group and the Computational Biology Graduate Group.

Here's my NIH biosketch.

Research Interests

Current research projects include:

1. De novo prediction of ncRNAs from comparative genomic data, and particularly the Drosophila 12fly data. Analysis of large-scale genomic datasets. Not just flies; to be used for multiple organisms for modENCODE.
   • Twelve Fly Screen Predictions
2. RNA multiple alignment. Sensitive and specific.
   • Stemloc-AMA
3. Ancestral inference on multiple homologous ncRNAs (using the methods of structural alignment, or simultaneous sequence alignment and structure prediction). In-depth analysis of single ncRNA families. Statistical alignment for structured RNAs.
   • my poster from RECOMB 2007)
4. The transducer framework for statistical alignment.
   • Transducer Composition
5. Simulating the evolution of syntenic blocks of the genome.
   • SIMGENOME

I've also worked on:

• Pseudogene classification and ancestral inference with a probabilistic evolutionary model (a phylogenetic tree-like graphical model with hidden states, if you must know).
• Evolutionary rate measurements in stems and loops of ncRNAs predicted in the 12fly data (see AAA and the 12fly Nature paper).
• Visualization of rate matrices of Markov chains for interpreting phylo-grammar evolutionary models (see Bubble Plots).

Publications

In prep:

1. Varadarajan A, Bradley RK, Holmes I. "SIMGENOME: Trainable transducers and flexible phylo-grammars for simulating evolution." In prep.

Submitted:

1. Bradley RK, Pachter L, Holmes I. "Specific Alignment of Structured RNA: Stochastic Grammars and Sequence Annealing." Submitted.
2. Bradley RK, Uzilov AK, Skinner M, Bendana YR, Varadarajan A, Holmes I. "Non-Coding RNA Gene Predictors in Drosophila." Submitted.
3. Varadarajan A, Bradley RK, Holmes I. "Pinpointing Ancestral Pseudogenes Reveals Independent Parallel Gene Losses." Submitted.

Published:

1. Clark AG et al.  Evolution of genes and genomes on the Drosophila phylogeny.  Nature. 2007 Nov 8;450(7167):203-218.
2. Bradley RK, Holmes I.  Transducers: An Emerging Probabilistic Framework for Modeling Indels on Trees.  Bioinformatics. 2007 Sep 5;. (pdf)
3. Klosterman PS, Uzilov AV, Bendana YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.  XRate: a fast prototyping, training and annotation tool for phylo-grammars.  BMC Bioinformatics. 2006 Oct 3;7:428. (main paper, pdf) (supplement, pdf)

And from my days in high-energy physics:

1. S. Gubser and R. Bradley. “Degenerate eigenvalues for Hamiltonians with no obvious symmetries.” Adv. Theor. Math. Physics. Vol 9, 2005. (pdf)
2. R. Bradley. “Search for Superjets using the D0 detector at the Tevatron.” APS April 2003 meeting (Philadelphia). Session U13: “Physics Beyond the Standard Model.”

About Me

My brother works on structure learning in graphical models at Carnegie Mellon. You can check out his webpage.

Links and all that

Apropos of nothing, computer-related stuff which I like or find useful:

• Rex Swain's Perl5 Guide
• Perl one-liners: One-liners 101 and 102
• GNU gnuplot, make, screen, m4 and bc (increasing order of obscurity)
• changing my Mac OS X key bindings to make them emacs-ified
• attempting to change my Firefox key bindings to make them emacs-ified (your mileage may vary)
• reading about OS X: What is Mac OS X?
• LaTeX Tips
• R for statistics

I have a (short) page of random computer notes here at Robert Bradley Notes.

Here are some miscellaneous useful bio tools:

• Sequence formats
• EMBL user manual
• DOTLET
• Tools for multiple alignments
• Translate DNA->AA
• ATV
• Phylodendron