| James Bullard's Homepage |
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I am a recent graduate from the division of biostatistics at
UC Berkeley. I am currently employed at pacific biosciences. My research interests include: Statistical Software design
and implementation, High-throughput gene expression analysis,
and Model Selection, and Metagenomics.
A current resume can be found here. |
| Software | |
| DSA | The D/S/A is an algorithm for model selection. |
| affxparser | Affxparser is an R/Bioconductor parsing library for dealing with various Affymetrix file formats. |
| GenomeGraphs | GenomeGraphs is an R/Bioconductor package for plotting annotation and experimentally derived data along the genome. |
| panjo | panjo is a parallel implementation of the popular neighbor-joining algorithm using distributed memory. |
| Newick Parser | Newick parser is a fast C parser written using flex and bison |
| Genominator | Genominator is an R/Bioconductor package which facilitates analysis of data oriented along a chromosome. |
| Courses | |
| Fall-06 | Computational Methods For Biostatistics 240C You can also check out the wiki for the class at: wiki |
| Fall-08 | A Short Course on R and Bioconductor taught at the UNAM mexico website |
| Summer-08 | A Short Course on R and Statistics taught at Berkeley website |
| Summer-09 | A Short Course on R/Bioconductor for the Analysis of Next Generation Sequencing Data for the Conference on Computational and Systems Bioinformatics course download |
| Publications |
| Statistical Inference in mRNA-Seq: Exploratory Data Analysis and Differential Expression James H. Bullard, Elizabeth A. Purdom, Kasper D. Hansen, Steffen Durinck, and Sandrine Dudoit Working Paper 247, UC Berkeley Division of Biostatistics Working Paper Series, 2009 |
| GenomeGraphs: Integrated Genomic Data Visualization with R Steffen Durinck, James H. Bullard (joint first author), Paul T. Spellman, and Sandrine Dudoit BMC Bioinformatics, 2009 |
| Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species Albert Lee, Kasper D. Hansen, James H. Bullard (joint first author), Sandrine Dudoit, Gavin Sherlock PLoS Genetics, 2008 |
| aroma.affymetrix: A Generic Framework in R for Analyzing Small to Very Large Affymetrix Data Sets in Bounded Memory Henrik Bengtsson, Ken Simpson, James H. Bullard, Kasper D. Hansen Berkeley Statistics Technical Report, 2008 |
| Book review of "R Graphics" James H. Bullard, Journal of Statistical Software, 2007 |