James Bullard's Homepage
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.

  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.

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

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