Definition and evolution of CpG islands (pdf, 2014-05)
A pair HMM for chained alignments (pdf, 2013-05)
Alignment sets: a fundamental unsolved problem? (html, 2012-11)
Counting k-mers by sorting (html, 2012-09)
Genome assembly by radix sort, with some thoughts on dealing with contained reads and transitive overlaps (pdf, 2012-09)
Applying hidden Markov models to uncertain (fastq) sequences (pdf, 2012-06)
Split alignment (pdf, 2012-04)
Pairwise sequence alignment and pair hidden Markov models (pdf, 2012-04)
Aligning a color sequence to a DNA sequence (pdf, 2010-12)