academic article

• A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome.  PLoS Genetics.  6. 2010
• Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs.  BMC Genomics.  10:641. 2009
• Reliability and efficiency of algorithms for computing the significance of the Mann-Whitney test.  Computational Statistics.  24:605-622. 2009
• Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast.  BMC Bioinformatics.  9. 2008
• FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.  Bioinformatics.  24:577-578. 2008
• Factoring local sequence composition in motif significance analysis.  Genome Inform.  21:15-26. 2008
• GIMSAN: a Gibbs motif finder with significance analysis.  Bioinformatics.  24:2256-2257. 2008
• A conservative parametric approach to motif significance analysis.  Genome Inform.  19:61-72. 2007
• Correcting base-assignment errors in repeat regions of shotgun assembly.  IEEE/ACM Trans Comput Biol Bioinform.  4:54-64. 2007
• A fast and numerically robust method for exact multinomial goodness-of-fit test.  Journal of Computational and Graphical Statistics.  15:779-802. 2006
• Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.  Bioinformatics.  22. 2006
• Computing the P-value of the information content from an alignment of multiple sequences (vol 21, pg I311, 2005).  Bioinformatics.  21:3700-3700. 2005
• Designing seeds for similarity search in genomic DNA.  Journal of Computer and System Sciences.  70:342-363. 2005
• sFFT: A faster accurate computation of the p-value of the entropy score.  Journal of Computational Biology.  12:416-430. 2005
• A faster reliable algorithm to estimate the p-value of the multinomial llr statistic.  Algorithms in Bioinformatics, Proceedings.  3240:111-122. 2004
• On spaced seeds for similarity search.  Discrete Applied Mathematics.  138:253-263. 2004