Publications
2003. Dynamic querying for pattern identification in microarray and genomic data. 2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings. 3
2004. Gene synteny and evolution of genome architecture in trypanosomatids.. Mol Biochem Parasitol. 134(2):183-91.
2004. Schistosoma mansoni genome project: an update. Parasitology InternationalParasitology International. 53
2004. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic acids researchNucleic Acids Research. 32
2005. Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics (Oxford, England)Bioinformatics (Oxford, England). 21
2007. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic acids researchNucleic Acids Research. 35
2008. Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques. IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM '08.
2009. Inexact Local Alignment Search over Suffix Arrays. IEEE International Conference on Bioinformatics and Biomedicine, 2009. BIBM '09.
2009. A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.. Bioinformatics. 25(13):1609-16.
2010. MetaPhyler: Taxonomic profiling for metagenomic sequences. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
2010. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature reviews. GeneticsNature reviews. Genetics. 11
2012. Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC bioinformaticsBMC Bioinformatics. 13
2012. The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC bioinformaticsBMC Bioinformatics. 13
2014. Epiviz: interactive visual analytics for functional genomics data.. Nat Methods. 11(9):938-40.