Research in my laboratory involves identification of the genetic basis of behavioral and psychiatric disorders. To complement ongoing efforts in human psychiatric genetics, my laboratory embarked over the last several years on two main projects: a screen for novel behavioral mutations in the mouse and the functional annotation of the mammalian genome using bioinformatics approaches. We are now less involved in studies of behavioral traits in the mouse and main projects in the laboratory involve human genetic studies of neurodevelopmental and psychiatric disorders.
"GenGen is a suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.
Some of the most useful and more stable programs in this package are:
• calculate_association.pl: perform genome-wide association analysis for cohorts with case-control design and trio design, with ability to handle PLINK-formatted TPED/TFAM files and handle phenotype permutations.
• calculate_gsea.pl, combine_gsea.pl: use pathway-based approaches to test the significane of genes within a pathway for genome-wide association studies (see reference below).
• scan_region.pl: scan two sets of genomic regions to find overlap (for example, scan most conserved genomic elements, scan transcription factor binding sites, scan segmental duplication regions, scan predicted microRNA sites, scan pseudogenes, scan EvoFold regions, etc.
• convert_mach.pl, convert_mach2snptest.pl, combine_snptest.pl: convert MACH-imputed genotype data sets into standard PED/MAP format or SNPTEST format for subsequent association test.
• convert_bim_allele.pl: convert SNP allele coding between Illumina A/B alleles, Illumina 1/2 alleles, Illumina TOP strand alleles and dbSNP forward strand alleles.
• retrieve_ensembl.pl, retrieve_variation.pl, retrieve_compara.pl: query the Ensembl databases to get the desired information on genes, transcripts, variations, cross-references, domains, predicted regulatory elements and so on."