@article{camara_topological_2016, abstract = {Meiotic recombination is a fundamental evolutionary process driving diversity in eukaryotes. In mammals, recombination is known to occur preferentially at specific genomic regions. Using topological data analysis ({TDA}), a branch of applied topology that extracts global features from large data sets, we developed an efficient method for mapping recombination at fine scales. When compared to standard linkage-based methods, {TDA} can deal with a larger number of {SNPs} and genomes without incurring prohibitive computational costs. We applied {TDA} to 1,000 Genomes Project data and constructed high-resolution whole-genome recombination maps of seven human populations. Our analysis shows that recombination is generally under-represented within transcription start sites. However, the binding sites of specific transcription factors are enriched for sites of recombination. These include transcription factors that regulate the expression of meiosis- and gametogenesis-specific genes, cell cycle progression, and differentiation blockage. Additionally, our analysis identifies an enrichment for sites of recombination at repeat-derived loci matched by piwi-interacting {RNAs}.}, author = {Camara, Pablo G. and Rosenbloom, Daniel I. S. and Emmett, Kevin J. and Levine, Arnold J. and Rabadan, Raul}, date = {2016-07}, doi = {10.1016/j.cels.2016.05.008}, issn = {2405-4712}, journaltitle = {Cell Systems}, keywords = {1 - Cell recombination, 1 - Chromosome mapping, 1 - Genetic linkage, 1 - Genetic recombination, 1 - Genetics, 1 - Meiosis, 2 - Persistent homology, 3 - Genomes}, number = {1}, pages = {83--94}, pmcid = {PMC4965322}, pmid = {27345159}, shortjournal = {Cell Syst}, title = {Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination}, volume = {3} }