Publications

Closely spaced clusters of tandemly duplicated genes (CTDGs) contribute to the diversity of many phenotypes, including chemosensation, snake venom, and animal body plans. CTDGs have traditionally been identified subjectively as genomic neighborhoods containing several gene duplicates in close proximity; however, CTDGs are often highly variable with respect to gene number, intergenic distance, and synteny. This lack of formal definition hampers the study of CTDG evolutionary dynamics and the discovery of novel CTDGs in the exponentially growing body of genomic data. To address this gap, we developed a novel homology-based algorithm, CTDGFinder, which formalizes and automates the identification of CTDGs by examining the physical distribution of individual members of families of duplicated genes across chromosomes.

Clusters of duplicated genes (CTDGs) are great contributors to the diversity exhibited by many phenotypes, like snake venom, animal body plans, and olfaction. To systematically study CTDGs, we developed CTDGFinder, a homology-based algorithm that statistically takes into account the size and spacing of duplicate gene locations in a genome, and has been shown to identify several well-known mammalian CTDGs (e.g., the Hox, globin, and protocadherin CTDGs). We found that more than 20% of human genes belong to CTDGs and that CTDGs span 7% of the total length of the human genome.

The genome, that wonderful land. We, humble explorers, have cataloged many genes, many hills. Even more, as we mapped genes in different genomes, we discovered that many genes come in clusters of duplicated genes! Those mountain ranges, spanning large sections of our genomes, provide a lush environment for diverse phenotypes: olfaction, immunity, and body plan architecture are just some examples.

Juan Felipe Ortiz, Antonis Rokas

Johana Carolina Soto, Juan Felipe Ortiz, Laura Perlaza-Jiménez, Andrea Ximena Vásquez, Luis Augusto Becerra Lopez-Lavalle, Boby Mathew, Jens Léon, Adriana Jimena Bernal, Agim Ballvora & Camilo Ernesto López

Luis Guillermo Leal, Alvaro Perez, Andres Quintero, Angela Bayona, Juan Felipe Ortiz, Anju Gangadharan, David MacKey, Camilo Lopez, Liliana Lopez-Kleine

Mario Arrieta-Ortiz [42 more including Ortiz, J. F.] Adriana Bernal

Kacy Richmond, Patrick Masterson, Juan Felipe Ortiz, Jessica Siltberg-Liberles

Juan Felipe Ortiz, Madolyn L. MacDonald, Patrick Masterson, Vladimir N. Uversky, Jessica Siltberg-Liberles

Juan Felipe Ortiz, Brigitte Gavio