19 papers · ranked by Valyu relevance
Yanhui Hu, Ben Ewen-Campen, Aram Comjean, Jonathan Rodiger + 2 more
Paralogs are genes which arose via gene duplication, and when such paralogs retain overlapping or redundant function, this poses a challenge to functional genetics research. Recent technological advancements have made it possible to systematically probe gene function for redundant genes using dual or multiplex gene…
Yibo Si, Kshitiz Adhikari, Laura E. Herring, Daniel Isom + 6 more
Paralogs engage in biological processes through both redundant and non-redundant functions. In the yeast Saccharomyces cerevisiae, approximately one-fifth of the genome consists of paralogs, with their encoded proteins involved in multiple pathways. However, the unique contributions of individual paralogs have remained…
Rohan Dandage, Christian R Landry
The protective redundancy of paralogous genes partly relies on the fact that they carry their functions independently. However, a significant fraction of paralogous proteins may form functionally dependent pairs, for instance, through heteromerization. As a consequence, one could expect these heteromeric paralogs to be…
Marit S Bratlie, Jostein Johansen, Brad T Sherman, Da Wei Huang + 2 more
'Richard A Lempicki' 'Finn Drabløs'] Background Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likely to be beneficial…
Rohan Dandage, Christian R Landry
Gene duplicates provide protection against loss-of-function mutations. This protective redundancy partly relies on the fact that paralogs carry their functions independently, i.e. the inactivation of one gene copy does not impair the function of the other copy. However, a significant fraction of paralogous proteins may…
Domenico Di Fraia, Mihaela Anitei, Marie-Therese Mackmull, Luca Parca + 7 more
Gene duplication enables the emergence of new functions by lowering the general evolutionary pressure. Previous studies have highlighted the role of specific paralog genes during cell differentiation, e.g., in chromatin remodeling complexes. It remains unexplored whether similar mechanisms extend to other biological…
Domenico Di Fraia, Mihaela Anitei, Marie-Therese Mackmull, Luca Parca + 7 more
'Luca Parca' 'Laura Behrendt' 'Amparo Andres-Pons' 'Darren Gilmour' 'Manuela Helmer Citterich' 'Christoph Kaether' 'Martin Beck' 'Alessandro Ori\u202c\u202c'] Paralog proteins promote fine tuning of protein complexes. The author identified a specific paralog signature conserved across vertebrate neuronal…
Jacob L. Steenwyk, Dayna C. Goltz, Thomas J. Buida, Yuanning Li + 2 more
Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of positive selection, often rely on gene families of single-copy orthologs (SC-OGs). In contrast, large gene families with multiple homologs in one or more species—a phenomenon observed among several important families of genes such as…
Brittany M Greco, Gerardo Zapata, Rohan Dandage, Mikhail Papkov + 6 more
'Vanessa Pereira' 'François Lefebvre' 'Guillaume Bourque' 'Leopold Parts' 'Elena Kuzmin' 'G Brown'] Title: Abstract Whole-genome duplication (WGD) events are common across various organisms; however, the retention and evolution of WGD paralogs is not fully understood. Quantitative measure of protein redistribution in…
Saurav Mallik, Angel F. Cisneros, Christian R. Landry, Emmanuel D. Levy
Homomeric proteins are ubiquitous and mediate myriads of cellular functions. When a gene encoding a homomer duplicates, the resulting paralogs can either form distinct homomers, or evolve into a heteromer containing both paralogs. While such events have extensively shaped proteomes, the molecular mechanisms driving…
Nabil Ibtehaz, Shafayat Ahmed, Bishwajit Saha, M. Sohel Rahman + 1 more
Identifying orthologous genes plays a pivotal role in comparative genomics as the orthologous genes remain less diverged in the course of evolution. However, identifying orthologous genes is often difficult, slow, and idiosyncratic, especially in the presence of multiplicity of domains in proteins, evolutionary…
Marc Hellmuth, Nicolas Wieseke
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged after a speciation) is crucial and lies at the heart of many genomic studies.…
Haiming Tang, Angela D. Wilkins
Gene duplication is a major mechanism through which new genetic material is generated. Although numerous methods have been developed to differentiate the ortholog and paralogs, very few differentiate the "Parent-Daughter" relationship among paralogous pairs. As coined by the Mira et al, we refer the "Parent" copy as…
Olivia Mendivil Ramos, David E. K. Ferrier
Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence…
Kun Gao, Jonathan Miller
Genomic subsequences conserved between closely related species such as human and chimpanzee exhibit an exponential length distribution, in contrast to the algebraic length distribution observed for sequences shared between distantly related genomes. We find that the former exponential can be further decomposed into an…
Mark M. Jones, Manuel Lafond, Céline Scornavacca
- 1 Delft Institute of Applied Mathematics, Delft University of Technology, P.O. Box 5, 2600 AA, Delft, the Netherlands M.E.L.Jones@tudelft.nl - 2 Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada, mlafond2@uOttawa.ca - 3 Institut des Sciences de l'Evolution, Université de Montpellier…
David Sankoff, Chunfang Zheng, Qian Zhu
Background Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial.…
Xiang Ji, Jeffrey L. Thorne
Interlocus gene conversion (IGC) homogenizes paralogs. Little is known regarding the mutation events that cause IGC and even less is known about the IGC mutations that experience fixation. To disentangle the rates of fixed IGC mutations from the tract lengths of these fixed mutations, we employ a composite likelihood…
Edélcio G. de Souza, Alexandre Costa-Leite, Diogo H. B. Dias
Dealing with consequence structures (i.e. logics) in a recent paper (see [4]), we have proposed a method to show that it is possible to turn any explosive logic into a system able to deal with contradictions, answering, therefore, a problem posed in [2]: how to convert a given explosive logic into a paraconsistent one?…