18 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…
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…
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…
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…
Olivier Dennler, Colm J Ryan
Gene duplication is the primary source of new genes, resulting in most genes having identifiable paralogs. Over time, paralog pairs may diverge in some respects but many retain the ability to perform the same functional role. Protein sequence identity is often used as a proxy for functional similarity and can predict…
Yanhui Hu, Ben Ewen-Campen, Aram Comjean, Jonathan Rodiger + 2 more
'Stephanie E. Mohr' 'Norbert Perrimon'] Title: Graphical abstract
Rohan Dandage, Mikhail Papkov, Brittany M. Greco, Dmytro Fishman + 9 more
'Helena Friesen' 'Kyle Wang' 'Erin Styles' 'Oren Kraus' 'Benjamin Grys' 'Charles Boone' 'Brenda Andrews' 'Leopold Parts' 'Elena Kuzmin'] Gene duplication is common across the tree of life, including yeast and humans, and contributes to genomic robustness. In this study, we examined changes in the subcellular…
Rohan Dandage, Mikhail Papkov, Brittany M. Greco, Vanessa Pereira + 13 more
'Dmytro Fishman' 'Helena Friesen' 'Kyle Wang' 'Erin B. Styles' 'Oren Kraus' 'Benjamin Grys' 'Gerardo Zapata' 'Francois Lefebvre' 'Guillaume Bourque' 'Charles Boone' 'Brenda J. Andrews' 'Leopold Parts' 'Elena Kuzmin'] Title: Summary Gene duplication is common across the Tree of Life and contributes to genomic…
Carlos A. Gandarilla-Perez, S. San José Pinilla, Anne‐Florence Bitbol, Martin Weigt
'Martin Weigt'] Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use phylogeny or residue coevolution to infer which paralogs are specific…
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…
Evgeny Fraimovitch, Tzachi Hagai
Background Gene duplication is thought to be a central process in evolution to gain new functions. The factors that dictate gene retention following duplication as well paralog gene divergence in sequence, expression and function have been extensively studied. However, relatively little is known about the evolution of…
Alexander S. Moffett, Andrea Falcón-Cortés, Michele Di Pierro
Gene duplication is a fundamental part of evolutionary innovation. While single-gene duplications frequently exhibit asymmetric evolutionary rates between paralogs, the extent to which this applies to multi-gene duplications remains unclear. In this study, we investigate the role of genetic context in shaping…
Alan J.S. Beavan, Bulat Fatkhullin, Juan Fontana, James O. McInerney + 2 more
Throughout eukaryotic evolution, the structure of the ribosome has been highly conserved, featuring 80 common protein gene families. However, in many eukaryotes, paralogs of these proteins are present. “Specialised ribosomes” have been documented across diverse groups of eukaryotes where they play an important role in…
Andonis Gerardos, Nicola Dietler, Anne‐Florence Bitbol
Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families. Does successful inference mainly rely on correlations from…
Oren Sultan, Dafna Shahaf
Analogy-making gives rise to reasoning, abstraction, flexible categorization and counterfactual inference – abilities lacking in even the best AI systems today. Much research has suggested that analogies are key to non-brittle systems that can adapt to new domains. Despite their importance, analogies received little…
Sankha S. Basu, Sayantan Roy
Paraconsistency is commonly defined and/or characterized as the failure of a principle of explosion. The various standard forms of explosion involve one or more logical operators or connectives, among which the negation operator is the most frequent. In this article, we ask whether a negation operator is essential for…
Kamaledin Ghiasi-Shirazi
How do you translate the English sentence "If both switches A and B are on, then the light L is on" into propositional logic? According to the teachings of logic [4, 10, 8], you would define the propositions "p: switch A is on", "q: switch B is on", and "r: light L is on", and translate this sentence as (p∧q) → r. Now…
Hiroyuki Kido
This paper gives a generative model of the interpretation of formal logic for data-driven logical reasoning. The key idea is to represent the interpretation as likelihood of a formula being true given a model of formal logic. Using the likelihood, Bayes' theorem gives the posterior of the model being the case given the…