24 papers · ranked by Valyu relevance
Marc Feuermann, Huaiyu Mi, Pascale Gaudet, Anushya Muruganujan + 4 more
'Suzanna E. Lewis' 'Dustin Ebert' 'Tremayne Mushayahama' '' 'Paul D. Thomas'] A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working…
Avinash Sreedasyam, Christopher Plott, Md Shakhawat Hossain, John T. Lovell + 59 more
Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression…
Rohan Shawn Sunil, Shan Chun Lim, Manoj Itharajula, Marek Mutwil
Elucidating gene function is one of the ultimate goals of plant science. Despite this, only ~15% of all genes in the model plant Arabidopsis thaliana have comprehensively experimentally verified functions. While bioinformatical gene function prediction approaches can guide biologists in their experimental efforts…
James A Birchler, Hua Yang
Gene duplications have long been recognized as a contributor to the evolution of genes with new functions. Multiple copies of genes can result from tandem duplication, from transposition to new chromosomes, or from whole-genome duplication (polyploidy). The most common fate is that one member of the pair is deleted to…
Jasmine A. Richman, Leah R. Davis, Michael P. Phelps
The genome of many plant and animal species are heavily influenced by ancestral whole genome duplication (WGD) events. These events transform the regulation and function of gene networks, yet the evolutionary forces at work on duplicated genomes are not fully understood. Genes involved in cell surface signaling…
Authors not listed
Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence (“genomic variation”) with disease risk and other phenotypes, many of which could…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Chun Fu, YaoJun Yang
With the continuous upgrading of high-throughput sequencing technology, a large amount of biological genome data has been deciphered and published. The research on functional genes of biological genomes urgently needs a collection of service websites with user-friendly and full annotation functions for a variety of…
IGVF Consortium
Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence ("genomic variation") with disease risk and other phenotypes, many of which could…
Mengyao Sun, Yanni Ma, Jia Yu
Pseudogenes, as important products of genomic evolution, play unique regulatory roles in species adaptation. This review systematically summarizes the major types, functions, and regulatory mechanisms of metazoans pseudogenes, with a particular focus on their formation during primate evolution and the mechanisms…
Reza Rahmanzadeh
First, mutations leading to genetic novelties in a given species during evolution should be guided by the environment surrounding that species. Second, environment and germline are connected with each other via soma-germline messengers e.g., non-coding RNAs (ncRNAs). Third, based on the information that germline…
Paulo Amaral, Sílvia Carbonell Sala, Francisco M. De La Vega, Tiago Faial + 17 more
'Tiago Faial' 'Adam Frankish' 'T Gingeras' 'Roderic Guigó' 'Jennifer Harrow' 'Artemis G. Hatzigeorgiou' 'Rory Johnson' 'Terence D. Murphy' 'Mihaela Pertea' 'Kim D. Pruitt' 'Shashikant Pujar' 'Hazuki Takahashi' 'Igor Ulitsky' 'Ales Varabyou' 'Christine A. Wells' 'Mark Yandell' 'Piero Carninci' 'Steven L. Salzberg']…
Michaela Drobek, Nihar R Nayak, Gary Sutkin, Sunil Jaiman
During evolution, gene duplications lead to a naturally increased gene dosage. Duplicated genes can be further retained or eliminated over time by purifying selection pressure. The retention probability is increased by functional diversification and by the acquisition of novel functions. Interestingly, functionally…
Jessica A. Comstock, Merrill E. Asp, Fatmagül Bahar, Isabella Lee + 2 more
Robustness to the impact of mutation can mitigate phenotypes that have the potential to inform gene function. This robustness is often encoded into the genome through gene duplication, among other mechanisms. Duplication is a source of structurally similar genes that can retain some functional overlap as they diverge…
Kevin J. Mitchell, Nick Cheney
How does the genome encode the form of the organism? What is the nature of this genomic code? Common metaphors, such as a "blueprint" or "program", fail to capture the complex, indirect, and evolutionarily dynamic relationship between the genome and organismal form, or the constructive, interactive processes that…
Syafiq Samsolnizam, Boas Pucker
Gene duplication is a fundamental evolutionary mechanism that contributes to genetic innovation, such as in the diversification of plant metabolic pathways. This study investigates the duplication of dihydroflavonol-4-reductase (DFR) genes in Fagopyrum, focusing on their evolutionary origin and implications for…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Zheng Wang, Yaning Wang, Takao Kasuga, Francesc Lopez-Giraldez + 8 more
As de novo elements of the genome, orphan genes have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. However, there is a lack of working hypotheses as to what role they play. Systematic investigation of the evolutionary history, genome structures, expression…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Milena Trabert, Jesper Boman, Elina Immonen
Gene family evolution – the turnover of duplicated homologous genes – shapes genome architecture and fuels phenotypic innovation. Repetitive elements (REs) facilitate gene duplication and genome expansion, yet whether variation in repeat abundance and genome size (GS) scales with gene family evolution across species…
Delfi Dorussen, Emilie Knight, James Simmonds, Philippa Borrill
Active transcriptional compensation between gene duplicates (paralogs or homoeologs) has been proposed to facilitate functional redundancy, whereby mutations in multiple gene copies are required before a phenotype is observed. We tested whether transcriptional compensation occurs between homoeologs in response to…
Authors not listed
RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…
Authors not listed
Researching the EEEV virus is challenging due to the virus's high lethality and significant risk. This study employed bioinformatics methods for domain search to investigate the pathogenesis and infection process of the EEEV virus P protein. The results demonstrated that the EEEV virus P protein contains domains that…
Rumiana Tenchov, Janet Sasso, Xinmei Wang, Qiongqiong Angela Zhou
Aging is a dynamic, time-dependent process characterized by a gradual accumulation of cell damage. Continual functional decline in the intrinsic ability of living organisms to accurately regulate homeostasis leads to increased susceptibility and vulnerability to diseases. Anti-aging research has a long history…