17 papers · ranked by Valyu relevance
Chao-Hsin Chen, Chao-Yu Pan, Wen-chang Lin
The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human…
Sean P. Leonard, Tiffany Halvorsen, Bentley Lim, Dan M. Park + 3 more
Overlapping genes–wherein two different proteins are translated from alternative frames of the same DNA sequence–provide a means to stabilize an engineered gene by directly linking its evolutionary fate with that of an overlapped gene. However, creating overlapping gene pairs is challenging as it requires redesign of…
Izabela Makałowska, Chiao-Feng Lin, Krisitina Hernandez
Background Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several mechanisms have been proposed to explain gene overlap origination the…
Sophie Lèbre, Olivier Gascuel
Overlapping genes exist in all domains of life and are much more abundant than expected upon their first discovery in the late 1970s. Assuming that the reference gene is read in frame +0, an overlapping gene can be encoded in two reading frames in the sense strand, denoted by +1 and +2, and in three reading frames in…
Giulia Soldà, Mikita Suyama, Paride Pelucchi, Silvia Boi + 5 more
'Alessandro Guffanti' 'Ermanno Rizzi' 'Peer Bork' 'Maria Luisa Tenchini' 'Francesca D Ciccarelli'] Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps…
Chaitanya R Sanna, Wen-Hsiung Li, Liqing Zhang
Background Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes. Results About 10% of the genes under study are overlapping…
Farhad Maleki, Anthony J. Kusalik
Gene set analysis methods are widely used to analyse data from high-throughput “omics” technologies. One drawback of these methods is their low specificity or high false positive rate. Over-representation analysis is one of the most commonly used gene set analysis methods. In this paper, we investigate the hypothesis…
Stefan Wichmann, Siegfried Scherer, Zachary Ardern
Overlapping genes (OLGs) with long protein-coding overlapping sequences are often excluded by genome annotation programs, with the exception of virus genomes. A recent study used a novel algorithm to construct OLGs from arbitrary protein domain pairs and concluded that virus genes are best suited for creating OLGs, a…
Ke Chen, Haohan Wang
Modern disease classification often overlooks molecular commonalities hidden beneath divergent clinical presentations. This study introduces a transcriptomics-driven framework for discovering disease relationships by analyzing over 1,300 disease–condition pairs using GenoMAS, a fully automated agentic AI system. Beyond…
Wei Vivian Li, Yiling Elaine Chen, Jingyi Jessica Li
Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and differentiation…
Diogo M. Ribeiro, Simone Rubinacci, Anna Ramisch, Robin J. Hofmeister + 2 more
Nearby genes are often expressed as a group. Yet, the prevalence, molecular mechanisms and genetic control of local gene co-expression are far from being understood. Here, by leveraging gene expression measurements across 49 human tissues and hundreds of individuals, we found that local gene co-expression occurs in 13%…
Anna Grandchamp, Katrin Berk, Elias Dohmen, Erich Bornberg-Bauer
De novo genes are novel genes which emerge from non-coding DNA. Until now, little is known about de novo genes properties, correlated to their age and mechanisms of emergence. In this study, we investigate four properties: introns, upstream regulatory motifs, 5’ UTRs and protein domains, in 23135 human proto-genes. We…
Henrike Heyne, Susann Lautenschläger, Ronald Nelson, François Besnier + 11 more
'François Besnier' 'Maxime Rotival' 'Alex Cagan' 'R. V. Kozhemyakina' 'Irina Z. Plyusnina' 'Lyudmila N. Trut' 'Örjan Carlborg' 'Enrico Petretto' 'Leonid Kruglyak' 'Svante Pääbo' 'Torsten Schöneberg' 'Frank W. Albert'] Henrike O. Heyne ,§ , Susann Lautenschläger§ , Ronald Nelson† , François Besnier†,‡ , Maxime Rotival*…
Andrew Brown, Lara M. Mangravite, Barbara E. Engelhardt
Genetic variants in cis-regulatory elements or trans-acting regulators commonly influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL) mapping has paralleled the adoption of genome-wide association studies (GWAS) for the analysis of…
Gerald Quon, Soheil Feizi, Daniel Marbach, Melina Claussnitzer + 1 more
Genomic regions associated with complex traits and diseases are primarily located in non-coding regions of the genome and have unknown mechanism of action. A critical step to understanding the genetics of complex traits is to fine-map each associated locus; that is, to find the causal variant(s) that underlie genetic…
Zhiwen Pan, Jan Dellith, Lothar Wondraczek
Understanding the multivariate origin of physical properties is particularly complex for polyionic glasses. As a concept, the term genome has been used to describe the entirety of structure-property relations in solid materials, based on functional genes acting as descriptors for a particular property, for example, for…
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…