19 papers · ranked by Valyu relevance
Adel Ait-hamlat, Diego Javier Zea, Antoine Labeeuw, Lélia Polit + 2 more
Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to…
Yann Christinat, Bernard ME Moret
Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals--some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite much research on exon and intron evolution, little is known…
Wend Yam D D Ouedraogo, Aida Ouangraoua
Eukaryotic genes can encode multiple distinct transcripts through the alternative splicing (AS) of genes. Interest in the AS mechanism and its evolution across different species has stimulated numerous studies, leading to several databases that provide information on AS and transcriptome data across multiple eukaryotic…
Wend Yam D. D. Ouedraogo, Aida Ouangraoua
Background SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of…
Casey W. Dunn, Mark Howison, Felipe Zapata
Background: In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a few genes to hundreds or thousands of genes. Phylogenetic studies now regularly include genes from…
Eva Jiménez-Guri, Jaime Huerta-Cepas, Luca Cozzuto, Karl R Wotton + 5 more
'Hui Kang' 'Heinz Himmelbauer' 'Guglielmo Roma' 'Toni Gabaldón' 'Johannes Jaeger'] Background Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular…
August Guang, Mark Howison, Felipe Zapata, Charles Lawrence + 1 more
One of the most common transcriptome assembly errors is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. It is difficult to identify these errors during assembly, but in a phylogenetic analysis these errors can be diagnosed from gene trees containing clades of tips…
Rafik Neme, Diethard Tautz
Even in the best studied Mammalian genomes, less than 5% of the total genome length is annotated as exonic. However, deep sequencing analysis in humans has shown that around 40% of the genome may be covered by poly-adenylated non-coding transcripts occurring at low levels^1^. Their functional significance is…
August Guang, Mark Howison, Felipe Zapata, Charles Lawrence + 2 more
'Casey W. Dunn' 'Zhong-Hua Chen'] A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where…
Yu-Hao Huang, Yi-Fei Sun, Hao Li, Hao-Sen Li + 1 more
The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, traditional methods typically involve intricate and time-consuming procedures prior to core analyses. These procedures encompass assembly from high-throughput reads, decontamination, gene prediction, homology search…
Luisa C. Teasdale, Frank Köhler, Kevin D. Murray, Tim O’Hara + 1 more
The qualification of orthology is a significant challenge when developing large, multi-loci phylogenetic datasets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts, and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we…
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…
Nicolas Delhomme, Görel Sundström, Neda Zamani, Henrik Lantz + 9 more
'Yao-Cheng Lin' 'Torgeir R. Hvidsten' 'Marc P. Höppner' 'Patric Jern' 'Yves Van de Peer' 'Joakim Lundeberg' 'Manfred G. Grabherr' 'Nathaniel R. Street' 'Wolfgang Arthofer'] After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies)…
Carlo G. Artieri, Hunter B. Fraser
- 30 short cycles are a hallmark of the earliest stages of insect development, we used Drosophila developmental timecourse expression data to test whether intron delay affects gene expression genome-wide, and to determine its consequences for the evolution of gene structure. We find that long zygotically expressed, but…
Rosa Fernández, Toni Gabaldón, Christophe Dessimoz
Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF). 08003 Barcelona, Spain 3 ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain Department of Computational Biology, University…
Huda Al-Nayyef, Christophe Guyeux, Jacques M. Bahi
—Variations in mitochondrial genes are usually considered to infer phylogenies. However some of these genes are lesser constraint than other ones, and thus may blur the phylogenetic signals shared by the majority of the mitochondrial DNA sequences. To investigate such effects, in this research work, the molecular…
Bethan S. Jones, Connie M. Ross, Gabriel Foley, Nico Kress + 5 more
Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the sub-terminal…
Pavel Kohout, Michal Vasina, Marika Majerova, Veronika Novakova + 5 more
Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among residues. Computational methodologies predominantly rely on evolutionary insights, leveraging homologous sequences to pinpoint conserved and functionally…
Sunzid Ahmed
Yersinia pestis is an infamous gram-negative, coccobacillus enterobacterium responsible for three devastating plague pandemics worldwide. The recent outbreak of this zoonotic disease demands in silico study of the hypothetical proteins for efficient drug and vaccine discovery. As hypothetical proteins constitute a…