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Search · four archives
18 papers · ranked by Valyu relevance
Yiru Sheng, R. Ayesha Ali, Andreas Heyland
Background Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, in whole organisms, tissues, and at the single cell level. Collectively, this is a vast comparative…
Elias Oziolor, Seda Arat, Matthew Martin
Background Comparisons of the molecular framework among organisms can be done on both structural and functional levels. One of the most common top-down approaches for functional comparisons is RNA sequencing. This estimation of organismal transcriptional responses is of interest for understanding evolution of molecular…
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…
Giovanni Piccinini, Liliana Milani
Background In Metazoa, the germline represents the cell lineage devoted to the transmission of genetic heredity across generations. Its functions intuitively evoke the crucial roles that it plays in organism development and species evolution, and its establishment is tightly tied to animal multicellularity itself. The…
Anthony Piron, Florian Szymczak, Maria Inês Alvelos, Matthieu Defrance + 3 more
High throughput omics technologies have generated a wealth of large protein, gene and transcript datasets that have exacerbated the need for new methods to analyse and compare big datasets. Rank-rank hypergeometric overlap is an important threshold-free method to combine and visualize two ranked lists of P-values or…
Amal Thomas
One of the main challenges in analyzing gene expression profiles across species is the dependence on determining corresponding genes between species. Homology-based approaches fail to account for the contribution of non-homologous genes to the phenotype, genes’ functional divergence, and rewiring of pathways.…
Tanweer Beckett, Uljana Hesse, Alexandra S. Dubrovina
Rooibos (Aspalathus linearis) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South Africa, is at risk as commercial rooibos longevity is in decline, mostly due to low…
Samuel Gornard, Pascaline Venon, Florian Lasfont, Thierry Balliau + 2 more
comparative transcriptomic and proteomic Authors: ['Samuel Gornard' 'Pascaline Venon' 'Florian Lasfont' 'Thierry Balliau' 'Laure Kaiser-Arnauld' 'Florence Mougel'] Background: Two strains of the endoparasitoid Cotesia typhae present a differential parasitism success on the host, Sesamia nonagrioides. One is virulent on…
Kenneth A. Barr, Yoav Gilad
Comparative functional genomic studies are often affected by biased read mapping across species due to inter-species differences in genome structure, sequence composition, and annotation quality. We developed CrossFilt, a filtering strategy that retains only sequencing reads that map reciprocally between genomes…
Samuel H. Church, Jasmine L. Mah, Casey W. Dunn
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as depicted with phylogenetic trees, that define relationships between species…
Mélina Gallopin, Christine Drevet, Vanesa S. Garcia de la Torre, Sarah Jelassi + 9 more
The remarkable capacity of plants to tolerate and accumulate tremendous amount of nickel is a complex adaptative trait that appeared independently in more than 700 species distributed in about fifty families. Nickel hyperaccumulation is thus proposed as a model to investigate the evolution of complex traits in plants.…
Peng Ken Lim, Ruoxi Wang, Shan Chun Lim, Jenet Princy Antony Velankanni + 1 more
Gene co-expression networks (GCNs) are widely used for gene function prediction, yet their performance often suffers from low dataset quality. To address this problem, we have developed TEA-GCN (Two-Tier Ensemble Aggregation-GCN), a novel method that constructs highly-performing ensemble GCNs by leveraging unsupervised…
Parul Tyagi, Deeksha Singh, Shivangi Mathur, Ayushi Singh + 1 more
'Rajiv Ranjan'] Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and…
Peng Ken Lim, Ruoxi Wang, Shan Chun Lim, Jenet Princy Antony Velankanni + 1 more
Gene co-expression networks (GCNs) can reveal useful gene co-functional and co-regulatory relationships. However, current GCN construction methodologies are sensitive to batch effects and sample composition, limiting their performance in generating GCNs from public RNA-seq samples abundant for many species. Here, we…
Tanner Stokes, Haoning Howard Cen, Philipp Kapranov, Iain J Gallagher + 7 more
'Iain J Gallagher' 'Andrew A. Pitsillides' 'Claude‐Henry Volmar' 'William E Kraus' 'James D. Johnson' 'Stuart M. Phillips' 'Claes Wahlestedt' 'James A. Timmons'] Title: Abstract Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug…
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Authors not listed
The WRN helicase has recently emerged as a promising therapeutic target for microsatellite instability (MSI)-high cancers. Here, we report LXW-P1, a potent WRN degrader derived from marine bromotyrosine alkaloids. Its molecular target was identified using an AI-guided, pathway-informed perturbation transcriptomics…
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann‐Apitius, Daniel Domingo‐Fernándéz
'Daniel Domingo‐Fernándéz'] Pathway enrichment analysis has become a widely used knowledge-based approach for the interpretation of biomedical data. Its popularity has led to an explosion of both enrichment methods and pathway databases. While the elegance of pathway enrichment lies in its simplicity, multiple factors…