Search · four archives
Search · four archives
14 papers · ranked by Valyu relevance
Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Comparative transcriptome analysis is the comparison of expression patterns between homologous genes in different species. Since most molecular mechanistic studies in plants have been performed in model species including Arabidopsis and rice, comparative transcriptome analysis is particularly important for functional…
Trevor J. Krabbenhoft, Thomas F. Turner
Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome-environment interactions. However, important data handling and quality control challenges remain, particularly when working with non-model species outside of a controlled laboratory…
Mária Šurinová, Štepán Stočes, Tomáš Dostálek, Andrea Jarošová + 1 more
Impatiens is a genus containing more than 1000 species. Thanks to its size, it is a unique system for studying species diversification in natural populations. This study focused on the characterization of novel transcriptomes from seven Impatiens species originating from Nepal. Leave transcriptome of Impatines…
Julien Roux, Marta Rosikiewicz, Marc Robinson-Rechavi
Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of…
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.…
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…
Ferhat Ay, Abhijit Chakraborty, Ramana V. Davuluri
Access to large-scale genomics and transcriptomics data from various tissues and cell lines allowed the discovery of wide-spread alternative splicing events and alternative promoter usage in mammalians. However, evolutionary studies that aim at identifying orthology relationships mostly focus on gene-level orthology…
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…
Megan Crow, Hamsini Suresh, John Lee, Jesse Gillis
What makes a mouse a mouse, and not a hamster? The answer lies in the genome, and more specifically, in differences in gene regulation between the two organisms: where and when each gene is expressed. To quantify differences, a typical study will either compare functional genomics data from homologous tissues, limiting…
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…
Ping-Han Hsieh, Yen-Jen Oyang, Chien-Yu Chen
Correct quantification of transcript expression is essential to understand the functional products of the genome in different physiological conditions and developmental stages. Recently, the development of high-throughput RNA sequencing (RNA-Seq) allows the researchers to perform transcriptome analysis for the…
Anish M.S. Shrestha, Joyce Emlyn B. Guiao, Kyle Christian R. Santiago
RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. Conventional differential expression analysis for organisms without reference sequences requires performing computationally…
Alexander J. Hart, Samuel Ginzburg, Muyang (Sam) Xu, Cera R. Fisher + 4 more
EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated…
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…