Search · four archives
Search · four archives
15 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…
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan + 1 more
'Thomas Shafee'] Transcriptomics technologies are the techniques used to study an organism’s [transcriptome](), the sum of all of its [RNA transcripts](). The information content of an organism is recorded in the DNA of its [genome]() and [expressed]() through [transcription](). Here, [mRNA]() serves as a transient…
Marc Robinson‐Rechavi, Julien Roux, Marta Rosikiewicz, Marc Robinson‐Rechavi
'Marc Robinson‐Rechavi'] Title: ABSTRACT 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.…
Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Background 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…
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…
Aitor Moruno-Cuenca, Sergio Picart-Armada, Rachael Bogle, Jennifer Fox + 5 more
Disease models are biological experimental systems to study human disease. These models are designed to mimic the pathophysiology, progression, and response to treatments observed in human conditions. These models serve as the backbone to drug discovery and early drug development activities; drug target validation and…
Yvonne Poeschl, Carolin Delker, Jana Trenner, Kristian Karsten Ullrich + 3 more
'Kristian Karsten Ullrich' 'Marcel Quint' 'Ivo Grosse' 'Ken Mills'] Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics…
Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo + 5 more
'José F. Muñoz' 'Jonathan Livny' 'Amol C. Shetty' 'Anup Mahurkar' 'Julie C. Dunning Hotopp'] Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to…
Jan Ihmels, Sven Bergmann, Judith Berman, Naama Barkai + 1 more
Candida Transcription Authors: ['Jan Ihmels' 'Sven Bergmann' 'Judith Berman' 'Naama Barkai' 'Leonid Kruglyak'] Differences in gene expression underlie many of the phenotypic variations between related organisms, yet approaches to characterize such differences on a genome-wide scale are not well developed. Here, we…
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…
İlksen Berfin Ekinci, Anna Sławińska, Kacper Żukowski, Małgorzata Olejnik
'Małgorzata Olejnik'] Salinomycin (Sal) is an antiparasitic agent used in veterinary medicine and is characterized by low therapeutic index and high toxicity. Among poultry, chickens are resistant to Sal toxicity, but turkeys are considered susceptible. However, underlying mechanisms of Sal toxicity are poorly…
José Caldas, Susana Vinga, Tanja Zeller
Transcriptomics meta-analysis aims at re-using existing data to derive novel biological hypotheses, and is motivated by the public availability of a large number of independent studies. Current methods are based on breaking down studies into multiple comparisons between phenotypes (e.g. disease vs. healthy), based on…
Fu-Yuan Zhu, Mo-Xian Chen, Neng-Hui Ye, Wang-Min Qiao + 11 more
Background The next-generation sequencing (NGS) technology has greatly facilitated genomic and transcriptomic studies, contributing significantly in expanding the current knowledge on genome and transcriptome. However, the continually evolving variety of sequencing platforms, protocols and analytical pipelines has led…
Emily Whiston, Hua Zhang Wise, Thomas J. Sharpton, Ginger Jui + 3 more
'Garry T. Cole' 'John W. Taylor' 'Yong-Sun Bahn'] Coccidioides immitis and C. posadasii, the causative agents of coccidioidomycosis, are dimorphic fungal pathogens, which grow as hyphae in the saprobic phase in the environment and as spherules in the parasitic phase in the mammalian host. In this study, we use…
Bas E Dutilh, Martijn A Huynen, Berend Snel
Background The massive scale of microarray derived gene expression data allows for a global view of cellular function. Thus far, comparative studies of gene expression between species have been based on the level of expression of the gene across corresponding tissues, or on the co-expression of the gene with another…