15 papers · ranked by Valyu relevance
Guy P Hunt, Rafael Henkin, Fabrizio Smeraldi, Michael R Barnes
Over the past three decades there have been numerous molecular biology developments that have led to an explosion in the number of gene expression studies being performed. Many of these gene expression studies publish their data to the public database GEO, making them freely available. By analysing gene expression…
Ta-Chun Liu, Peter N. Kalugin, Jennifer L. Wilding, Walter F. Bodmer
Cancer evolution consists of a stepwise acquisition of genetic and epigenetic changes, which alter the gene expression profiles of cells in a particular tissue and result in phenotypic alterations acted upon by natural selection. The recurrent appearance of specific genetic lesions across individual cancers and cancer…
Elna Dickson, Amoolya Sai Dwijesha, Natalie Andersson, Sofia Lundh + 3 more
Structural changes and neuropathology in the hypothalamus have been suggested to contribute to the non-motor manifestations of Huntington’s disease (HD), a neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin (HTT) gene. In the present study, we investigated whether transcriptional changes…
Samuel Bharti, Nikita Krishnan, Arian Veyssi, Maryam Momeni + 1 more
Microarray data enables biologists to extract differentially expressed genes (DEGs) across multiple phenotypes. While several pipelines and tools exist to perform microarray data analysis, they are targeted to users with moderate to advanced computational understanding and lack an easy-to-use, interactive and dynamic…
Yuto Amano, Masayuki Yamane, Hiroshi Honda
Chemical structure-based read-across represents a promising method for chemical toxicity evaluation without the need for animal testing; however, a chemical structure is not necessarily related to toxicity. Therefore, in vitro studies were often used for read-across reliability refinement; however, their external…
Neeraja M. Krishnan, Sarah I Rahman, Lars Røn Olsen, Binay Panda
Many biological studies could benefit from combining data from legacy microarray and high-throughput sequencing platforms, especially in clinical domains where collecting additional samples is not possible. However, incompatibility between platforms makes legacy data difficult to integrate, owing to differences in…
Chloe J. Bennett, Rodolfo Aramayo
RNA sequencing (RNA-seq) is a commonly used method to identify changes in gene expression between two conditions. The analysis of RNA-seq output is complicated, with the possibility of getting different results from the same raw data. We developed and deployed four parallel pipelines to reanalyze an existing dataset of…
Min Gi, Shugo Suzuki, Masayuki Kanki, Masanao Yokohira + 6 more
The development of a rapid and accurate model for determining the genotoxicity and carcinogenicity of chemicals is crucial for effective cancer risk assessment, and it also contributes to cancer prevention. This study aims to develop a one-day, single-dose model for identifying genotoxic hepatocarcinogens (GHCs) in…
Michael A. Bertagna, Lydia J. Bright, Fei Ye, Yu-Yang Jiang + 6 more
Although an established model organism, Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datasets and outdated algorithms. Here, we report a new approach to consolidating RNA-seq and microarray data based on a…
Erik Bot, Jose Davila-Velderrain
Gene expression specificity is a biological parameter relevant for understanding the molecular basis of evolutionary constraints and tissue-selective pathogenesis. Many efforts have tried to quantify the degree of tissue specificity of individual genes. The growing availability of single-cell transcriptomic data…
Aygun Azadova, Anthonia Ekperuoh, Greg N. Brooke, Antonio Marco
The popularity of microRNA expression analyses is reflected by the existence of thousands of works in the literature in which sRNAseq has been performed in myriads of samples, but for which no matched total RNAseq exists. The lack of paired sequencing experiments severely restricts the analysis of microRNA-gene…
Aygun Azadova, Anthonia Ekperuoh, Greg N. Brooke, Antonio Marco
The popularity of microRNA expression analyses is reflected by the existence of thousands of sRNA-seq studies where matched total RNA-seq data are often unavailable. The lack of paired sequencing experiments limits the analysis of microRNA-gene regulatory networks. We explore whether protein-coding gene expression can…
Rongrong Zhang, Yajia Huang, Mei Li, Lei Wang + 5 more
Synthetic biology relies on the screening and quantification of genetic components to assemble sophisticated gene circuits with specific functions. Microscopy is powerful tool for characterizing complex cellular phenotypes with increasing spatial and temporal resolution to library screening of genetic elements.…
Arun H. Patil, Andrea Baran, Zachary P. Brehm, Matthew N. McCall + 1 more
An incomplete picture of the expression distribution of microRNAs (miRNAs) across human cell types has long hindered our understanding of this important regulatory class of RNA. With the continued increase in available public small RNA sequencing datasets, there is an opportunity to more fully understand the general…
Nena Martin, Julie Kleine-Schultjann, Quentin Boussau, Agnès Dumont + 5 more
Gene expression regulation is a stochastic process that can be modified by mutations not only in a deterministic manner but also in a probabilistic way, for example by changing the extent of cell-to-cell variability in gene expression (also called “gene expression noise”) without necessarily changing the expected…