14 papers · ranked by Valyu relevance
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…
Luca Visentin, Luca Munaron, Federico Alessandro Ruffinatti
Tens of thousands of gene expression data sets describing a variety of model organisms in a many different pathophysiological conditions are currently stored in publicly available databases such as Gene Expression Omnibus (GEO) and ArrayExpress. As microarray technology is giving way to RNA-Seq, it becomes strategic to…
Sophie Bérubé, Tamaki Kobayashi, Amy Wesolowski, Douglas E. Norris + 3 more
Protein microarrays are a promising technology that measure protein levels in serum or plasma samples. Due to the high technical variability of these assays and high variation in protein levels across serum samples in any population, directly answering biological questions of interest using protein microarray…
Juwayria, Priyansh Shrivastava, Kaustar Yadav, Sourabh Das + 5 more
10X Visium, a popular Spatial transcriptomics (ST) method, faces limited adoption due to its high cost and restricted sample usage per slide. To address these issues, we propose Microarray Integrated Spatial Transcriptomics (MIST), combining conventional tissue microarray (TMA) with Visium, using laser-cutting and 3D…
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…
Keegan Flanagan, Steven Pelech, Yossef Av-Gay, Khanh Dao Duc
Analysis of signal transduction pathways relies on monitoring global changes in cellular response to perturbation or genetic manipulation. Antibody microarray data provides an increasingly viable tool for the monitoring and analyzing high throughput expression and protein phosphorylation data. However, computational…
Anderson A. Butler, Jason Kras, Karolina Chwalek, Enrique I. Ramos + 3 more
DNA methylation microarrays have become a widely used tool for investigating epigenetic modifications in various aspects of biomedical research. However, technical variability in methylation data poses challenges for downstream applications such as predictive modeling of health and disease. In this study, we measure…
Revanth Reddy, Liwei Yang, Jesse Liu, Zhuojie Liu + 1 more
Highly multiplexed analysis of biospecimens significantly advances the understanding of biological basics of diseases, but these techniques are limited by the number of multiplexity and the speed of processing. Here, we present a rapid multiplex method for quantitative detection of protein markers on brain sections…
Emi Suzuki, Masaki Serata, Tomoyuki Sako, Sumie Sato + 3 more
We previously identified a gene cluster of Lacticaseibacillus paracasei strain Shirota (YIT 9029) for cell surface long-chain polysaccharides (LCPS-1) biosynthesis, which modulates YIT 9029 activity to induce cytokine production in immune cells, and showed that a lectin microarray can be useful for distinguishing the…
David A. Russell, Erin M. Gorden, Michelle A. Peck, Christina M. Neal + 6 more
Microarray processing, which interrogates hundreds of thousands of single nucleotide polymorphisms (SNPs) across the human genome, has recently gained traction in forensics due to its use in forensic genetic genealogy, which is based on analysis using SNPs to compare distant relatives in publicly curated databases for…
Xingpeng Li, Wen He, Ying Zhang, Karen Page + 2 more
Atopic Dermatitis (AD) is a persistent inflammatory disease of the skin to which a few novel treatment options have recently become available. Multiple published datasets, from RNA sequencing (RNA-seq) and microarray experiments performed on lesional (LS) and non-lesional (NL) skin biopsies collected from AD patients…
Xianglin Ji, Peilin Fang, Xi Zhao, Chuanyin Xiong + 9 more
The importance of genetic or epi-genetic heterogeneity has been increasingly recognized, but it has been challenging to profile intracellular post-transcriptional targets with sufficient throughput and resolution at across large-scale tissue samples. This study describes a technique, Spectrum-FISH, for high-throughput…
Sijbren Kramer, Ryungeun Song, Yujia Huang, Soonwoo Hong + 3 more
Multiplexed methods for nucleic acid detection are immensely challenging to deploy outside of laboratory settings. Conversely, field-deployable methods are limited to low levels of multiplexing. During the COVID-19 pandemic, we developed Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a sensitive…
Yunming Wu, Wenjing Xu, Limei Ma, Zulin Yu + 2 more
We describe a cost-effective, highly sensitive, and quantitative method for in situ detection of single RNA molecules in tissue sections. This method, dubbed Yn situ, standing for Y-branched probe in situ hybridization, uses a single-strand DNA preamplifier with multiple initiation sites that trigger hybridization…