27 papers · ranked by Valyu relevance
Peijian Cao, Ki-Hong Jung, Daeseok Choi, Daehee Hwang + 2 more
'Pamela C Ronald'] Background Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. Results In this study, we developed…
Ming Zhang, Yudong Zhang, Li Liu, Lijuan Yu + 6 more
'Jing Tan' 'Wenhua Yao' 'Manjit S Kang' 'Yongqiang An' 'Xingming Fan'] Background In the last decade, a large amount of microarray gene expression data has been accumulated in public repositories. Integrating and analyzing high-throughput gene expression data have become key activities for exploring gene functions…
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…
Fadi Alharbi, Aleksandar Vakanski
Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after cardiovascular diseases. Gene expression can play a fundamental role in the early…
Eric Bair
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA microarray experiments is to identify genes associated with biological…
Miroslav Blumenberg
Recent years witnessed the birth of bioinformatics technologies, which greatly advanced biological research. These ‘omics’ technologies address comprehensively the entire genome, transcriptome, proteome, microbiome etc. A large impetus in development of bioinformatics was the introduction of DNA microarrays for…
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…
Yuerong Zhu, Yuelin Zhu, Wei Xu
Background Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. With accumulating…
Markus Weniger, Julia C Engelmann, Jörg Schultz
Background Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure the expression level of thousands of mRNAs at the same time, allowing insight into or comparison of different cellular…
Khalid Raza
Microarray is one of the essential technologies used by the biologist to measure genome-wide expression levels of genes in a particular organism under some particular conditions or stimuli. As microarrays technologies have become more prevalent, the challenges of analyzing these data for getting better insight about…
Greg Gibson
Microarrays can survey genome-wide expression patterns. Not only can these gene expression profiles be used to identify a few genes of interest, they are now being creatively applied for hypothesis generation and testing
Dmytro Fishman
Accurate information about protein content in the organism is instrumental for a better understanding of human biology and disease mechanisms. While the presence of certain types of proteins can be life-threatening, the abundance of others is an essential condition for an individual's overall well-being. Protein…
Mrutyunjaya Panda
Gene is the basic unit of storage containing hereditary information in living beings. For the technical point of view,it can be treated as a distinct sequence of nucleotides constituting part of a chromosome. Microarrays data analysis is relatively a new technology that aims to help in finding the right treatment for…
Pratik Jaluria, Konstantinos Konstantopoulos, Michael Betenbaugh, Joseph Shiloach
'Joseph Shiloach'] With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as…
Khalid Raza, Akhilesh Mishra
The high-throughput data generated by microarray experiments provides complete set of genes being expressed in a given cell or in an organism under particular conditions. The analysis of these enormous data has opened a new dimension for the researchers. In this paper we describe a novel algorithm to microarray data…
Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo + 1 more
Protein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while existing solutions are either outdated or challenging to use without programming skills. The typical data analysis…
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…
Ernur Saka, Benjamin J. Harrison, Kirk West, Jeffrey C. Petruska + 1 more
Since the introduction of microarrays in 1995, researchers world-wide have used both commercial and custom-designed microarrays for understanding differential expression of transcribed genes. Public databases such as ArrayExpress and the Gene Expression Omnibus (GEO) have made millions of samples readily available. One…
Alina Frolova, Vladyslav Bondarenko, Maria Obolenska
According to major public repositories statistics an overwhelming majority of the existing and newly uploaded data originates from microarray experiments. Unfortunately, the potential of this data to bring new insights is limited by the effects of individual study-specific biases due to small number of biological…
Nikita Bhandari, Rahee Walambe, Ketan Kotecha, Satyajeet P. Khare
Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous amounts of data. Traditionally, statistical methods are used for comparative…
Chin Hong Ooi, Nam-Trung Nguyen, Gregor Kijanka
Protein arrays are systematically arranged, large collections of annotated proteins on planar surfaces commonly used for the characterisation of protein binding events against a wide range of possible probes. These may include analyses of protein-protein, peptide-protein, enzyme-substrate or antibody-antigen…
Nathaniel Lim, Stepan Tesar, Manuel Belmadani, Guillaume Poirier-Morency + 6 more
Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing…
Shadman Khan, Amid Shakeri, Jonathan Monteiro, Simrun Tariq + 5 more
With both foodborne illness and food spoilage detrimentally impacting human health and the economy, there is growing interest in the development of in situ sensors that offer real-time monitoring of food quality within enclosed food packages. While oligonucleotide-based fluorescent sensors have illustrated significant…
Authors not listed
Microarrays are widely used for detecting target analytes and biomarkers, with fabrication methods ranging from non-contact to contact bioprinting techniques. Microcontact bioprinting (μCP), which utilizes elastomeric stamps to transfer biorecognition molecules (bioinks) onto substrates, offers advantages such as…
Authors not listed
Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA…
Authors not listed
The nanosafety domain has seen significant advancements in data generation and sharing, yet challenges remain in ensuring data interoperability and reuse. This article focuses on developing a semantic interoperability framework for nanosafety data to maximize the FAIRness (Findability, Accessibility, Interoperability…
Eric W Deutsch, Juan Antonio Vizcaíno, Andrew R Jones, Pierre-Alain Binz + 25 more
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception twenty years ago. Here we describe the general…