23 papers · ranked by Valyu relevance
Itamar José Guimarães Nunes, Mariana Recamonde-Mendoza, Bruno César Feltes
fast, versatile and ready-to-use microarray analysis platform Authors: ['Itamar José Guimarães Nunes' 'Mariana Recamonde-Mendoza' 'Bruno César Feltes'] Title: Abstract There are still numerous challenges to be overcome in microarray data analysis because advanced, state-of-the-art analyses are restricted to programming…
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…
Mahmoud M. Abdelwahab, Khamis A. Al-Karawi, Hatem E. Semary, Natalia V. Gulyaeva
'Natalia V. Gulyaeva'] Alzheimer’s disease is a genetically complex disorder, and microarray technology provides valuable insights into it. However, the high dimensionality of microarray datasets and small sample sizes pose challenges. Gene selection techniques have emerged as a promising solution to this challenge…
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…
Hatim Z Almarzouki
The quantity of data required to give a valid analysis grows exponentially as machine learning dimensionality increases. In a single experiment, microarrays or gene expression profiling assesses and determines gene expression levels and patterns in various cell types or tissues. The advent of DNA microarray technology…
George I. Lambrou, Myrto Poulou, Krinio Giannikou, Marios Themistocleous + 4 more
'Marios Themistocleous' 'Apostolos Zaravinos' 'Maria Braoudaki' 'David Wong' 'Francesca Orso'] Simple Summary Epigenetic mechanisms, that are modifications of the genome without the presence of mutations, are known to play a crucial role in central nervous system (CNS) tumors during childhood. Two well-known epigenetic…
Hanaa Fathi, Hussain AlSalman, Abdu Gumaei, Ibrahim I. M. Manhrawy + 2 more
'Abdelazim G. Hussien' 'Passent El-Kafrawy'] Cancer can be considered as one of the leading causes of death widely. One of the most effective tools to be able to handle cancer diagnosis, prognosis, and treatment is by using expression profiling technique which is based on microarray gene. For each data point (sample)…
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…
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, Giorgia Scarpellino, Giorgia Chinigò, Luca Munaron + 3 more
'Federico Alessandro Ruffinatti' 'Ioannis Michalopoulos' 'Apostolos Malatras'] Simple Summary Researchers are often interested in detecting whether there are any differences in gene expression levels between two types of cells. To do this, gene expression levels are measured, and specific computer programs are used to…
Anahita Banaei, Shadrokh Samavi, Ebrahim Nasr Esfahani
Microarray technology is a new and powerful tool for the concurrent monitoring of a large number of gene expressions. Each microarray experiment produces hundreds of images. Each digital image requires a large storage space. Hence, real-time processing of these images and transmission of them necessitates efficient and…
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…
Emine Akpinar, Batuhan Hangun, Murat Oduncuoglu, Oguz Altun + 2 more
'Onder Eyecioglu' 'Zeynel Yalcin'] Abstract—DNA microarray technology enables the simultaneous measurement of expression levels of thousands of genes, thereby facilitating the understanding of the molecular mechanisms underlying complex diseases such as brain tumors and the identification of diagnostic genetic…
Maryam Eshraghi Evari, Md. Nasir Sulaiman, Amir Behjat
Data Authors: ['Maryam Eshraghi Evari' 'Md. Nasir Sulaiman' 'Amir Behjat'] DNA microarray gene-expression data has been widely used to identify cancerous gene signatures. Microarray can increase the accuracy of cancer diagnosis and prognosis. However, analyzing the large amount of gene expression data from microarray…
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…
Xiongshi Deng, Min Li, Shaobo Deng, Lei Wang
Microarray gene expression data are often accompanied by a large number of genes and a small number of samples. However, only a few of these genes are relevant to cancer, resulting in significant gene selection challenges. Hence, we propose a two-stage gene selection approach by combining extreme gradient boosting…
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…
Essam H. Houssein, Hager N. Hassan, Nagwan Abdel Samee, Mona M. Jamjoom + 2 more
'Mona M. Jamjoom' 'Dechang Chen' 'Wei Shao'] It is crucial to accurately categorize cancers using microarray data. Researchers have employed a variety of computational intelligence approaches to analyze gene expression data. It is believed that the most difficult part of the problem of cancer diagnosis is determining…
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…
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…
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…
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…
Amal Homer, Andrea Knoll, Uschi Gruber, Oliver Seitz
Fluorogenic hybridization probes allow the detection and localization of specific mRNA molecules in living cells without the need for genetic engineering. However, with the fluorescence properties of currently available oligonucleotide probes, detection in live cells is difficult when the mRNA target is expressed at…