26 papers · ranked by Valyu relevance
John H Malone, Brian Oliver
Microarrays first made the analysis of the transcriptome possible, and have produced much important information. Today, however, researchers are increasingly turning to direct high-throughput sequencing - RNA-Seq - which has considerable advantages for examining transcriptome fine structure - for example in the…
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
Robert Plomin, Leonard C Schalkwyk
Microarrays are revolutionizing genetics by making it possible to genotype hundreds of thousands of DNA markers and to assess the expression (RNA transcripts) of all of the genes in the genome. Microarrays are slides the size of a postage stamp that contain millions of DNA sequences to which single-stranded DNA or RNA…
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…
Sten Z Cekan
This review deals with the methods of identifying genes that have been activated by inner or outer impulses. The activation and subsequent expression of a gene can be detected by its transcription into a corresponding messenger ribonucleic acid (mRNA). Principles of the methods for identification of individual…
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…
Gregory P. Way, Ted Natoli, Adeniyi Adeboye, Lev Litichevskiy + 16 more
Morphological and gene expression profiling can cost-effectively capture thousands of features in thousands of samples across perturbations by disease, mutation, or drug treatments, but it is unclear to what extent the two modalities capture overlapping versus complementary information. Here, using both the L1000 and…
David Murray, Peter Doran, Padraic MacMathuna, Alan C Moss
Efforts aimed at deciphering the molecular basis of complex disease are underpinned by the availability of high throughput strategies for the identification of biomolecules that drive the disease process. The completion of the human genome-sequencing project, coupled to major technological developments, has afforded…
Mihails Delmans, Martin Hemberg
The advent of high throughput RNA-seq at the single-cell level has opened up new opportunities to elucidate the heterogeneity of gene expression. One of the most widespread applications of RNA-seq is to identify genes which are differentially expressed between two experimental conditions. Here, we present a discrete…
Carlos P. Roca, Susana I.L. Gomes, Mónica J.B. Amorim, Janeck J. Scott‐Fordsmand
'Janeck J. Scott‐Fordsmand'] RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit…
Neil R. Clark, Kevin Hu, Edward Y. Chen, Qioanan Duan + 1 more
Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers set up experiments where control samples are compared to a treatment condition…
Trevor Martin, Hunter B. Fraser
Phylogenetic profiling, which infers functional relationships between genes based on patterns of gene presence/absence across species, has proven to be highly effective. Here we introduce a complementary approach, phylogenetic expression profiling (PEP), which detects gene sets with correlated expression levels across…
Alexandra Lee, Taylor Reiter, Georgia Doing, Julia Oh + 2 more
'Deborah A. Hogan' 'Casey S. Greene'] A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a tremendous opportunity for gaining a systems…
Balakrishnan Venkatesh, Ursula Hettwer, Birger Koopmann, Petr Karlovský
'Petr Karlovský'] Background: Gene expression studies on non-model organisms require open-end strategies for transcription profiling. Gel-based analysis of cDNA fragments allows to detect alterations in gene expression for genes which have neither been sequenced yet nor are available in cDNA libraries. Commonly used…
David Angeles-Albores, Carmie Puckett Robinson, Brian A. Williams, Paul W. Sternberg
RNA-seq is commonly used to identify genetic modules that respond to a perturbation. Although transcriptomes have been mainly used for target gene discovery, their quantitative nature makes them attractive structures with which to study genetic interactions. To understand whether whole-organism RNA-seq is suitable for…
Rita M. Cantor, Heather J. Cordell
Background We currently have the ability to quantify transcript abundance of messenger RNA (mRNA), genome-wide, using microarray technologies. Analyzing genotype, phenotype and expression data from 20 pedigrees, the members of our Genetic Analysis Workshop (GAW) 19 gene expression group published 9 papers, tackling…
Georg Kustatscher, Piotr Grabowski, Tina A. Schrader, Josiah B. Passmore + 2 more
The annotation of protein function is a longstanding challenge of cell biology that suffers from the sheer magnitude of the task. Here we present ProteomeHD, which documents the response of 10,323 human proteins to 294 biological perturbations, measured by isotope-labelling mass spectrometry. Using this data matrix and…
Mohammad H Rohban, Shantanu Singh, Xiaoyun Wu, Julia B Berthet + 5 more
We hypothesized that human genes and disease-associated alleles might be systematically functionally annotated using morphological profiling of cDNA constructs, via a microscopy-based Cell Painting assay. Indeed, 50% of the 220 tested genes yielded detectable morphological profiles, which grouped into biologically…
Paulo Amaral, Sílvia Carbonell Sala, Francisco M. De La Vega, Tiago Faial + 17 more
'Tiago Faial' 'Adam Frankish' 'T Gingeras' 'Roderic Guigó' 'Jennifer Harrow' 'Artemis G. Hatzigeorgiou' 'Rory Johnson' 'Terence D. Murphy' 'Mihaela Pertea' 'Kim D. Pruitt' 'Shashikant Pujar' 'Hazuki Takahashi' 'Igor Ulitsky' 'Ales Varabyou' 'Christine A. Wells' 'Mark Yandell' 'Piero Carninci' 'Steven L. Salzberg']…
Authors not listed
One Health seeks to integrate and balance the health of humans, animals, and environmental systems. These three spheres are intricately interconnected through microbiomes, which are universally present and exchange microbes and genes, influencing not only human and animal health but also key environmental…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Zahir Ali, Maged Serag, Gozde Demirer, Bruno Torre + 4 more
Efficient delivery of DNA, RNA, and genome engineering machinery to plant cells will enable efforts to genetically modify plants for global food security, sustainable energy production, synthetic biology applications, and climate change resilience. For the delivery of functional genetic units into plant cells, charged…
Authors not listed
Plasma proteomics has regained attention in recent years through advancements in mass spectrometry instrumentation and sample preparation, as well as new high-throughput affinity-based technologies. Here, we evaluate the analytical performance of the new Olink Reveal platform, a proximity extension assay (PEA)-based…
Authors not listed
Therapeutic oligonucleotides (ONs) are short synthetic DNA or RNA strands used to modulate protein expression in disease treatment. Besides the full-length product (FLP), ON samples contain many closely related impurities that must be profiled to ensure drug quality. Separation techniques, such as ion-pairing…
Authors not listed
MALDI MS analysis of liquid biopsy combined with ML enables non-invasive disease screening and monitoring. Presented an open-source R-based workflow covering all steps from raw data preprocessing to predictive model evaluation. The pipeline is customizable, transparent, and validated on clinical plasma samples from…