27 papers · ranked by Valyu relevance
Simon Anders, Davis J. McCarthy, Yunshun Chen, Michał Okoniewski + 3 more
'Gordon K. Smyth' 'Wolfgang Huber' 'Mark D. Robinson'] | 1Genome Biology Unit, European Molecular Biology Laboratory, Mayerhofstrasse 1, 69117 | | --- | | Heidelberg, Germany | | 2Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, | | United Kingdom | | 3Wellcome Trust Centre for Human…
Robert Petryszak, Tony Burdett, Benedetto Fiorelli, Nuno A. Fonseca + 17 more
'Mar Gonzalez-Porta' 'Emma Hastings' 'Wolfgang Huber' 'Simon Jupp' 'Maria Keays' 'Nataliya Kryvych' 'Julie McMurry' 'John C. Marioni' 'James Malone' 'Karine Megy' 'Gabriella Rustici' 'Amy Y. Tang' 'Jan Taubert' 'Eleanor Williams' 'Oliver Mannion' 'Helen E. Parkinson' 'Alvis Brazma'] Expression Atlas…
Miriam Shiffman, Ryan Giordano, Tamara Broderick
C O U L D D R O P P I N G A F E W C E L L S C H A N G E T H E TA K E A W AY S F R O M D I F F E R E N T I A L E X P R E S S I O N ?
Franziska Hoerbst, Gurpinder Singh Sidhu, Thelonious Omori, Melissa Tomkins + 1 more
Advances in sequencing technologies have revolutionised our ability to capture the complete RNA profile in tissue samples, allowing for comparative analyses of RNA levels between developmental processes, environmental responses, or treatments. However, quantifying changes in gene expression remains challenging, given…
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…
Juliana Costa-Silva, Douglas Silva Domingues, David Menotti, Mariangela Hungría + 1 more
'Mariangela Hungría' 'Fabricio M Lopes'] The analysis of differential gene expression from RNA-Seq data has become a standard for several research areas mainly involving bioinformatics. The steps for the computational analysis of these data include many data types and file formats, and a wide variety of computational…
Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar + 5 more
'Tsung-Jung Wu' 'Cheng Yan' 'Haichen Zhang' 'Raja Mazumder'] BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. The…
Ionas Erb, Thomas Quinn, David Lovell, Cedric Notredame
Gene expression data, such as those generated by next generation sequencing technologies (RNA-seq), are of an inherently relative nature: the total number of sequenced reads has no biological meaning. This issue is most often addressed with various normalization techniques which all face the same problem: once…
Yingye Zheng, Margaret Pepe
Consider a gene expression array study comparing two groups of subjects where the goal is to explore a large number of genes in order to select for further investigation a subset that appear to be differently expressed. There has been much statistical research into the development of formal methods for designating…
Robert A Rubin
Background The disparate results from the methods commonly used to determine differential expression in Affymetrix microarray experiments may well result from the wide variety of probe set and probe level models employed. Here we take the approach of making the fewest assumptions about the structure of the microarray…
Mykhaylo M. Malakhov, Ben Dai, Xiaotong T. Shen, Wei Pan
Understanding how genetic variation affects gene expression is essential for a complete picture of the functional pathways that give rise to complex traits. Although numerous studies have established that many genes are differentially expressed in distinct human tissues and cell types, no tools exist for identifying…
Yanglan Gan, Shanshan Liang, Qingting Wei, Guobing Zou
A complex tissue contains a variety of cells with distinct molecular signatures. Single-cell RNA sequencing has characterized the transcriptomes of different cell types and enables researchers to discover the underlying mechanisms of cellular heterogeneity. A critical task in single-cell transcriptome studies is to…
Pedro L. Baldoni, Lizhong Chen, Mengbo Li, Yunshun Chen + 1 more
Differential transcript usage (DTU) refers to changes in the relative abundance of transcript isoforms of the same gene between experimental conditions, even when the total expression of the gene doesn’t change. DTU analysis requires the quantification of individual isoforms from RNA-seq data, which has a high level of…
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…
Christophe Le Priol, Chloé-Agathe Azencott, Xavier Gidrol, Saurabh Sinha
'Saurabh Sinha'] The majority of gene expression studies focus on the search for genes whose mean expression is different between two or more populations of samples in the so-called “differential expression analysis” approach. However, a difference in variance in gene expression may also be biologically and…
Ciaran Evans, Johanna Hardin, Daniel M. Stoebel
Johanna Hardin is Professor of Mathematics at Pomona College. She works on different types of analyses of high-throughput genetic data that don't conform to the usual assumptions needed for statistical analyses. Daniel Stoebel is Associate Professor of Biology at Harvey Mudd College. He works on the molecular biology…
Franziska Hoerbst, G. S. Sidhu, Melissa Tomkins, Richard J. Morris
in Gene Expression using Bayes Factors Authors: ['Franziska Hoerbst' 'G. S. Sidhu' 'Melissa Tomkins' 'Richard J. Morris'] Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for…
Sumanta Ray, Snehalika Lall, Sanghamitra Bandyopadhyay
Differential coexpression has recently emerged as a new way to establish a fundamental difference in expression pattern among a group of genes between two populations. Earlier methods used some scoring techniques to detect changes in correlation patterns of a gene pair in two conditions. However, modeling differential…
Sumanta Ray, Snehalika Lall, Sanghamitra Bandyopadhyay
Differential coexpression has recently emerged as a new way to establish a fundamental difference in expression pattern among a group of genes between two populations. Earlier methods used some scoring techniques to detect changes in correlation patterns of a gene pair in two conditions. However, modeling differential…
Sk Md Mosaddek Hossain, Aanzil Akram Halsana, Lutfunnesa Khatun, Sumanta Ray + 1 more
Pancreatic Ductal Adenocarcinoma (PDAC) is the most lethal type of pancreatic cancer (PC), late detection of which leads to its therapeutic failure. This study aims to find out key regulatory genes and their impact on the progression of the disease helping the etiology of the disease which is still largely unknown. We…
Thomas P. Quinn
It is largely taken for granted that differential abundance analysis is, by default, the best first step when analyzing genomic data. We argue that this is not necessarily the case. In this article, we identify key limitations that are intrinsic to differential abundance analysis: it is (a) dependent on unverifiable…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
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
Chinese hamster ovary (CHO) cells are the industrial workhorse for manufacturing biopharmaceuticals, including monoclonal antibodies. CHO cell line development requires a more data-driven approach for the accelerated identification of hyper-productive cell lines. Traditional methods, which rely on time-consuming…
Hafeez Haniff, Laurent Knerr, Xiaohui Liu, Gogce Crynen + 5 more
Vascular Endothelial Growth Factor A (VEGFA) stimulates angiogenesis in human endothelial cells and increasing its expression is a potential treatment for heart failure, currently accomplished via gene or mRNA therapy. Herein, we describe a designed small molecule (TGP-377) that specifically and potently enhances VEGFA…
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…