14 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…
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…
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…
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…
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…
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…
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…