Machine learning in genomic medicine: a review of computational problems and data sets
In this paper, we provide an introduction to machine learning tasks that address important
problems in genomic medicine. One of the goals of genomic medicine is to determine how …
problems in genomic medicine. One of the goals of genomic medicine is to determine how …
RNA sequencing data: hitchhiker's guide to expression analysis
K Van den Berge, KM Hembach… - Annual Review of …, 2019 - annualreviews.org
Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …
regulatory programs are observable. The measurement of transcriptome-wide gene …
The human splicing code reveals new insights into the genetic determinants of disease
INTRODUCTION Advancing whole-genome precision medicine requires understanding how
gene expression is altered by genetic variants, especially those that are far outside of …
gene expression is altered by genetic variants, especially those that are far outside of …
Deep learning of the tissue-regulated splicing code
Motivation: Alternative splicing (AS) is a regulated process that directs the generation of
different transcripts from single genes. A computational model that can accurately predict …
different transcripts from single genes. A computational model that can accurately predict …
An internal promoter underlies the difference in disease severity between N-and C-terminal truncation mutations of Titin in zebrafish
J Zou, D Tran, M Baalbaki, LF Tang, A Poon… - elife, 2015 - elifesciences.org
Truncating mutations in the giant sarcomeric protein Titin result in dilated cardiomyopathy
and skeletal myopathy. The most severely affected dilated cardiomyopathy patients harbor …
and skeletal myopathy. The most severely affected dilated cardiomyopathy patients harbor …
Regulation of alternative splicing in Drosophila by 56 RNA binding proteins
Alternative splicing is regulated by RNA binding proteins (RBPs) that recognize pre-mRNA
sequence elements and activate or repress adjacent exons. Here, we used RNA …
sequence elements and activate or repress adjacent exons. Here, we used RNA …
Cardiac circRNAs arise mainly from constitutive exons rather than alternatively spliced exons
S Aufiero, MMG van den Hoogenhof, YJ Reckman… - Rna, 2018 - rnajournal.cshlp.org
Circular RNAs (circRNAs) are a relatively new class of RNA molecules, and knowledge
about their biogenesis and function is still in its infancy. It was recently shown that alternative …
about their biogenesis and function is still in its infancy. It was recently shown that alternative …
Intron-centric estimation of alternative splicing from RNA-seq data
DD Pervouchine, DG Knowles, R Guigo - Bioinformatics, 2013 - academic.oup.com
Motivation: Novel technologies brought in unprecedented amounts of high-throughput
sequencing data along with great challenges in their analysis and interpretation. The …
sequencing data along with great challenges in their analysis and interpretation. The …
Methods to study splicing from high-throughput RNA sequencing data
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq)
has provided a very powerful mean to study splicing under multiple conditions at …
has provided a very powerful mean to study splicing under multiple conditions at …
Revealing the history and mystery of RNA-seq
A Gondane, HM Itkonen - Current Issues in Molecular Biology, 2023 - mdpi.com
Advances in RNA-sequencing technologies have led to the development of intriguing
experimental setups, a massive accumulation of data, and high demand for tools to analyze …
experimental setups, a massive accumulation of data, and high demand for tools to analyze …