A survey of best practices for RNA-seq data analysis

A Conesa, P Madrigal, S Tarazona, D Gomez-Cabrero… - Genome biology, 2016 - Springer
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …

From big data analysis to personalized medicine for all: challenges and opportunities

A Alyass, M Turcotte, D Meyre - BMC medical genomics, 2015 - Springer
Recent advances in high-throughput technologies have led to the emergence of systems
biology as a holistic science to achieve more precise modeling of complex diseases. Many …

[HTML][HTML] Multi-omics and metabolic modelling pipelines: challenges and tools for systems microbiology

M Fondi, P Liò - Microbiological research, 2015 - Elsevier
Integrated-omics approaches are quickly spreading across microbiology research labs,
leading to (i) the possibility of detecting previously hidden features of microbial cells like …

[HTML][HTML] Statistical single cell multi-omics integration

M Colomé-Tatché, FJ Theis - Current Opinion in Systems Biology, 2018 - Elsevier
Single cell high throughput genomic measurements are revolutionizing the fields of biology
and medicine, providing a means to tackle biological problems that have thus far been …

Data integration challenges for machine learning in precision medicine

M Martínez-García, E Hernández-Lemus - Frontiers in medicine, 2022 - frontiersin.org
A main goal of Precision Medicine is that of incorporating and integrating the vast corpora on
different databases about the molecular and environmental origins of disease, into analytic …

Multi-omics data integration in extracellular vesicle biology—utopia or future reality?

L Chitoiu, A Dobranici, M Gherghiceanu… - International journal of …, 2020 - mdpi.com
Extracellular vesicles (EVs) are membranous structures derived from the endosomal system
or generated by plasma membrane shedding. Due to their composition of DNA, RNA …

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape

N Alcaraz, J Pauling, R Batra, E Barbosa, A Junge… - BMC systems …, 2014 - Springer
Background Over the last decade network enrichment analysis has become popular in
computational systems biology to elucidate aberrant network modules. Traditionally, these …

Complexities of JC polyomavirus receptor-dependent and-independent mechanisms of infection

J Morris-Love, WJ Atwood - Viruses, 2022 - mdpi.com
JC polyomavirus (JCPyV) is a small non-enveloped virus that establishes lifelong, persistent
infection in most of the adult population. Immune-competent patients are generally …

Integrative omics-from data to biology

H Dihazi, AR Asif, T Beißbarth, R Bohrer… - Expert review of …, 2018 - Taylor & Francis
Introduction: Multi-omic approaches are promising a broader view on cellular processes and
a deeper understanding of biological systems. with strongly improved high-throughput …

转录组测序在林草植物抗逆性研究中的应用

高慧娟, 吕昕培, 王润娟, 任伟, 程济南, 汪永平… - 草业 …, 2019 - cyxb.magtech.com.cn
生物和非生物胁迫对农作物产量和生态环境造成极大的威胁, 林草植物对外界环境具有较强的
适应能力, 因此挖掘林草植物抗逆基因, 分析其抗逆机制已经成为当下的研究趋势 …