Ten years of pathway analysis: current approaches and outstanding challenges
Pathway analysis has become the first choice for gaining insight into the underlying biology
of differentially expressed genes and proteins, as it reduces complexity and has increased …
of differentially expressed genes and proteins, as it reduces complexity and has increased …
Methods and approaches in the topology-based analysis of biological pathways
C Mitrea, Z Taghavi, B Bokanizad, S Hanoudi… - Frontiers in …, 2013 - frontiersin.org
The goal of pathway analysis is to identify the pathways significantly impacted in a given
phenotype. Many current methods are based on algorithms that consider pathways as …
phenotype. Many current methods are based on algorithms that consider pathways as …
Gateways to the FANTOM5 promoter level mammalian expression atlas
M Lizio, J Harshbarger, H Shimoji, J Severin… - Genome biology, 2015 - Springer
The FANTOM5 project investigates transcription initiation activities in more than 1,000
human and mouse primary cells, cell lines and tissues using CAGE. Based on manual …
human and mouse primary cells, cell lines and tissues using CAGE. Based on manual …
graphite - a Bioconductor package to convert pathway topology to gene network
Background Gene set analysis is moving towards considering pathway topology as a crucial
feature. Pathway elements are complex entities such as protein complexes, gene family …
feature. Pathway elements are complex entities such as protein complexes, gene family …
Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges
S Chowdhury, RR Sarkar - Database, 2015 - academic.oup.com
Elucidating the complexities of cell signaling pathways is of immense importance to gain
understanding about various biological phenomenon, such as dynamics of gene/protein …
understanding about various biological phenomenon, such as dynamics of gene/protein …
[HTML][HTML] Pathway analysis of complex diseases for GWAS, extending to consider rare variants, multi-omics and interactions
Background Genome-wide association studies (GWAS) is a major method for studying the
genetics of complex diseases. Finding all sequence variants to explain fully the aetiology of …
genetics of complex diseases. Finding all sequence variants to explain fully the aetiology of …
Data sharing: convert challenges into opportunities
AS Figueiredo - Frontiers in public health, 2017 - frontiersin.org
Initiatives for sharing research data are opportunities to increase the pace of knowledge
discovery and scientific progress. The reuse of research data has the potential to avoid the …
discovery and scientific progress. The reuse of research data has the potential to avoid the …
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data
Metagenomic approaches are increasingly recognized as a baseline for understanding the
ecology and evolution of microbial ecosystems. The development of methods for pathway …
ecology and evolution of microbial ecosystems. The development of methods for pathway …
Recent advances in modeling languages for pathway maps and computable biological networks
T Slater - Drug discovery today, 2014 - Elsevier
Highlights•The importance of biological models to systems biology is discussed.•The
principal role and desired characteristics of modeling languages in the development of …
principal role and desired characteristics of modeling languages in the development of …
Network‐based approaches for pathway level analysis
Identification of impacted pathways is an important problem because it allows us to gain
insights into the underlying biology beyond the detection of differentially expressed genes …
insights into the underlying biology beyond the detection of differentially expressed genes …