Learning from co-expression networks: possibilities and challenges

EAR Serin, H Nijveen, HWM Hilhorst… - Frontiers in plant …, 2016 - frontiersin.org
Plants are fascinating and complex organisms. A comprehensive understanding of the
organization, function and evolution of plant genes is essential to disentangle important …

Methods for biological data integration: perspectives and challenges

V Gligorijević, N Pržulj - Journal of the Royal Society …, 2015 - royalsocietypublishing.org
Rapid technological advances have led to the production of different types of biological data
and enabled construction of complex networks with various types of interactions between …

EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study

Z **ong, F Yang, M Li, Y Ma, W Zhao… - Nucleic acids …, 2022 - academic.oup.com
Abstract Epigenome-Wide Association Study (EWAS) has become a standard strategy to
discover DNA methylation variation of different phenotypes. Since 2018, we have developed …

Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles

DR Rhodes, S Kalyana-Sundaram, V Mahavisno… - Neoplasia, 2007 - Elsevier
DNA microarrays have been widely applied to cancer transcriptome analysis; however, the
majority of such data are not easily accessible or comparable. Furthermore, several …

Marker-assisted plant breeding: principles and practices

BD Singh, AK Singh - 2015 - Springer
Improved genotypes developed by plant breeding remain pivotal to global food security. In
the wake of ever-increasing human population, declining agricultural resources and the …

Integrated omics analysis of specialized metabolism in medicinal plants

A Rai, K Saito, M Yamazaki - The Plant Journal, 2017 - Wiley Online Library
Medicinal plants are a rich source of highly diverse specialized metabolites with important
pharmacological properties. Until recently, plant biologists were limited in their ability to …

The Connectivity Map: a new tool for biomedical research

J Lamb - Nature reviews cancer, 2007 - nature.com
The ultimate objective of biomedical research is to connect human diseases with the genes
that underlie them and drugs that treat them. But this remains a daunting task, and even the …

Sharing detailed research data is associated with increased citation rate

HA Piwowar, RS Day, DB Fridsma - PloS one, 2007 - journals.plos.org
Background Sharing research data provides benefit to the general scientific community, but
the benefit is less obvious for the investigator who makes his or her data available. Principal …

Reuse of public genome-wide gene expression data

J Rung, A Brazma - Nature Reviews Genetics, 2013 - nature.com
Our understanding of gene expression has changed dramatically over the past decade,
largely catalysed by technological developments. High-throughput experiments …

Affinity‐purification coupled to mass spectrometry: Basic principles and strategies

WH Dunham, M Mullin, AC Gingras - Proteomics, 2012 - Wiley Online Library
Identifying the interactions established by a protein of interest can be a critical step in
understanding its function. This is especially true when an unknown protein of interest is …