eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis

(2019) Guangyan Zhou et al.   NUCLEIC ACIDS RESEARCH

Notch3 is involved in adipogenesis of human adipose-derived stromal/stem cells

(2018) Demi A. Sandel et al.   BIOCHIMIE

Causal network reconstruction from time series: From theoretical assumptions to practical estimation

(2018) J. Runge   CHAOS

GTRD: a database on gene transcription regulation—2019 update

(2018) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Subcutaneous adipose tissue gene expression and DNA methylation respond to both short- and long-term weight loss

(2017) S Bollepalli et al.   INTERNATIONAL JOURNAL OF OBESITY

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae

(2017) Miguel C Teixeira et al.   NUCLEIC ACIDS RESEARCH

Non-canonical NOTCH3 signalling limits tumour angiogenesis

(2017) Shuheng Lin et al.   Nature Communications

Computational dynamic approaches for temporal omics data with applications to systems medicine

(2017) Yulan Liang et al.   BioData Mining

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

Effects of Moderate and Subsequent Progressive Weight Loss on Metabolic Function and Adipose Tissue Biology in Humans with Obesity

(2016) Faidon Magkos et al.   Cell Metabolism

Adipose tissue gene expression is differentially regulated with different rates of weight loss in overweight and obese humans

(2016) R G Vink et al.   INTERNATIONAL JOURNAL OF OBESITY

Can we open the black box of AI?

(2016) Davide Castelvecchi   NATURE

The effect of rate of weight loss on long-term weight regain in adults with overweight and obesity

(2016) Roel G. Vink et al.   Obesity

Discretization of gene expression data revised

(2015) Cristian A. Gallo et al.   BRIEFINGS IN BIOINFORMATICS

SLC transporters as therapeutic targets: emerging opportunities

(2015) Lawrence Lin et al.   NATURE REVIEWS DRUG DISCOVERY

ABCA1 in adipocytes regulates adipose tissue lipid content, glucose tolerance, and insulin sensitivity

(2014) Willeke de Haan et al.   JOURNAL OF LIPID RESEARCH

Quantifying ‘Causality’ in Complex Systems: Understanding Transfer Entropy

(2014) Fatimah Abdul Razak et al.   PLoS One

Mining differential top-k co-expression patterns from time course comparative gene expression datasets

(2013) Yu-Cheng Liu et al.   BMC BIOINFORMATICS

Regulation of splicing by SR proteins and SR protein-specific kinases

(2013) Zhihong Zhou et al.   CHROMOSOMA

HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolism

(2013) Chi-Yi Yu et al.   HUMAN MOLECULAR GENETICS

Obesity induced a leptin-Notch signaling axis in breast cancer

(2013) Monica Battle et al.   INTERNATIONAL JOURNAL OF CANCER

Differential Proinflammatory and Oxidative Stress Response and Vulnerability to Metabolic Syndrome in Habitual High-Fat Young Male Consumers Putatively Predisposed by Their Genetic Background

(2013) Pedro González-Muniesa et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Differential gene expression in adipose tissue from obese human subjects during weight loss and weight maintenance

(2012) Lovisa E Johansson et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

“Good Enough Solutions” and the Genetics of Complex Diseases

(2012) James N. Weiss et al.   CIRCULATION RESEARCH

A Survey of Discretization Techniques: Taxonomy and Empirical Analysis in Supervised Learning

(2012) Salvador Garcia et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

CMRules: Mining sequential rules common to several sequences

(2011) Philippe Fournier-Viger et al.   KNOWLEDGE-BASED SYSTEMS

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

Gene association analysis: a survey of frequent pattern mining from gene expression data

(2009) R. Alves et al.   BRIEFINGS IN BIOINFORMATICS

Semantic Similarity in Biomedical Ontologies

(2009) Catia Pesquita et al.   PLoS Computational Biology

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining

Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity

(2008) Corneliu Henegar et al.   GENOME BIOLOGY