PathVisio 3: An Extendable Pathway Analysis Toolbox

Proteome-Based Systems Biology Analysis of the Diabetic Mouse Aorta Reveals Major Changes in Fatty Acid Biosynthesis as Potential Hallmark in Diabetes Mellitus-Associated Vascular Disease

(2014) H. Husi et al.   Circulation-Cardiovascular Genetics

Metabolomic changes in Caenorhabditis elegans lifespan mutants as evident from GC–EI–MS and GC–APCI–TOF–MS profiling

(2014) Carsten Jaeger et al.   Metabolomics

TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling

(2014) J. Zhong et al.   Database-The Journal of Biological Databases and Curation

ProfileDB: A resource for proteomics and cross-omics biomarker discovery

(2013) Chris Bauer et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways

(2013) J. Y. Fried et al.   BIOINFORMATICS

Whole blood transcriptome comparison of pigs with extreme production of in vivo dsRNA-induced serum IFN-a

(2013) Xiangdong Liu et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

The Immediate Early Gene Product EGR1 and Polycomb Group Proteins Interact in Epigenetic Programming during Chondrogenesis

(2013) Frank Spaapen et al.   PLoS One

Into the Eye of the Cytokine Storm

(2012) J. R. Tisoncik et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Molecular Pathways Involved in Prostate Carcinogenesis: Insights from Public Microarray Datasets

(2012) Sarah C. Baetke et al.   PLoS One

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations

(2011) Kumar Chandan et al.   BIOINFORMATICS

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)

(2011) Augustin Luna et al.   BIOINFORMATICS

Plug-and-play macroscopes

(2011) Katy Börner   COMMUNICATIONS OF THE ACM

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

(2010) Martijn P van Iersel et al.   BMC BIOINFORMATICS

Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes

(2010) Danyel G.J. Jennen et al.   DRUG DISCOVERY TODAY

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example

(2009) Heiko Neuweger et al.   BMC Systems Biology

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

Presenting and exploring biological pathways with PathVisio

(2008) Martijn P van Iersel et al.   BMC BIOINFORMATICS

KEGG Atlas mapping for global analysis of metabolic pathways

(2008) S. Okuda et al.   NUCLEIC ACIDS RESEARCH