Publications

Selected publications from the Computational Biology Facility.

Deciphering the complex role of thrombospondin-1 in glioblastoma development (Nat Commun. – 2019)

MzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics (Analytical Chemistry, 2019)

Chemical hazard prediction and hypothesis testing using quantitative adverse outcome pathways (ALTEX, 2019)

Non-specific effects of oral vaccination with live-attenuated Salmonella Typhi strain Ty21a (Science Advances, 2019)

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets (Molecular & Cellular Proteomics, 2018)

Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants (Journal of Proteomics, 2018)

Incorporating suborganismal processes into dynamic energy budget models for ecological risk assessment (Integrated Environmental Assessment Management, 2018)

In Silico Computational Transcriptomics Reveals Novel Endocrine Disruptors in Largemouth Bass (Micropterus salmoides) (Environmental Science Technology, 2018)

Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions (Molecular Immunology, 2018)

The role of Eif6 in Skeletal Muscle Homeostasis Revealed by Endurance Training Co-Expression networks (Cell Rep, 2017)

Transcriptional mechanism of vascular endothelial growth factor-induced expression of protein kinase CBII in chronic lymphocytic leukaemia cells (Sci Rep, 2017)

Glaerosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus (Open Biology, 2017)

A network biology approach identifies molecular cross-talk between normal prostate epithelial and prostate carcinoma cells (PloS Computational Biology, 2016)

The centrosomal deubiquitylase UP21 regulates Gly1 trancriptional activity and stability (Journal of Cell Science, 2016)

Inference of low and high-grade glioma gene regulatory networks delineates the role of Rnd3 in establishing multiple hallmarks of cancer (PLoS Genetics, 2015)

Systems Biology Approach Reveals a Calcium-Dependent mechanism for basal toxicity in Daphnia Magna (Environmental Science Technology, 2015)

Adverse outcome pathways for regulatory applications: examination of four case studies with different degrees of completeness and scientific confidence (Toxicological Sciences, 2015)

Lpg0393 of Legionella pneumophila Is a Guanine-Nucleotide Exchange Factor for Rab5, Rab21 and Rab22 ( PloS One, 2015)

Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations (Nucleic Acids Research, 2014)

ProteomeXchange provides globally coordinated proteomics data submission and dissemination (Nature Biotechnology, 2014)