Plasma lipidome variation during the second half of the human lifespan is associated with age and sex but minimally with BMI

Wong et al., PLoS ONE 2019

Single cell data explosion: Deep learning to the rescue

Azad et al., arXiv. 2019

CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes

Bayati et al. Scientific Reports, bioRxiv, 424960

Deep Learning meets single-cell omics to personalise medicine.

Fatemeh Vafaee and A. K. M. Azad, Briefings in Bioinformatics [under review]

Prognostic utility of lncRNAs in ovarian cancer-associated fibroblasts.

Conlvin et al., Cancers [under review]

Global redox proteome and phosphoproteome analysis reveals widespread crosstalk and signal dysregulation induced by oxidative stress

Su et al., Nature Communiations [under review]

Serum exosome microRNAs predict multiple sclerosis disease activity after fingolimod treatment

Ebrahimkhani et al., Frontiers in Neurology [under review]


Deep sequencing of circulating exosomal microRNA allows non-invasive glioblastoma diagnosis

Ebrahimkhani et al., NPJ precision oncology, Nature; 2018

A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis

Vafaee et al., NPJ Syst Biol Appl. 2018 Jun 1;4:20

Bayesian network hybrid learning using an elite-guided genetic algorithm

Contaldi et al., Artificial Intelligence Review. 2018; 1-28

The transcriptional response to oxidative stress is part of, but not sufficient for, insulin resistance in adipocytes

Chaudhuri et al., Scientific reports. 2018; 8 (1), 1774

Transcriptomic Data Normalization

Vafaee et al., Encyclopedia Of Bioinformatics and Computational Biology, Reference Module in Life Sciences, Elsevier


Functional prediction of long non-coding RNAs in ovarian cancer-associated fibroblasts indicate a role in metastasis

Vafaee et al., Scientific Reports, Nature; 2017

Exosomal microRNA signatures in multiple sclerosis reflect disease status

Ebrahimkhani et al., Scientific Reports, Nature; 2017


ORTI: an open-access repository of transcriptional interactions for interrogating mammalian gene expression data

Vafaee et al., PLoS One; 2016

Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases

Vafaee et al., Scientific Reports; 2016

Intratumoral heterogeneity of DNA repair pathways in glioblastoma

Nicole et al., Scientific Reports; 2016

Identifying kinase substrate relationships using temporal data from large-scale phosphoproteomics studies

Domanova et al., PLoS One; 2016


Unravelling the mechanistic complexity of Alzheimer’s disease with systems biology

Rollo et al., Alzheimer’s & Dementia; 2015


In silico prediction of physical protein interactions and characterization of interactome orphans

Kotlyar et al., Nature Methods; 2014


Novel semantic similarity measure improves an integrative approach to predicting gene functional associations

Vafaee et al., BMC Systems Biolog; 2013