Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC.

Subramanian S; Thoms JAI; Huang Y; Cornejo Paramo CP; Koch FC; Jacquelin S; Shen S; Song E; Joshi S; Brownlee CP; Woll PS; Chacon-Fajardo D; Beck D; Curtis DJ; Yehson K; Antonenas V; O'Brien T; Trickett A; Powell JA; Lewis ID; Pitson SM; Gandhi MK; Lane SW; Vafaee F; Wong E; Gottgens B; Rokny H; Wong JWH; Pimanda JE, Blood

Extracellular vesicles from biological fluids as potential markers in castration resistant prostate cancer

Choi WWY; Sánchez C; Li JJ; Dinarvand M; Adomat H; Ghaffari M; Khoja L; Vafaee F; Joshua AM; Chi KN; Guns EST; Hosseini-Beheshti E, Journal of Cancer Research and Clinical Oncology, 149, pp. 4701 - 4717

Fotomics: fourier transform-based omics imagification for deep learning-based cell-identity mapping using single-cell omics profiles

Zandavi SM; Liu D; Chung V; Anaissi A; Vafaee F, Artificial Intelligence Review, 56, pp. 7263 - 7278

Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis

Safari F; Kehelpannala C; Safarchi A; Batarseh AM; Vafaee F, Cancers, 15, pp. 2780 - 2780

Small and Large Extracellular Vesicles Derived from Pleural Mesothelioma Cell Lines Offer Biomarker Potential

Ahmadzada T; Vijayan A; Vafaee F; Azimi A; Reid G; Clarke S; Kao S; Grau GE; Hosseini-Beheshti E, Cancers, 15, pp. 2364 - 2364

Computer-Aided Diagnosis of Melanoma Subtypes Using Reflectance Confocal Images

Mandal A; Priyam S; Chan HH; Gouveia BM; Guitera P; Song Y; Baker MAB; Vafaee F, Cancers, 15, pp. 1428 - 1428

Pan-Cancer Analysis Reveals Functional Similarity of Three lncRNAs across Multiple Tumors

Khazaal A; Zandavi SM; Smolnikov A; Fatima S; Vafaee F, International Journal of Molecular Sciences, 24, pp. 4796 - 4796

Anti-cancer potential of synergistic phytochemical combinations is influenced by the genetic profiles of prostate cancer cell lines

Gano C; Fatima S; Failes T; Arndt G; Sajinovic M; Mahns D; Saedisomeolia A; Coorssen J; Bucci J; DeSouza P; Vafaee F; Scott K, Frontiers in Nutrition

Investigation of Plasma-Derived Lipidome Profiles in Experimental Cerebral Malaria in a Mouse Model Study

Batarseh AM; Vafaee F; Hosseini-Beheshti E; Safarchi A; Chen A; Cohen A; Juillard A; Hunt NH; Mariani M; Mitchell T; Grau GER, International Journal of Molecular Sciences, 24, pp. 501 - 501

An introduction to representation learning for single-cell data analysis

Gunawan I; Vafaee F; Meijering E; Lock JG, Cell Reports Methods, pp. 100547 - 100547


Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods

Vijayan A; Fatima S; Sowmya A; Vafaee F, Briefings in Bioinformatics, 23

Disentangling single-cell omics representation with a power spectral density-based feature extraction

Zandavi SM; Koch FC; Vijayan A; Zanini F; Mora FV; Ortega DG; Vafaee F, Nucleic Acids Research, 50, pp. 5482 - 5492

Harnessing Liquid Biopsies to Guide Immune Checkpoint Inhibitor Therapy

Fatima S; Ma Y; Safrachi A; Haider S; Spring KJ; Vafaee F; Scott KF; Roberts TL; Becker TM; de Souza P, Cancers, 14, pp. 1669 - 1669

3D-IncNet: Head and Neck (H&N) Primary Tumors Segmentation and Survival Prediction

Qayyum A; Benzinou A; Razzak I; Mazher M; Nguyen TT; Puig D; Vafaee F, IEEE Journal of Biomedical and Health Informatics, pp. 1 - 9

dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data

Dinarvand M; Koch FC; Mouiee DA; Vuong K; Vijayan A; Tanzim AF; Azad AKM; Penesyan A; Castaño-Rodríguez N; Vafaee F, Microbial Genomics, 8


An update on novel approaches for diagnosis and treatment of SARS-CoV-2 infection

Safarchi A; Fatima S; Ayati Z; Vafaee F, Cell and Bioscience, 11

Human group iia phospholipase A2 —three decades on from its discovery

Scott KF; Mann TJ; Fatima S; Sajinovic M; Razdan A; Kim RR; Cooper A; Roohullah A; Bryant KJ; Gamage KK; Harman DG; Vafaee F; Graham GG; Church WB; Russell PJ; Dong Q; de Souza P, Molecules, 26, pp. 7267 - 7267

Dynamic Hybrid Model to Forecast the Spread of COVID-19 Using LSTM and Behavioral Models Under Uncertainty

Zandavi SM; Rashidi TH; Vafaee F, IEEE Transactions on Cybernetics, pp. 1 - 13

Supervised application of internal validation measures to benchmark dimensionality reduction methods in scRNA-seq data

Koch FC; Sutton GJ; Voineagu I; Vafaee F, Briefings in Bioinformatics, 22

A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond

Azad AKM; Dinarvand M; Nematollahi A; Swift J; Lutze-Mann L; Vafaee F, Briefings in Bioinformatics, 22

COVIDSpread: real-time prediction of COVID-19 spread based on time-series modelling

Shahriari S; Hossein Rashidi T; Azad AKM; Vafaee F, F1000Research, 10, pp. 1110 - 1110

Integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action

Azad AKM; Fatima S; Capraro A; Waters SA; Vafaee F, Patterns, pp. 100325

Ageing impairs the airway epithelium defence response to SARS-CoV-2

Capraro A; Wong S; Adhikari A; Allan K; Patel H; Zhong L; Raftery M; Jaffe A; Yeang M; Aggarwal A; Wu L; Pandzic E; Whan R; Turville S; Vittorio O; Bull R; Kaakoush N; Rawlinson W; Tedla N; Vafaee F; Waters S,


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

Bayati M; Rabiee HR; Mehrbod M; Vafaee F; Ebrahimi D; Forrest ARR; Alinejad-Rokny H, Scientific Reports, 10, pp. 1286

Pharmacodynamic Functions of Synthetic Derivatives for Treatment of Methicillin-Resistant Staphylococcus aureus (MRSA) and Mycobacterium tuberculosis

Dinarvand M; Spain MP; Vafaee F, Frontiers in Microbiology, 11

An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action

Azad AKM; Fatima S; Vafaee F,

TDAview: An online visualization tool for topological data analysis

Walsh K; Voineagu MA; Vafaee F; Voineagu I, Bioinformatics, 36, pp. 4805 - 4809

Expression of long noncoding RNAs in cancer-associated fibroblasts linked to patient survival in ovarian cancer

Colvin EK; Howell VM; Mok SC; Samimi G; Vafaee F, Cancer Science, 111, pp. 1805 - 1817

Serum Exosome MicroRNAs Predict Multiple Sclerosis Disease Activity after Fingolimod Treatment

Ebrahimkhani S; Beadnall HN; Wang C; Suter CM; Barnett MH; Buckland ME; Vafaee F, Molecular Neurobiology, 57, pp. 1245 - 1258


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