Publications
Explore our publications and learn more about the latest published outcomes of our research.
Explore the most recent research publications
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- A review on graph neural networks for predicting synergistic drug combinations
Besharatifard M; Vafaee F, 2024, Artificial Intelligence Review, 57 - Genomic Ancestry Inference of Admixed Population by Identifying Approximate Boundaries of Ancestry Change
Alizadeh F; Jazayeriy H; Jazayeri O; Vafaee F, 2024, International Journal of Engineering, Transactions A: Basics, 37, pp. 412 - 424 - BloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells
Thoms JAI; Koch FC; Raei A; Subramanian S; Wong JWH; Vafaee F; Pimanda JE, 2024, Nucleic Acids Research, 52, pp. D1131 - D1137
- A review on graph neural networks for predicting synergistic drug combinations
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- 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 - 50 - An introduction to representation learning for single-cell data analysis
Gunawan I; Vafaee F; Meijering E; Lock JG, Cell Reports Methods, pp. 100547 - 100547
- Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC.
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- 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
- Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods
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- 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,
- An update on novel approaches for diagnosis and treatment of SARS-CoV-2 infection
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- 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
- CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes
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- 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]
- Plasma lipidome variation during the second half of the human lifespan is associated with age and sex but minimally with BMI
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- 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
- Deep sequencing of circulating exosomal microRNA allows non-invasive glioblastoma diagnosis
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- 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
- Functional prediction of long non-coding RNAs in ovarian cancer-associated fibroblasts indicate a role in metastasis
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- 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
- ORTI: an open-access repository of transcriptional interactions for interrogating mammalian gene expression data
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- Unravelling the mechanistic complexity of Alzheimer’s disease with systems biology
Rollo et al., Alzheimer’s & Dementia; 2015
- Unravelling the mechanistic complexity of Alzheimer’s disease with systems biology
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- In silico prediction of physical protein interactions and characterization of interactome orphans
Kotlyar et al., Nature Methods; 2014
- In silico prediction of physical protein interactions and characterization of interactome orphans
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- Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
Vafaee et al., BMC Systems Biolog; 2013
- Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
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