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Select Publications

Journal articles

Qayyum A; Benzinou A; Razzak I; Mazher M; Nguyen TT; Puig D; Vafaee F, 2024, '3D-IncNet: Head and Neck (H&N) Primary Tumors Segmentation and Survival Prediction', IEEE Journal of Biomedical and Health Informatics, 28, pp. 1185 - 1194,

Besharatifard M; Vafaee F, 2024, 'A review on graph neural networks for predicting synergistic drug combinations', Artificial Intelligence Review, 57,

Alizadeh F; Jazayeriy H; Jazayeri O; Vafaee F, 2024, 'Genomic Ancestry Inference of Admixed Population by Identifying Approximate Boundaries of Ancestry Change', International Journal of Engineering, Transactions A: Basics, 37, pp. 412 - 424,

Thoms JAI; Koch FC; Raei A; Subramanian S; Wong JWH; Vafaee F; Pimanda JE, 2024, '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', Nucleic Acids Research, 52, pp. D1131 - D1137,

Alizadeh F; Jazayeriy H; Jazayeri O; Vafaee F, 2023, 'AICRF: ancestry inference of admixed population with deep conditional random field', Journal of Genetics, 102,

Subramanian S; Thoms JAI; Huang Y; Cornejo-Páramo P; Koch FC; Jacquelin S; Shen S; Song E; Joshi S; Brownlee C; 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 ES; Göttgens B; Alinejad-Rokny H; Wong JWH; Pimanda JE, 2023, 'Genome-wide transcription factor–binding maps reveal cell-specific changes in the regulatory architecture of human HSPCs', Blood, 142, pp. 1448 - 1462,

Gunawan I; Vafaee F; Meijering E; Lock JG, 2023, 'An introduction to representation learning for single-cell data analysis', Cell Reports Methods, 3,

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, 2023, 'Extracellular vesicles from biological fluids as potential markers in castration resistant prostate cancer', Journal of Cancer Research and Clinical Oncology, 149, pp. 4701 - 4717,

Zandavi SM; Liu D; Chung V; Anaissi A; Vafaee F, 2023, 'Fotomics: fourier transform-based omics imagification for deep learning-based cell-identity mapping using single-cell omics profiles', Artificial Intelligence Review, 56, pp. 7263 - 7278,

Safari F; Kehelpannala C; Safarchi A; Batarseh AM; Vafaee F, 2023, 'Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis', Cancers, 15, pp. 2780,

Ahmadzada T; Vijayan A; Vafaee F; Azimi A; Reid G; Clarke S; Kao S; Grau GE; Hosseini-Beheshti E, 2023, 'Small and Large Extracellular Vesicles Derived from Pleural Mesothelioma Cell Lines Offer Biomarker Potential', Cancers, 15,

Mandal A; Priyam S; Chan HH; Gouveia BM; Guitera P; Song Y; Baker MAB; Vafaee F, 2023, 'Computer-Aided Diagnosis of Melanoma Subtypes Using Reflectance Confocal Images', Cancers, 15,

Khazaal A; Zandavi SM; Smolnikov A; Fatima S; Vafaee F, 2023, 'Pan-Cancer Analysis Reveals Functional Similarity of Three lncRNAs across Multiple Tumors', International Journal of Molecular Sciences, 24,

Gano C; Fatima S; Failes T; Arndt G; Sajinovic M; Mahns D; Saedisomeolia A; Coorssen J; Bucci J; DeSouza P; Vafaee F; Scott K, 2023, 'Anti-cancer potential of synergistic phytochemical combinations is influenced by the genetic profiles of prostate cancer cell lines', Frontiers in Nutrition,

Batarseh AM; Vafaee F; Hosseini-Beheshti E; Safarchi A; Chen A; Cohen A; Juillard A; Hunt NH; Mariani M; Mitchell T; Grau GER, 2023, 'Investigation of Plasma-Derived Lipidome Profiles in Experimental Cerebral Malaria in a Mouse Model Study', International Journal of Molecular Sciences, 24,

Vijayan A; Fatima S; Sowmya A; Vafaee F, 2022, 'Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods', Briefings in Bioinformatics, 23,

Zandavi SM; Koch FC; Vijayan A; Zanini F; Mora FV; Ortega DG; Vafaee F, 2022, 'Disentangling single-cell omics representation with a power spectral density-based feature extraction', Nucleic Acids Research, 50, pp. 5482 - 5492,

Fatima S; Ma Y; Safrachi A; Haider S; Spring KJ; Vafaee F; Scott KF; Roberts TL; Becker TM; de Souza P, 2022, 'Harnessing Liquid Biopsies to Guide Immune Checkpoint Inhibitor Therapy', Cancers, 14,

Dinarvand M; Koch FC; Mouiee DA; Vuong K; Vijayan A; Tanzim AF; Azad AKM; Penesyan A; Castaño-Rodríguez N; Vafaee F, 2022, 'dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data', Microbial Genomics, 8,

Safarchi A; Fatima S; Ayati Z; Vafaee F, 2021, 'An update on novel approaches for diagnosis and treatment of SARS-CoV-2 infection', Cell and Bioscience, 11,

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, 2021, 'Human group iia phospholipase A2 —three decades on from its discovery', Molecules, 26,

Zandavi SM; Rashidi TH; Vafaee F, 2021, 'Dynamic Hybrid Model to Forecast the Spread of COVID-19 Using LSTM and Behavioral Models Under Uncertainty', IEEE Transactions on Cybernetics,

Koch FC; Sutton GJ; Voineagu I; Vafaee F, 2021, 'Supervised application of internal validation measures to benchmark dimensionality reduction methods in scRNA-seq data', Briefings in Bioinformatics, 22,

Azad AKM; Dinarvand M; Nematollahi A; Swift J; Lutze-Mann L; Vafaee F, 2021, 'A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond', Briefings in Bioinformatics, 22,

Shahriari S; Hossein Rashidi T; Azad AKM; Vafaee F, 2021, 'COVIDSpread: real-time prediction of COVID-19 spread based on time-series modelling', F1000Research, 10,

Azad AKM; Fatima S; Capraro A; Waters SA; Vafaee F, 2021, 'Integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action', Patterns, 2, pp. 100325,

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, 2021, 'Ageing impairs the airway epithelium defence response to SARS-CoV-2', ,

Bayati M; Rabiee HR; Mehrbod M; Vafaee F; Ebrahimi D; Forrest ARR; Alinejad-Rokny H, 2020, 'CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes', Scientific Reports, 10, pp. 1286,

Dinarvand M; Spain MP; Vafaee F, 2020, 'Pharmacodynamic Functions of Synthetic Derivatives for Treatment of Methicillin-Resistant Staphylococcus aureus (MRSA) and Mycobacterium tuberculosis', Frontiers in Microbiology, 11,

Azad AKM; Fatima S; Vafaee F, 2020, 'An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action', ,

Walsh K; Voineagu MA; Vafaee F; Voineagu I, 2020, 'TDAview: An online visualization tool for topological data analysis', Bioinformatics, 36, pp. 4805 - 4809,

Colvin EK; Howell VM; Mok SC; Samimi G; Vafaee F, 2020, 'Expression of long noncoding RNAs in cancer-associated fibroblasts linked to patient survival in ovarian cancer', Cancer Science, 111, pp. 1805 - 1817,

Ebrahimkhani S; Beadnall HN; Wang C; Suter CM; Barnett MH; Buckland ME; Vafaee F, 2020, 'Serum Exosome MicroRNAs Predict Multiple Sclerosis Disease Activity after Fingolimod Treatment', Molecular Neurobiology, 57, pp. 1245 - 1258,

Su Z; Burchfield JG; Yang P; Humphrey SJ; Yang G; Francis D; Yasmin S; Shin SY; Norris DM; Kearney AL; Astore MA; Scavuzzo J; Fisher-Wellman KH; Wang QP; Parker BL; Neely GG; Vafaee F; Chiu J; Yeo R; Hogg PJ; Fazakerley DJ; Nguyen LK; Kuyucak S; James DE, 2019, 'Global redox proteome and phosphoproteome analysis reveals redox switch in Akt', Nature Communications, 10,

Wong MWK; Braidy N; Pickford R; Vafaee F; Crawford J; Muenchhoff J; Schofield P; Attia J; Brodaty H; Sachdev P; Poljak A, 2019, 'Plasma lipidome variation during the second half of the human lifespan is associated with age and sex but minimally with BMI', PLoS ONE, 14, pp. e0214141,

Ebrahimkhani S; Vafaee F; Hallal S; Wei H; Lee MYT; Young PE; Satgunaseelan L; Beadnall H; Barnett MH; Shivalingam B; Suter CM; Buckland ME; Kaufman KL, 2018, 'Deep sequencing of circulating exosomal microRNA allows non-invasive glioblastoma diagnosis', npj Precision Oncology, 2,

Chaudhuri R; Krycer JR; Fazakerley DJ; Fisher-Wellman KH; Su Z; Hoehn KL; Yang JYH; Kuncic Z; Vafaee F; James DE, 2018, 'The transcriptional response to oxidative stress is part of, but not sufficient for, insulin resistance in adipocytes', Scientific Reports, 8, pp. 1774,

Vafaee F; Diakos C; Kirschner M; Reid G; Michael M; Horvath LISA; Alinejad-Rokny H; Cheng ZJ; Kuncic Z; Clarke S, 2018, 'A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis', npj Systems Biology and Applications, 4, pp. 20 - 20,

Vafaee F; Dashti H; Alinejad-Rokny H, 2018, 'Transcriptomic Data Normalization', Encyclopedia of Bioinformatics and Computational Biology, Elsevier,

Contaldi C; Vafaee F; Nelson P, 2018, 'Bayesian network hybrid learning using an elite-guided genetic algorithm', Artificial Intelligence Review, pp. 1 - 1,

Vafaee F; Colvin EK; Mok SC; Howell VM; Samimi G, 2017, 'Functional prediction of long non-coding RNAs in ovarian cancer-Associated fibroblasts indicate a potential role in metastasis', Scientific Reports, 7, pp. 10374,

Ebrahimkhani S; Vafaee F; Young PE; Hur SSJ; Hawke S; Devenney E; Beadnall H; Barnett MH; Suter CM; Buckland ME, 2017, 'Exosomal microRNA signatures in multiple sclerosis reflect disease status', Scientific Reports, 7, pp. 14293,

Domanova W; Krycer JR; Chaudhuri R; Yang P; Vafaee F; Fazakerley DJ; Humphrey SJ; James DE; Kuncic Z, 2017, 'Erratum: Unraveling kinase activation dynamics using kinase-substrate relationships from temporal large-scale phosphoproteomics studies (PLoS ONE (2016) 11: 6 (e0157763) DOI: 10.1371/journal.pone.0157763)', PLoS ONE, 12,

Vafaee F; Krycer JR; Ma X; Burykin T; James DE; Kuncic Z, 2016, 'ORTI: An open-access Repository of transcriptional interactions for interrogating mammalian gene expression data', PLoS ONE, 11, pp. e0164535,

Domanova W; Krycer J; Chaudhuri R; Yang P; Vafaee F; Fazakerley D; Humphrey S; James D; Kuncic Z, 2016, 'Unraveling kinase activation dynamics using kinase-substrate relationships from temporal Large-Scale phosphoproteomics studies', PLoS ONE, 11, pp. e0157763,

Rollo JL; Banihashemi N; Vafaee F; Crawford JW; Kuncic Z; Holsinger RMD, 2016, 'Unraveling the mechanistic complexity of Alzheimer's disease through systems biology', Alzheimer's and Dementia, 12, pp. 708 - 718,

Parker NR; Hudson AL; Khong P; Parkinson JF; Dwight T; Ikin RJ; Zhu Y; Cheng ZJ; Vafaee F; Chen J; Wheeler HR; Howell VM, 2016, 'Intratumoral heterogeneity identified at the epigenetic, genetic and transcriptional level in glioblastoma', Scientific Reports, 6,

Wilkins K; Hassan M; Francescatto M; Jespersen J; Parra RG; Cuypers B; DeBlasio D; Junge A; Jigisha A; Rahman F; Laenen G; Willems S; Thorrez L; Moreau Y; Raju N; Chothani SP; Ramakrishnan C; Sekijima M; Gromiha MM; Slator PJ; Burroughs NJ; Szałaj P; Tang Z; Michalski P; Luo O; Li X; Ruan Y; Plewczynski D; Fiscon G; Weitschek E; Ciccozzi M; Bertolazzi P; Felici G; Cuypers B; Meysman P; Vanaerschot M; Berg M; Imamura H; Dujardin J-C; Laukens K; Domanova W; Krycer JR; Chaudhuri R; Yang P; Vafaee F; Fazakerley DJ; Humphrey SJ; James DE; Kuncic Z, 2016, 'Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015.', BMC Bioinformatics, 17 Suppl 3, pp. 95,

Vafaee F, 2016, 'Using multi-objective optimization to identify dynamical network biomarkers as early-warning signals of complex diseases', Scientific Reports, 6,

Kotlyar M; Pastrello C; Pivetta F; Lo Sardo A; Cumbaa C; Li H; Naranian T; Niu Y; Ding Z; Vafaee F; Broackes-Carter F; Petschnigg J; Mills GB; Jurisicova A; Stagljar I; Maestro R; Jurisica I, 2014, 'In silico prediction of physical protein interactions and characterization of interactome orphans', Nature Methods, 12, pp. 79 - 84,

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