Select Publications

Journal articles

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, vol. 10, pp. 1286, http://dx.doi.org/10.1038/s41598-020-58107-2

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, vol. 11, http://dx.doi.org/10.3389/fmicb.2020.551189

Walsh K; Voineagu MA; Vafaee F; Voineagu I, 2020, 'TDAview: an online visualization tool for topological data analysis', Bioinformatics (Oxford, England), vol. 36, pp. 4805 - 4809, http://dx.doi.org/10.1093/bioinformatics/btaa600

Azad AKM; Dinarvand M; Nematollahi A; Swift J; Lutze-Mann L; Vafaee F, 2020, 'A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond.', Brief Bioinform, http://dx.doi.org/10.1093/bib/bbaa126

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, vol. 111, pp. 1805 - 1817, http://dx.doi.org/10.1111/cas.14350

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, vol. 57, pp. 1245 - 1258, http://dx.doi.org/10.1007/s12035-019-01792-6

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, vol. 10, pp. 5486, http://dx.doi.org/10.1038/s41467-019-13114-4

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, vol. 14, pp. e0214141, http://dx.doi.org/10.1371/journal.pone.0214141

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, vol. 2, http://dx.doi.org/10.1038/s41698-018-0071-0

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, vol. 8, http://dx.doi.org/10.1038/s41598-018-20104-x

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, vol. 4, pp. 20 - 20, http://dx.doi.org/10.1038/s41540-018-0056-1

Vafaee F; Dashti H; Alinejad-Rokny H, 2018, 'Transcriptomic Data Normalization', Encyclopedia of Bioinformatics and Computational Biology, Elsevier, http://dx.doi.org/10.1016/B978-0-12-809633-8.20209-4

Contaldi C; Vafaee F; Nelson P, 2018, 'Bayesian network hybrid learning using an elite-guided genetic algorithm', Artificial Intelligence Review, pp. 1 - 1, http://dx.doi.org/10.1007/s10462-018-9615-5

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, vol. 7, http://dx.doi.org/10.1038/s41598-017-10869-y

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, vol. 7, http://dx.doi.org/10.1038/s41598-017-14301-3

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, vol. 12, pp. e0185871, http://dx.doi.org/10.1371/journal.pone.0185871

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, vol. 11, http://dx.doi.org/10.1371/journal.pone.0164535

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, vol. 11, http://dx.doi.org/10.1371/journal.pone.0157763

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, vol. 12, pp. 708 - 718, http://dx.doi.org/10.1016/j.jalz.2015.10.010

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, vol. 6, http://dx.doi.org/10.1038/srep22477

Vafaee F, 2016, 'Using multi-objective optimization to identify dynamical network biomarkers as early-warning signals of complex diseases', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep22023

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, vol. 12, pp. 79 - 84, http://dx.doi.org/10.1038/nmeth.3178

Vafaee F; Rosu D; Broackes-Carter F; Jurisica I, 2013, 'Novel semantic similarity measure improves an integrative approach to predicting gene functional associations.', BMC systems biology, vol. 7, pp. 22, http://dx.doi.org/10.1186/1752-0509-7-22

Vafaee F; Nelson PC; Zhou C; Xiao W, 2008, 'Dynamic adaptation of genetic operators' probabilities', Studies in Computational Intelligence, vol. 129, pp. 159 - 168, http://dx.doi.org/10.1007/978-3-540-78987-1_15


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