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

Conference Papers

Alizadeh F; Jazayeriy H; Jazayeri O; Vafaee F, 2020, 'SMIA: a simple way for inference of admixed population ancestors', in 2020 10th International Conference on Computer and Knowledge Engineering (ICCKE), IEEE, presented at 2020 10th International Conference on Computer and Knowledge Engineering (ICCKE), 29 October 2020 - 30 October 2020, http://dx.doi.org/10.1109/iccke50421.2020.9303686

Ebrahimkhani S; Vafaee F; Barnett MH; Suter CM; Buckland ME, 2017, 'Exosomal microRNA signatures in multiple sclerosis reflect disease status', in MULTIPLE SCLEROSIS JOURNAL, SAGE PUBLICATIONS LTD, MS Res Australia, Sydney, AUSTRALIA, pp. NP17 - NP17, presented at Progress in MS Research Conference, MS Res Australia, Sydney, AUSTRALIA, 11 October 2017 - 13 October 2017, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000414783200046&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Contaldi, C ; Vafaee F; Nelson, PC , 2017, 'The role of crossover operator in bayesian network structure learning performance: a comprehensive comparative study and new insights', in GECCO 2017 - Proceedings of the 2017 Genetic and Evolutionary Computation Conference, ACM New York, NY, USA ©2017, Berlin, Germany, pp. 769 - 776, presented at in GECCO 2017 - Proceedings of the 2017 Genetic and Evolutionary Computation Conference, Berlin, Germany, 15 July 2017 - 19 July 2017, http://dx.doi.org/10.1145/3071178.3071240

Domanova W; Krycer JR; Chaudhuri R; Yang P; Vafaee F; Fazakerley DJ; Humphrey SJ; James DE; Kuncic Z, 2015, 'Unravelling signal coordination from large scale phosphorylation kinetic data', in BMC BIOINFORMATICS, BIOMED CENTRAL LTD, Dublin, IRELAND, pp. 208 - 209, presented at 11th ISCB-Student-Council Symposium held in conjunction with the Intelligent Systems for Molecular Biology (ISMB) Conference / European Conference on Computational Biology (ECCB), Dublin, IRELAND, 10 July 2015, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000371886800009&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Parker NR; Hudson AL; Khong P; Parkinson JF; Ikin R; Cheng ZJ; Vafaee F; Wheeler HR; Howell VM, 2015, 'Intratumoral heterogeneity of DNA repair pathways in glioblastoma', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, Washington, DC, presented at AACR Special Conference on Advances in Brain Cancer Research, Washington, DC, 27 May 2015 - 30 May 2015, http://dx.doi.org/10.1158/1538-7445.BRAIN15-B39

Vafaee F; Turán G; Nelson PC; Berger-Wolf TY, 2014, 'Among-site rate variation: Adaptation of genetic algorithm mutation rates at each single site', in GECCO 2014 - Proceedings of the 2014 Genetic and Evolutionary Computation Conference, pp. 863 - 870, http://dx.doi.org/10.1145/2576768.2598216

Vafaee F; Turán G; Nelson PC; Berger-Wolf TY, 2014, 'Balancing the exploration and exploitation in an adaptive diversity guided genetic algorithm', in Proceedings of the 2014 IEEE Congress on Evolutionary Computation, CEC 2014, pp. 2570 - 2577, http://dx.doi.org/10.1109/CEC.2014.6900257

Vafaee F, 2014, 'Learning the structure of large-scale Bayesian Networks using genetic algorithm', in GECCO 2014 - Proceedings of the 2014 Genetic and Evolutionary Computation Conference, pp. 855 - 862, http://dx.doi.org/10.1145/2576768.2598223

Vafaee F; Nelson PC, 2010, 'An explorative and exploitative mutation scheme', in 2010 IEEE World Congress on Computational Intelligence, WCCI 2010 - 2010 IEEE Congress on Evolutionary Computation, CEC 2010, http://dx.doi.org/10.1109/CEC.2010.5586142

Vafaee F; Turán G; Nelson PC, 2010, 'Optimizing genetic operator rates using a Markov chain model of Genetic Algorithms', in Proceedings of the 12th Annual Genetic and Evolutionary Computation Conference, GECCO '10, pp. 721 - 728, http://dx.doi.org/10.1145/1830483.1830613

Vafaee F; Nelson PC, 2009, 'A genetic algorithm that incorporates an adaptive mutation based on an evolutionary model', in 8th International Conference on Machine Learning and Applications, ICMLA 2009, pp. 101 - 107, http://dx.doi.org/10.1109/ICMLA.2009.101

Xu B; Vafaee F; Wolfson O, 2009, 'In-network query processing in mobile P2P databases', in GIS: Proceedings of the ACM International Symposium on Advances in Geographic Information Systems, pp. 207 - 216, http://dx.doi.org/10.1145/1653771.1653802

Vafaee F; Nelson PC, 2009, 'Self-adaptation of genetic operator probabilities using differential evolution', in SASO 2009 - 3rd IEEE International Conference on Self-Adaptive and Self-Organizing Systems, pp. 274 - 275, http://dx.doi.org/10.1109/SASO.2009.13

Vafaee F; Xiao W; Nelson PC; Zhou C, 2008, 'Adaptively evolving probabilities of genetic operators', in Proceedings - 7th International Conference on Machine Learning and Applications, ICMLA 2008, pp. 292 - 299, http://dx.doi.org/10.1109/ICMLA.2008.45

Conference Abstracts

Colvin EK; Howell VM; Mok SC; Samimi G; Vafaee F, 2018, 'EXPRESSION OF LNCRNAS IN OVARIAN CANCER-ASSOCIATED FIBROBLASTS IS ASSOCIATED WITH PATIENT SURVIVAL', in CLINICAL CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, Seattle, WA, Vol. 25, pp. 154 - 154, presented at 12th Rivkin-Centre Biennial Ovarian Cancer Research Symposium, Seattle, WA, 13 September 2018 - 15 September 2018, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000497337700092&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Colvin EK; Vafaee F; Mok SC; Howell VM; Samimi G, 2015, 'Differential expression of long non-coding RNAs in ovarian cancer-associated fibroblasts versus normal ovarian fibroblasts', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, Philadelphia, PA, Vol. 75, presented at 106th Annual Meeting of the American-Association-for-Cancer-Research (AACR), Philadelphia, PA, 18 April 2015 - 22 April 2015, http://dx.doi.org/10.1158/1538-7445.AM2015-2885


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