Fatemeh Vafaee

Senior Lecturer

Academic Experience:

  • 2017 - Present: Senior Lecturer, School of BABS, UNSW Sydney
  • 2013 - 2017: Research Fellow, Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney
  • 2011 - 2013: Postdoctral Research Associate, University of Toronto, University Health Network and Ontario Cancer Institute
  • 2007 - 2011: PhD computer Science, Artificial Intelligence (AI), University of Illinois in Chicago

Research Interests and Contribution:

Dr Vafaee is a Senior Lecturer in Computational Biomedicine and Bioinformatics. She has launched (2017) and leads AI-enhanced Biomedicine Laboratory at UNSW (www.VafaeeLab.com) which currently holds 15 members collaboratively working on deploying advanced AI techniques to address variety of biomedical pressing problems. Relying on multidisciplinary expertise and cross-faculty collaborations, Dr Vafaee and her team are developing advanced machine-learning methods and deep-learning models that leverage large omics data to find hidden structures within them, account for complex interactions among the measurements, integrate heterogeneous data and make accurate predictions in different biomedical applications ranging from single-cell sequencing analysis and multi-omics biomarker discovery to disease functional genomics and drug repositioning.

Dr Vafaee has a strong track record of multidisciplinary research leadership and industrial engagement. Her research has been attracted >$5.7M for over 10 research projects and industrial partnership grants including prestigious schemes of Cooperative Research Centre Project (CRC-P, 2019) and Medical Research Future Fund (MRFF, 2020). She has co-authored 35 publications (68% first/corresponding author) in prestigious venues—e.g., Briefings in Bioinformatics, Nature Methods, npj Systems Biology & Applications, Molecular Neurobiology, Precision Oncology and Nature Communications—demonstrating her research leadership and substantive contribution in methodological changes. Dr Vafaee's research has been featured in Faculty of Science Capability Statement in Health Science and UNSW Capability Statement in Biomedical Research.

Leadership Activities and Executive memberships:

Editorial Activities:

  • Associate Editor of Artificial Intelligence Review (IF: 5.095, Q1 in AI and Computer Science)
  • Associate Editor of PLoS One (IF: 2.776, Q1 in Genetics and Molecular Biology)
  • Associate Editor of Entropy, Genomics Special Issue (IF: 2.305, Q1 in Physics)

PUBLICATIONS

Journal articles
add
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
2020
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
2020
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
2020
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
2020
Walsh K; Voineagu MA; Vafaee F; Voineagu I, 2020, 'TDAview: an online visualization tool for topological data analysis.', Bioinformatics, http://dx.doi.org/10.1093/bioinformatics/btaa600
2020
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
2019
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
2019
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
2018
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
2018
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
2018
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
2018
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
2018
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
2017
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
2017
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
2017
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
2016
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
2016
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
2016
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
2016
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
2016
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
2014
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
2013
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
2008
Conference Abstracts
add
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
2018
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
2015
Conference Papers
add
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=891bb5ab6ba270e68a
2017
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
2017
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
2015
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
2015
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
2014
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
2014
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
2014
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
2010
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
2010
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
2009
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
2009
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
2009
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
2008