By Associate Professor Fatemeh Vafaee

Journal articles

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, http://dx.doi.org/10.1186/s12859-016-0901-4

Vafaee F, 2016, 'Using multi-objective optimization to identify dynamical network biomarkers as early-warning signals of complex diseases', Scientific Reports, 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, 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, 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, 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 10h International Conference on Computer and Knowledge Engineering, ICCKE 2020, pp. 540 - 543, http://dx.doi.org/10.1109/ICCKE50421.2020.9303686

Colvin EK; Howell VM; Mok SC; Samimi G; Vafaee F, 2019, 'Abstract TMIM-067: EXPRESSION OF LNCRNAS IN OVARIAN CANCER-ASSOCIATED FIBROBLASTS IS ASSOCIATED WITH PATIENT SURVIVAL', in Clinical Cancer Research, American Association for Cancer Research (AACR), http://dx.doi.org/10.1158/1557-3265.ovcasymp18-tmim-067

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, AUSTRALIA, MS Res Australia, Sydney, pp. NP17 - NP17, presented at Progress in MS Research Conference, AUSTRALIA, MS Res Australia, Sydney, 11 October 2017 - 13 October 2017, https://www.webofscience.com/api/gateway?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', 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, IRELAND, Dublin, 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), IRELAND, Dublin, 10 July 2015, https://www.webofscience.com/api/gateway?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, DC, Washington, presented at AACR Special Conference on Advances in Brain Cancer Research, DC, Washington, 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, '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; 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, 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

de St Groth BF; McGuire H; Kao S; McNeil C; Hersey P; Boyer M; Vafaee F; Choi C; Kwong C-TJ, 2021, 'Predictive immune signatures for cancer immunotherapy - From bench to bedside', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, Vol. 17, pp. 69 - 70, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000693805000133&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

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, WA, Seattle, Vol. 25, pp. 154 - 154, presented at 12th Rivkin-Centre Biennial Ovarian Cancer Research Symposium, WA, Seattle, 13 September 2018 - 15 September 2018, https://www.webofscience.com/api/gateway?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, PA, Philadelphia, Vol. 75, presented at 106th Annual Meeting of the American-Association-for-Cancer-Research (AACR), PA, Philadelphia, 18 April 2015 - 22 April 2015, http://dx.doi.org/10.1158/1538-7445.AM2015-2885

Working Papers

Vafaee F; Gallego-Ortega D; Zanini F; Zandavi SM; Koch F; Valdes Mora F, 2021, Disentangling single-cell omics representation with a power spectral density-based feature extraction, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/2021.10.25.465657

Preprints

Su Z; Fang M; Smolnikov A; Vafaee F; Dinger M; Oates E, 2024, Genes in Humans and Mice: Insights from Deep learning of 777K Bulk Transcriptomes, http://dx.doi.org/10.1101/2024.04.01.587517

Su Z; Fang M; Smolnikov A; Dinger M; Oates E; Vafaee F, 2024, Multifaceted Representation of Genes via Deep Learning of Gene Expression Networks, http://dx.doi.org/10.1101/2024.03.07.583777

Lock J; Gunawan I; Kohane F; Nguyen K; Zheng Y; Neumann D; Vafaee F; Meijering E, 2024, Seeing more with less: Extensible Immunofluorescence (ExIF) accessibly generates high-plexity datasets by integrating standard 4-plex imaging data, http://dx.doi.org/10.21203/rs.3.rs-4872456/v1

Aminzadeh F; Wu J; He J; Saberi M; Vafaee F, 2024, Single-Cell Data Integration and Cell Type Annotation through Contrastive Adversarial Open-set Domain Adaptation, http://dx.doi.org/10.1101/2024.10.04.616599

Besharatifard M; Vafaee F, 2023, A Review on Graph Neural Networks for Predicting Synergistic Drug Combinations, http://dx.doi.org/10.21203/rs.3.rs-3318384/v1

Subramanian S; Subramanian S; Thoms JAI; Huang Y; Cornejo P; Koch F; Jacquelin S; Shen S; Song E; Joshi S; Brownlee C; Woll P; Fajardo DC; Beck D; Curtis D; Yehson K; Antonenas V; Brien TO; Trickett A; Powell J; Lewis I; Pitson S; Gandhi M; Lane S; Vafaee F; Wong E; Göttgens B; Rokny HA; Wong JWH; Pimanda J, 2023, Cell Type-Specific Regulation by a Heptad of Transcription Factors in Human Hematopoietic Stem and Progenitor Cells, http://dx.doi.org/10.1101/2023.04.18.537282

Anaissi A; Zandavi SM; Suleiman B; Alyassine W; Braytee A; Vafaee F, 2022, A Benchmark of Pre-processing Effect on Single Cell RNA Sequencing Integration Methods, http://dx.doi.org/10.21203/rs.3.rs-2249309/v1

Choi WY; Sánchez C; Li JJ; Dinarvand M; Adomat H; Ghaffari M; Khoja L; Vafaee F; Joshua AM; Chi KN; Guns EST; Hosseini-Beheshti E, 2022, Extracellular vesicles from biological fluids as potential biomarkers for prostate cancer, http://dx.doi.org/10.21203/rs.3.rs-1948091/v1

Liu D; Zandavi SM; Chung V; Anaissi A; Vafaee F, 2022, Omics Imagification: Transforming High-throughput Molecular Representation of a Cell into an Image, http://dx.doi.org/10.21203/rs.3.rs-1919175/v1

Vijayan A; Fatima S; Sowmya A; Vafaee F, 2022, Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods, http://dx.doi.org/10.1101/2022.03.13.483368

Mandal A; Priyam S; Chan HH; Gouveia BM; Guitera P; Song Y; Baker MAB; Vafaee F, 2022, Computer-aided diagnosis of reflectance confocal images to differentiate between lentigo maligna (LM) and atypical intraepidermal melanocytic proliferation (AIMP), http://dx.doi.org/10.1101/2022.05.10.491423

Dinarvand M; Kock F; Al Mouiee D; Vuong K; Vijayan A; Tanzim AF; Azad AKM; Penesyan A; Castaño-Rodríguez N; Vafaee F, 2022, dSeqSb: A systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data, http://dx.doi.org/10.1101/2022.02.28.482417

Zandavi SM; Liu D; Chung V; Anaissi A; Vafaee F, 2022, Fotomics: Fourier transform-based omics imagification for deep learning-based cell-identity mapping using single-cell omics profiles, http://dx.doi.org/10.1101/2022.07.08.499309

Khazaal A; Zandavi SM; Smolnikov A; Fatima S; Vafaee F, 2022, Pan-cancer Analyses reveal functional similarities of three lncRNAs across multiple tumors, http://dx.doi.org/10.1101/2022.03.14.22272396

Azad AKM; Fatima S; Capraro A; Waters SA; Vafaee F, 2021, An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action, http://dx.doi.org/10.33774/chemrxiv-2021-tk6rt-v2

Azad AKM; Fatima S; Capraro A; Waters SA; Vafaee F, 2021, An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action, http://dx.doi.org/10.26434/chemrxiv-2021-tk6rt-v2

Safarchi A; Fatima S; Ayati Z; Vafaee F, 2021, An Update on Novel Approaches for Diagnosis and Treatment of SARS-CoV-2 Infection, http://dx.doi.org/10.31219/osf.io/xg6z5

Azad AKM; Fatima S; Vafaee F, 2020, An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action, http://dx.doi.org/10.26434/chemrxiv.13271096

Batarseh AM; Vafaee F; Hosseini-Beheshti E; Chen A; Cohen A; Juillard A; Hunt NH; Mariani M; Mitchell T; Raymond Grau GE, 2020, Lipidome profiles of plasma microvesicles differ in experimental cerebral malaria, compared to malaria without neurological complications, http://dx.doi.org/10.1101/2020.07.28.224170

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, http://dx.doi.org/10.26434/chemrxiv.12376505.v1

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, http://dx.doi.org/10.26434/chemrxiv.12376505

Zandavi SM; Rashidi TH; Vafaee F, 2020, Forecasting the Spread of Covid-19 Under Control Scenarios Using LSTM and Dynamic Behavioral Models, http://dx.doi.org/10.48550/arxiv.2005.12270

Rashidi TH; Shahriari S; Azad AKM; Vafaee F, 2020, Real-time time-series modelling for prediction of COVID-19 spread and intervention assessment, http://dx.doi.org/10.1101/2020.04.24.20078923

Koch F; Sutton G; Voineagu I; Vafaee F, 2020, Supervised Application of Internal Validation Measures to Benchmark Dimensionality Reduction Methods in scRNA-seq Data, http://dx.doi.org/10.1101/2020.10.29.361451

Bayati M; Rabiee HR; Mehrbod M; Vafaee F; Ebrahimi D; Forrest A; Alinejad-Rokny H, 2018, CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes, http://dx.doi.org/10.1101/424960

Ebrahimkhani S; Vafaee F; Hallal S; Wei H; Lee MYT; Young PE; Satgunaseelan L; Shivalingam B; Suter CM; Buckland ME; Kaufman KL, 2018, Deep sequencing of circulating exosomal microRNA allows non-invasive glioblastoma diagnosis, http://dx.doi.org/10.1101/342154

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