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F. Vafaee · SciRah

Researcher profile · Semantic Scholar

F. Vafaee

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F. Vafaee — researcher profile on SciRah

h-index: 22
Works: 100
Citations: 1,892

Most-cited papers

Exosomal microRNA signatures in multiple sclerosis reflect disease status
S. Ebrahimkhani, F. Vafaee, P. Young, Suzy S. J. Hur +6 more
2017Scientific Reports251 citations Open access
Semantic Scholar
Intratumoral heterogeneity identified at the epigenetic, genetic and transcriptional level in glioblastoma
Nicole R. Parker, A. Hudson, Peter Khong, J. Parkinson +8 more
2016Scientific Reports159 citations Open access
Semantic Scholar
Deep sequencing of circulating exosomal microRNA allows non-invasive glioblastoma diagnosis
S. Ebrahimkhani, F. Vafaee, S. Hallal, H. Wei +9 more
2018bioRxiv148 citations Open access
Semantic Scholar
In silico prediction of physical protein interactions and characterization of interactome orphans
M. Kotlyar, C. Pastrello, Flavia Pivetta, A. L. Sardo +13 more
2014Nature Methods145 citations
Semantic Scholar
Global redox proteome and phosphoproteome analysis reveals redox switch in Akt
Zhiduan Su, James G. Burchfield, Peng-Yi Yang, Sean J. Humphrey +20 more
2019Nature Communications128 citations Open access
Semantic Scholar
Bayesian network hybrid learning using an elite-guided genetic algorithm
C. Contaldi, F. Vafaee, P. Nelson
2019Artificial Intelligence Review56 citations
Semantic Scholar
A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis
F. Vafaee, C. Diakos, M. Kirschner, G. Reid +6 more
2018npj Systems Biology and Applications52 citations Open access
Semantic Scholar
Serum Exosome MicroRNAs Predict Multiple Sclerosis Disease Activity after Fingolimod Treatment
S. Ebrahimkhani, H. Beadnall, Chen-Yu Wang, C. Suter +3 more
2019Molecular Neurobiology49 citations
Semantic Scholar
Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC
Shruthi Subramanian, J. Thoms, Y. Huang, P. Cornejo +25 more
2023Blood47 citations Open access
Semantic Scholar
Plasma lipidome variation during the second half of the human lifespan is associated with age and sex but minimally with BMI
M. Wong, N. Braidy, Russell Pickford, F. Vafaee +7 more
2019PLoS ONE46 citations Open access
Semantic Scholar
In-network query processing in mobile P2P databases
Bo Xu, F. Vafaee, O. Wolfson
2009ACM SIGSPATIAL International Workshop on Advances in Geographic Information Systems42 citations
Semantic Scholar
Functional prediction of long non-coding RNAs in ovarian cancer-associated fibroblasts indicate a potential role in metastasis
F. Vafaee, E. Colvin, S. Mok, V. Howell +1 more
2017Scientific Reports40 citations Open access
Semantic Scholar
Expression of long noncoding RNAs in cancer‐associated fibroblasts linked to patient survival in ovarian cancer
E. Colvin, V. Howell, S. Mok, G. Samimi +1 more
2020Cancer Science33 citations Open access
Semantic Scholar
Unraveling the mechanistic complexity of Alzheimer's disease through systems biology
J. Rollo, Nahid Banihashemi, F. Vafaee, John W. Crawford +2 more
2016Alzheimer's & Dementia32 citations
Semantic Scholar
Benchmarking ensemble machine learning algorithms for multi-class, multi-omics data integration in clinical outcome prediction
Annette Spooner, M. K. Moridani, Barbra Toplis, J. Behary +5 more
2024Briefings Bioinform.28 citations Open access
Semantic Scholar
CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes
M. Bayati, H. Rabiee, M. Mehrbod, F. Vafaee +3 more
2018Scientific Reports26 citations Open access
Semantic Scholar
The Quest for Non-Invasive Diagnosis: A Review of Liquid Biopsy in Glioblastoma
M. Elias, Harry Hadjiyiannis, F. Vafaee, K. Scott +3 more
2025Cancers25 citations Open access
Semantic Scholar
Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis
F. Safari, Cheka Kehelpannala, Azadeh Safarchi, A. Batarseh +1 more
2023Cancers24 citations Open access
Semantic Scholar
Dynamic Hybrid Model to Forecast the Spread of COVID-19 Using LSTM and Behavioral Models Under Uncertainty
S. M. Zandavi, T. Rashidi, F. Vafaee
2020IEEE Transactions on Cybernetics23 citations Open access
Semantic Scholar
Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases
F. Vafaee
2016Scientific Reports23 citations Open access
Semantic Scholar
Learning the structure of large-scale bayesian networks using genetic algorithm
F. Vafaee
2014Annual Conference on Genetic and Evolutionary Computation23 citations
Semantic Scholar
A Genetic Algorithm that Incorporates an Adaptive Mutation Based on an Evolutionary Model
F. Vafaee, P. Nelson
2009International Conference on Machine Learning and Applications23 citations
Semantic Scholar
Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs
J. Thoms, Feng Yan, Henry R. Hampton, S. Davidson +52 more
2025Nature Communications20 citations Open access
Semantic Scholar
An introduction to representation learning for single-cell data analysis
Ihuan Gunawan, F. Vafaee, Erik H. W. Meijering, J. Lock
2023Cell Reports Methods20 citations Open access
Semantic Scholar
ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data
F. Vafaee, J. Krycer, Xiuquan Ma, T. Burykin +2 more
2016PLoS ONE20 citations Open access
Semantic Scholar
An explorative and exploitative mutation scheme
F. Vafaee, P. Nelson
2010IEEE Congress on Evolutionary Computation20 citations Open access
Semantic Scholar
Supervised Application of Internal Validation Measures to Benchmark Dimensionality Reduction Methods in scRNA-seq Data
Forrest C Koch, G. J. Sutton, I. Voineagu, F. Vafaee
2020bioRxiv19 citations Open access
Semantic Scholar
The transcriptional response to oxidative stress is part of, but not sufficient for, insulin resistance in adipocytes
Rima Chaudhuri, J. Krycer, D. Fazakerley, Kelsey H. Fisher-Wellman +6 more
2018Scientific Reports18 citations Open access
Semantic Scholar
Anti-cancer potential of synergistic phytochemical combinations is influenced by the genetic profile of prostate cancer cell lines
C. Gano, S. Fatima, T. Failes, G. Arndt +8 more
2023Frontiers in Nutrition17 citations Open access
Semantic Scholar
Harnessing Liquid Biopsies to Guide Immune Checkpoint Inhibitor Therapy
S. Fatima, Ya-Feng Ma, Azadeh Safrachi, S. Haider +6 more
2022Cancers17 citations Open access
Semantic Scholar
A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond
A. Azad, M. Dinarvand, A. Nematollahi, J. Swift +2 more
2020Briefings Bioinform.16 citations Open access
Semantic Scholar
Balancing the exploration and exploitation in an adaptive diversity guided genetic algorithm
F. Vafaee, György Turán, P. Nelson, T. Berger-Wolf
2014IEEE Congress on Evolutionary Computation16 citations
Semantic Scholar
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
F. Vafaee, D. Rosu, Fiona Broackes-Carter, I. Jurisica
2013BMC Systems Biology16 citations Open access
Semantic Scholar
Fotomics: fourier transform-based omics imagification for deep learning-based cell-identity mapping using single-cell omics profiles
S. M. Zandavi, Derong Liu, Vera Chung, Ali Anaissi +1 more
2022bioRxiv14 citations Open access
Semantic Scholar
An update on novel approaches for diagnosis and treatment of SARS-CoV-2 infection
Azadeh Safarchi, S. Fatima, Z. Ayati, F. Vafaee
2021Cell & Bioscience14 citations Open access
Semantic Scholar
Small and Large Extracellular Vesicles Derived from Pleural Mesothelioma Cell Lines Offer Biomarker Potential
T. Ahmadzada, Abhishek Vijayan, F. Vafaee, Ali Azimi +5 more
2023Cancers13 citations Open access
Semantic Scholar
Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies
W. Domanova, J. Krycer, Rima Chaudhuri, Peng-Yi Yang +5 more
2016PLoS ONE13 citations Open access
Semantic Scholar
Adaptively Evolving Probabilities of Genetic Operators
F. Vafaee, Wei-Min Xiao, P. Nelson, Chi Zhou
20082008 Seventh International Conference on Machine Learning and Applications13 citations
Semantic Scholar
AI‐powered prediction of HCC recurrence after surgical resection: Personalised intervention opportunities using patient‐specific risk factors
S. M. Zandavi, Christy Kim, Thomas Goodwin, Cynthuja Thilakanathan +16 more
2024Liver international (Print)12 citations Open access
Semantic Scholar
Human Group IIA Phospholipase A2—Three Decades on from Its Discovery
K. Scott, T. J. Mann, S. Fatima, Mila Sajinovic +13 more
2021Molecules12 citations Open access
Semantic Scholar
Pharmacodynamic Functions of Synthetic Derivatives for Treatment of Methicillin-Resistant Staphylococcus aureus (MRSA) and Mycobacterium tuberculosis
M. Dinarvand, M. Spain, F. Vafaee
2020Frontiers in Microbiology12 citations Open access
Semantic Scholar
3D-IncNet: Head and Neck (H&N) Primary Tumors Segmentation and Survival Prediction
Abdul Qayyum, A. Benzinou, Imran Razzak, Moona Mazher +3 more
2024IEEE journal of biomedical and health informatics10 citations
Semantic Scholar
Extracellular vesicles from biological fluids as potential markers in castration resistant prostate cancer
Wendy W Y Choi, Catherine Sánchez, Jiao-Jiao Li, M. Dinarvand +8 more
2022Journal of Cancer Research and Clinical Oncology10 citations Open access
Semantic Scholar
Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods
Abhishek Vijayan, S. Fatima, A. Sowmya, F. Vafaee
2022bioRxiv10 citations Open access
Semantic Scholar
Integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action
A. M. Azad, S. Fatima, A. Capraro, Shafagh A. Waters +1 more
2021Patterns10 citations Open access
Semantic Scholar
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
J. Thoms, Forrest C. Koch, Alireza Raei, Shruthi Subramanian +3 more
2023Nucleic Acids Research9 citations Open access
Semantic Scholar
Disentangling single-cell omics representation with a power spectral density-based feature extraction
S. M. Zandavi, Forrest C Koch, Abhishek Vijayan, Fabio Zanini +3 more
2021bioRxiv9 citations Open access
Semantic Scholar
TDAview: an online visualization tool for topological data analysis
Kieran Walsh, Mircea A. Voineagu, F. Vafaee, I. Voineagu
2020Bioinform.9 citations
Semantic Scholar
Ageing impairs the airway epithelium defence response to SARS-CoV-2
A. Capraro, S. Wong, A. Adhikari, K. Allan +17 more
2021bioRxiv8 citations Open access
Semantic Scholar
The role of crossover operator in bayesian network structure learning performance: a comprehensive comparative study and new insights
C. Contaldi, F. Vafaee, P. Nelson
2017Annual Conference on Genetic and Evolutionary Computation8 citations
Semantic Scholar

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