By Associate Professor Fatemeh Vafaee

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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