By Professor Fatemeh Vafaee

Preprints

Chen S; Zahedi R; Chhuo L; Nguyen R; BaghGolshani M; Beheshti A; Grosser M; Yang M; Farbehi N; Lovell N; Argha A; Porntaveetusm T; Vafaee F; Ye Y; Alinejad-Rokny H, 2026, Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation, http://dx.doi.org/10.48550/arxiv.2607.17227

Beheshti E; Dharwal V; Lay W; Zelei R; Azimi A; Wang L; Huang T; Zhuang L; Grau G; Clarke S; Kao S; Vafaee F; Kovacevic Z, 2026, miRNA cargo from pleural mesothelioma-derived extracellular vesicles reprograms fibroblasts to a cancer-associated phenotype, http://dx.doi.org/10.21203/rs.3.rs-9648282/v1

Thoms JAI; Hampton HR; Boon PLS; Stonehouse O; Zou X; Chung HM; Koch FC; Yan F; Joshi S; Nguyen MNT; Hung D; Wright DC; Vafaee F; Polizzotto MN; Swarbrick A; Huang Y; Jolly CJ; Zanini F; Pimanda JE, 2026, Single cell multiomics reveal clonal and functional dynamics of MDS stem/progenitor cells during hypomethylating therapy, http://dx.doi.org/10.64898/2026.03.13.711488

Khazaal A; Vafaee F, 2025, From Static to Dynamic: Exploring Temporal Networks in Systems Biology, http://dx.doi.org/10.48550/arxiv.2505.10741

Frisendahl C; Gemzell-Danielsson K; Nair K; Koch F; Menezes J; Sheikhi M; Dahlgren K; Alnahal W; Lindgren K; Bohlin T; Olofsson J; Töhönen V; Vafaee F; Lalitkumar PG; Boggavarapu NR; Faridani O, 2025, Blastocoel fluid RNA predicts pregnancy outcome in assisted reproduction, http://dx.doi.org/10.1101/2025.03.09.641486

Rafeie M; Vafaee F; Faridani O, 2025, Medlib: A Feature-Rich C/C++ Library for Exact Alignment of Nanopore Sequences Using Multiple Edit Distance, http://dx.doi.org/10.1101/2025.05.01.651420

Spooner A; Moridani MK; Safarchi A; Maher S; Vafaee F; Zekry A; Sowmya A, 2024, Multi-omics data integration for early diagnosis of hepatocellular carcinoma (HCC) using machine learning, http://dx.doi.org/10.48550/arxiv.2409.13791

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

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

Shahriari S; Hossein Rashidi T; Azad AKM; Vafaee F, 2021, COVIDSpread: real-time prediction of COVID-19 spread based on time-series modelling, http://dx.doi.org/10.12688/f1000research.73969.1

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

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

Azad AKM; Vafaee F, 2019, Single cell data explosion: Deep learning to the rescue, http://dx.doi.org/10.48550/arxiv.1901.06105

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

Azad A; Dinarvand M; Nematollahi A; Swift J; Lutze-Mann L; Vafaee F, A Comprehensive Integrated Drug Similarity Resource for In-Silico Drug Repositioning and Beyond, http://dx.doi.org/10.26434/chemrxiv.12376505.v1

Azad A; Dinarvand M; Nematollahi A; Swift J; Lutze-Mann L; Vafaee F, A Comprehensive Integrated Drug Similarity Resource for In-Silico Drug Repositioning and Beyond, http://dx.doi.org/10.26434/chemrxiv.12376505

Huang T; Koch FC; Peake DA; Adam K-P; David M; Li D; Heffernan K; Lim A; Hurrell JGH; Preston S; Baterseh A; Vafaee F, A Cross-Cohort Validated Plasma Lipid Biomarker Assay for Early Breast Cancer Detection Using Machine Learning, http://dx.doi.org/10.64898/2026.04.23.26351564

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

Azad A; Fatima S; Vafaee F, 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

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

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

Bayati M; Rabiee HR; Mehrbod M; Vafaee F; Ebrahimi D; Forrest ARR; Alinejad-Rokny H, 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

Subramanian S; Thoms JAI; Huang Y; Cornejo P; Koch FC; Jacquelin S; Shen S; Song E; Joshi S; Brownlee C; Woll PS; Fajardo DC; Beck D; Curtis DJ; Yehson K; Antonenas V; Brien TO; Trickett A; Powell JA; Lewis ID; Pitson SM; Gandhi MK; Lane SW; Vafaee F; Wong ES; Göttgens B; Rokny HA; Wong JWH; Pimanda JE, 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

Bhuyan GS; Yan F; Nguyen MNT; Chung HM; Zou X; Gullapalli V; Vaughan L; Stonehouse O; Hampton HR; Shen S; Truong P; Dissanayake R; Ghodousi ES; Joshi S; Koch FC; Zanini F; Vafaee F; Huang Y; Thoms JAI; Faridani OR; Jolly CJ; Pimanda JE, Cell-state-specific mechanisms of 5-azacytidine response in myelodysplastic neoplasms, http://dx.doi.org/10.64898/2026.04.26.720516

Mann TJ; Zheng Y; Khan T; Huang T; Nindra U; Ma Y; James A; Neumann DP; Kohane FV; Gunawan I; Vafaee F; Chua W; de Souza P; Roberts TL; Becker TM; Lock JG, Deep multiplexed 50-marker imaging of circulating tumor cells expands actionable biomarker profiling for precision oncology, http://dx.doi.org/10.1101/2025.10.23.684075

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

Dinarvand M; Kock F; Al Mouiee D; Vuong K; Vijayan A; Tanzim AF; Azad A; Penesyan A; Castaño-Rodríguez N; Vafaee F, 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

Kohane FV; Johnstone C; Neumann DP; Gunawan I; Huang T; Vafaee F; Chaffer CL; Lock JG, Epithelial–mesenchymal cell state heterogeneity predetermines differential phospho-signaling responses to EGF stimulation, http://dx.doi.org/10.1101/2025.07.05.658545

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, Extracellular vesicles from biological fluids as potential biomarkers for prostate cancer, http://dx.doi.org/10.21203/rs.3.rs-1948091/v1

Zandavi SM; Liu D; Chung V; Anaissi A; Vafaee F, 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

Safari F; Tree JJ; Vafaee F, From Nucleotides to Numbers: A Comprehensive Review of RNA Feature Extraction Methods for Computational Modelling, http://dx.doi.org/10.20944/preprints202508.1739.v1

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

Safari F; Mediati DG; Alquethamy S; Tree JJ; Vafaee F, Molecular Determinants of Functional Bacterial sRNA–mRNA Interactions Revealed by Integrating RNA Interactomes and Interpretable Machine Learning, http://dx.doi.org/10.64898/2026.08.26.747384

Nguyen R; Vafaee F, Multi-Omics Prognostic Marker Discovery and Survival Modeling: A Case Study on Pan-Cancer Survival Analyses in Women’s Cancers, http://dx.doi.org/10.1101/2025.01.08.25320212

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

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

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

Lock J; Gunawan I; Kohane F; Nguyen K; Zheng Y; Neumann D; Vafaee F; Meijering E, 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

Umashankar B; Capraro A; Vijayan A; Wong SL; Nielsen BU; Zhong L; Raftery M; Allan K; Ooi CY; Sivam S; Visser S; Prentice BJ; Fawcett L; Kovacevic Z; Eliasson L; Faurholt-Jepsen D; Jaffe A; Shaw JA; Vafaee F; Waters SA, Serum Exosomal Multi-Omic Signatures Stratify Glucose Tolerance in Cystic Fibrosis and Reveal Partial Therapeutic Reprogramming by CFTR Modulators, http://dx.doi.org/10.1101/2025.07.07.25331056

Aminzadeh F; Wu J; He J; Saberi M; Vafaee F, 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

Koch FC; Sutton GJ; Voineagu I; Vafaee F, 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

Elias MG; Hadjiyiannis H; Vafaee F; Scott KF; de Souza P; Becker TM; Fatima S, The Quest for Non-Invasive Diagnosis: A Review of Liquid Biopsy in Glioblastoma, http://dx.doi.org/10.20944/preprints202508.0558.v1

Heydari MJ; Lye B; Mansouri P; Marsland T; Pamulapati K; Vary R; Allen H; Simpson KJ; Lock JG; McKenna J; Vafaee F, Uncertainty-Aware Deep Learning for Multi-Metric and Dose-Specific Prediction of Drug Synergy, http://dx.doi.org/10.1101/2025.11.05.686895

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