By Dr Nona Farbehi

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

Liang Y; Chhuo L; Argha A; Farbehi N; Chen L; Alizadehsani R; Hosseinzadeh M; Yang M; Porntaveetusm T; Ye Y; Alinejad-Rokny H, 2026, Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability, http://dx.doi.org/10.48550/arxiv.2604.05478

Zahedi R; Argha A; Farbehi N; Bakhshayeshi I; Ye Y; Lovell NH; Alinejad-Rokny H, 2025, SemanticST: Spatially Informed Semantic Graph Learning for Clustering, Integration, and Scalable Analysis of Spatial Transcriptomics, http://dx.doi.org/10.48550/arxiv.2506.11491

Haghighattalab M; Karimi F; Farbehi N; Rnjak-Kovacina J, 2025, Evaluating Flow-Focused Microfluidic Device Fabrication Techniques for Silk Fibroin Microgel Production, http://dx.doi.org/10.1101/2025.02.02.636143

Liang Y; Abedini S; Farbehi N; Alinejad-Rokny H, 2024, How chromatin interactions shed light on interpreting non-coding genomic variants: opportunities and future direc-tions, http://dx.doi.org/10.48550/arxiv.2411.17956

Valdes-Mora F; Salomon R; Gloss B; Law AM; Castillo L; Murphy K; Venhuizen J; Magenau A; Papanicolau M; de la Fuente LR; Roden DL; Colino-Sanguino Y; Kikhtyak Z; Farbehi N; Conway JR; Oakes SR; Sikta N; O'Donoghue SI; Cox TR; Timpson P; Ormandy CJ; Ortega DG, 2020, Single Cell Transcriptomics Reveals Involution Mimicry During the Specification of the Basal Breast Cancer Subtype, http://dx.doi.org/10.2139/ssrn.3634808

Nazeen S; Wang X; Zielinski D; Lam I; Hallacli E; Xu P; Ethier E; Strom R; Zanella CA; Nithianandam V; Ritter D; Henderson A; Saurat N; Afroz J; Nutter-Upham A; Benyamini H; Copty J; Ravishankar S; Morrow A; Mitchel J; Neavin D; Gupta R; Farbehi N; Grundman J; Myers RH; Scherzer CR; Trojanowski JQ; Van Deerlin VM; Cooper AA; Lee EB; Erlich Y; Lindquist S; Peng J; Geschwind DH; Powell J; Studer L; Feany MB; Sunyaev SR; Khurana V, Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies, http://dx.doi.org/10.1101/2024.03.03.583145

Asli NS; Xaymardan M; Patrick R; Farbehi N; Cornwell J; Forte E; Waardenberg AJ; Janbandhu V; Kesteven S; Chandrakanthan V; Malinowska H; Reinhard H; Schofield P; Christ D; Ahmed I; Bouveret R; Srivastava S; Mishra RK; Dhawan J; Chong JJH; Nordon R; Macdonald P; Graham RM; Feneley M; Harvey RP, PDGFRα signaling in cardiac fibroblasts modulates quiescence, metabolism and self-renewal, and promotes anatomical and functional repair, http://dx.doi.org/10.1101/225979

Daniszewski MS; Senabouth A; Liang HH; Han X; Lidgerwood GE; Hernández D; Sivakumaran P; Clarke JE; Lim SY; Lees JG; Rooney L; Gulluyan L; Souzeau E; Graham SL; Chan C-L; Nguyen U; Farbehi N; Gnanasambandapillai V; McCloy RA; Clarke L; Kearns L; Mackey DA; Craig JE; MacGregor S; Powell JE; Pébay A; Hewitt AW, Retinal ganglion cell-specific genetic regulation in primary open angle glaucoma, http://dx.doi.org/10.1101/2021.07.14.452417

Valdes-Mora F; Salomon R; Gloss B; Law AM; Castillo L; Murphy KJ; Venhuizen J; Magenau A; Papanicolau M; de la Fuente LR; Roden DL; Colino-Sanguino Y; Kikhtyak Z; Farbehi N; Conway JR; Oakes SR; Sikta N; O’Donoghue SI; Cox TR; Timpson P; Ormandy CJ; Gallego-Ortega D, Single cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtype, http://dx.doi.org/10.1101/624890

Senabouth A; Daniszewski M; Lidgerwood GE; Liang HH; Hernández D; Mirzaei M; Zhang R; Han X; Neavin D; Rooney L; Sanchez IL; Gulluyan L; Paulo JA; Clarke L; Kearns LS; Gnanasambandapillai V; Chan C-L; Nguyen U; Steinmann AM; Zekanovic R; Farbehi N; Gupta VK; Mackey DA; Bylsma G; Verma N; MacGregor S; Guymer RH; Powell JE; Hewitt AW; Pébay A, Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration, http://dx.doi.org/10.1101/2021.08.19.457044

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