Author

Shadi Darvish Shafighi

Cancer Research UK Cambridge CenterORCID 0000-0003-0367-8864Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:human· 2 Approach:statistical model· 2 Approach:benchmark study· 1 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:clustering· 1 Research Focus:deconvolution· 1

Frequent Co-Authors

Ewa SzczurekiD· 2 shared Agnieszka GerasiD· 1 shared Akane Ota· 1 shared Alicja RączkowskaiD· 1 shared Amy E CulleniD· 1 shared Anna PiskorziD· 1 shared Cornelis A.M. van BergeniD· 1 shared Dominika NowisiD· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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2 shared papersBioinformatics

Ewa SzczurekORCID

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3 papers

Recent·Most cited

Cancer BiologybioRxivPreprintApr 30, 2026

scUnique: Measuring Ongoing Chromosomal Instability

Michael P Schneider, Shadi Darvish Shafighi, Amy E Cullen…·Florian M. Markowetz

scUnique measures ongoing chromosomal instability from single-cell whole genome sequencing data by identifying recent copy number aberrations in phylogenetic trees.

1 citation

humanwhole-genome sequencing

𝕏 PostBluesky

BioinformaticsGenome biologyPeer-reviewedNov 5, 2024

CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants

Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Darvish Shafighi…·Ewa Szczurek

CaClust integrates exomic, scRNA-seq, and BCR data to infer clone genotypes and cell-to-clone mappings in follicular lymphoma, revealing genotype-phenotype links.

3 citations

humanscRNA-seq

𝕏 PostBluesky

BioinformaticsGenome biologyPeer-reviewedMay 17, 2023

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

Agnieszka Geras, Shadi Darvish Shafighi, Kacper Domżał…·Ewa Szczurek

Celloscope deconvolves cell types in spatial transcriptomics data using marker genes, outperforming existing methods and accurately identifying brain structures and immune infiltrates.

32 citations

mousespatial transcriptomics

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