Author

Boaz Nadler

Weizmann Institute of ScienceORCID 0000-0002-9777-4576Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:clustering· 2 Approach:deep learning· 2 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Assay:scRNA-seq· 1 Assay:spatial transcriptomics· 1 Approach:statistical model· 1

Frequent Co-Authors

Nir YosefiD· 2 shared Artemii Bakulin· 1 shared Can ErgeniD· 1 shared Florian IngelfingeriD· 1 shared Giacomo CinnirellaiD· 1 shared Nathan LevyiD· 1 shared Pierre BoyeauiD· 1 shared Pini ZilberiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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2 shared papersEvolutionary Biology

Nir YosefORCID

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2 papers

Recent·Most cited

Can you trust your reconstructed lineage tree? A homoplasy-based approach for irreversible evolution

Pini Zilber, Sebastian Prillo, Yaara Neumeier, Nir Yosef, Boaz Nadler

This paper introduces a homoplasy-based method to assess lineage tree reliability using Cas9-induced mutations, showing it outperforms parsimony in simulations.

bioRxiv · Jul 27, 2025 · PreprintEvolutionary Biology

scVIVA: a probabilistic framework for representation of cells and their environments in spatial transcriptomics

Nathan Levy, Florian Ingelfinger, Artemii Bakulin, Giacomo Cinnirella, Pierre Boyeau, Boaz Nadler, Can Ergen, Nir Yosef

scVIVA is a deep generative model that integrates cell-intrinsic and neighboring gene expression to produce embeddings and gene profiles, revealing spatially restricted tumor-promoting endothelial cells and niche-associated T cell states in breast cancer.

bioRxiv · Jun 1, 2025 · PreprintBioinformatics