Author

Russell Kunes

Howard Hughes Medical Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:cell type annotation· 2 Research Focus:clustering· 2 Research Focus:gene regulatory network inference· 2 Assay:spatial transcriptomics· 2 Approach:statistical model· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Alejandra BrunaiD· 2 shared Andrew J. L. RothiD· 2 shared Andrew McPhersoniD· 2 shared Anubhav SinhaiD· 2 shared Bernd BodenmilleriD· 2 shared Carlos CaldasiD· 2 shared Ciara H. O’FlanaganiD· 2 shared Claire M. MulveyiD· 2 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Alejandra BrunaORCID

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Author profile →

3 papers

Recent·Most cited

Serval: A modular framework for decoding imaging based spatial transcriptomics data

Jenkin Tsui, Naila Adam, Woongcheol Choi, Luna Y Liu, C. Cárcamo Flores, Shadi Ansari, Esther Kong, Yukta Thapliyal, Hakwoo Lee, Shahid Haider, Issac Von Riedemann, Ciara H. O’Flanagan, Mohammad Al Sa’d, Bruno Albuquerque, Hamid Raza Ali, , Nicholas A. Walton

Serval is a modular framework for decoding spatial transcriptomics data that introduces Cosine, a method improving transcript recovery and correlation with expression references.

Bioinformatics · Sep 27, 2026Peer-reviewedBioinformatics

Supervised discovery of interpretable gene programs from single-cell data

Russell Kunes, Thomas Walle, Max Land, Tal Nawy, Dana Pe’er

This paper introduces Spectra, an algorithm that identifies and refines gene programs from single-cell data, outperforming existing methods in tumor immune contexts by improving interpretability and capturing cell-state changes.

Nature Biotechnology · Sep 21, 2023Peer-reviewedBioinformatics

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

Shahar Alon, Daniel Goodwin, Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G. Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C. Payne, Chun‐Chen Yao, Ho‐Jun Suk, , Kirsty Sawicka

ExSeq enables multiplexed RNA mapping at nanoscale resolution by expanding biological specimens for in situ sequencing.

Science · Jan 28, 2021Peer-reviewedGenomics