Leaderboards/Single-cell and spatial transcriptomics

Single-cell and spatial transcriptomics

Last updated July 15, 2026

Rising Stars

Fresh ink, massive impact

Researchers

1
Yuhan Hao
Jilin University
2
Haotian Cui
University Health Network
3
Sunny Z. Wu
Garvan Institute of Medical Research
4
Danielle Maeser
University of Minnesota
5
Dylan Cable
University of Michigan
6
Vitalii Kleshchevnikov
Wellcome Sanger Institute
7
Hansruedi Mathys
University of Pittsburgh
8
Cecilia Domínguez Conde
Human Technopole
9
Giovanni Palla
Helmholtz Zentrum München
10
Zhuoqing Fang
Stanford Medicine

Papers

1
scGPT: toward building a foundation model for single-cell multi-omics using generative AI
Nature Methods|2024
1k cit.
2
Single-cell multiregion dissection of Alzheimer’s disease
Nature|2024
267 cit.
3
Towards multimodal foundation models in molecular cell biology
Nature|2025
88 cit.
4
DeepVelo: deep learning extends RNA velocity to multi-lineage systems with cell-specific kinetics
Genome biology|2024
55 cit.
5
Integration of Computational Pipeline to Streamline Efficacious Drug Nomination and Biomarker Discovery in Glioblastoma
Cancers|2024
4 cit.
6
Fibroblastic FLT3L supports lymph node dendritic cells in the interfollicular niche
Nature Immunology|2025
4 cit.
7
Multi-Dimensional Geometric Feature-Based Calibration Method for LiDAR and Camera Fusion
Unknown Journal|2024
3 cit.
8
Abstract A015: Predicting efficacious drugs and drug-biomarker relationships for targeted glioblastoma treatment
Cancer Research|2024
0 cit.
9
Fibroblast TGF-β3 promotes tissue-residency and survival of CD8 T cells in barrier tissues and tumors
bioRxiv (Cold Spring Harbor Laboratory)|2026
0 cit.

Emerging Leaders

Drafting the new consensus

Researchers

1
Peter Smibert
10X Genomics (United States)
2
Evan Z. Macosko
Broad Institute
3
Orit Rozenblatt–Rosen
Broad Institute
4
Fei Chen
Broad Institute
5
Benjamin Izar
Columbia University Irving Medical Center
6
Marius Pachitariu
Janelia Research Campus
7
Sanja Vicković
Science for Life Laboratory
8
Guoji Guo
Zhejiang University
9
Smita Krishnaswamy
Yale University
10
Fredrik Salmén
HES-SO Genève

Papers

1
Cellpose 2.0: how to train your own model
Nature Methods|2022
1.4k cit.
2
Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease
Nature Neuroscience|2022
563 cit.
3
Spike sorting with Kilosort4
Nature Methods|2024
390 cit.
4
Cellpose3: one-click image restoration for improved cellular segmentation
Nature Methods|2025
306 cit.
5
High-throughput total RNA sequencing in single cells using VASA-seq
Nature Biotechnology|2022
241 cit.
6
Dissecting the treatment-naive ecosystem of human melanoma brain metastasis
Cell|2022
211 cit.
7
Early Alzheimer’s disease pathology in human cortex involves transient cell states
Cell|2023
208 cit.
8
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics
Nature|2023
198 cit.
9
SM-Omics is an automated platform for high-throughput spatial multi-omics
Nature Communications|2022
193 cit.
10
The molecular cytoarchitecture of the adult mouse brain
Nature|2023
183 cit.

Current Senior Leaders

Wrote the book, still writing it

Researchers

1
Aviv Regev
Broad Institute
2
Rahul Satija
New York Genome Center
3
Ash A. Alizadeh
California Institute for Regenerative Medicine
4
Fabian J. Theis
Helmholtz Zentrum München
5
Sarah A. Teichmann
Stem Cell Institute
6
Cole Trapnell
University of Washington
7
John C. Marioni
European Bioinformatics Institute
8
Sten Linnarsson
Karolinska Institutet
9
Jay Shendure
Brotman Baty Institute
10
Garry P. Nolan
Stanford University

Papers

1
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Nature Biotechnology|2011
22.6k cit.
2
Comprehensive Integration of Single-Cell Data
Cell|2019
16.9k cit.
3
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Nature Biotechnology|2010
16.5k cit.
4
Integrated analysis of multimodal single-cell data
Cell|2021
16k cit.
5
Robust enumeration of cell subsets from tissue expression profiles
Nature Methods|2015
14.1k cit.
6
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Nature Protocols|2012
12.9k cit.
7
TopHat: discovering splice junctions with RNA-Seq
Bioinformatics|2009
12.1k cit.
8
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
Nature|2000
10k cit.
9
SCANPY: large-scale single-cell gene expression data analysis
Genome biology|2018
9.3k cit.
10
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Nature Protocols|2013
9.1k cit.

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