Insights, opportunities, and challenges provided by large cell atlases

Martin Hemberg; Federico Marini; Shila Ghazanfar; Ahmad Al Ajami; Najla Abassi; Benedict Anchang; Bérénice A. Benayoun; Yue Cao; Ken Chen; Yesid Cuesta-Astroz; Zachary DeBruine; Calliope A. Dendrou; Iwijn De Vlaminck; Katharina Imkeller; Ilya Korsunsky; Alex R. Lederer; Jessica Jingyi Li; Pieter Meysman; Clint L. Miller; Kerry A. Mullan; Uwe Ohler; Pratibha Panwar; Nikolaos Patikas; Jonas Schuck; Jacqueline H.Y. Siu; Timothy J. Triche; Alex Tsankov; Sander W. van der Laan; Masanao Yajima; Jean Yang; Fabio Zanini; Ivana Jelic

doi:10.1186/s13059-025-03771-8

Insights, opportunities, and challenges provided by large cell atlases

Martin Hemberg^*
, Federico Marini^*
, Shila Ghazanfar^*
, Ahmad Al Ajami
, Najla Abassi
, Benedict Anchang
, Bérénice A. Benayoun
, Yue Cao
, Ken Chen
, Yesid Cuesta-Astroz
, Zachary DeBruine
, Calliope A. Dendrou
, Iwijn De Vlaminck
, Katharina Imkeller
, Ilya Korsunsky
, Alex R. Lederer
, Jessica Jingyi Li
, Pieter Meysman
, Clint L. Miller
, Kerry A. Mullan

Uwe Ohler, Pratibha Panwar, Nikolaos Patikas, Jonas Schuck, Jacqueline H.Y. Siu, Timothy J. Triche, Alex Tsankov, Sander W. van der Laan, Masanao Yajima, Jean Yang, Fabio Zanini, Ivana Jelic^*

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

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Abstract

The field of single-cell biology is growing rapidly, generating large amounts of data from a variety of species, disease conditions, tissues, and organs. Coordinated efforts such as CZI CELLxGENE, HuBMAP, Broad Institute Single Cell Portal, and DISCO allow researchers to access large volumes of curated datasets, including more than just scRNA-seq data. These resources have created an opportunity to build and expand the computational biology ecosystem to develop tools necessary for data reuse and for extracting novel biological insights. We highlight achievements made so far, areas where further development is needed, and specific challenges that need to be overcome.

Original language	English
Article number	358
Number of pages	18
Journal	Genome Biology
Volume	26
Issue number	1
DOIs	https://doi.org/10.1186/s13059-025-03771-8
Publication status	Published - 20 Oct 2025

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Hemberg, M., Marini, F., Ghazanfar, S., Al Ajami, A., Abassi, N., Anchang, B., Benayoun, B. A., Cao, Y., Chen, K., Cuesta-Astroz, Y., DeBruine, Z., Dendrou, C. A., De Vlaminck, I., Imkeller, K., Korsunsky, I., Lederer, A. R., Li, J. J., Meysman, P., Miller, C. L., ... Jelic, I. (2025). Insights, opportunities, and challenges provided by large cell atlases. Genome Biology, 26(1), Article 358. https://doi.org/10.1186/s13059-025-03771-8

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title = "Insights, opportunities, and challenges provided by large cell atlases",

abstract = "The field of single-cell biology is growing rapidly, generating large amounts of data from a variety of species, disease conditions, tissues, and organs. Coordinated efforts such as CZI CELLxGENE, HuBMAP, Broad Institute Single Cell Portal, and DISCO allow researchers to access large volumes of curated datasets, including more than just scRNA-seq data. These resources have created an opportunity to build and expand the computational biology ecosystem to develop tools necessary for data reuse and for extracting novel biological insights. We highlight achievements made so far, areas where further development is needed, and specific challenges that need to be overcome.",

author = "Martin Hemberg and Federico Marini and Shila Ghazanfar and \{Al Ajami\}, Ahmad and Najla Abassi and Benedict Anchang and Benayoun, \{B{\'e}r{\'e}nice A.\} and Yue Cao and Ken Chen and Yesid Cuesta-Astroz and Zachary DeBruine and Dendrou, \{Calliope A.\} and \{De Vlaminck\}, Iwijn and Katharina Imkeller and Ilya Korsunsky and Lederer, \{Alex R.\} and Li, \{Jessica Jingyi\} and Pieter Meysman and Miller, \{Clint L.\} and Mullan, \{Kerry A.\} and Uwe Ohler and Pratibha Panwar and Nikolaos Patikas and Jonas Schuck and Siu, \{Jacqueline H.Y.\} and Triche, \{Timothy J.\} and Alex Tsankov and \{van der Laan\}, \{Sander W.\} and Masanao Yajima and Jean Yang and Fabio Zanini and Ivana Jelic",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = oct,

day = "20",

doi = "10.1186/s13059-025-03771-8",

language = "English",

volume = "26",

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Hemberg, M, Marini, F, Ghazanfar, S, Al Ajami, A, Abassi, N, Anchang, B, Benayoun, BA, Cao, Y, Chen, K, Cuesta-Astroz, Y, DeBruine, Z, Dendrou, CA, De Vlaminck, I, Imkeller, K, Korsunsky, I, Lederer, AR, Li, JJ, Meysman, P, Miller, CL, Mullan, KA, Ohler, U, Panwar, P, Patikas, N, Schuck, J, Siu, JHY, Triche, TJ, Tsankov, A, van der Laan, SW, Yajima, M, Yang, J, Zanini, F & Jelic, I 2025, 'Insights, opportunities, and challenges provided by large cell atlases', Genome Biology, vol. 26, no. 1, 358. https://doi.org/10.1186/s13059-025-03771-8

TY - JOUR

T1 - Insights, opportunities, and challenges provided by large cell atlases

AU - Hemberg, Martin

AU - Marini, Federico

AU - Ghazanfar, Shila

AU - Al Ajami, Ahmad

AU - Abassi, Najla

AU - Anchang, Benedict

AU - Benayoun, Bérénice A.

AU - Cao, Yue

AU - Chen, Ken

AU - Cuesta-Astroz, Yesid

AU - DeBruine, Zachary

AU - Dendrou, Calliope A.

AU - De Vlaminck, Iwijn

AU - Imkeller, Katharina

AU - Korsunsky, Ilya

AU - Lederer, Alex R.

AU - Li, Jessica Jingyi

AU - Meysman, Pieter

AU - Miller, Clint L.

AU - Mullan, Kerry A.

AU - Ohler, Uwe

AU - Panwar, Pratibha

AU - Patikas, Nikolaos

AU - Schuck, Jonas

AU - Siu, Jacqueline H.Y.

AU - Triche, Timothy J.

AU - Tsankov, Alex

AU - van der Laan, Sander W.

AU - Yajima, Masanao

AU - Yang, Jean

AU - Zanini, Fabio

AU - Jelic, Ivana

PY - 2025/10/20

Y1 - 2025/10/20

N2 - The field of single-cell biology is growing rapidly, generating large amounts of data from a variety of species, disease conditions, tissues, and organs. Coordinated efforts such as CZI CELLxGENE, HuBMAP, Broad Institute Single Cell Portal, and DISCO allow researchers to access large volumes of curated datasets, including more than just scRNA-seq data. These resources have created an opportunity to build and expand the computational biology ecosystem to develop tools necessary for data reuse and for extracting novel biological insights. We highlight achievements made so far, areas where further development is needed, and specific challenges that need to be overcome.

AB - The field of single-cell biology is growing rapidly, generating large amounts of data from a variety of species, disease conditions, tissues, and organs. Coordinated efforts such as CZI CELLxGENE, HuBMAP, Broad Institute Single Cell Portal, and DISCO allow researchers to access large volumes of curated datasets, including more than just scRNA-seq data. These resources have created an opportunity to build and expand the computational biology ecosystem to develop tools necessary for data reuse and for extracting novel biological insights. We highlight achievements made so far, areas where further development is needed, and specific challenges that need to be overcome.

UR - https://www.scopus.com/pages/publications/105019391833

U2 - 10.1186/s13059-025-03771-8

DO - 10.1186/s13059-025-03771-8

M3 - Review article

C2 - 41116172

AN - SCOPUS:105019391833

SN - 1474-7596

VL - 26

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 358

ER -

Insights, opportunities, and challenges provided by large cell atlases

Abstract

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