Mohammad Lotfollahi

Wellcome/MRC Cambridge Stem Cell Institute

Also affiliated with University of Cambridge, Wellcome Sanger Institute, Helmholtz Zentrum München, Bridge University

Biochemistry, Genetics and Molecular BiologyImmunology and Microbiology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

15.6Author DataRank

Indexed papers

11in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 11 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology(2023)10.1038/s41587-023-01733-8

Top 4%

5.4DataRank

Top 4%353 citations

Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso +29 more

Papers

Driven by 37 papers — median percentile 56. Top paper: “A Python library for probabilistic analysis of single-cell omics data”.

A Python library for probabilistic analysis of single-cell omics data

Nature Biotechnology(2022)10.1038/s41587-021-01206-w

N/A

9.4DataRank · unranked

825 citations

Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong +24 more

The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology(2023)10.1038/s41587-023-01733-8

Top 4%

5.4DataRank

Top 4%353 citations

Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso +29 more

An integrated cell atlas of the lung in health and disease

Nature Medicine(2023)10.1038/s41591-023-02327-2

Top 4%

5.0DataRank

Top 4%781 citations

Ciro Ramírez-Suástegui, Tessa E. Gillett, Luke Zappia, Elo Madissoon, Nikolay S. Markov +87 more

Machine learning for perturbational single-cell omics

Cell Systems(2021)10.1016/j.cels.2021.05.016

N/A

3.6DataRank · unranked

136 citations

Mohammad Lotfollahi, Francesca Finotello, Fabian Joachim Theis, Florian Wolf, Yuge Ji

Conditional out-of-distribution generation for unpaired data using transfer VAE

Bioinformatics(2020)10.1093/bioinformatics/btaa800

N/A

3.1DataRank · unranked

139 citations

Mohsen Naghipourfar, Fabian Joachim Theis, Francesca Finotello, Florian Wolf, Mohammad Lotfollahi

Squidpy: a scalable framework for spatial single cell analysis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.19.431994

N/A

3.0DataRank · unranked

71 citations

Hannah Spitzer, Michal Klein, David S. Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle +8 more

An integrated cell atlas of the human lung in health and disease

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.10.483747

Top 8%

2.8DataRank

Top 8%97 citations

Daniel Strobl, Luke Zappia, Nikolay S. Markov, Laure-Emmanuelle Zaragosi, Marie-Jeanne Arguel +77 more

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

Nature Methods(2023)10.1038/s41592-023-01994-w

N/A

2.3DataRank · unranked

123 citations

Herbert B. Schiller, Mohammad Lotfollahi, Dominik Klein, Michal Klein, Aaron Streets +3 more

scvi-tools: a library for deep probabilistic analysis of single-cell omics data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.28.441833

N/A

2.3DataRank · unranked

72 citations

Romain Lopez, Galen Xing, Pierre Boyeau, Katherine Wu, Michael Jayasuriya +20 more

Integration and querying of multimodal single-cell data with PoE-VAE

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.16.484643

N/A

2.1DataRank · unranked

64 citations

Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi +2 more

Population-level integration of single-cell datasets enables multi-scale analysis across samples

Nature Methods(2023)10.1038/s41592-023-02035-2

N/A

2.0DataRank · unranked

108 citations

Soroor Hediyeh-zadeh, Amir Ali Moinfar, Marco Wagenstetter, Luke Zappia, Mohammad Lotfollahi +2 more

Learning interpretable cellular responses to complex perturbations in high-throughput screens

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.14.439903

N/A

1.9DataRank · unranked

52 citations

Anna Klimovskaia Susmelj, Carlo De Donno, Yuge Ji, Ignacio Ibarra Del Río, Francesca Finotello +5 more

The future of rapid and automated single-cell data analysis using reference mapping

Cell(2024)10.1016/j.cell.2024.03.009

N/A

1.7DataRank · unranked

71 citations

Yuhan Hao, Fabian Joachim Theis, Rahul Satija, Mohammad Lotfollahi

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.12.503709

N/A

1.4DataRank · unranked

33 citations

Herbert B. Schiller, Mohammad Lotfollahi, Dominik Klein, Michal Klein, Aaron Streets +3 more

Learning interpretable latent autoencoder representations with annotations of feature sets

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.02.401182

N/A

1.2DataRank · unranked

24 citations

Mohammad Lotfollahi, Fabian Joachim Theis, Francesca Finotello, Sergei Rybakov

Towards multimodal foundation models in molecular cell biology

Nature(2025)10.1038/s41586-025-08710-y

N/A

1.2DataRank · unranked

88 citations

Alejandro Tejada-Lapuerta, Maria Brbić, Julio Saez-Rodriguez, Simona Cristea, Hani Goodarzi +4 more

Best practices for single-cell analysis across modalities

Nature Reviews Genetics(2023)10.1038/s41576-023-00586-w

N/A

1.0DataRank · unranked

1013 citations

Anna Christina Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia +34 more

Single-cell reference mapping to construct and extend cell-type hierarchies

NAR Genomics and Bioinformatics(2023)10.1093/nargab/lqad070

Top 20%

1.0DataRank

Top 20%38 citations

Mohammad Lotfollahi, Daniel Strobl, Avi Srivastava, Marcel J.T. Reinders, Fabian Joachim Theis +2 more

scGen predicts single-cell perturbation responses

Nature Methods(2019)10.1038/s41592-019-0494-8

N/A

0.975DataRank · unranked

666 citations

Francesca Finotello, Fabian Joachim Theis, Mohammad Lotfollahi

Mapping single-cell data to reference atlases by transfer learning

Nature Biotechnology(2021)10.1038/s41587-021-01001-7

N/A

0.962DataRank · unranked

610 citations

Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter +9 more

Population-level integration of single-cell datasets enables multi-scale analysis across samples

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.28.517803

Top 22%

0.932DataRank

Top 22%27 citations

Soroor Hediyeh-zadeh, Marco Wagenstetter, Amir Ali Moinfar, Luke Zappia, Mohammad Lotfollahi +2 more

Predicting cellular responses to complex perturbations in high‐throughput screens

Molecular Systems Biology(2023)10.15252/msb.202211517

N/A

0.832DataRank · unranked

256 citations

Anna Klimovskaia Susmelj, Carlo De Donno, Leon Hetzel, Yuge Ji, Ignacio Ibarra Del Río +16 more

Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

Nature Neuroscience(2024)10.1038/s41593-024-01806-0

N/A

0.691DataRank · unranked

29 citations

Gonçalo Castelo-Branco, Fei Chen, Simone Codeluppi, M. Ryan Corces, Jean Fan +26 more

Quantitative characterization of cell niches in spatial atlases

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.21.581428

N/A

0.653DataRank · unranked

18 citations

Irene Bonafonte-Pardàs, Adib Miraki Feriz, Adam Boxall, Eneritz Agirre, Fani Memi +8 more

Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data

(2021)10.1101/2021.09.01.458535

N/A

0.550DataRank · unranked

9 citations

Leander Dony, Harshita Agarwala, Fabian Joachim Theis, Mohammad Lotfollahi

Predicting cell morphological responses to perturbations using generative modeling

Nature Communications(2025)10.1038/s41467-024-55707-8

N/A

0.457DataRank · unranked

20 citations

Fabian Joachim Theis, Mohammad Lotfollahi, Alessandro Palma

Single-cell reference mapping to construct and extend cell-type hierarchies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.07.499109

Top 44%

0.423DataRank

Top 44%7 citations

Mohammad Lotfollahi, Daniel Strobl, Avi Srivastava, Marcel J.T. Reinders, Fabian Joachim Theis +2 more

Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/478503

N/A

0.396DataRank · unranked

13 citations

Francesca Finotello, Fabian Joachim Theis, Mohammad Lotfollahi, Florian Wolf

Integration and Querying of Multimodal Single-Cell Data with PoE-VAE

Lecture Notes in Computer Science(2025)10.1007/978-3-031-90252-9_36

N/A

0.165DataRank · unranked

2 citations

Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi +2 more

An integrated cell atlas of the human lung in health and disease

Research Square(2022)10.21203/rs.3.rs-1438584/v1

Top 71%

0.127DataRank

Top 71%1 citations

Avi Srivastava, Daniel Strobl, Luke Zappia, Elo Madissoon, Nikolay S. Markov +80 more

Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

Nature Neuroscience(2024)10.1038/s41593-024-01858-2

N/A

0.118DataRank · unranked

1 citations

Gonçalo Castelo-Branco, Fei Chen, Simone Codeluppi, M. Ryan Corces, Jean Fan +26 more

Mapping cells to gene programs

Research Square(2023)10.21203/rs.3.pex-2092/v1

N/A

0.104DataRank · unranked

1 citations

Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-zadeh, Alexander V. Misharin, Fabian Joachim Theis +2 more

ArchMap: A web-based platform for reference-based analysis of single-cell datasets

Research Square(2024)10.21203/rs.3.rs-5110946/v1

N/A

0.104DataRank · unranked

1 citations

Mohammad Lotfollahi, Fabian Joachim Theis, Ronald Skorobogat, Xavier George, Simon Richter +4 more

mvTCR - trained models

Zenodo (CERN European Organization for Nuclear Research)(2024)10.5281/zenodo.7215446

Top 100%

0DataRank

Top 100%0 citations

Yang An, Irene Bonafonte-Pardàs, Lisa M. Dratva, Rik G.H. Lindeboom, Muzlifah Haniffa +5 more

mvTCR - trained models

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.8112246

Top 100%

0DataRank

Top 100%0 citations

Yang An, Irene Bonafonte-Pardàs, Lisa M. Dratva, Rik G.H. Lindeboom, Muzlifah Haniffa +5 more

Predicting cell morphological responses to perturbations using generative modeling

Zenodo (CERN European Organization for Nuclear Research)(2024)10.5281/zenodo.8307628

Top 100%

0DataRank

Top 100%0 citations

Fabian Joachim Theis, Mohammad Lotfollahi, Alessandro Palma

Predicting cell morphological responses to perturbations using generative modeling

Zenodo (CERN European Organization for Nuclear Research)(2023)10.5281/zenodo.8307629

Top 100%

0DataRank

Top 100%0 citations

Fabian Joachim Theis, Mohammad Lotfollahi, Alessandro Palma

Mohammad Lotfollahi

Indexed papers

Top data-sharing exemplar

Papers