Integrative Genomics by the Lücken Lab at the Computational Health Center

Research

Our research so far has focused on building atlases, using these atlases, and designing quality standards for single cell analyses.

Here’s a list of the latest papers from the lab.

Highlighted

An integrated cell atlas of the lung in health and disease
An integrated cell atlas of the lung in health and disease
Lisa Sikkema, Ciro Ramírez-Suástegui, Daniel C. Strobl, Tessa E. Gillett, Luke Zappia, ..., Sara A. Teichmann, Alexander V. Misharin, Martijn C. Nawijn, Malte D. Luecken, Fabian J. Theis
Nature Medicine   ·   01 Jun 2023   ·   doi:10.1038/s41591-023-02327-2
lung atlas single-cell
Benchmarking atlas-level data integration in single-cell genomics
Benchmarking atlas-level data integration in single-cell genomics
Malte D. Luecken, M. Büttner, K. Chaichoompu, A. Danese, M. Interlandi, ..., D. C. Strobl, L. Zappia, M. Dugas, M. Colomé-Tatché, Fabian J. Theis
Nature Methods   ·   23 Dec 2021   ·   doi:10.1038/s41592-021-01336-8
open science benchmarking single-cell

All

2025

funkyheatmap: Visualising data frames with mixed data types
funkyheatmap: Visualising data frames with mixed data types
Robrecht Cannoodt*, Louise Deconinck*, Artuur Couckuyt*, Nikolay S. Markov*, Luke Zappia, Malte D. Luecken, Marta Interlandi, Yvan Saeys†, Wouter Saelens†
Journal of Open Source Software   ·   11 Apr 2025   ·   doi:10.21105/joss.07698
Feature selection methods affect the performance of scRNA-seq data integration and querying
Feature selection methods affect the performance of scRNA-seq data integration and querying
Luke Zappia, Sabrina Richter, Ciro Ramírez-Suástegui, Raphael Kfuri-Rubens, Larsen Vornholz, Weixu Wang, Oliver Dietrich, Amit Frishberg, Malte D. Luecken, Fabian J. Theis
Nature Methods   ·   13 Mar 2025   ·   doi:10.1038/s41592-025-02624-3
Biases in machine-learning models of human single-cell data
Biases in machine-learning models of human single-cell data
Theresa Willem, Vladimir A. Shitov, Malte D. Luecken, Niki Kilbertus, Stefan Bauer, Marie Piraud, Alena Buyx, Fabian J. Theis
Nature Cell Biology   ·   19 Feb 2025   ·   doi:10.1038/s41556-025-01619-8

2024

Probe set selection for targeted spatial transcriptomics
Probe set selection for targeted spatial transcriptomics
Louis B. Kuemmerle, Malte D. Luecken, Alexandra B. Firsova, Lisa Barros de Andrade e Sousa, Lena Straßer, ..., Peter Horvath, Marie Piraud, Ali Ertürk, Christos Samakovlis, Fabian J. Theis
Nature Methods   ·   18 Nov 2024   ·   doi:10.1038/s41592-024-02496-z
ArchMap: A web-based platform for reference-based analysis of single-cell datasets
ArchMap: A web-based platform for reference-based analysis of single-cell datasets
Mohammad Lotfollahi, Chelsea Bright, Ronald Skorobogat, Mohammad Dehkordi, Xavier George, Simon Richter, Vladimir Shitov, Alexandra Topalova, Malte D. Luecken, Fabian J. Theis
Cold Spring Harbor Laboratory   ·   19 Sep 2024   ·   doi:10.1101/2024.09.19.613883
Defining and benchmarking open problems in single-cell analysis
Defining and benchmarking open problems in single-cell analysis
Malte Luecken, Scott Gigante, Daniel Burkhardt, Robrecht Cannoodt, Daniel Strobl, ..., Drausin Wulsin, Luca Pinello, Yvan Saeys, Fabian Theis, Smita Krishnaswamy
Research Square Platform LLC   ·   04 Apr 2024   ·   doi:10.21203/rs.3.rs-4181617/v1
open science benchmarking single-cell

2023

Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus
Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus
Aron Kos, Juan Pablo Lopez, Joeri Bordes, Carlo de Donno, Julien Dine, ..., Rainer Stoffel, Cornelia Flachskamm, Fabian J. Theis, Mathias V. Schmidt, Alon Chen
Science Advances   ·   01 Dec 2023   ·   doi:10.1126/sciadv.adj3793
Integrated multi-omics single cell atlas of the human retina
Integrated multi-omics single cell atlas of the human retina
Rui Chen, Jin Li, Jun Wang, Ignacio Ibarra, Xuesen Cheng, ..., Tim Stout, Shiming Chen, Yumei Li, Margaret DeAngelis, Fabian Theis
Research Square Platform LLC   ·   17 Nov 2023   ·   doi:10.21203/rs.3.rs-3471275/v1
An integrated cell atlas of the lung in health and disease
An integrated cell atlas of the lung in health and disease
Lisa Sikkema, Ciro Ramírez-Suástegui, Daniel C. Strobl, Tessa E. Gillett, Luke Zappia, ..., Sara A. Teichmann, Alexander V. Misharin, Martijn C. Nawijn, Malte D. Luecken, Fabian J. Theis
Nature Medicine   ·   01 Jun 2023   ·   doi:10.1038/s41591-023-02327-2
lung atlas single-cell
Best practices for single-cell analysis across modalities
Best practices for single-cell analysis across modalities
Lukas Heumos, Anna C. Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, ..., Jovan Tanevski, Isaac Virshup, Philipp Weiler, Herbert B. Schiller, Fabian J. Theis
Nature Reviews Genetics   ·   31 Mar 2023   ·   doi:10.1038/s41576-023-00586-w
Synthetic enforcement of STING signaling in cancer cells appropriates the immune microenvironment for checkpoint inhibitor therapy
Synthetic enforcement of STING signaling in cancer cells appropriates the immune microenvironment for checkpoint inhibitor therapy
Larsen Vornholz, Sophie E. Isay, Zsuzsanna Kurgyis, Daniel C. Strobl, Patricia Loll, ..., Christof Winter, Florian R. Greten, Henner F. Farin, Fabian J. Theis, Jürgen Ruland
Science Advances   ·   17 Mar 2023   ·   doi:10.1126/sciadv.add8564

2022

Probe set selection for targeted spatial transcriptomics
Probe set selection for targeted spatial transcriptomics
Louis B. Kuemmerle, Malte D. Luecken, Alexandra B. Firsova, Lisa Barros de Andrade e Sousa, Lena Straßer, ..., Peter Horvath, Marie Piraud, Ali Ertürk, Christos Samakovlis, Fabian J. Theis
Cold Spring Harbor Laboratory   ·   17 Aug 2022   ·   doi:10.1101/2022.08.16.504115
Primary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease
Primary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease
Sebastian Schmidt, Malte D. Luecken, Dietrich Trümbach, Sina Hembach, Kristina M. Niedermeier, ..., Jürgen Winkler, Daniela M. Vogt Weisenhorn, Florian Giesert, Fabian J. Theis, Wolfgang Wurst
Nature Communications   ·   16 Aug 2022   ·   doi:10.1038/s41467-022-32229-9
Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation
Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation
Kevin Baßler, Wataru Fujii, Theodore S. Kapellos, Erika Dudkin, Nico Reusch, ..., Thomas Ulas, Jan Hasenauer, Fabian J. Theis, Dirk Skowasch, Joachim L. Schultze
Frontiers in Immunology   ·   28 Jul 2022   ·   doi:10.3389/fimmu.2022.917232
Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2
Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2
Juan Pablo Lopez, Malte D. Lücken, Elena Brivio, Stoyo Karamihalev, Aron Kos, ..., Jan M. Deussing, Matthias Eder, Julien Dine, Fabian J. Theis, Alon Chen
Neuron   ·   01 Jul 2022   ·   doi:10.1016/j.neuron.2022.05.001
Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage
Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage
Konstantin Lutz, Andrea Musumeci, Christopher Sie, Ezgi Dursun, Elena Winheim, ..., Barbara U. Schraml, Fabian J. Theis, Wolfgang Enard, Thomas Korn, Anne B. Krug
Nature Communications   ·   16 Jun 2022   ·   doi:10.1038/s41467-022-31054-4
Multimodal single cell data integration challenge: results and lessons learned
Multimodal single cell data integration challenge: results and lessons learned
Christopher Lance, Malte D. Luecken, Daniel B. Burkhardt, Robrecht Cannoodt, Pia Rautenstrauch, ..., , Angela Oliveira Pisco, Jonathan Bloom, Smita Krishnaswamy, Fabian J. Theis
Cold Spring Harbor Laboratory   ·   12 Apr 2022   ·   doi:10.1101/2022.04.11.487796
Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons
Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons
Jessica Giehrl‐Schwab, Florian Giesert, Benedict Rauser, Chu Lan Lao, Sina Hembach, ..., Sabine M Hölter, Daniela M Vogt Weisenhorn, Fabian J Theis, Magdalena Götz, Wolfgang Wurst
EMBO Molecular Medicine   ·   04 Apr 2022   ·   doi:10.15252/emmm.202114797
An integrated cell atlas of the human lung in health and disease
An integrated cell atlas of the human lung in health and disease
Malte Luecken, Lisa Sikkema, Daniel Strobl, Luke Zappia, Elo Madissoon, ..., Lorraine Ware, Kun Zhang, Alexander Misharin, Martijn Nawijn, Fabian Theis
Research Square Platform LLC   ·   15 Mar 2022   ·   doi:10.21203/rs.3.rs-1438584/v1
An integrated cell atlas of the human lung in health and disease
An integrated cell atlas of the human lung in health and disease
L Sikkema, D Strobl, L Zappia, E Madissoon, NS Markov, ..., JL Schultze, AV Misharin, MC Nawijn, MD Luecken, F Theis
Cold Spring Harbor Laboratory   ·   11 Mar 2022   ·   doi:10.1101/2022.03.10.483747
The discovAIR project: a roadmap towards the Human Lung Cell Atlas
The discovAIR project: a roadmap towards the Human Lung Cell Atlas
Malte D. Luecken, Laure-Emmanuelle Zaragosi, Elo Madissoon, Lisa Sikkema, Alexandra B. Firsova, ..., Michael von Papen, Fabian J. Theis, Christos Samakovlis, Kerstin B. Meyer, Martijn C. Nawijn
European Respiratory Journal   ·   27 Jan 2022   ·   doi:10.1183/13993003.02057-2021

2021

Benchmarking atlas-level data integration in single-cell genomics
Benchmarking atlas-level data integration in single-cell genomics
Malte D. Luecken, M. Büttner, K. Chaichoompu, A. Danese, M. Interlandi, ..., D. C. Strobl, L. Zappia, M. Dugas, M. Colomé-Tatché, Fabian J. Theis
Nature Methods   ·   23 Dec 2021   ·   doi:10.1038/s41592-021-01336-8
open science benchmarking single-cell
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
Daniel Wendisch, Oliver Dietrich, Tommaso Mari, Saskia von Stillfried, Ignacio L. Ibarra, ..., Thorsten Wolff, Peter Boor, Matthias Selbach, Antoine-Emmanuel Saliba, Leif Erik Sander
Cell   ·   01 Dec 2021   ·   doi:10.1016/j.cell.2021.11.033
Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice
Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice
Alexandra Aliluev, Sophie Tritschler, Michael Sterr, Lena Oppenländer, Julia Hinterdobler, ..., Matthias H. Tschöp, Malte D. Luecken, Fabian J. Theis, Heiko Lickert, Anika Böttcher
Nature Metabolism   ·   22 Sep 2021   ·   doi:10.1038/s42255-021-00458-9
Mapping single-cell data to reference atlases by transfer learning
Mapping single-cell data to reference atlases by transfer learning
Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, ..., Nir Yosef, Marta Interlandi, Sergei Rybakov, Alexander V. Misharin, Fabian J. Theis
Nature Biotechnology   ·   30 Aug 2021   ·   doi:10.1038/s41587-021-01001-7
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Christoph Muus, Malte D. Luecken, Gökcen Eraslan, Lisa Sikkema, Avinash Waghray, ..., Laure-Emmanuelle Zaragosi, Darin Zerti, Hongbo Zhang, Kun Zhang, Xiaohui Zhang
Nature Medicine   ·   01 Mar 2021   ·   doi:10.1038/s41591-020-01227-z

2020

Query to reference single-cell integration with transfer learning
Query to reference single-cell integration with transfer learning
Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, Ziga Avsec, Alexander V. Misharin, Fabian J. Theis
Cold Spring Harbor Laboratory   ·   16 Jul 2020   ·   doi:10.1101/2020.07.16.205997
RAAS blockade, kidney disease, and expression of<i>ACE2</i>, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells
RAAS blockade, kidney disease, and expression ofACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells
Ayshwarya Subramanian, Katherine A Vernon, Michal Slyper, Julia Waldman, Malte D Luecken, ..., Orit Rozenblatt-Rosen, Astrid Weins, , Aviv Regev, Anna Greka
Cold Spring Harbor Laboratory   ·   23 Jun 2020   ·   doi:10.1101/2020.06.23.167098
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
Kevin Baßler, Wataru Fujii, Theodore S. Kapellos, Arik Horne, Benedikt Reiz, ..., Thomas Ulas, Jan Hasenauer, Fabian J. Theis, Dirk Skowasch, Joachim L. Schultze
Cold Spring Harbor Laboratory   ·   30 May 2020   ·   doi:10.1101/2020.05.28.121541
Benchmarking atlas-level data integration in single-cell genomics
Benchmarking atlas-level data integration in single-cell genomics
MD Luecken, M Büttner, K Chaichoompu, A Danese, M Interlandi, ..., DC Strobl, L Zappia, M Dugas, M Colomé-Tatché, FJ Theis
Cold Spring Harbor Laboratory   ·   23 May 2020   ·   doi:10.1101/2020.05.22.111161
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
Christoph Muus, Malte D. Luecken, Gokcen Eraslan, Avinash Waghray, Graham Heimberg, ..., Wenjun Yan, William Zhao, Carly G. K. Ziegler, ,
Cold Spring Harbor Laboratory   ·   20 Apr 2020   ·   doi:10.1101/2020.04.19.049254

2019

Current best practices in single‐cell RNA‐seq analysis: a tutorial
Current best practices in single‐cell RNA‐seq analysis: a tutorial
Malte D Luecken, Fabian J Theis
Molecular Systems Biology   ·   01 Jun 2019   ·   doi:10.15252/msb.20188746

2017

CommWalker: correctly evaluating modules in molecular networks in light of annotation bias
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias
M D Luecken, M J T Page, A J Crosby, S Mason, G Reinert, C M Deane
Bioinformatics   ·   03 Nov 2017   ·   doi:10.1093/bioinformatics/btx706