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 human lung in health and disease

L Sikkema, D Strobl, L Zappia, E Madissoon, NS Markov, ..., AV Misharin, MC Nawijn, MD Luecken, F Theis,

Cold Spring Harbor Laboratory   ·   11 Mar 2022   ·   doi:10.1101/2022.03.10.483747

lung atlas single-cell

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

2022

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

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

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

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

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

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   ·   31 May 2022   ·   pmid:35649415

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

L Sikkema, D Strobl, L Zappia, E Madissoon, NS Markov, ..., AV Misharin, MC Nawijn, MD Luecken, F Theis,

Cold Spring Harbor Laboratory   ·   11 Mar 2022   ·   doi:10.1101/2022.03.10.483747

lung atlas single-cell

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

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

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

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

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.

Christoph Muus, Malte D Luecken, Gökcen Eraslan, Lisa Sikkema, Avinash Waghray, ..., Wenjun Yan, William Zhao, Carly G K Ziegler, ,

Nature medicine   ·   02 Mar 2021   ·   pmid:33654293

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, ..., 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

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 ACE2, 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

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

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

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

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

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

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