Publications of 2022

202248 publications

1. High-throughput profiling of drug interactions in Gram-positive bacteria

   Elisabetta Cacace, Vladislav Kim, Michael Knopp, …, Kemal Inecik, …, Athanasios Typas

   bioRxivPreprintOpen accessDOIPDF
   Topic: Perturbation responses

2. Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases

   A. Schäbitz, C. Hillig, M. Mubarak, …, F. Theis, …, S. Eyerich

   Nature CommunicationsOpen accessDOIPDF
   Topic: Immunity and inflammation

3. T cells modulate the microglial response to brain ischemia

   Corinne Benakis, Alba Simats, Sophie Tritschler, …, Fabian J Theis, …, Arthur Liesz

   eLifeOpen accessDOIPDF
   Topic: Immunity and inflammation

4. Spatial proteomics in three-dimensional intact specimens

   Harsharan Singh Bhatia, Andreas-David Brunner, Furkan Öztürk, …, Fabian Theis, …, Ali Ertürk

   CellOpen accessDOI
   Topic: Spatial omics

5. A transcriptional cross species map of pancreatic islet cells

   Sophie Tritschler, Moritz Thomas, Anika Böttcher, …, Fabian J. Theis

   Molecular MetabolismOpen accessDOIPDF
   Topic: Metabolism and diabetes

6. TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury

   Alessandro Zambusi, Klara Tereza Novoselc, Saskia Hutten, …, Fabian Theis, …, Jovica Ninkovic

   Nature NeuroscienceDOI
   Topic: Immunity and inflammation

7. Network reconstruction for trans acting genetic loci using multi-omics data and prior information

   Johann S. Hawe, Ashis Saha, Melanie Waldenberger, …, Fabian J. Theis, …, Matthias Heinig

   Genome MedicineOpen accessDOIPDF
   Topic: Networks and graphs

8. Modeling intercellular communication in tissues using spatial graphs of cells

   David S. Fischer, Anna C. Schaar, Fabian J. Theis

   Nature BiotechnologyOpen accessDOIPDF
   Topic: Deep learning and generative models

9. Pytometry: Flow and mass cytometry analytics in Python

   Maren Büttner, Felix Hempel, Thomas Ryborz, Fabian J. Theis, Joachim L. Schultze

   bioRxivPreprintOpen accessDOIPDF
   Topic: Single-cell genomics

10. Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps

    Luca Vincent Eyring, Dominik Klein, Giovanni Palla, Soeren Becker, Philipp Weiler, Niki Kilbertus, Fabian J. Theis

    bioRxivPreprintOpen accessDOIPDF
    Topic: Cell fate and dynamics

11. Ex vivo modeling of human lung fibrogenesis and drug mode of action screens using single cell RNA-seq in precision-cut lung slices

    N J Lang, M Ansari, L Yang, …, F J Theis, …, H B Schiller

    03.03 - Mechanisms of lung injury and repairConference paperDOI
    Topic: Perturbation responses

12. Single cell transcriptomic dissection of virus induced immunopathology in interferon gamma receptor null mice

    L Yang, L Heumos, I Angelidis, …, F J. Theis, …, H Schiller

    10.01 - Respiratory infections and bronchiectasisConference paperDOI
    Topic: Immunity and inflammation

13. Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa

    Anne M. van der Does, Rashad M. Mahbub, Dennis K. Ninaber, …, Fabian J. Theis, …, Alen Faiz

    Respiratory ResearchOpen accessDOIPDF
    Topic: Bulk omics and genetics

14. Probing cell identity hierarchies by fate titration and collision during direct reprogramming

    Bob A Hersbach, David S Fischer, Giacomo Masserdotti, …, Fabian J Theis, …, Stefan H Stricker

    Molecular Systems BiologyOpen accessDOIPDF
    Topic: Cell fate and dynamics

15. Primary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease

    Sebastian Schmidt, Malte D. Luecken, Dietrich Trümbach, …, Fabian J. Theis, Wolfgang Wurst

    Nature CommunicationsOpen accessDOIPDF
    Topic: Brain and mental health

16. Variant-risk-exon interplay impacts circadian rhythm and dopamine signaling pathway in severe psychiatric disorders

    Karolina Worf, Natalie Matosin, Nathalie Gerstner, …, Fabian J. Theis, …, Nikola S. Mueller

    medRxivPreprintOpen accessDOIPDF
    Topic: Brain and mental health

17. Interpretable surface-based detection of focal cortical dysplasias: a Multi-centre Epilepsy Lesion Detection study

    Hannah Spitzer, Mathilde Ripart, Kirstie Whitaker, …, Fabian J Theis, …, Konrad Wagstyl

    BrainOpen accessDOIPDF
    Topic: Imaging

18. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies

    Daniel Reichart, Eric L. Lindberg, Henrike Maatz, …, Fabian J. Theis, …, Christine E. Seidman

    ScienceOpen accessDOIPDF
    Topic: Single-cell genomics

19. Synaptotagmin-13 orchestrates pancreatic endocrine cell egression and islet morphogenesis

    Mostafa Bakhti, Aimée Bastidas-Ponce, Sophie Tritschler, …, Fabian J. Theis, …, Heiko Lickert

    Nature CommunicationsOpen accessDOIPDF
    Topic: Metabolism and diabetes

20. CIARA: a cluster-independent algorithm for the identification of markers of rare cell types from single-cell RNA seq data

    Gabriele Lubatti, Marco Stock, Ane Iturbide, …, Fabian J. Theis, …, Antonio Scialdone

    bioRxivPreprintOpen accessDOIPDF
    Topic: Single-cell genomics

21. Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response

    Elise M. A. Slob, Alen Faiz, Jos van Nijnatten, …, Fabian Theis, …, Gerard H. Koppelman

    Clinical and Translational AllergyOpen accessDOIPDF
    Topic: Immunity and inflammation

22. Proteomics of spatially identified tissues in whole organs

    Molecular & Cellular ProteomicsDOI
    Topic: Spatial omics

23. Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation

    Kevin Baßler, Wataru Fujii, Theodore S. Kapellos, …, Fabian J. Theis, …, Joachim L. Schultze

    Frontiers in ImmunologyOpen accessDOIPDF
    Topic: Immunity and inflammation

24. Origin and function of activated fibroblast states during zebrafish heart regeneration

    Bo Hu, Sara Lelek, Bastiaan Spanjaard, …, Fabian Theis, …, Jan Philipp Junker

    Nature GeneticsOpen accessDOIPDF
    Topic: Single-cell genomics

25. MultiCPA: Multimodal Compositional Perturbation Autoencoder

    Kemal Inecik, Andreas Uhlmann, Mohammad Lotfollahi, Fabian Theis

    bioRxivPreprintOpen accessDOIPDF
    Topic: Perturbation responses

26. Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2

    Juan Pablo Lopez, Malte D. Lücken, Elena Brivio, …, Fabian J. Theis, Alon Chen

    NeuronOpen accessDOI
    Topic: Brain and mental health

27. Heterogeneous Development of β-Cell Populations in Diabetes-Resistant and -Susceptible Mice

    Pascal Gottmann, Thilo Speckmann, Mandy Stadion, …, Fabian J. Theis, …, Annette Schürmann

    DiabetesOpen accessDOIPDF
    Topic: Metabolism and diabetes

28. Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage

    Konstantin Lutz, Andrea Musumeci, Christopher Sie, …, Fabian J. Theis, …, Anne B. Krug

    Nature CommunicationsOpen accessDOIPDF
    Topic: Cell fate and dynamics

29. Mature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19

    Amit Frishberg, Emma Kooistra, Melanie Nuesch-Germano, …, Fabian J. Theis, …, Matthijs Kox

    Cell Reports MedicineOpen accessDOIPDF
    Topic: Immunity and inflammation

30. Gene expression based molecular test proves clinical validity as diagnostic aid for the differential diagnosis of psoriasis and eczema in formalin fixed and paraffin embedded tissue

    Felix Fischer, Sophie Roenneberg, Larissa Graner, …, Fabian J. Theis, …, Stefanie Eyerich

    medRxivPreprintOpen accessDOIPDF
    Topic: Immunity and inflammation

31. Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study

    Cristiana Cruceanu, Leander Dony, Anthi C. Krontira, …, Fabian J. Theis, Elisabeth B. Binder

    American Journal of PsychiatryOpen accessDOI
    Topic: Brain and mental health

32. Multimodal single cell data integration challenge: results and lessons learned

    Christopher Lance, Malte D. Luecken, Daniel B. Burkhardt, …, Fabian J. Theis

    bioRxivPreprintOpen accessDOIPDF
    Topic: Benchmarks and best practices

33. Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons

    Jessica Giehrl‐Schwab, Florian Giesert, Benedict Rauser, …, Fabian J Theis, …, Wolfgang Wurst

    EMBO Molecular MedicineOpen accessDOIPDF
    Topic: Cell fate and dynamics

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

    Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, Fabian Theis

    bioRxivPreprintOpen accessDOIPDF
    Topic: Data integration

35. Concept of the Munich/Augsburg Consortium Precision in Mental Health for the German Center of Mental Health

    Peter Falkai, Nikolaos Koutsouleris, Katja Bertsch, …, Fabian J. Theis, …, Josef Priller

    Frontiers in PsychiatryReviewOpen accessDOIPDF
    Topic: Brain and mental health

36. Toward modeling metabolic state from single-cell transcriptomics

    Karin Hrovatin, David S. Fischer, Fabian J. Theis

    Molecular MetabolismReviewOpen accessDOIPDF
    Topic: Metabolism and diabetes

37. Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

    Andreas‐David Brunner, Marvin Thielert, Catherine Vasilopoulou, …, Fabian J Theis, Matthias Mann

    Molecular Systems BiologyOpen accessDOIPDF
    Topic: Single-cell genomics

38. Rapid Inhibitor Discovery by Exploiting Synthetic Lethality

    Jacob D. Muscato, Heidi G. Morris, Aaron Mychack, …, Kemal İnecik, …, Suzanne Walker

    Journal of the American Chemical SocietyOpen accessDOIPDF
    Topic: Perturbation responses

39. Spatial components of molecular tissue biology

    Giovanni Palla, David S. Fischer, Aviv Regev, Fabian J. Theis

    Nature BiotechnologyReviewOpen accessDOIPDF
    Topic: Spatial omics

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

    Adam Gayoso, Romain Lopez, Galen Xing, …, Fabian J. Theis, …, Nir Yosef

    Nature BiotechnologyOpen accessDOIPDF
    Topic: Open-source software

41. Effect of Atmospheric Aging on Soot Particle Toxicity in Lung Cell Models at the Air–Liquid Interface: Differential Toxicological Impacts of Biogenic and Anthropogenic Secondary Organic Aerosols (SOAs)

    Svenja Offer, Elena Hartner, Sebastiano Di Bucchianico, …, Fabian Theis, …, Ralf Zimmermann

    Environmental Health PerspectivesOpen accessDOIPDF
    Topic: Perturbation responses

42. Squidpy: a scalable framework for spatial omics analysis

    Giovanni Palla, Hannah Spitzer, Michal Klein, …, Fabian J. Theis

    Nature MethodsOpen accessDOIPDF
    Topic: Spatial omics

43. The discovAIR project: a roadmap towards the Human Lung Cell Atlas

    Malte D. Luecken, Laure-Emmanuelle Zaragosi, Elo Madissoon, …, Fabian J. Theis, …, Martijn C. Nawijn

    European Respiratory JournalReviewOpen accessDOIPDF
    Topic: Cell atlases

44. Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development

    Margaret E. Magaletta, Macrina Lobo, Eric M. Kernfeld, Hananeh Aliee, Jack D. Huey, Teagan J. Parsons, Fabian J. Theis, René Maehr

    Nature CommunicationsOpen accessDOIPDF
    Topic: Gene regulation

45. CellRank for directed single-cell fate mapping

    Marius Lange, Volker Bergen, Michal Klein, …, Fabian J. Theis

    Nature MethodsOpen accessDOIPDF
    Topic: Cell fate and dynamics

46. Repeated toxic injuries of murine liver are tolerated through microsteatosis and mild inflammation

    Seddik Hammad, Christoph Ogris, Amnah Othman, …, Fabian J. Theis, …, Nikola S. Mueller

    bioRxivPreprintOpen accessDOIPDF
    Topic: Perturbation responses

47. Noise Transfer for Unsupervised Domain Adaptation of Retinal OCT Images

    Valentin Koch, Olle Holmberg, Hannah Spitzer, Johannes Schiefelbein, Ben Asani, Michael Hafner, Fabian J. Theis

    Lecture Notes in Computer ScienceBook chapterOpen accessDOI
    Topic: Imaging

48. Benchmarking atlas-level data integration in single-cell genomics - integration task datasets

    Malte Luecken, Maren Buttner, Anna Danese, …, Fabian Theis, Kridsadakorn Chaichoompu

    figshareDatasetOpen accessDOI
    Topic: Data integration