Publications of 2019

201942 publications

1. S.11.01 Brain organoids as models of the developing human brain: deciphering the molecular signature of prenatal stress

   C. Cruceanu, L. Dony, A.C. Kontira, …, F. Theis, E.B. Binder

   European NeuropsychopharmacologyDOI
   Topic: Brain and mental health

2. Establishment of a high-resolution 3D modeling system for studying pancreatic epithelial cell biology in vitro

   Mostafa Bakhti, Katharina Scheibner, Sophie Tritschler, Aimée Bastidas-Ponce, Marta Tarquis-Medina, Fabian J. Theis, Heiko Lickert

   Molecular MetabolismOpen accessDOIPDF
   Topic: Cell fate and dynamics

3. ggplot.multistats: Multiple Summary Statistics for Binned Stats/Geometries

   Philipp Angerer

   CRAN: Contributed PackagesDatasetOpen accessDOI
   Topic: Open-source software

4. knn.covertree: An Accurate kNN Implementation with Multiple Distance Measures

   Philipp Angerer, David Crane

   CRAN: Contributed PackagesDatasetOpen accessDOI
   Topic: Open-source software

5. Aldh1b1 expression defines progenitor cells in the adult pancreas and is required for Kras-induced pancreatic cancer

   Ekaterina Mameishvili, Ioannis Serafimidis, Sara Iwaszkiewicz, …, Fabian Theis, …, Anthony Gavalas

   Proceedings of the National Academy of SciencesOpen accessDOIPDF
   Topic: Cell fate and dynamics

6. MPRAnalyze: statistical framework for massively parallel reporter assays

   Tal Ashuach, David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian J. Theis, Nir Yosef

   Genome BiologyOpen accessDOIPDF
   Topic: Statistical inference

7. Pheno-seq – linking visual features and gene expression in 3D cell culture systems

   Stephan M. Tirier, Jeongbin Park, Friedrich Preußer, …, Fabian Theis, …, Christian Conrad

   Scientific ReportsOpen accessDOIPDF
   Topic: Data integration

8. BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis

   Fatma Uzbas, Florian Opperer, Can Sönmezer, …, Fabian J. Theis, …, Micha Drukker

   Genome BiologyOpen accessDOIPDF
   Topic: Single-cell genomics

9. scGen predicts single-cell perturbation responses

   Mohammad Lotfollahi, F. Alexander Wolf, Fabian J. Theis

   Nature MethodsOpen accessDOI
   Topic: Deep learning and generative models

10. Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration

    Maximilian Strunz, Lukas M. Simon, Meshal Ansari, …, Fabian J. Theis, Herbert B. Schiller

    bioRxivPreprintOpen accessDOIPDF
    Topic: Cell fate and dynamics

11. Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

    Juan C. Caicedo, Jonathan Roth, Allen Goodman, …, Fabian J. Theis, Anne E. Carpenter

    Cytometry Part AOpen accessDOIPDF
    Topic: Benchmarks and best practices

12. scSLAM-seq reveals core features of transcription dynamics in single cells

    Florian Erhard, Marisa A. P. Baptista, Tobias Krammer, …, Fabian J. Theis, …, Lars Dölken

    NatureOpen accessDOIPDF
    Topic: Single-cell genomics

13. Faculty Opinions recommendation of Deep generative modeling for single-cell transcriptomics.

    Fabian Theis

    Faculty Opinions – Post-Publication Peer Review of the Biomedical LiteratureDatasetOpen accessDOI
    Topic: Single-cell genomics

14. Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology

    Subarna Palit, Christoph Heuser, Gustavo P. de Almeida, Fabian J. Theis, Christina E. Zielinski

    Frontiers in ImmunologyReviewOpen accessDOIPDF
    Topic: Single-cell genomics

15. The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease

    Herbert B. Schiller, Daniel T. Montoro, Lukas M. Simon, …, Fabian J. Theis, …, Martijn C. Nawijn

    American Journal of Respiratory Cell and Molecular BiologyReviewOpen accessDOIPDF
    Topic: Cell atlases

16. A cellular census of human lungs identifies novel cell states in health and in asthma

    Felipe A. Vieira Braga, Gozde Kar, Marijn Berg, …, Fabian J. Theis, …, Sarah A. Teichmann

    Nature MedicineOpen accessDOI
    Topic: Single-cell genomics

17. Concepts and limitations for learning developmental trajectories from single cell genomics

    Sophie Tritschler, Maren Büttner, David S. Fischer, Marius Lange, Volker Bergen, Heiko Lickert, Fabian J. Theis

    DevelopmentReviewOpen accessDOI
    Topic: Cell fate and dynamics

18. Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis

    Aimée Bastidas-Ponce, Sophie Tritschler, Leander Dony, …, Fabian J. Theis, …, Mostafa Bakhti

    DevelopmentOpen accessDOI
    Topic: Cell fate and dynamics

19. Inferring Interaction Networks From Multi-Omics Data

    Johann S. Hawe, Fabian J. Theis, Matthias Heinig

    Frontiers in GeneticsReviewOpen accessDOIPDF
    Topic: Networks and graphs

20. Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns

    Darina Czamara, Gökçen Eraslan, Christian M. Page, …, Fabian J. Theis, …, Elisabeth B. Binder

    Nature CommunicationsOpen accessDOIPDF
    Topic: Bulk omics and genetics

21. Current best practices in single‐cell RNA‐seq analysis: a tutorial

    Malte D Luecken, Fabian J Theis

    Molecular Systems BiologyReviewOpen accessDOIPDF
    Topic: Benchmarks and best practices

22. Deep learning does not outperform classical machine learning for cell-type annotation

    Niklas D. Köhler, Maren Büttner, Niry Andriamanga, Fabian J. Theis

    bioRxivPreprintOpen accessDOIPDF
    Topic: Benchmarks and best practices

23. Dynamic modelling of an ACADS genotype in fatty acid oxidation – Application of cellular models for the analysis of common genetic variants

    Kerstin Matejka, Ferdinand Stückler, Michael Salomon, …, Fabian J. Theis, …, Helmut Laumen

    PLOS ONEOpen accessDOIPDF
    Topic: Metabolism and diabetes

24. A map of β-cell differentiation pathways supports cell therapies for diabetes

    Fabian J. Theis, Heiko Lickert

    NatureOpen accessDOIPDF
    Topic: Cell fate and dynamics

25. Altered relaxation times in MRI indicate bronchopulmonary dysplasia

    Kai Förster, Birgit Ertl-Wagner, Harald Ehrhardt, …, Fabian Theis, …, Anne Hilgendorff

    ThoraxOpen accessDOIPDF
    Topic: Imaging

26. Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation

    M. Laimighofer, R. Lickert, R. Fuerst, F. J. Theis, C. Winkler, E. Bonifacio, A.-G. Ziegler, J. Krumsiek

    Scientific ReportsOpen accessDOIPDF
    Topic: Immunity and inflammation

27. Deep learning: new computational modelling techniques for genomics

    Gökcen Eraslan, Žiga Avsec, Julien Gagneur, Fabian J. Theis

    Nature Reviews GeneticsReviewDOI
    Topic: Deep learning and generative models

28. Inferring population dynamics from single-cell RNA-sequencing time series data

    David S. Fischer, Anna K. Fiedler, Eric M. Kernfeld, …, Fabian J. Theis

    Nature BiotechnologyOpen accessDOIPDF
    Topic: Cell fate and dynamics

29. A strategy for high‐dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors

    Norbert Krautenbacher, Nicolai Flach, Andreas Böck, …, Fabian J. Theis, …, Bianca Schaub

    AllergyOpen accessDOIPDF
    Topic: Immunity and inflammation

30. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

    F. Alexander Wolf, Fiona K. Hamey, Mireya Plass, …, Fabian J. Theis

    Genome BiologyOpen accessDOIPDF
    Topic: Single-cell genomics

31. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

    Ilias Angelidis, Lukas M. Simon, Isis E. Fernandez, …, Fabian J. Theis, Herbert B. Schiller

    Nature CommunicationsOpen accessDOIPDF
    Topic: Single-cell genomics

32. IRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling

    Xia Sheng, Hatice Zeynep Nenseth, Su Qu, …, Fabian Theis, …, Fahri Saatcioglu

    Nature CommunicationsOpen accessDOIPDF
    Topic: Perturbation responses

33. Single-cell RNA-seq denoising using a deep count autoencoder

    Gökcen Eraslan, Lukas M. Simon, Maria Mircea, Nikola S. Mueller, Fabian J. Theis

    Nature CommunicationsOpen accessDOIPDF
    Topic: Deep learning and generative models

34. A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease

    F.A. Vieira Braga, G. Kar, M. Berg, …, F.J. Theis, …, S.A. Teichmann

    bioRxivPreprintOpen accessDOIPDF
    Topic: Immunity and inflammation

35. Editorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine

    Lars Kaderali, Fabian Theis, Vitaly V. Ganusov, Stanca M. Ciupe, Ramit Mehr, Ruy M. Ribeiro, Esteban A. Hernandez-Vargas

    Frontiers in MicrobiologyOpen accessDOIPDF
    Topic: Immunity and inflammation

36. Artificial Neural Networks and Machine Learning – ICANN 2019: Theoretical Neural Computation

    Lecture Notes in Computer ScienceOtherDOI
    Topic: Deep learning and generative models

37. Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions

    Lecture Notes in Computer ScienceOtherDOI
    Topic: Deep learning and generative models

38. WHAT SHAPES THE CHILD'S EPIGENOME: GENOTYPE, PRENATAL ENVIRONMENT OR BOTH?

    Darina Czamara, Goekcen Eraslan, Anna Suarez, …, Fabian J. Theis, …, Elisabeth B. Binder

    European NeuropsychopharmacologyDOI
    Topic: Gene regulation

39. POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGICAL FEATURES IN A CROSS-DIAGNOSTIC GROUP OF INDIVIDUALS WITH SEVERE MENTAL ILLNESS

    Eva Schulte, Ivan Kondofersky, Monika Budde, …, Fabian J. Theis, …, Thomas G. Schulze

    European NeuropsychopharmacologyDOI
    Topic: Brain and mental health

40. GENOTYPE, PRENATAL ENVIRONMENT OR BOTH–WHAT SHAPES THE NEWBORN'S EPIGENOME?

    Darina Czamara, Goekcen Eraslan, Jari Lahti, …, Fabian J. Theis, …, Elisabeth Binder

    European NeuropsychopharmacologyDOI
    Topic: Gene regulation

41. F96POLYGENIC RISK SCORE ANALYSIS OF TRAJECTORIES OF COGNITIVE PERFORMANCE IN PSYCHIATRIC PATIENTS

    Sabrina Schaupp, Monika Budde, Ivan Kondofersky, …, Fabian J. Theis, Thomas Schulze

    European NeuropsychopharmacologyDOI
    Topic: Brain and mental health

42. SA125POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGICAL FEATURES IN A CROSS-DIAGNOSTIC GROUP OF INDIVIDUALS WITH SEVERE MENTAL ILLNESS

    Eva Schulte, Ivan Kondofersky, Monika Budde, …, Fabian J. Theis, …, Thomas G. Schulze

    European NeuropsychopharmacologyDOI
    Topic: Brain and mental health