Publications of 2024

202445 publications

1. Delineating the effective use of self-supervised learning in single-cell genomics

   Till Richter, Mojtaba Bahrami, Yufan Xia, David S. Fischer, Fabian J. Theis

   Nature Machine IntelligenceOpen accessDOIPDF
   Topic: Benchmarks and best practices

2. ProCyon: A multimodal foundation model for protein phenotypes

   Owen Queen, Yepeng Huang, Robert Calef, …, Fabian J. Theis, …, Marinka Zitnik

   bioRxivPreprintOpen accessDOI
   Topic: Deep learning and generative models

3. Considerations for building and using integrated single-cell atlases

   Karin Hrovatin, Lisa Sikkema, Vladimir A. Shitov, …, Fabian J. Theis, Malte D. Luecken

   Nature MethodsReviewDOI
   Topic: Cell atlases

4. inVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps

   Hananeh Aliee, Ferdinand Kapl, Duy Pham, …, Fabian J. Theis

   bioRxivPreprintOpen accessDOIPDF
   Topic: Deep learning and generative models

5. Heterogeneity-driven phenotypic plasticity and treatment response in branched-organoid models of pancreatic ductal adenocarcinoma

   Aristeidis Papargyriou, Mulham Najajreh, David P. Cook, …, Fabian J. Theis, …, Maximilian Reichert

   Nature Biomedical EngineeringOpen accessDOIPDF
   Topic: Perturbation responses

6. Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution

   Nicolò Caporale, Davide Castaldi, Marco Tullio Rigoli, …, Fabian J. Theis, …, Giuseppe Testa

   Nature MethodsOpen accessDOIPDF
   Topic: Brain and mental health

7. HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

   Rigney E. Turnham, Adriana Pitea, Gwendolyn M. Jang, …, Fabian J. Theis, …, John D. Gordan

   Cancer ResearchOpen accessDOIPDF
   Topic: Immunity and inflammation

8. Modulation of TCR stimulation and pifithrin-α improve the genomic safety profile of CRISPR-engineered human T cells

   Laurenz T. Ursch, Jule S. Müschen, Julia Ritter, …, Fabian J. Theis, …, Kathrin Schumann

   Cell Reports MedicineOpen accessDOIPDF
   Topic: Immunity and inflammation

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

   Boyan Bonev, Gonçalo Castelo-Branco, Fei Chen, …, Fabian Theis, …, Tomasz J. Nowakowski

   Nature NeuroscienceReviewOpen accessDOIPDF
   Topic: Brain and mental health

10. An integrated transcriptomic cell atlas of human neural organoids

    Zhisong He, Leander Dony, Jonas Simon Fleck, …, Fabian J. Theis, Barbara Treutlein

    NatureOpen accessDOIPDF
    Topic: Single-cell genomics

11. Probe set selection for targeted spatial transcriptomics

    Louis B. Kuemmerle, Malte D. Luecken, Alexandra B. Firsova, …, Fabian J. Theis

    Nature MethodsOpen accessDOIPDF
    Topic: Spatial omics

12. Disentangling cellular heterogeneity into interpretable biological factors through structured latent representations

    Amir Ali Moinfar, Fabian J. Theis

    bioRxivPreprintOpen accessDOI
    Topic: Deep learning and generative models

13. Mapping lineage-traced cells across time points with moslin

    Marius Lange, Zoe Piran, Michal Klein, Bastiaan Spanjaard, Dominik Klein, Jan Philipp Junker, Fabian J. Theis, Mor Nitzan

    Genome BiologyOpen accessDOIPDF
    Topic: Cell fate and dynamics

14. Vitessce: integrative visualization of multimodal and spatially resolved single-cell data

    Mark S. Keller, Ilan Gold, Chuck McCallum, Trevor Manz, Peter V. Kharchenko, Nils Gehlenborg

    Nature MethodsOpen accessDOIPDF
    Topic: Open-source software

15. An open-source framework for electronic health record and patient fate exploration

    Nature MedicineDOI
    Topic: Clinical and cohort data

16. Endothelial regulatory circuits control cranial neural crest migration and plasticity

    Zhiyuan Hu, Sarah Mayes, Weixu Wang, José M. Santos-Pereira, Fabian Theis, Tatjana Sauka-Spengler

    bioRxivPreprintOpen accessDOIPDF
    Topic: Gene regulation

17. anndata: Access and store annotated data matrices

    Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, F. Alexander Wolf

    Journal of Open Source SoftwareOpen accessDOIPDF
    Topic: Open-source software

18. Mode of actions of nanomaterial-induced respiratory toxicity

    Carola Voss, Lianyong Han, Meshal Ansari, …, Fabian J. Theis, …, Tobias Stoeger

    Occupational and environmental healthConference paperDOI
    Topic: Perturbation responses

19. An open-source framework for end-to-end analysis of electronic health record data

    Lukas Heumos, Philipp Ehmele, Tim Treis, …, Fabian J. Theis

    Nature MedicineOpen accessDOIPDF
    Topic: Clinical and cohort data

20. Small data methods in omics: the power of one

    Kevin G. Johnston, Steven F. Grieco, Qing Nie, Fabian J. Theis, Xiangmin Xu

    Nature MethodsReviewOpen accessDOIPDF
    Topic: Data integration

21. Scalable and universal prediction of cellular phenotypes enables in silico experiments

    Yuge Ji, Alejandro Tejada-Lapuerta, Niklas A. Schmacke, …, Fabian J. Theis

    bioRxivPreprintOpen accessDOIPDF
    Topic: Deep learning and generative models

22. scTab: Scaling cross-tissue single-cell annotation models

    Felix Fischer, David S. Fischer, Roman Mukhin, Andrey Isaev, Evan Biederstedt, Alexandra-Chloé Villani, Fabian J. Theis

    Nature CommunicationsOpen accessDOIPDF
    Topic: Single-cell genomics

23. Polyploidisation pleiotropically buffers ageing in hepatocytes

    Kelvin Yin, Maren Büttner, Ioannis K. Deligiannis, …, Fabian Theis, …, Celia P. Martinez-Jimenez

    Journal of HepatologyOpen accessDOI
    Topic: Single-cell genomics

24. Transformers in single-cell omics: a review and new perspectives

    Artur Szałata, Karin Hrovatin, Sören Becker, Alejandro Tejada-Lapuerta, Haotian Cui, Bo Wang, Fabian J. Theis

    Nature MethodsReviewDOI
    Topic: Deep learning and generative models

25. Weakly supervised learning uncovers phenotypic signatures in single-cell data

    Anastasia Litinetskaya, Soroor Hediyeh-zadeh, Amir Ali Moinfar, Mohammad Lotfollahi, Fabian J. Theis

    bioRxivPreprintOpen accessDOI
    Topic: Deep learning and generative models

26. Evaluation of OCT biomarker changes in treatment-naive neovascular AMD using a deep semantic segmentation algorithm

    Ben Asani, Olle Holmberg, Johannes B. Schiefelbein, …, Fabian J. Theis, Siegfried G. Priglinger

    EyeOpen accessDOIPDF
    Topic: Imaging

27. A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection

    Miriam Bosch, Nina Kallin, Sainitin Donakonda, …, Fabian Theis, …, Percy A. Knolle

    NatureOpen accessDOIPDF
    Topic: Immunity and inflammation

28. Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

    Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, …, Fabian J. Theis, Calliope A. Dendrou

    Genome BiologyOpen accessDOIPDF
    Topic: Single-cell genomics

29. Mapping the human hematopoietic stem and progenitor cell hierarchy through integrated single-cell proteomics and transcriptomics

    Benjamin Furtwängler, Nil Üresin, Sabrina Richter, …, Fabian J. Theis, …, Bo T Porse

    bioRxivPreprintOpen accessDOI
    Topic: Single-cell genomics

30. Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data

    Felix Drost, Yang An, Irene Bonafonte-Pardàs, …, Fabian Theis, …, Benjamin Schubert

    Nature CommunicationsOpen accessDOIPDF
    Topic: Data integration

31. GraphCompass: spatial metrics for differential analyses of cell organization across conditions

    Mayar Ali, Merel Kuijs, Soroor Hediyeh-zadeh, Tim Treis, Karin Hrovatin, Giovanni Palla, Anna C Schaar, Fabian J Theis

    BioinformaticsOpen accessDOIPDF
    Topic: Spatial omics

32. CellRank 2: unified fate mapping in multiview single-cell data

    Philipp Weiler, Marius Lange, Michal Klein, Dana Pe’er, Fabian Theis

    Nature MethodsOpen accessDOIPDF
    Topic: Cell fate and dynamics

33. Machine learning integrative approaches to advance computational immunology

    Fabiola Curion, Fabian J. Theis

    Genome MedicineReviewOpen accessDOIPDF
    Topic: Data integration

34. MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery

    Till Siebenmorgen, Filipe Menezes, Sabrina Benassou, …, Fabian J. Theis, …, Grzegorz M. Popowicz

    Nature Computational ScienceOpen accessDOIPDF
    Topic: Mechanistic modelling

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

    Mohammad Lotfollahi, Yuhan Hao, Fabian J. Theis, Rahul Satija

    CellReviewOpen accessDOIPDF
    Topic: Data integration

36. hadge: a comprehensive pipeline for donor deconvolution in single-cell studies

    Fabiola Curion, Xichen Wu, Lukas Heumos, …, Fabian J. Theis

    Genome BiologyOpen accessDOIPDF
    Topic: Single-cell genomics

37. Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex

    Christina Koupourtidou, Veronika Schwarz, Hananeh Aliee, …, Fabian J. Theis, Jovica Ninkovic

    Nature CommunicationsOpen accessDOIPDF
    Topic: Brain and mental health

38. SpatialData: an open and universal data framework for spatial omics

    Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, …, Fabian J. Theis, Oliver Stegle

    Nature MethodsOpen accessDOIPDF
    Topic: Spatial omics

39. longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types

    Jonas Hagenberg, Monika Budde, Teodora Pandeva, …, Fabian J Theis, …, Janine Knauer-Arloth

    BioinformaticsOpen accessDOIPDF
    Topic: Open-source software

40. Quantitative characterization of cell niches in spatial atlases

    Sebastian Birk, Irene Bonafonte-Pardàs, Adib Miraki Feriz, …, Fabian J. Theis, …, Mohammad Lotfollahi

    bioRxivPreprintOpen accessDOIPDF
    Topic: Deep learning and generative models

41. Community effort to unravel the complex human neuronal landscape exemplified for the striatum

    Joachim Schultze, Shobhit Agrawal, Rebekka Scholz, …, Fabian Theis, …, Marc Beyer

    Research SquarePreprintOpen accessDOIPDF
    Topic: Brain and mental health

42. Cell circuits underlying nanomaterial specific respiratory toxicology

    Carola Voss, Lianyong Han, Meshal Ansari, …, Fabian J. Theis, …, Tobias Stoeger

    bioRxivPreprintOpen accessDOIPDF
    Topic: Single-cell genomics

43. Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts

    Christoph H. Mayr, Arunima Sengupta, Sara Asgharpour, …, Fabian J. Theis, …, Herbert B. Schiller

    European Respiratory JournalOpen accessDOIPDF
    Topic: Cell fate and dynamics

44. Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma

    Daniel Kirschenbaum, Ken Xie, Florian Ingelfinger, …, Fabian J. Theis, …, Ido Amit

    CellOpen accessDOI
    Topic: Cell fate and dynamics

45. Single cell transcriptomic analysis of epithelial and mesenchymal tumour cells

    Aristeidis Papargyriou, Till Richter, Malte Luecken, Fabian J. Theis, Maximilian Reichert

    ZenodoDatasetDOI
    Topic: Single-cell genomics