Brain Region-Specific Oligodendrocyte States Highlight Mitochondrial Gene Upregulation and Loss of Canonical Identity Signatures in Alzheimer’s Disease
Preprint (Jan. 2026)
#p-theis
SPG+25
Modeling Microenvironment Trajectories on Spatial Transcriptomics With NicheFlow
NeurIPS 2025
#p-guennemann#p-theis
GWZ+25
Language May Be All Omics Needs: Harmonizing Multimodal Data for Omics Understanding With CellHermes
Preprint (Nov. 2025)
#p-theis
BTB+25
ScConcept: Contrastive Pretraining for Technology-Agnostic Single-Cell Representations Beyond Reconstruction
Preprint (Oct. 2025)
#p-kilbertus#p-theis
UER+25
Disentangled Representation Learning With the Gromov-Monge Gap
ICLR 2025
#p-akata#p-theis
CDW+25
Transformers and Genome Language Models
Nature Machine Intelligence. Mar. 2025
#p-theis
BVT+25
A Scalable Gene Network Model of Regulatory Dynamics in Single Cells
Preprint (Mar. 2025)
#p-bauer-s#p-theis
Wei25
Deep Generative Modeling of Transcriptional Dynamics and Data-View Agnostic Inference of Cellular State Changes With Single-Cell Omics Data
Dissertation TU München. Jan. 2025
#p-theis
KLF+24a
Probe Set Selection for Targeted Spatial Transcriptomics
Nature Methods 21. Dec. 2024
#p-theis
SHB+24
Transformers in Single-Cell Omics: A Review and New Perspectives
Nature Methods 21. Aug. 2024
#p-kilbertus#p-theis
UER+24
Disentangled Representation Learning Through Geometry Preservation With the Gromov-Monge Gap
SPIGM @ICML 2024
#p-akata#p-theis
AKH+24
GraphCompass: Spatial Metrics for Differential Analyses of Cell Organization Across Conditions
Bioinformatics 40.Supplement 1. Jul. 2024
#p-theis
WKH+24
Expressivity and Generalization: Fragment-Biases for Molecular GNNs
Preprint (Jun. 2024)
#p-guennemann#p-theis
EKU+24
Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation
ICLR 2024
#p-kilbertus#p-theis
GWL+24
Deep Generative Modeling of Transcriptional Dynamics for RNA Velocity Analysis in Single Cells
Nature Methods 21. Jan. 2024
#p-theis
LSD+23
Predicting Cellular Responses to Complex Perturbations in High‐throughput Screens
Molecular Systems Biology 19.e11517. Jun. 2023
#p-guennemann#p-theis
SHL+23
The Power of Motifs as Inductive Bias for Learning Molecular Distributions
Preprint (Jun. 2023)
#p-guennemann#p-theis
FST23
Modeling Intercellular Communication in Tissues Using Spatial Graphs of Cell
Nature Biotechnology 41. Mar. 2023
#p-theis
HSL+23
Best Practices for Single-Cell Analysis Across Modalities
Nature Reviews Genetics 24. Mar. 2023
#p-theis
ARS+22
Sparsity in Continuous-Depth Neural Networks
NeurIPS 2022
#p-kilbertus#p-theis
HBK+22
Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution
Modeling Dynamical Biological Processes Through the Lens of Single-Cell Genomics
Dissertation TU München. Oct. 2022
#p-theis
HFM+22
Probing Cell Identity Hierarchies by Fate Titration and Collision During Direct Reprogramming
Molecular Systems Biology 18.e11129. Sep. 2022
#p-theis
SFN+22
Association of Bronchial Steroid Inducible Methylation Quantitative Trait Loci With Asthma and Chronic Obstructive Pulmonary Disease Treatment Response
Clinical and Translational Allergy 12.8. Aug. 2022
#p-theis
LNL+22
Mapping Single-Cell Data to Reference Atlases by Transfer Learning
Nature Biotechnology 40. Aug. 2022
#p-theis
HBK+22a
Predicting Single-Cell Perturbation Responses for Unseen Drugs
MLDD @ICML 2022
#p-guennemann#p-kilbertus#p-theis
BFK+22
Alveolar Macrophages in Early Stage COPD Show Functional Deviations With Properties of Impaired Immune Activation
Frontiers in Immunology 13. Jul. 2022
#p-theis
PSK+22
Squidpy: A Scalable Framework for Spatial Omics Analysis
Nature Methods 19. Jan. 2022
#p-theis
LBK+22
CellRank for Directed Single-Cell Fate Mapping
Nature Methods 19.2. Jan. 2022
#p-theis
HFG+21
Graph Representation Learning for Single-Cell Biology
Current Opinion in Systems Biology 28.100347. Dec. 2021
#p-guennemann#p-theis
SHC+21
ScPower Accelerates and Optimizes the Design of Multi-Sample Single Cell Transcriptomic Studies
Nature Communications 12.6625. Nov. 2021
#p-theis
VFH+21
Group Testing for SARS-CoV-2 Allows for Up to 10-Fold Efficiency Increase Across Realistic Scenarios and Testing Strategies
Frontiers in Public Health 9. Aug. 2021
#p-krahmer#p-theis
FDK+21
Sfaira Accelerates Data and Model Reuse in Single Cell Genomics
Genome Biology 22.248. Aug. 2021
#p-theis
BSK+21
RNA Velocity—current Challenges and Future Perspectives
Molecular Systems Biology 17.e10282. Aug. 2021
#p-theis
FAW+21
Single-Cell RNA Sequencing Reveals Ex Vivo Signatures of SARS-CoV-2-Reactive T Cells Through ‘Reverse Phenotyping’
Nature Communications 12.1. Jul. 2021
#p-theis
JLW+21
Machine Learning for Perturbational Single-Cell Omics
Cell Systems 12.6. Jun. 2021
#p-theis
FST21
Learning Cell Communication From Spatial Graphs of Cells
Preprint (Jun. 2021)
#p-theis
LSD+21
Compositional Perturbation Autoencoder for Single-Cell Response Modeling
Preprint (May. 2021)
#p-theis
PSK+21
Squidpy: A Scalable Framework for Spatial Single Cell Analysis
Preprint (Apr. 2021)
#p-theis
MKB+21
Deep Learning the Collisional Cross Sections of the Peptide Universe From a Million Experimental Values
Nature Communications 12.1185. Feb. 2021
#p-theis
LBS+21a
Single-Cell Molecular Profiling of All Three Components of the HPA Axis Reveals Adrenal ABCB1 as a Regulator of Stress Adaptation
Science Advances 7.5. Jan. 2021
#p-theis
LNT+20
Conditional Out-of-Distribution Generation for Unpaired Data Using Transfer VAE
Bioinformatics 36.Supplement 2. Dec. 2020
#p-theis
CKF+20
A Sparse Deep Learning Approach for Automatic Segmentation of Human Vasculature in Multispectral Optoacoustic Tomography
Photoacoustics 20.100203. Dec. 2020
#p-theis
CRB+20
Predicting Single-Cell Gene Expression Profiles of Imaging Flow Cytometry Data With Machine Learning
Nucleic Acids Research 48.20. Nov. 2020
#p-theis
FWS+20
Predicting Antigen Specificity of Single T Cells Based on TCR CDR3 Regions
Molecular Systems Biology 16.8. Aug. 2020
#p-theis
BLP+20
Generalizing RNA Velocity to Transient Cell States Through Dynamical Modeling
Nature Biotechnology 38. Aug. 2020
#p-theis
KCR+20
In Vivo Identification of Apoptotic and Extracellular Vesicle-Bound Live Cells Using Image-Based Deep Learning
Journal of Extracellular Vesicles 9.1. Jul. 2020
#p-theis
LNL+20
Query to Reference Single-Cell Integration With Transfer Learning
Preprint (Jul. 2020)
#p-theis
BFK+20
Alterations of Multiple Alveolar Macrophage States in Chronic Obstructive Pulmonary Disease
Preprint (May. 2020)
#p-theis
SBT+20
Targeted Pharmacological Therapy Restores Β-Cell Function for Diabetes Remission
Nature Metabolism 2. Feb. 2020
#p-theis
LWT19
ScGen Predicts Single-Cell Perturbation Responses
Nature Methods 16.8. Jul. 2019
#p-theis
EBK+19
ScSLAM-Seq Reveals Core Features of Transcription Dynamics in Single Cells
Nature 571. Jul. 2019
#p-theis
LT19
Current Best Practices in Single‐cell RNA‐seq Analysis: A Tutorial