Dissecting the logical types of network control in gene expression profiles. - Carsten Marr; Marcel Geertz; Marc-Thorsten Hütt; Georgi Muskhelishvili (BMC Syst. Biol., 2008)

Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli. - Carsten Marr; Fabian J. Theis; Larry S. Liebovitch; Marc-Thorsten Hütt (PLoS Comput. Biol., 2010)

Cellular Automata on Graphs: Topological Properties of ER Graphs Evolved towards Low-Entropy Dynamics. - Carsten Marr; Marc-Thorsten Hütt (Entropy, 2012)

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. - Felix Buggenthin; Carsten Marr; Michael Schwarzfischer; Philipp S. Hoppe; Oliver Hilsenbeck; Timm Schroeder; Fabian J. Theis (BMC Bioinform., 2013)

Centroid Clustering of Cellular Lineage Trees. - Valeriy Khakhutskyy; Michael Schwarzfischer; Nina C. Hubig; Claudia Plant; Carsten Marr; Michael A. Rieger; Timm Schroeder; Fabian J. Theis (ITBAM, 2014)

MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data. - Justin Feigelman; Fabian J. Theis; Carsten Marr (BMC Bioinform., 2014)

Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics. - Carolin Loos; Carsten Marr; Fabian J. Theis; Jan Hasenauer (CMSB, 2015)

Anatomic-landmark detection using graphical context modelling. - Lichao Wang; Vasileios Belagiannis; Carsten Marr; Fabian J. Theis; Guang-Zhong Yang; Nassir Navab (ISBI, 2015)

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy. - Michael K. Strasser; Justin Feigelman; Fabian J. Theis; Carsten Marr (BMC Syst. Biol., 2015)

Structure-based assessment of cancerous mitochondria using deep networks. - Manish Mishra; Sabine Schmitt; Lichao Wang; Michael K. Strasser; Carsten Marr; Nassir Navab; Hans Zischka; Tingying Peng (ISBI, 2016)

destiny: diffusion maps for large-scale single-cell data in R. - Philipp Angerer; Laleh Haghverdi; Maren Büttner; Fabian J. Theis; Carsten Marr; Florian A. Büttner (Bioinform., 2016)

An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson's rule. - Sabine Hug; Michael Schwarzfischer; Jan Hasenauer; Carsten Marr; Fabian J. Theis (Stat. Comput., 2016)

fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy. - Oliver Hilsenbeck; Michael Schwarzfischer; Dirk Loeffler; Sotiris Dimopoulos; Simon Hastreiter; Carsten Marr; Fabian J. Theis; Timm Schroeder (Bioinform., 2017)

Abstract: Digital Cytomorphology - Deep Learning on an Image Data Set of Cell Morphologies in Acute Myeloid Leukemia. - Christian Matek; Carsten Marr; Karsten Spiekermann (Bildverarbeitung für die Medizin, 2018)

LNA++: Linear Noise Approximation with First and Second Order Sensitivities. - Justin Feigelman; Daniel Weindl; Fabian J. Theis; Carsten Marr; Jan Hasenauer (CMSB, 2018)

Quantifying Structural Heterogeneity of Healthy and Cancerous Mitochondria Using a Combined Segmentation and Classification USK-Net. - Manish Mishra; Sabine Schmitt; Hans Zischka; Michael K. Strasser; Nassir Navab; Carsten Marr; Tingying Peng (ICANN (Workshop), 2019)

Evaluation of Domain Adaptation Approaches for Robust Classification of Heterogeneous Biological Data Sets. - Michael Schneider; Lichao Wang; Carsten Marr (ICANN (2), 2019)

In-Silico Staining from Bright-Field and Fluorescent Images Using Deep Learning. - Dominik Jens Elias Waibel; Ulf Tiemann; Valerio Lupperger; Henrik Semb; Carsten Marr (ICANN (3), 2019)

Multi-task Learning of a Deep K-Nearest Neighbour Network for Histopathological Image Classification and Retrieval. - Tingying Peng; Melanie Boxberg; Wilko Weichert; Nassir Navab; Carsten Marr (MICCAI (1), 2019)

Multiclass Deep Active Learning for Detecting Red Blood Cell Subtypes in Brightfield Microscopy. - Ario Sadafi; Niklas Koehler; Asya Makhro; Anna Bogdanova; Nassir Navab; Carsten Marr; Tingying Peng (MICCAI (1), 2019)

Human-level recognition of blast cells in acute myeloid leukaemia with convolutional neural networks. - Christian Matek; Simone Schwarz; Karsten Spiekermann; Carsten Marr (Nat. Mach. Intell., 2019)

Abstract: Recognition of AML Blast Cells in a Curated Single-Cell Dataset of Leukocyte Morphologies Using Deep Convolutional Neural Networks. - Christian Matek; Simone Schwarz; Karsten Spiekermann; Carsten Marr (Bildverarbeitung für die Medizin, 2020)

Background and Illumination Correction for Time-Lapse Microscopy Data with Correlated Foreground. - Tingying Peng; Lorenz Lamm; Dirk Loeffler; Nouraiz Ahmed; Nassir Navab; Timm Schroeder; Carsten Marr (MICCAI (5), 2020)

Attention Based Multiple Instance Learning for Classification of Blood Cell Disorders. - Ario Sadafi; Asya Makhro; Anna Bogdanova; Nassir Navab; Tingying Peng; Shadi Albarqouni; Carsten Marr (MICCAI (5), 2020)

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data. - Philipp Angerer; David S. Fischer; Fabian J. Theis; Antonio Scialdone; Carsten Marr (Bioinform., 2020)

Fourier Transform of Percoll Gradients Boosts CNN Classification of Hereditary Hemolytic Anemias. - Ario Sadafi; Lucía María Moya Sans; Asya Makhro; Leonid Livshits; Nassir Navab; Anna Bogdanova; Shadi Albarqouni; Carsten Marr (ISBI, 2021)

Sickle Cell Disease Severity Prediction from Percoll Gradient Images Using Graph Convolutional Networks. - Ario Sadafi; Asya Makhro; Leonid Livshits; Nassir Navab; Anna Bogdanova; Shadi Albarqouni; Carsten Marr (DART/FAIR@MICCAI, 2021)

Structure-Preserving Multi-domain Stain Color Augmentation Using Style-Transfer with Disentangled Representations. - Sophia J. Wagner; Nadieh Khalili; Raghav Sharma; Melanie Boxberg; Carsten Marr; Walter de Back; Tingying Peng (MICCAI (8), 2021)

InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification. - Dominik Jens Elias Waibel; Sayedali Shetab Boushehri; Carsten Marr (BMC Bioinform., 2021)

Abstract: A Database and Neural Network for Highly Accurate Classification of Single Bone Marrow Cells. - Christian Matek; Sebastian Krappe; Christian Münzenmayer; Torsten Haferlach; Carsten Marr (Bildverarbeitung für die Medizin, 2022)

Systematic Comparison of Incomplete-Supervision Approaches for Biomedical Image Classification. - Sayedali Shetab Boushehri; Ahmad Bin Qasim; Dominik Jens Elias Waibel; Fabian Schmich; Carsten Marr (ICANN (1), 2022)

Anomaly-Aware Multiple Instance Learning for Rare Anemia Disorder Classification. - Salome Kazeminia; Ario Sadafi; Asya Makhro; Anna Bogdanova; Shadi Albarqouni; Carsten Marr (MICCAI (8), 2022)

DeStripe: A Self2Self Spatio-Spectral Graph Neural Network with Unfolded Hessian for Stripe Artifact Removal in Light-Sheet Microscopy. - Yu Liu; Kurt Weiss; Nassir Navab; Carsten Marr; Jan Huisken; Tingying Peng (MICCAI (4), 2022)

Unsupervised Cross-Domain Feature Extraction for Single Blood Cell Image Classification. - Raheleh Salehi; Ario Sadafi; Armin Gruber; Peter Lienemann; Nassir Navab; Shadi Albarqouni; Carsten Marr (MICCAI (3), 2022)

Capturing Shape Information with Multi-scale Topological Loss Terms for 3D Reconstruction. - Dominik Jens Elias Waibel; Scott Atwell; Matthias Meier; Carsten Marr; Bastian Rieck (MICCAI (4), 2022)

Altered expression response upon repeated gene repression in single yeast cells. - Lea Schuh; Igor Kukhtevich; Poonam Bheda; Melanie Schulz; Maria Bordukova; Robert Schneider; Carsten Marr (PLoS Comput. Biol., 2022)

A Study of Age and Sex Bias in Multiple Instance Learning Based Classification of Acute Myeloid Leukemia Subtypes. - Ario Sadafi; Matthias Hehr; Nassir Navab; Carsten Marr (CLIP/FAIMI/EPIMI@MICCAI, 2023)

Pixel-Level Explanation of Multiple Instance Learning Models in Biomedical Single Cell Images. - Ario Sadafi; Oleksandra Adonkina; Ashkan Khakzar; Peter Lienemann; Rudolf Matthias Hehr; Daniel Rueckert; Nassir Navab; Carsten Marr (IPMI, 2023)

Active Learning Enhances Classification of Histopathology Whole Slide Images with Attention-Based Multiple Instance Learning. - Ario Sadafi; Nassir Navab; Carsten Marr (ISBI, 2023)

BEL: A Bag Embedding Loss for Transformer Enhances Multiple Instance Whole Slide Image Classification. - Daniel Sens; Ario Sadafi; Francesco Paolo Casale; Nassir Navab; Carsten Marr (ISBI, 2023)

A Diffusion Model Predicts 3D Shapes from 2D Microscopy Images. - Dominik Jens Elias Waibel; Ernst Röell; Bastian Rieck; Raja Giryes; Carsten Marr (ISBI, 2023)

BigFUSE: Global Context-Aware Image Fusion in Dual-View Light-Sheet Fluorescence Microscopy with Image Formation Prior. - Yu Liu; Gesine Müller; Nassir Navab; Carsten Marr; Jan Huisken; Tingying Peng (MICCAI (8), 2023)

A Continual Learning Approach for Cross-Domain White Blood Cell Classification. - Ario Sadafi; Raheleh Salehi; Armin Gruber; Sayedali Shetab Boushehri; Pascal Giehr; Nassir Navab; Carsten Marr (DART@MICCAI, 2023)

Imbalanced Domain Generalization for Robust Single Cell Classification in Hematological Cytomorphology. - Rao Muhammad Umer; Armin Gruber; Sayedali Shetab Boushehri; Christian Metak; Carsten Marr (CoRR, 2023)

Topologically-Regularized Multiple Instance Learning for Red Blood Cell Disease Classification. - Salome Kazeminia; Ario Sadafi; Asya Makhro; Anna Bogdanova; Carsten Marr; Bastian Rieck (CoRR, 2023)

A Data-Driven Solution for The Cold Start Problem in Biomedical Image Classification. - Salome Kazeminia; Miroslav Brezík; Sayedali Shetab Boushehri; Carsten Marr (ISBI, 2024)

Low-Resource Finetuning of Foundation Models Beats State-of-the-Art in Histopathology. - Benedikt Roth; Valentin Koch; Sophia J. Wagner; Julia A. Schnabel; Carsten Marr; Tingying Peng (ISBI, 2024)

Neural Cellular Automata for Lightweight, Robust and Explainable Classification of White Blood Cell Images. - Michael Deutges; Ario Sadafi; Nassir Navab; Carsten Marr (MICCAI (3), 2024)

DinoBloom: A Foundation Model for Generalizable Cell Embeddings in Hematology. - Valentin Koch; Sophia J. Wagner; Salome Kazeminia; Ece Sancar; Matthias Hehr; Julia A. Schnabel; Tingying Peng; Carsten Marr (MICCAI (12), 2024)

EchoVisuAL: Efficient Segmentation of Echocardiograms Using Deep Active Learning. - Isabella Galter; Elida Schneltzer; Carsten Marr; IMPC Consortium; Nadine Spielmann; Martin Hrabé de Angelis (MIUA (2), 2024)

Self-Supervised Multiple Instance Learning for Acute Myeloid Leukemia Classification. - Salome Kazeminia; Max Joosten; Dragan Bosnacki; Carsten Marr (CoRR, 2024)

M-HOF-Opt: Multi-Objective Hierarchical Output Feedback Optimization via Multiplier Induced Loss Landscape Scheduling. - Xudong Sun 002; Nutan Chen; Alexej Gossmann; Yu Xing; Carla Feistner; Emilio Dorigatt; Felix Drost; Daniele Scarcella; Lisa Beer; Carsten Marr (CoRR, 2024)

DomainLab: A modular Python package for domain generalization in deep learning. - Xudong Sun 002; Carla Feistner; Alexej Gossmann; George Schwarz; Rao Muhammad Umer; Lisa Beer; Patrick Rockenschaub; Rahul Babu Shrestha; Armin Gruber; Nutan Chen; Sayedali Shetab Boushehri; Florian Buettner 001; et al. (CoRR, 2024)

Multimodal Analysis of White Blood Cell Differentiation in Acute Myeloid Leukemia Patients using a β-Variational Autoencoder. - Gizem Mert; Ario Sadafi; Raheleh Salehi; Nassir Navab; Carsten Marr (CoRR, 2024)

UNICORN: A Deep Learning Model for Integrating Multi-Stain Data in Histopathology. - Valentin Koch; Sabine Bauer; Valerio Lupperger; Michael Joner; Heribert Schunkert; Julia A. Schnabel; Moritz von Scheidt; Carsten Marr (CoRR, 2024)

SCAS dashboard: A tool to intuitively and interactively analyze Slurm cluster usage. - Thomas Walzthoeni; Bom Bahadur Singiali; N. William Rayner; Francesco Paolo Casale; Christoph Feest; Carsten Marr; Alf Wachsmann (J. Open Source Softw., 2024)

M-HOF-Opt: Multi-Objective Hierarchical Output Feedback Optimization via Multiplier Induced Loss Landscape Scheduling. - Xudong Sun 002; Nutan Chen; Alexej Gossmann; Yu Xing; Matteo Wohlrapp; Emilio Dorigatti; Carla Feistner; Felix Drost; Daniele Scarcella; Lisa Beer; Carsten Marr (AISTATS, 2025)

Hierarchical Neural Cellular Automata for Lightweight Microscopy Image Classification. - Chen Yang; Michael Deutges; Nassir Navab; Ario Sadafi; Carsten Marr (IPMI (1), 2025)

CellPilot: A Unified Approach to Automatic and Interactive Segmentation in Histopathology. - Philipp Endres; Valentin Koch; Julia A. Schnabel; Carsten Marr (ISBI, 2025)

The role of single cell transcriptomics for efficacy and toxicity profiling of chimeric antigen receptor (CAR) T cell therapies. - Moritz Thomas; Ruben Brabenec; Lisa Gregor; David Andreu-Sanz; Emanuele Carlini; Philipp Jie Müller; Adrian Gottschlich; Donjete Simnica; Sebastian Kobold; Carsten Marr (Comput. Biol. Medicine, 2025)

FL-W3S: Cross-domain federated learning for weakly supervised semantic segmentation of white blood cells. - Hussain Ahmad Madni; Rao Muhammad Umer; Silvia Zottin; Carsten Marr; Gian Luca Foresti (Int. J. Medical Informatics, 2025)

Addressing pitfalls in implicit unobserved confounding synthesis using explicit block hierarchical ancestral sampling. - Xudong Sun 002; Alex Markham; Pratik Misra; Carsten Marr (CoRR, 2025)

AI-Driven Cytomorphology Image Synthesis for Medical Diagnostics. - Jan Carreras Boada; Rao Muhammad Umer; Carsten Marr (CoRR, 2025)

CytoSAE: Interpretable Cell Embeddings for Hematology. - Muhammed Furkan Dasdelen; Hyesu Lim; Michèle Buck; Katharina S. Götze; Carsten Marr; Steffen Schneider 004 (CoRR, 2025)

Continual Multiple Instance Learning for Hematologic Disease Diagnosis. - Zahra Ebrahimi; Raheleh Salehi; Nassir Navab; Carsten Marr; Ario Sadafi (CoRR, 2025)