C. Marr

发表

Outer-totalistic cellular automata on graphs

C. Marr, M. Hütt, 2008, 0812.2408.

Hierarchical Differentiation of Myeloid Progenitors Is Encoded in the Transcription Factor Network

Fabian J Theis, C. Marr, T. Schroeder, 2011, PloS one.

Human-level recognition of blast cells in acute myeloid leukaemia with convolutional neural networks

K. Spiekermann, C. Marr, Christian Matek, 2019, Nat. Mach. Intell..

Tissue-Specific Target Analysis of Disease-Associated MicroRNAs in Human Signaling Pathways

Fabian J. Theis, Andreas Kowarsch, Carsten Marr, 2010, PloS one.

Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer.

Michael M. Saint-Antoine, A. Raj, Abhyudai Singh, 2020, Cell systems.

A geometric analysis of fast-slow models for stochastic gene expression

Carsten Marr, Nikola Popović, P. Swain, 2015, Journal of Mathematical Biology.

Evaluation of domain adaptation approaches for robust classification of heterogeneous biological data sets

C. Marr, Michael Schneider, Lichao Wang, 2019, bioRxiv.

Multi‐scale modeling of GMP differentiation based on single‐cell genealogies

Fabian J Theis, Michael K. Strasser, C. Marr, 2012, The FEBS journal.

Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression.

Fabian J Theis, Michael K. Strasser, C. Marr, 2011, Biophysical journal.

Determining the Properties of Gene Regulatory Networks from Expression Data

L. Liebovitch, Viktor Jirsa, C. Marr, 2009 .

Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks.

Dominik M. Wittmann, Fabian J Theis, C. Marr, 2010, Journal of theoretical biology.

Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies

Fabian J Theis, C. Marr, S. Cremer, 2012, PLoS biology.

miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs.

Fabian J Theis, C. Marr, A. Kowarsch, 2011, RNA.

Prospective identification of hematopoietic lineage choice by deep learning

Fabian J Theis, Michael K. Strasser, Philipp S. Hoppe, 2017, Nature Methods.

Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis.

Fabian J Theis, Michael K. Strasser, J. Hasenauer, 2018, Cell reports.

Subtle Changes in Clonal Dynamics Underlie the Age-Related Decline in Neurogenesis

Fabian J Theis, Michael K. Strasser, J. Hasenauer, 2017, bioRxiv.

Reoccurring neural stem cell divisions in the adult zebrafish telencephalon are sufficient for the emergence of aggregated spatiotemporal patterns

C. Marr, V. Lupperger, P. Chapouton, 2020, PLoS biology.

Aggregated spatio-temporal division patterns emerge from reoccurring divisions of neural stem cells

C. Marr, V. Lupperger, P. Chapouton, 2020, bioRxiv.

Regularizing capacity of metabolic networks.

Marc-Thorsten Hütt, Mark Müller-Linow, Carsten Marr, 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine

Carsten Marr, Fabian J Theis, Wolfgang Wurst, 2009, Genome Biology.

Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots.

Carsten Marr, Sui Huang, Joseph X Zhou, 2016, Current opinion in biotechnology.

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios

Carsten Marr, Fabian J Theis, Oliver Hilsenbeck, 2016, Nature.

Network plasticity of pluripotency transcription factors in embryonic stem cells

Fabian J. Theis, Jan Hasenauer, Carsten Marr, 2015, Nature Cell Biology.

Live cell-lineage tracing and machine learning reveal patterns of organ regeneration

C. Marr, H. López-Schier, V. Lupperger, 2018, eLife.

SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins

Rolf Backofen, Carsten Marr, Fabian Theis, 2015, RNA biology.

Computational modeling reveals cell-cycle dependent kinetics of H4K20 methylation states during Xenopus embryogenesis

C. Marr, L. Schuh, A. Imhof, 2020, bioRxiv.

H4K20 Methylation Is Differently Regulated by Dilution and Demethylation in Proliferating and Cell-Cycle-Arrested Xenopus Embryos.

C. Marr, L. Schuh, A. Imhof, 2020, Cell systems.

Domain Model Explains Propagation Dynamics and Stability of Histone H3K27 and H3K36 Methylation Landscapes.

J. Hasenauer, C. Marr, A. Groth, 2020, Cell reports.

cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics

Fabian J Theis, Michael K. Strasser, F. Buettner, 2016, bioRxiv.

cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics

Fabian J Theis, Michael K. Strasser, F. Buettner, 2016, bioRxiv.

Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate

Fabian J Theis, Edward S. Allgeyer, F. Buettner, 2018, The EMBO journal.

Single-Cell Gene Expression Profiling and Cell State Dynamics: Collecting Data, Correlating Data Points and Connecting the Dots

Sui Huang, C. Marr, J. Zhou, 2016, bioRxiv.

destiny: diffusion maps for large-scale single-cell data in R

Fabian J. Theis, Florian Buettner, Carsten Marr, 2015, Bioinform..

Human-level recognition of blast cells in acute myeloid leukaemia with convolutional neural networks

K. Spiekermann, C. Marr, Christian Matek, 2019, Nature Machine Intelligence.

Opposing effects of allogrooming on disease transmission in ant societies

Fabian J Theis, C. Marr, S. Cremer, 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

Systematic comparison of incomplete-supervision approaches for biomedical imaging classification

Sayedali Shetab Boushehri, Dominik Jens Elias Waibel, C. Marr, 2020, bioRxiv.

Built to last? Reproducibility and Reusability of Deep Learning Algorithms in Computational Pathology

Sayedali Shetab Boushehri, Dominik Jens Elias Waibel, C. Marr, 2022, medRxiv.

Sickle Cell Disease Severity Prediction from Percoll Gradient Images using Graph Convolutional Networks

Nassir Navab, Shadi Albarqouni, Ario Sadafi, 2021, DART/FAIR@MICCAI.

DeStripe: A Self2Self Spatio-Spectral Graph Neural Network with Unfolded Hessian for Stripe Artifact Removal in Light-sheet Microscopy

N. Navab, J. Huisken, C. Marr, 2022, 2206.13419.

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

Fabian J Theis, J. Hasenauer, C. Marr, 2016, Cell systems.

Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cells

Fabian J Theis, C. Marr, T. Schroeder, 2016, bioRxiv.

Unsupervised Cross-Domain Feature Extraction for Single Blood Cell Image Classification

Shadi Albarqouni, N. Navab, C. Marr, 2022, MICCAI.

Anomaly-aware multiple instance learning for rare anemia disorder classification

Shadi Albarqouni, C. Marr, A. Makhro, 2022, MICCAI.

Attention based Multiple Instance Learning for Classification of Blood Cell Disorders pdf

Nassir Navab, Tingying Peng, Shadi Albarqouni, 2020, MICCAI.

Early myeloid lineage choice is not induced by random PU.1 / GATA1 protein ratios

Michael K. Strasser, Philipp S. Hoppe, C. Marr, 2015 .

The value of longitudinal clinical data and paired CT scans in predicting the deterioration of COVID-19 revealed by an artificial intelligence system

C. Marr, F. Shan, Botao Zhao, 2022, iScience.

DESTINY

Fabian J Theis, M. Büttner, F. Buettner, 2004, Destiny.

Altered expression response upon repeated gene repression in single yeast cells

C. Marr, L. Schuh, Poonam Bheda, 2022, PLoS Comput. Biol..

CHIP & HIPs: Clonal Hematopoiesis is Common in Hip Arthroplasty Patients and Associates with Autoimmune Disease.

K. Metzeler, K. Götze, F. Bassermann, 2021, Blood.

A geometric analysis of fast-slow models for stochastic gene expression

P. Swain, N. Popović, C. Marr, 2016, Journal of mathematical biology.

An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule

Fabian J Theis, J. Hasenauer, C. Marr, 2015, Statistics and Computing.

Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory.

S. Maerkl, C. Marr, T. Höfer, 2020, Molecular cell.

A generalizable brain extraction net (BEN) for multimodal MRI data from rodents, nonhuman primates, and humans

Jianfeng Feng, C. Marr, Jie Zhang, 2022, eLife.

BEN: a generalizable Brain Extraction Net for multimodal MRI data from rodents, nonhuman primates, and humans

Jianfeng Feng, C. Marr, Jie Zhang, 2022, bioRxiv.

T cells armed with the C-X-C chemokine receptor type 6 enhance adoptive cell therapy for pancreatic tumours

N. Halama, C. Marr, E. Tartour, 2021, Nature Biomedical Engineering.

destiny: diffusion maps for large-scale single-cell data in R

Fabian J. Theis, Florian Buettner, Carsten Marr, 2015, Bioinform..

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data

Carsten Marr, Fabian J Theis, David S. Fischer, 2020, bioRxiv.

Automatic identification of relevant genes from low-dimensional embeddings of single cell RNAseq data

Fabian J. Theis, Carsten Marr, Fabian J Theis, 2020, bioRxiv.

A BaSiC tool for background and shading correction of optical microscopy images

Nassir Navab, Tingying Peng, Carsten Marr, 2017, Nature Communications.

Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm

Carsten Marr, Fabian J Theis, Dirk Loeffler, 2018, Nature Communications.

Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells.

Carsten Marr, Fabian J Theis, Michael Schwarzfischer, 2016, Cell systems.

scifAI: Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies

C. Marr, M. Bacac, K. Essig, 2022, bioRxiv.

Twist1 induces distinct cell states depending on TGFBR1-activation

C. Marr, L. K. Meixner, Uwe J. Kloos, 2016, Oncotarget.

Twist1 induces distinct cell states depending on TGFBR1-activation

C. Marr, L. K. Meixner, Uwe J. Kloos, 2016, Oncotarget.

fastER: a user‐friendly tool for ultrafast and robust cell segmentation in large‐scale microscopy

Fabian J. Theis, Carsten Marr, Sotiris Dimopoulos, 2017, Bioinform..

Efficient fluorescence image normalization for time lapse movies

Fabian J. Theis, Carsten Marr, Fabian J Theis, 2011 .

Highly accurate differentiation of bone marrow cell morphologies using deep neural networks on a large image data set

Christian Münzenmayer, Carsten Marr, Sebastian Krappe, 2021, Blood.

MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data

Fabian J. Theis, Carsten Marr, Fabian J Theis, 2014, BMC Bioinformatics.

Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects

Carsten Marr, Dominik Lutter, Fabian J Theis, 2010, BMC Genomics.

Dissecting the logical types of network control in gene expression profiles

Marc-Thorsten Hütt, Carsten Marr, Marcel Geertz, 2008, BMC Systems Biology.

Two distinct logical types of network control in gene expression profiles

C. Marr, Marcel Geertz, G. Muskhelishvili, 2007, 0709.3156.

Gene networks with transcriptional bursting recapitulate rare transient coordinated expression states in cancer

Michael M. Saint-Antoine, A. Raj, Abhyudai Singh, 2019, bioRxiv.

Combined tumor-directed recruitment and protection from immune suppression enable CAR T cell efficacy in solid tumors

C. Marr, S. Endres, T. Mempel, 2021, Science Advances.

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy

Fabian J. Theis, Carsten Marr, Fabian J Theis, 2013, BMC Bioinformatics.

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy

Fabian J. Theis, Carsten Marr, Fabian J Theis, 2015, BMC Systems Biology.

Software tools for single-cell tracking and quantification of cellular and molecular properties

Carsten Marr, Fabian J Theis, Oliver Hilsenbeck, 2016, Nature Biotechnology.

Image analysis of neural stem cell division patterns in the zebrafish brain

C. Marr, F. Buggenthin, V. Lupperger, 2017, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

Domain model explains propagation dynamics and stability of K27 and K36 methylation landscapes

J. Hasenauer, C. Marr, A. Groth, 2019, bioRxiv.

Computational modeling of stem and progenitor cell kinetics identifies plausible hematopoietic lineage hierarchies

K. Götze, C. Marr, R. Oostendorp, 2021, iScience.

Centroid Clustering of Cellular Lineage Trees

Fabian J. Theis, Valeriy Khakhutskyy, Claudia Plant, 2014, ITBAM.

A case study on the use of scale separation-based analytic propagators for parameter inference in stochastic gene regulation

N. Popović, C. Marr, Justin Feigelman, 2015 .

Explainable AI identifies diagnostic cells of genetic AML subtypes

T. Haferlach, K. Spiekermann, C. Marr, 2023, PLOS digital health.

InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification

Carsten Marr, Dominik Jens Elias Waibel, Sayedali Shetab Boushehri, 2021, BMC bioinformatics.

InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification

Carsten Marr, Sayedali Shetab Boushehri, Dominik Waibel, 2020, BMC Bioinformatics.

A single-cell micro-trench platform for automatic monitoring of cell division and apoptosis after chemotherapeutic drug administration

A. Vollmar, C. Marr, J. Rädler, 2018, Scientific Reports.

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy

Fabian J Theis, Philipp S. Hoppe, C. Marr, 2013, BMC Bioinformatics.

MicroRNA as an Integral Part of Cell Communication: Regularized Target Prediction and Network Prediction

Fabian J. Theis, Rolf Backofen, Klaus Palme, 2018 .

Tens of images can suffice to train neural networks for malignant leukocyte detection

C. Marr, D. Bosnacki, C. Matek, 2021, Scientific Reports.

MitoSegNet: Easy-to-use Deep Learning Segmentation for Analyzing Mitochondrial Morphology

Carsten Marr, Christian A. Fischer, Laura Besora-Casals, 2020, iScience.

Multi-task learning of a deep k-nearest neighbour network for histopathological image classification and retrieval

Nassir Navab, Tingying Peng, Carsten Marr, 2019, bioRxiv.

Injury triggers fascia fibroblast collective cell migration to drive scar formation through N-cadherin

T. Volz, C. Marr, H. Schiller, 2020, Nature Communications.

Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli

Marc-Thorsten Hütt, Fabian J. Theis, Larry S. Liebovitch, 2010, PLoS Comput. Biol..

Parameter inference with analytical propagators for stochastic models of autoregulated gene expression

Carsten Marr, Nikola Popović, Frits Veerman, 2018, bioRxiv.

Imbalanced Domain Generalization for Robust Single Cell Classification in Hematological Cytomorphology

Rao Muhammad Umer, Sayedali Shetab Boushehri, C. Marr, 2023, ArXiv.

NG2-Glia Transiently Overcome Their Homeostatic Network and Contribute to Wound Closure After Brain Injury

C. Marr, F. Buggenthin, C. Straube, 2021, Frontiers in Cell and Developmental Biology.

LNA++: Linear Noise Approximation with First and Second Order Sensitivities

Fabian J. Theis, Jan Hasenauer, Carsten Marr, 2018, CMSB.

Histopathology-Based Deep-Learning Predicts Atherosclerotic Lesions in Intravascular Imaging

M. Joner, A. Kastrati, C. Marr, 2021, Frontiers in Cardiovascular Medicine.

Single-cell transcriptomic atlas-guided development of CAR-T cells for the treatment of acute myeloid leukemia

B. Vick, I. Jeremias, C. Marr, 2023, Nature Biotechnology.

An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule

Fabian J. Theis, Jan Hasenauer, Carsten Marr, 2015, Statistics and Computing.

Time-dependent propagators for stochastic models of gene expression: an analytical method

N. Popović, C. Marr, Frits Veerman, 2017, Journal of Mathematical Biology.

ELECTRONIC SUPPLEMENTARY MATERIAL TO A GEOMETRIC ANALYSIS OF FAST-SLOW MODELS FOR STOCHASTIC GENE EXPRESSION (JOURNAL OF MATHEMATICAL BIOLOGY)

P. Swain, C. Marr, 2015 .

Cellular connectomes as arbiters of local circuit models in the cerebral cortex

Fabian J Theis, M. Helmstaedter, C. Marr, 2021, Nature Communications.

A sparse deep learning approach for automatic segmentation of human vasculature in multispectral optoacoustic tomography

Vasilis Ntziachristos, Fabian J. Theis, Carsten Marr, 2019, bioRxiv.

Spatial proteomics in neurons at single-protein resolution

Sayedali Shetab Boushehri, C. Marr, E. Fornasiero, 2023, bioRxiv.

Fourier Transform of Percoll Gradients Boosts CNN Classification of Hereditary Hemolytic Anemias

Shadi Albarqouni, Nassir Navab, Ario Sadafi, 2021, 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI).

Multiclass Deep Active Learning for Detecting Red Blood Cell Subtypes in Brightfield Microscopy

Nassir Navab, Tingying Peng, Ario Sadafi, 2019, MICCAI.

Structure-Preserving Multi-Domain Stain Color Augmentation using Style-Transfer with Disentangled Representations

Walter de Back, Tingying Peng, Carsten Marr, 2021, MICCAI.

Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies

Sayedali Shetab Boushehri, C. Marr, M. Bacac, 2023, bioRxiv.

PXPermute: Unveiling staining importance in multichannel fluorescence microscopy

Sayedali Shetab Boushehri, C. Marr, F. Schmich, 2023, bioRxiv.

A Topological Characterization of Medium-Dependent Essential Metabolic Reactions

Marc-Thorsten Hütt, Carsten Marr, Nikolaus Sonnenschein, 2012, Metabolites.

SHAPR predicts 3D cell shapes from 2D microscopic images

Dominik Jens Elias Waibel, C. Marr, A. Sadafi, 2021, bioRxiv.

Bispecific antibodies redirect synthetic agonistic receptor modified T cells against melanoma

M. Heppt, C. Marr, S. Endres, 2023, Journal for ImmunoTherapy of Cancer.

Exact Bayesian lineage tree-based inference identi-1 fies Nanog negative autoregulation in mouse em-2 bryonic stem cells 3

Fabian J Theis, C. Marr, T. Schroeder, 2016 .

N6-methyladenosine (m6A) depletion regulates pluripotency exit by activating signaling pathways in embryonic stem cells

C. Marr, K. Anastassiadis, A. Klungland, 2021, Proceedings of the National Academy of Sciences.

DABC-Net for robust pneumonia segmentation and prediction of COVID-19 progression on chest CT scans

X. Xue, C. Marr, Botao Zhao, 2020 .

Annotation-efficient classification combining active learning, pre-training and semi-supervised learning for biomedical images

Carsten Marr, Sayedali Shetab Boushehri, Ahmad Bin Qasim, 2020 .

Progressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS

Fabian J Theis, K. Metzeler, K. Götze, 2023, iScience.

Pixel-Level Explanation of Multiple Instance Learning Models in Biomedical Single Cell Images

D. Rueckert, C. Marr, P. Lienemann, 2023, IPMI.

Cellular Automata on Graphs: Topological Properties of ER Graphs Evolved towards Low-Entropy Dynamics

Marc-Thorsten Hütt, Carsten Marr, C. Marr, 2012, Entropy.

Topology regulates the distribution pattern of excitations in excitable dynamics on graphs.

Marc-Thorsten Hütt, Mark Müller-Linow, Carsten Marr, 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

A Study of Age and Sex Bias in Multiple Instance Learning based Classification of Acute Myeloid Leukemia Subtypes

C. Marr, N. Navab, A. Sadafi, 2023, ArXiv.

Structure-based assessment of cancerous mitochondria using deep networks

Nassir Navab, Lichao Wang, Tingying Peng, 2016, 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI).

Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells.

Fabian J Theis, C. Marr, T. Schroeder, 2016, Cell Systems.

A case study on the use of scale separation-based analytical propagators for parameter inference in models of stochastic gene regulation

N. Popović, C. Marr, Justin Feigelman, 2015 .

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy

Fabian J Theis, Michael K. Strasser, C. Marr, 2015, BMC Systems Biology.