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List of works by Fabian J. Theis

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

scientific article published on 08 June 2017

A Fast Predictive Lossless Coder for fMRI Data Sets

A Python library for probabilistic analysis of single-cell omics data

scientific article published on 07 February 2022

A Vine-copula Based Adaptive MCMC Sampler for Efficient Inference of Dynamical Systems

A bilinear algorithm for sparse representations

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

scientific article published on 17 June 2019

A computational model to predict severity of atopic eczema from 30 serum proteins

scientific article published on 13 May 2016

A critical period for postnatal adaptive plasticity in a model of motor axon miswiring

scientific article

A field guide to cultivating computational biology

scientific article published on 08 October 2021

A geometric algorithm for overcomplete linear ICA

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

scientific article published on 01 May 2019

A modular framework for gene set analysis integrating multilevel omics data

scientific article

A new concept for separability problems in blind source separation

scientific article published in September 2004

A new ica method based on a lattice of the observation space

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst ⬇️

scientific article published on September 15, 2012

A novel molecular disease classifier for psoriasis and eczema

scientific article published on 19 May 2016

A robust model for spatiotemporal dependencies

A scalable moment-closure approximation for large-scale biochemical reaction networks

scientific article published on July 2017

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

scientific article published on 10 September 2020

A strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes

article

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

scientific article published on 31 March 2019

A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion

scientific article published on 19 November 2013

A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling

scientific article published on 19 January 2015

A test metric for assessing single-cell RNA-seq batch correction

scientific article published on 20 December 2018

A transcriptional cross species map of pancreatic islet cells

scientific article published in 2022

A unilateral negative feedback loop between miR-200 microRNAs and Sox2/E2F3 controls neural progenitor cell-cycle exit and differentiation

scientific article published on September 2012

AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients

scientific article published on 02 January 2017

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

scientific article published on 23 September 2019

Allergic contact dermatitis in psoriasis patients: typical, delayed, and non-interacting.

scientific article

Altered relaxation times in MRI indicate bronchopulmonary dysplasia

scientific article published on 02 May 2019

Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis

scientific article published on 16 July 2020

An Affine Equivariant Robust Second-Order BSS Method

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

An atlas of genetic influences on human blood metabolites

scientific article

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

scientific article published on 27 February 2019

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

scientific article

An ensemble approach for inferring semi-quantitative regulatory dynamics for the differentiation of mouse embryonic stem cells using prior knowledge

scientific article published in January 2012

An evolutionary and structural characterization of mammalian protein complex organization

scientific article

An integrated cell atlas of the lung in health and disease

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

scientific article published on November 2016

Analyzing M-CSF dependent monocyte/macrophage differentiation: expression modes and meta-modes derived from an independent component analysis

scientific article

Anatomic-landmark detection using graphical context modelling

Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics

Asc-1 regulates white versus beige adipocyte fate in a subcutaneous stromal cell population

scientific article published on 11 March 2021

Assessment of batch-correction methods for scRNA-seq data with a new test metric

Asthma in farm children is more determined by genetic polymorphisms and in non-farm children by environmental factors

scientific article published on 30 September 2020

Atrx promotes heterochromatin formation at retrotransposons

scientific article published on 26 May 2015

Author Correction: Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates

correction of a scholarly article

Author Correction: Targeted pharmacological therapy restores β-cell function for diabetes remission

correction of a scholarly article

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

scientific article published on 24 March 2020

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

scientific article published on 06 August 2019

Bayesian Fuzzy Clustering of Colored Graphs

Bayesian Inference of Latent Causes in Gene Regulatory Dynamics

article

Bayesian blind source separation for data with network structure

scientific article

Bayesian independent component analysis recovers pathway signatures from blood metabolomics data

scientific article

Bayesian model selection validates a biokinetic model for zirconium processing in humans

scientific article

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.

scientific article published in July 2018

Benchmarking atlas-level data integration in single-cell genomics

scientific article published on 23 December 2021

Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series

scholarly article published 14 November 2017

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

scientific article published on 21 July 2010

Blind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data

Blind Source Separation Techniques For The Decomposition Of Multiply Labeled Fluorescence Images

Blind source separation based on self-organizing neural network

Blind source separation techniques for the decomposition of multiply labeled fluorescence images

scientific article published on May 2009

Body fat free mass is associated with the serum metabolite profile in a population-based study

scientific article

CD23 LEVELS ON B CELLS DETERMINE LONG-TERM THERAPEUTIC RESPONSE IN ATOPIC ECZEMA PATIENTS TREATED WITH SELECTIVE IGE IMMUNE APHERESIS

scientific article published on 16 September 2020

CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

scientific article

Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma

scientific article

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

scientific article published on 19 April 2018

Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study

scientific article published on 26 October 2021

CellRank for directed single-cell fate mapping

scientific article published on 13 January 2022

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

scientific article published on 13 May 2021

Centroid Clustering of Cellular Lineage Trees

article

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies

scientific article published on 20 September 2018

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies

scholarly article published 11 February 2018

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

scientific article published on 24 March 2013

Clinical impact of GATA2 mutations in acute myeloid leukemia patients harboring CEBPA mutations: a study of the AML study group

scientific article published on 4 July 2016

Cloning and sequencing of the genes encoding the periplasmic-cytochrome B-containing selenate reductase of Thauera selenatis

scientific article (publication date: 2000)

Clustering of dependent components: a new paradigm for fMRI signal detection

Colored Subspace Analysis: Dimension Reduction Based on a Signal's Autocorrelation Structure

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions

scientific article

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

scientific article

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

scientific article published on 18 April 2019

Comparison of maximum entropy and minimal mutual information in a nonlinear setting

Complex Principal Component and Correlation Structure of 16 Yeast Genomic Variables

scientific article published on 28 March 2011

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems

scientific article

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

scientific article published on 17 June 2019

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

scientific article

Computational approaches for systems metabolomics

scientific article

Concept of the Munich/Augsburg Consortium Precision in Mental Health for the German Center of Mental Health

scientific article published on 04 March 2022

Concepts and limitations for learning developmental trajectories from single cell genomics

scientific article published on 27 June 2019

Copy number aberrations from Affymetrix SNP 6.0 genotyping data-how accurate are commonly used prediction approaches?

article

Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies

scientific article published on 24 September 2017

Correction: Lessons Learned from Quantitative Dynamical Modeling in Systems Biology.

scientific article

Correction: The Nature and Perception of Fluctuations in Human Musical Rhythms

scientific article published in PLoS ONE

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

scientific article published on 19 June 2019

Cytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells

scientific article

Data-Driven Modelling of Biological Multi-Scale Processes

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems

scientific article

Decoding the regulatory network of early blood development from single-cell gene expression measurements.

scientific article

Deep learning the collisional cross sections of the peptide universe from a million experimental values

scientific article published on 20 February 2021

Deep learning: new computational modelling techniques for genomics

scientific article published on 01 July 2019

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

scientific article published on 03 February 2020

Dependent component analysis

Determinants of SARS-CoV-2 receptor gene expression in upper and lower airways

scientific article published on 02 September 2020

Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice

scientific article published on 27 September 2021

Diffusion maps for high-dimensional single-cell analysis of differentiation data.

scientific article

Diffusion pseudotime robustly reconstructs lineage branching

scientific article published on 29 August 2016

Discovery of sexual dimorphisms in metabolic and genetic biomarkers

scientific article

Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy

scientific article

Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-cell lymphoma allows prediction of therapeutic targets

scientific article published on 2 December 2010

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

scientific article published on 23 May 2019

Dynamic regimes of random fuzzy logic networks

Early Identification of Bronchopulmonary Dysplasia Using Novel Biomarkers by Proteomic Screening

scientific article published on 20 October 2017

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

scientific article published on 13 July 2016

Editorial overview: Systems biology-the intersection of experiments and computation, underpinning biotechnology

scientific article published on 9 May 2016

Editorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine

scientific article published in 2018

Effect of Atmospheric Aging on Soot Particle Toxicity in Lung Cell Models at the Air–Liquid Interface: Differential Toxicological Impacts of Biogenic and Anthropogenic Secondary Organic Aerosols (SOAs)

scientific article published on 03 February 2022

Effective Emission Tomography Image Reconstruction Algorithms for SPECT Data

Effective parameters determining the information flow in hierarchical biological systems

scientific article published on 23 December 2010

Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study

scientific article

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model

scientific article published on 28 November 2018

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

EpiScanpy: integrated single-cell epigenomic analysis

scientific article published on 01 September 2021

Epigenetic germline inheritance of diet-induced obesity and insulin resistance.

scientific article

Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

scientific article published on 12 January 2018

Episode-specific differential gene expression of peripheral blood mononuclear cells in rapid cycling supports novel treatment approaches

scientific article published on September 2008

Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2

scientific article published on 27 February 2020

Epithelial cell plasticity drives endoderm formation during gastrulation

scientific article published on 24 June 2021

Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes

article

Erratum to: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer

scientific article published on 31 July 2015

Erratum: Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

article

Erratum: Publisher Correction: Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection

scientific article published on 07 March 2019

Erythropoietin enhances hippocampal long-term potentiation and memory

scientific article

Essstörungen im Internet: Eine experimentelle Studie zu den Auswirkungen von Pro-Essstörungs- und Selbsthilfewebsites

scientific article published on 14 February 2012

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

scientific article published on 24 September 2019

Estimating Hidden Influences in Metabolic and Gene Regulatory Networks

Estimating Non-Gaussian Subspaces by Characteristic Functions

article

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

scholarly article published 31 May 2018

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

scientific article published on 16 July 2019

Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone

scientific article published on 2 March 2015

Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes

scientific article published on 4 September 2014

From binary to multivalued to continuous models: the lac operon as a case study

scientific article published on December 14, 2010

Functional MRI Analysis by a Novel Spatiotemporal ICA Algorithm

GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency

scientific article published on 25 October 2017

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

scientific article

Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells

Gender-specific pathway differences in the human serum metabolome

scientific article

Gene regulatory networks simplified by nonlinear balanced truncation

article

Generalizing RNA velocity to transient cell states through dynamical modeling

scientific article published on 03 August 2020

Genome-wide association analyses identify 18 new loci associated with serum urate concentrations

scientific article published in February 2013

Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies

scientific article published on 05 May 2020

Hierarchical Extraction of Independent Subspaces of Unknown Dimensions

Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network

scientific article

High-dimensional Bayesian parameter estimation: case study for a model of JAK2/STAT5 signaling

scientific article published on 16 April 2013

Huge splicing frequency in human Y chromosomal UTY gene

scientific article published on 17 February 2011

Hybridizing Sparse Component Analysis with Genetic Algorithms for Blind Source Separation

Hypergraphs and cellular networks

scientific article

Hypothalamic miR-103 protects from hyperphagic obesity in mice.

scientific article published in August 2014

ICA over Finite Fields

ICA over finite fields—Separability and algorithms

scholarly article by Harold W. Gutch et al published August 2012 in Signal Processing

ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data

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

scientific article published in Nature Communications

Identification and Quantification of 1-Hydroxybutene-2-yl Mercapturic Acid in Human Urine by UPLC- HILIC-MS/MS as a Novel Biomarker for 1,3-Butadiene Exposure

scientific article published on 27 July 2012

Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice

scientific article published on 30 November 2020

Identifying latent dynamic components in biological systems

scientific article

Impact of Brain Fatty Acid Signaling on Peripheral Insulin Action in Mice

scholarly article by Susanne Neschen et al published 5 November 2018 in Experimental and Clinical Endocrinology and Diabetes

Impulse model-based differential expression analysis of time course sequencing data

scientific article published on 01 November 2018

In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning

scientific article published on 16 July 2020

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

scientific article published on 01 December 2018

Inductive and Selective Effects of GSK3 and MEK Inhibition on Nanog Heterogeneity in Embryonic Stem Cells

scientific article published on 17 May 2018

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion

scientific article

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

scientific article published on 21 September 2015

Inferring Interaction Networks From Multi-Omics Data

scientific article published on 12 June 2019

Inferring catalysis in biological systems

scientific article published on December 2016

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

scientific article published on 01 April 2019

Information Theoretic Concepts to Unravel Cell–Cell Communication

Information-Theoretic Model Selection for Independent Components

article

Inhibition of LTβR signalling activates WNT-induced regeneration in lung

scientific article published on 04 November 2020

Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data

scientific article

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

scientific article published on 11 June 2019

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

scientific article published on 22 March 2021

Integrated single cell analysis of human lung fibrosis resolves cellular origins of predictive protein signatures in body fluids ⬇️

journal article from 'medRxiv' published in 2020

Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development

scientific article published on 24 January 2022

Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1.

scientific article

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers

scientific article published on 02 March 2021

Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma

scientific article

Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways.

scientific article published on 18 November 2015

Intraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema

scientific article published in July 2014

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

scientific article

Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability

scientific article published on 31 December 2012

Joint Diagonalization of Several Scatter Matrices for ICA

Joint low-rank approximation for extracting non-Gaussian subspaces

Knowledge-based gene expression classification via matrix factorization

scientific article published on 5 June 2008

Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation

scientific article

LSC Abstract – Early biomarkers indicating the development of neonatal chronic lung disease defined by clinical and imaging parameters

article

Label-free cell cycle analysis for high-throughput imaging flow cytometry.

scientific article published on 7 January 2016

Lactation is associated with altered metabolomic signatures in women with gestational diabetes

scientific article published on 16 July 2016

Lessons learned from quantitative dynamical modeling in systems biology

scientific article

LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 07 September 2020

Lifetime study in mice after acute low-dose ionizing radiation: a multifactorial study with special focus on cataract risk

scientific article

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

scientific article published on 12 July 2018

Linear Geometric ICA: Fundamentals and Algorithms

scientific article published on 01 February 2003

Live imaging of astrocyte responses to acute injury reveals selective juxtavascular proliferation.

scientific article

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

scientific article

MEMO: multi-experiment mixture model analysis of censored data

scientific article

MIPS: curated databases and comprehensive secondary data resources in 2010

scientific article

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

scientific article published in 2024

MPRAnalyze: statistical framework for massively parallel reporter assays

scientific article published on 02 September 2019

Mapping single-cell data to reference atlases by transfer learning

scientific article published on 30 August 2021

Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin

scientific article

Measuring Non-Gaussianity by Phi-Transformed and Fuzzy Histograms

article

Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

scientific article published on 01 December 2018

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

scientific article published on 03 July 2019

MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data

scholarly article published 30 September 2018

MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data

scholarly article published 22 February 2018

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

scientific article published in June 2018

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

scientific article

Metabolism gene signatures and surgical site infections in abdominal surgery

scientific article published on 16 January 2015

Metabolite profiling reveals new insights into the regulation of serum urate in humans

scientific article published on 20 July 2013

Metabolomic profiles in individuals with negative affectivity and social inhibition: a population-based study of Type D personality

scientific article published on 10 December 2012

Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns

scientific article published on 8 March 2016

Metabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema

scientific article published on 12 November 2015

Method of conditional moments (MCM) for the Chemical Master Equation: a unified framework for the method of moments and hybrid stochastic-deterministic models

scientific article

MicroRNA loss enhances learning and memory in mice

scientific article

MicroRNA-138 promotes acquired alkylator resistance in glioblastoma by targeting the Bcl-2-interacting mediator BIM.

scientific article

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma

scientific article published on 18 December 2015

MicroRNAs coordinately regulate protein complexes

scientific article

Mining the unknown: a systems approach to metabolite identification combining genetic and metabolic information

scientific article

Mobile decision support for transplantation patient data

scientific article

Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib.

scientific article published on 9 October 2017

Model selection using limiting distributions of second-order blind source separation algorithms

scholarly article by Katrin Illner et al published August 2015 in Signal Processing

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines

scientific article published on 02 March 2020

Model-based branching point detection in single-cell data by K-Branches clustering ⬇️

scientific article

Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis

scientific article

Modeling of stochastic biological processes with non-polynomial propensities using non-central conditional moment equation

Moderne Informations- und Kommunikationstechnologie in der Rehabilitation

scientific article published on 01 April 2011

Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns

article

Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain

scientific article published on 20 August 2014

Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection

Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection

Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection.

scientific article published on 10 December 2018

Multi-omic signature of body weight change: results from a population-based cohort study

scientific article

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

scientific article published on 3 July 2012

Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway

scientific article published on 14 November 2017

Network plasticity of pluripotency transcription factors in embryonic stem cells

scientific article published on 21 September 2015

Network-based approach for analyzing intra- and interfluid metabolite associations in human blood, urine, and saliva

scientific article published on 9 December 2014

Network-based metabolite ratios for an improved functional characterization of genome-wide association study results

Neurodevelopment. Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain

scientific article published in May 2015

Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer

scientific article published on 25 April 2015

Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates

scientific article published on 04 January 2021

Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses

scientific article

ODE constrained mixture modelling: a method for unraveling subpopulation structures and dynamics

scientific article

OME-Zarr: a cloud-optimized bioimaging file format with international community support

scientific article published in 2023

Odefy--from discrete to continuous models.

scientific article

On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies

scientific article

On the use of simulated annealing to automatically assign decorrelated components in second-order blind source separation.

scientific article

On the use of sparse signal decomposition in the analysis of multi-channel surface electromyograms

Opposing effects of allogrooming on disease transmission in ant societies.

scientific article published on May 2015

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

scientific article published on 29 October 2021

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

scientific article published on 19 March 2019

Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models

scientific article published on 10 January 2017

Parameter estimation for dynamical systems with discrete events and logical operations

scientific article published on 31 December 2016

Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

scientific article

Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons

scientific article published on 04 April 2022

Pattern Repulsion Revisited

Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli

scientific article

Peptide serum markers in islet autoantibody-positive children

scientific article

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

scientific article published on 26 August 2019

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

scientific article

PhenomiR: microRNAs in human diseases and biological processes

scientific article published on January 2012

Pitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedgehog Pathway Activation

scientific article

Post-surgical adhesions are triggered by calcium-dependent membrane bridges between mesothelial surfaces

scientific article published on 17 June 2020

Posterior subcapsular cataracts are a late effect after acute exposure to 0.5 Gy ionizing radiation in mice

scientific article published on 19 January 2021

Posttranscriptional regulatory networks: from expression profiling to integrative analysis of mRNA and microRNA data.

scientific article

Predicting antigen specificity of single T cells based on TCR CDR3 regions

scientific article published on 01 August 2020

Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning

scientific article published on 29 October 2020

Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young

scientific article published on 11 July 2017

Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data

scientific article

Prospective identification of hematopoietic lineage choice by deep learning.

scientific article published on 20 February 2017

Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts

scientific article

Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)

scientific article published on 03 May 2020

Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)

scientific article published on 30 June 2020

Publisher Correction to: Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)

scientific article published on 01 September 2020

Publisher Correction: Inhibition of LTβR signalling activates WNT-induced regeneration in lung

scientific article published on 22 December 2020

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 17 March 2021

Publisher Correction: Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway

scientific article published on 13 February 2018

Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma.

scientific article published on 06 April 2017

Quantification of regenerative potential in primary human mammary epithelial cells

scientific article

Quantitative comparison of competing PDE models for Pomlp dynamics in fission yeast * *The authors acknowledge financial support from the Postdoctoral Fellowship Program (PFP) of the Helmholtz Zentrum Munchen

RAMONA: a Web application for gene set analysis on multilevel omics data

scientific article

RNA velocity—current challenges and future perspectives

scientific article published on 26 August 2021

Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis

Reconstructing cell cycle and disease progression using deep learning

scientific article published on 6 September 2017

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data

scientific article

Reconstruction of graphs based on random walks

Rejoinder

Robust Second-Order Source Separation Identifies Experimental Responses in Biomedical Imaging

article

Robust Sparse Component Analysis Based on a Generalized Hough Transform

Robust stability analysis and design under consideration of multiple feedback loops of the tryptophan regulatory network of Escherichia coli.

scientific article published on January 2010

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

scientific article published on 27 April 2020

SCANPY: large-scale single-cell gene expression data analysis.

scientific article

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

scientific article (publication date: 2017)

Second Order Subspace Analysis and Simple Decompositions

Second-Order Blind Source Separation Based on Multi-dimensional Autocovariances

Second-Order Source Separation Based on Prior Knowledge Realized in a Graph Model

Separation of Uncorrelated Stationary time series using Autocovariance Matrices

article by Jari Petteri Miettinen et al published 9 September 2015 in Journal of Time Series Analysis

Sfaira accelerates data and model reuse in single cell genomics

scientific article published on 25 August 2021

Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation

scientific article

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

scientific article

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

scientific article published in Nature Communications

Single-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation

scientific article published on 27 January 2021

Single-cell reference mapping to construct and extend cell type hierarchies

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Social transfer of pathogenic fungus promotes active immunisation in ant colonies

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Sparse Component Analysis: a New Tool for Data Mining

Sparse Nonnegative Matrix Factorization Applied to Microarray Data Sets

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Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary

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Spatial components of molecular tissue biology

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Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus

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The nature and perception of fluctuations in human musical rhythms

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The quinone-reactive Ni/Fe-hydrogenase of Wolinella Succinogenes.

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Tree-Dependent and Topographic Independent Component Analysis for fMRI Analysis

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

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

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

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

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iVUN: interactive Visualization of Uncertain biochemical reaction Networks

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miR-23a-3p causes cellular senescence by targeting hyaluronan synthase 2: possible implication for skin aging

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miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm

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netReg: Network-regularized linear models for biological association studies.

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pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms

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scGen predicts single-cell perturbation responses

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scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies

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