Fabian J. Theis

According to our database1, Fabian J. Theis authored at least 172 papers between 2001 and 2020.

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Bibliography

2020
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines.
PLoS Comput. Biol., 2020

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.
PLoS Comput. Biol., 2020

Munich School for Data Science (MUDS) - Eine Graduiertenschule für Data Science in München.
Inform. Spektrum, 2020

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data.
Bioinform., 2020

Copy number aberrations from Affymetrix SNP 6.0 genotyping data - how accurate are commonly used prediction approaches?
Briefings Bioinform., 2020

Learning Tn5 Sequence Bias from ATAC-seq on Naked Chromatin.
Proceedings of the Artificial Neural Networks and Machine Learning - ICANN 2020, 2020

2019
12 Grand Challenges in Single-Cell Data Science.
PeerJ Prepr., 2019

Conditional out-of-sample generation for unpaired data using trVAE.
CoRR, 2019

2018
netReg: network-regularized linear models for biological association studies.
Bioinform., 2018

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.
Bioinform., 2018

LNA++: Linear Noise Approximation with First and Second Order Sensitivities.
Proceedings of the Computational Methods in Systems Biology, 2018

2017
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.
PLoS Comput. Biol., 2017

Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies.
Comput. Math. Methods Medicine, 2017

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems.
BMC Syst. Biol., 2017

pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms.
BMC Bioinform., 2017

A scalable moment-closure approximation for large-scale biochemical reaction networks.
Bioinform., 2017

fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy.
Bioinform., 2017

Parameter estimation for dynamical systems with discrete events and logical operations.
Bioinform., 2017

Model-based branching point detection in single-cell data by K-branches clustering.
Bioinform., 2017

2016
An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson's rule.
Stat. Comput., 2016

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion.
PLoS Comput. Biol., 2016

Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression.
J. Comput. Biol., 2016

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints.
BMC Syst. Biol., 2016

MEMO: multi-experiment mixture model analysis of censored data.
Bioinform., 2016

<i>destiny</i>: diffusion maps for large-scale single-cell data in R.
Bioinform., 2016

Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields.
Proceedings of the Machine Learning in Medical Imaging - 7th International Workshop, 2016

2015
Model selection using limiting distributions of second-order blind source separation algorithms.
Signal Process., 2015

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy.
BMC Syst. Biol., 2015

RAMONA: a Web application for gene set analysis on multilevel omics data.
Bioinform., 2015

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
Bioinform., 2015

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.
Bioinform., 2015

Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Bioinform., 2015

Anatomic-landmark detection using graphical context modelling.
Proceedings of the 12th IEEE International Symposium on Biomedical Imaging, 2015

An Affine Equivariant Robust Second-Order BSS Method.
Proceedings of the Latent Variable Analysis and Signal Separation, 2015

Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics.
Proceedings of the Computational Methods in Systems Biology, 2015

2014
ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics.
PLoS Comput. Biol., 2014

Bayesian Blind Source Separation for Data with Network Structure.
J. Comput. Biol., 2014

MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data.
BMC Bioinform., 2014

Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data.
Bioinform., 2014

Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain.
Database J. Biol. Databases Curation, 2014

Centroid Clustering of Cellular Lineage Trees.
Proceedings of the Information Technology in Bio- and Medical Informatics, 2014

Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More.
Proceedings of the Computational Methods in Systems Biology, 2014

Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis.
Proceedings of the Computational Methods in Systems Biology, 2014

2013
Truth-Content and Phase Transitions of Random Boolean Networks with Generic Logics.
SIAM J. Appl. Dyn. Syst., 2013

Dependent component analysis.
EURASIP J. Adv. Signal Process., 2013

Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation.
BMC Syst. Biol., 2013

iVUN: interactive Visualization of Uncertain biochemical reaction Networks.
BMC Bioinform., 2013

Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis.
BMC Bioinform., 2013

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy.
BMC Bioinform., 2013

Visualizing edge-edge relations in graphs.
Proceedings of the IEEE Pacific Visualization Symposium, 2013

2012
The signal separation evaluation campaign (2007-2010): Achievements and remaining challenges.
Signal Process., 2012

ICA over finite fields - Separability and algorithms.
Signal Process., 2012

Uniqueness of linear factorizations into independent subspaces.
J. Multivar. Anal., 2012

Bayesian model selection validates a biokinetic model for zirconium processing in humans.
BMC Syst. Biol., 2012

On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies.
BMC Bioinform., 2012

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst.
Bioinform., 2012

Measuring Non-Gaussianity by Phi-Transformed and Fuzzy Histograms.
Adv. Artif. Neural Syst., 2012

Bayesian Fuzzy Clustering of Colored Graphs.
Proceedings of the Latent Variable Analysis and Signal Separation, 2012

Joint Diagonalization of Several Scatter Matrices for ICA.
Proceedings of the Latent Variable Analysis and Signal Separation, 2012

Bayesian Inference of Latent Causes in Gene Regulatory Dynamics.
Proceedings of the Latent Variable Analysis and Signal Separation, 2012

To Infinity and Beyond: On ICA over Hilbert Spaces.
Proceedings of the Latent Variable Analysis and Signal Separation, 2012

2011
Uniqueness of Non-Gaussianity-Based Dimension Reduction.
IEEE Trans. Signal Process., 2011

MIPS: curated databases and comprehensive secondary data resources in 2010.
Nucleic Acids Res., 2011

Modularity maximization and tree clustering: Novel ways to determine effective geographic borders
CoRR, 2011

MicroRNAs coordinately regulate protein complexes.
BMC Syst. Biol., 2011

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data.
BMC Syst. Biol., 2011

An ISA algorithm with unknown group sizes identifies meaningful clusters in metabolomics data.
Proceedings of the 19th European Signal Processing Conference, 2011

2010
Colored Subspace Analysis: Dimension Reduction Based on a Signal's Autocorrelation Structure.
IEEE Trans. Circuits Syst. I Regul. Pap., 2010

Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of <i>Escherichia coli</i>.
PLoS Comput. Biol., 2010

From Binary to Multivalued to Continuous Models: The Lac Operon as a Case Study.
J. Integr. Bioinform., 2010

Odefy -- From discrete to continuous models.
BMC Bioinform., 2010

Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation.
BMC Bioinform., 2010

Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs.
BMC Bioinform., 2010

Robust Second-Order Source Separation Identifies Experimental Responses in Biomedical Imaging.
Proceedings of the Latent Variable Analysis and Signal Separation, 2010

Information-Theoretic Model Selection for Independent Components.
Proceedings of the Latent Variable Analysis and Signal Separation, 2010

Second Order Subspace Analysis and Simple Decompositions.
Proceedings of the Latent Variable Analysis and Signal Separation, 2010

ICA over Finite Fields.
Proceedings of the Latent Variable Analysis and Signal Separation, 2010

Second-Order Source Separation Based on Prior Knowledge Realized in a Graph Model.
Proceedings of the Latent Variable Analysis and Signal Separation, 2010

The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Biomedical Source Separation.
Proceedings of the Latent Variable Analysis and Signal Separation, 2010

The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Audio Source Separation.
Proceedings of the Latent Variable Analysis and Signal Separation, 2010

Uncovering the Structure of Heterogenous Biological Data: Fuzzy Graph Partitioning in the k-partite Setting.
Proceedings of the German Conference on Bioinformatics 2010, 2010

Robust Stability Analysis of Multi-Time Scale Genetic Regulatory Networks under Parametric Uncertainties.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2010

Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops in the Tryptophan Regulatory Network of E. coli.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2010

2009
Reconstruction of graphs based on random walks.
Theor. Comput. Sci., 2009

Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary.
PLoS Comput. Biol., 2009

Hypergraphs and Cellular Networks.
PLoS Comput. Biol., 2009

ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data.
Eng. Appl. Artif. Intell., 2009

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.
BMC Syst. Biol., 2009

Blind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data.
Proceedings of the Independent Component Analysis and Signal Separation, 2009

Soft Dimension Reduction for ICA by Joint Diagonalization on the Stiefel Manifold.
Proceedings of the Independent Component Analysis and Signal Separation, 2009

Hierarchical Extraction of Independent Subspaces of Unknown Dimensions.
Proceedings of the Independent Component Analysis and Signal Separation, 2009

Estimating Hidden Influences in Metabolic and Gene Regulatory Networks.
Proceedings of the Independent Component Analysis and Signal Separation, 2009

2008
Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns.
IEEE Pervasive Comput., 2008

A robust model for spatiotemporal dependencies.
Neurocomputing, 2008

Hybridizing sparse component analysis with genetic algorithms for microarray analysis.
Neurocomputing, 2008

Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis.
BMC Bioinform., 2008

Knowledge-based gene expression classification via matrix factorization.
Bioinform., 2008

Effective Emission Tomography Image Reconstruction Algorithms for SPECT Data.
Proceedings of the Computational Science, 2008

Stochastic Stability Analysis of the Heat Shock Response in E. Coli.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

2007
Joint low-rank approximation for extracting non-Gaussian subspaces.
Signal Process., 2007

Robust Sparse Component Analysis Based on a Generalized Hough Transform.
EURASIP J. Adv. Signal Process., 2007

A bilinear algorithm for sparse representations.
Comput. Optim. Appl., 2007

Sparse Nonnegative Matrix Factorization with Genetic Algorithms for Microarray Analysis.
Proceedings of the International Joint Conference on Neural Networks, 2007

Statistical Analysis of Sample-Size Effects in ICA.
Proceedings of the Intelligent Data Engineering and Automated Learning, 2007

Blind Matrix Decomposition Via Genetic Optimization of Sparseness and Nonnegativity Constraints.
Proceedings of the Artificial Neural Networks, 2007

Exploiting Blind Matrix Decomposition Techniques to Identify Diagnostic Marker Genes.
Proceedings of the Artificial Neural Networks, 2007

Colored Subspace Analysis.
Proceedings of the Independent Component Analysis and Signal Separation, 2007

Blind Matrix Decomposition Techniques to Identify Marker Genes from Microarrays.
Proceedings of the Independent Component Analysis and Signal Separation, 2007

Independent Subspace Analysis Is Unique, Given Irreducibility.
Proceedings of the Independent Component Analysis and Signal Separation, 2007

A Toolbox for Model-Free Analysis of fMRI Data.
Proceedings of the Independent Component Analysis and Signal Separation, 2007

Identifiability Conditions and Subspace Clustering in Sparse BSS.
Proceedings of the Independent Component Analysis and Signal Separation, 2007

Pivot Selection Strategies in Jacobi Joint Block-Diagonalization.
Proceedings of the Independent Component Analysis and Signal Separation, 2007

2006
On the use of simulated annealing to automatically assign decorrelated components in second-order blind source separation.
IEEE Trans. Biomed. Eng., 2006

Median-based clustering for underdetermined blind signal processing.
IEEE Signal Process. Lett., 2006

On the use of sparse signal decomposition in the analysis of multi-channel surface electromyograms.
Signal Process., 2006

Separation of water artifacts in 2D NOESY protein spectra using congruent matrix pencils.
Neurocomputing, 2006

Denoising using local projective subspace methods.
Neurocomputing, 2006

Blind source separation based on self-organizing neural network.
Eng. Appl. Artif. Intell., 2006

Towards a general independent subspace analysis.
Proceedings of the Advances in Neural Information Processing Systems 19, 2006

On the use of joint diagonalization in blind signal processing.
Proceedings of the International Symposium on Circuits and Systems (ISCAS 2006), 2006

New Riemannian metrics for speeding-up the convergence of over- and underdetermined ICA.
Proceedings of the International Symposium on Circuits and Systems (ISCAS 2006), 2006

Stability Analysis of an Unsupervised Competitive Neural Network.
Proceedings of the International Joint Conference on Neural Networks, 2006

Region of Interest Based Independent Component Analysis.
Proceedings of the Neural Information Processing, 13th International Conference, 2006

A Fast Predictive Lossless Coder for fMRI Data Sets.
Proceedings of the International Conference on Image Processing, 2006

Sparseness by Iterative Projections Onto Spheres.
Proceedings of the 2006 IEEE International Conference on Acoustics Speech and Signal Processing, 2006

Uniqueness of Non-Gaussian Subspace Analysis.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2006

Sparse Nonnegative Matrix Factorization Applied to Microarray Data Sets.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2006

Estimating Non-Gaussian Subspaces by Characteristic Functions.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2006

Grassmann clustering.
Proceedings of the 14th European Signal Processing Conference, 2006

2005
Sparse component analysis and blind source separation of underdetermined mixtures.
IEEE Trans. Neural Networks, 2005

On model identifiability in analytic postnonlinear ICA.
Neurocomputing, 2005

Extended Sparse Nonnegative Matrix Factorization.
Proceedings of the Computational Intelligence and Bioinspired Systems, 2005

A Hybridization of Simulated Annealing and Local PCA for Automatic Component Assignment Within ICA.
Proceedings of the Computational Intelligence and Bioinspired Systems, 2005

Hybridizing Sparse Component Analysis with Genetic Algorithms for Blind Source Separation.
Proceedings of the Biological and Medical Data Analysis, 6th International Symposium, 2005

Blind signal separation into groups of dependent signals using joint block diagonalization.
Proceedings of the International Symposium on Circuits and Systems (ISCAS 2005), 2005

A Fast and Efficient Method for Compressing fMRI Data Sets.
Proceedings of the Artificial Neural Networks: Formal Models and Their Applications, 2005

Functional MRI Analysis by a Novel Spatiotemporal ICA Algorithm.
Proceedings of the Artificial Neural Networks: Biological Inspirations, 2005

Bispectrum-Based Statistical Tests for VAD.
Proceedings of the Artificial Neural Networks: Formal Models and Their Applications, 2005

AutoAssign - An Automatic Assignment Tool for Independent Components.
Proceedings of the Pattern Recognition and Image Analysis, Second Iberian Conference, 2005

First results on uniqueness of sparse non-negative matrix factorization.
Proceedings of the 13th European Signal Processing Conference, 2005

Spatiotemporal blind source separation using double-sided approximate joint diagonalization.
Proceedings of the 13th European Signal Processing Conference, 2005

Multidimensional independent component analysis using characteristic functions.
Proceedings of the 13th European Signal Processing Conference, 2005

2004
Uniqueness of complex and multidimensional independent component analysis.
Signal Process., 2004

A New Concept for Separability Problems in Blind Source Separation.
Neural Comput., 2004

A geometric algorithm for overcomplete linear ICA.
Neurocomputing, 2004

Mobile decision support for transplantation patient data.
Int. J. Medical Informatics, 2004

Blind source separation and sparse component analysis of overcomplete mixtures.
Proceedings of the 2004 IEEE International Conference on Acoustics, 2004

Second-Order Blind Source Separation Based on Multi-dimensional Autocovariances.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2004

Postnonlinear Overcomplete Blind Source Separation Using Sparse Sources.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2004

Tree-Dependent and Topographic Independent Component Analysis for fMRI Analysis.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2004

3D Spatial Analysis of fMRI Data on a Word Perception Task.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2004

Denoising Using Local ICA and a Generalized Eigendecomposition with Time-Delayed Signals.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2004

Blind Source Separation of Linear Mixtures with Singular Matrices.
Proceedings of the Independent Component Analysis and Blind Signal Separation, 2004

Uniqueness of real and complex linear independent component analysis revisited.
Proceedings of the 2004 12th European Signal Processing Conference, 2004

Linearization identification and an application to BSS using a SOM.
Proceedings of the ESANN 2004, 2004

Robust overcomplete matrix recovery for sparse sources using a generalized Hough transform.
Proceedings of the ESANN 2004, 2004

Separability of analytic postnonlinear blind source separation with bounded sources.
Proceedings of the ESANN 2004, 2004

2003
Geometric source separation: algorithms and applications.
PhD thesis, 2003

Mathematics in independent component analysis.
PhD thesis, 2003

Linear Geometric ICA: Fundamentals and Algorithms.
Neural Comput., 2003

Generalizing Geometric ICA to Nonlinear Settings.
Proceedings of the Artificial Neural Nets Problem Solving Methods, 2003

An Improved Geometric Overcomplete Blind Source Separation Algorithm.
Proceedings of the Artificial Neural Nets Problem Solving Methods, 2003

An Adaptive Approach to Blind Source Separation Using a Self-Organzing Map and a Neural Gas.
Proceedings of the Artificial Neural Nets Problem Solving Methods, 2003

A Generalized Eigendecomposition Approach Using Matrix Pencils to Remove Artefacts from 2D NMR Spectra.
Proceedings of the Artificial Neural Nets Problem Solving Methods, 2003

Neural network signal analysis in immunology.
Proceedings of the Seventh International Symposium on Signal Processing and Its Applications, 2003

Mathematics in independent component analysis.
Proceedings of the Seventh International Symposium on Signal Processing and Its Applications, 2003

Removing water artefacts from 2D protein NMR spectra using GEVD with congruent matrix pencils.
Proceedings of the Seventh International Symposium on Signal Processing and Its Applications, 2003

2002
Comparison of maximum entropy and minimal mutual information in a nonlinear setting.
Signal Process., 2002

Overcomplete ICA with a Geometric Algorithm.
Proceedings of the Artificial Neural Networks, 2002

Geometric overcomplete ICA.
Proceedings of the ESANN 2002, 2002

How to generalize geometric ICA to higher dimensions.
Proceedings of the ESANN 2002, 2002

2001
Pattern Repulsion Revisited.
Proceedings of the Bio-inspired Applications of Connectionism, 2001


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