Fabian J. Theis

Fabian J. Theis, Elmar Wolfgang Lang, Susanne Krauss-Etschmann, 2003, Seventh International Symposium on Signal Processing and Its Applications, 2003. Proceedings..

Denoising Using Local ICA and a Generalized Eigendecomposition with Time-Delayed Signals

Fabian J. Theis, Peter Gruber, Kurt Stadlthanner, 2004, ICA.

Conditional out-of-sample generation for unpaired data using trVAE pdf

Fabian J. Theis, Mohammad Lotfollahi, Fabian J Theis, 2019, ArXiv.

Uniqueness of Non-Gaussian Subspace Analysis

Motoaki Kawanabe, Fabian J. Theis, Fabian J Theis, 2006, ICA.

A Generalized Eigendecomposition Approach Using Matrix Pencils to Remove Artefacts from 2D NMR Spectra

Fabian J. Theis, Kurt Stadlthanner, Elmar Wolfgang Lang, 2003, IWANN.

An ISA algorithm with unknown group sizes identifies meaningful clusters in metabolomics data

Harold W. Gutch, Fabian J. Theis, Fabian J Theis, 2011, 2011 19th European Signal Processing Conference.

First results on uniqueness of sparse non-negative matrix factorization

Toshihisa Tanaka, Fabian J. Theis, Kurt Stadlthanner, 2005, 2005 13th European Signal Processing Conference.

Optimization Techniques for Date Representions with Biomedical Applications

Fabian J. Theis, Fabian J Theis, Pando G. Georgiev, 2009 .

Linearization identification and an application to BSS using a SOM

Fabian J. Theis, Elmar Wolfgang Lang, Fabian J Theis, 2004, ESANN.

CellRank for directed single-cell fate mapping

Fabian J. Theis, Fabian J Theis, Heiko Lickert, 2020, Nature Methods.

Recent Advances in Biomedical Signal Processing

Sabine Van Huffel, Misha Pavel, Alberto Olivares, 2012 .

Sparse Component Analysis: a New Tool for Data Mining

Fabian J. Theis, Andrzej Cichocki, Hovagim Bakardjian, 2004 .

A geometric algorithm for overcomplete linear ICA

Fabian J. Theis, Elmar Wolfgang Lang, Carlos García Puntonet, 2004, Neurocomputing.

Pivot Selection Strategies in Jacobi Joint Block-Diagonalization

Fabian J. Theis, Fabian J Theis, Cédric Févotte, 2007, ICA.

Mobile decision support for transplantation patient data

Andreas Krause, Fabian J. Theis, Dominik Hartl, 2004, Int. J. Medical Informatics.

Handbook of Optimization in Complex Networks

Fabian J. Theis, Dirk Brockmann, Christian Thiemann, 2011 .

Blind Matrix Decomposition Techniques to Identify Marker Genes from Microarrays

Fabian J. Theis, Dominik Lutter, Juan Manuel Górriz, 2007, ICA.

Bayesian Inference of Latent Causes in Gene Regulatory Dynamics

Fabian J. Theis, Sabine Hug, 2012, LVA/ICA.

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

Fabian J. Theis, Elmar Wolfgang Lang, Fabian J Theis, 2002, Signal Process..

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

Wei Li, Fabian J. Theis, Sabine Hug, 2012, BMC Systems Biology.

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.

AutoAssign - An Automatic Assignment Tool for Independent Components

Fabian J. Theis, Peter Gruber, Kurt Stadlthanner, 2005, IbPRIA.

Scalable parameter estimation for genome-scale biochemical reaction networks

Fabian J. Theis, Barbara Kaltenbacher, Jan Hasenauer, 2016 .

An Improved Geometric Overcomplete Blind Source Separation Algorithm

Fabian J. Theis, Elmar Wolfgang Lang, Carlos García Puntonet, 2009, IWANN.

Sparse Nonnegative Matrix Factorization with Genetic Algorithms for Microarray Analysis

Fabian J. Theis, Dominik Lutter, Kurt Stadlthanner, 2007, 2007 International Joint Conference on Neural Networks.

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

Fabian J. Theis, Jan Hasenauer, Fabian Fröhlich, 2016, PloS one.

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

Fabian J. Theis, Berthold Göttgens, Florian Buettner, 2014, Bioinform..

MEMO: multi-experiment mixture model analysis of censored data

Fabian J. Theis, Nicole Radde, Eva-Maria Geissen, 2016, Bioinform..

FASTGenomics: An analytical ecosystem for single-cell RNA sequencing data

Fabian J. Theis, Christian Sauer, Joachim L. Schultze, 2018, bioRxiv.

Estimating Hidden Influences in Metabolic and Gene Regulatory Networks

Fabian J. Theis, Florian Blöchl, 2009, ICA.

Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields

Nassir Navab, Fabian J. Theis, Lichao Wang, 2016, MLMI@MICCAI.

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

Fabian J. Theis, Sarah A. Teichmann, Fabian J Theis, 2017, bioRxiv.

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

Fabian J. Theis, Jan Hasenauer, Fabian J Theis, 2013, BMC Bioinformatics.

Measuring Non-Gaussianity by Phi-Transformed and Fuzzy Histograms

Anke Meyer-Bäse, Fabian J. Theis, Claudia Plant, 2012, Adv. Artif. Neural Syst..

Sfaira accelerates data and model reuse in single cell genomics

Luke Zappia, Fabian J. Theis, Hananeh Aliee, 2020, bioRxiv.

On the use of joint diagonalization in blind signal processing

Fabian J. Theis, Yujiro Inouye, Fabian J Theis, 2006, 2006 IEEE International Symposium on Circuits and Systems.

Mathematics in independent component analysis

Fabian J. Theis, Fabian J Theis, 2003, Seventh International Symposium on Signal Processing and Its Applications, 2003. Proceedings..

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

Fabian J. Theis, Edda Klipp, Ursula Klingmüller, 2015, Bioinform..

Sparse Representation of Data and Support Vector Machines (in: Proceedings)

Fabian J. Theis, Anca L. Ralescu, Pando Georgiev, 2004 .

Network reconstruction for trans acting genetic loci using multi-omics data and prior information

Christian Gieger, Fabian J. Theis, Johann S. Hawe, 2020, bioRxiv.

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

Christian Gieger, Fabian J. Theis, Michael Laimighofer, 2018, Metabolomics.

From Discrete to Continuous Gene Regulation Models – A Tutorial Using the Odefy Toolbox

Fabian J. Theis, Dominik M. Wittmann, Fabian J Theis, 2011 .

Statistical single cell multi-omics integration

Fabian J. Theis, Fabian J Theis, Maria Colomé-Tatché, 2018 .

Anatomic-landmark detection using graphical context modelling

Nassir Navab, Guang-Zhong Yang, Fabian J. Theis, 2015, 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI).

Uniqueness of linear factorizations into independent subspaces

Harold W. Gutch, Fabian J. Theis, Fabian J Theis, 2012, J. Multivar. Anal..

Workshop Report IV of the Windberg Meeting 2004

Fabian J. Theis, Bernhard Rieder, Christian Schüller, 2004 .

Automated clustering of ICA results for fMRI data analysis

Fabian J. Theis, Peter Gruber, Ana Maria Tomé, 2005 .

Design and power analysis for multi-sample single cell genomics experiments

Fabian J. Theis, Matthias Heinig, Fabian J Theis, 2020, bioRxiv.

Multidimensional independent component analysis using characteristic functions

Fabian J. Theis, Fabian J Theis, 2005, 2005 13th European Signal Processing Conference.

Self-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy

Fabian J. Theis, Olle G. Holmberg, Jakob Siedlecki, 2020 .

A New Concept for Separability Problems in Blind Source Separation

Fabian J. Theis, Fabian J Theis, 2004, Neural Computation.

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

Fabian J. Theis, Dirk Brockmann, D. Brockmann, 2008, IEEE Pervasive Computing.

Separability of analytic postnonlinear blind source separation with bounded sources

Fabian J. Theis, Peter Gruber, Fabian J Theis, 2004, ESANN.

Scanpy for analysis of large-scale single-cell gene expression data

Fabian J. Theis, Fabian J Theis, F. Alexander Wolf, 2017, bioRxiv.

Hierarchical Extraction of Independent Subspaces of Unknown Dimensions

Harold W. Gutch, Fabian J. Theis, Peter Gruber, 2009, ICA.

Robust Stability Analysis of Multi-Time Scale Genetic Regulatory Networks under Parametric Uncertainties

Anke Meyer-Bäse, Fabian J. Theis, Claudia Plant, 2010, BIOCOMP.

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

Steffen Klamt, Fabian J. Theis, Julio Saez-Rodriguez, 2009, BMC Systems Biology.

An Affine Equivariant Robust Second-Order BSS Method

Klaus Nordhausen, Hannu Oja, Fabian J. Theis, 2015, LVA/ICA.

netReg: network-regularized linear models for biological association studies

Fabian J. Theis, Simon Dirmeier, Christiane Fuchs, 2017, Bioinform..

Removing water artefacts from 2D protein NMR spectra using GEVD with congruent matrix pencils

Fabian J. Theis, Kurt Stadlthanner, Elmar Wolfgang Lang, 2003, Seventh International Symposium on Signal Processing and Its Applications, 2003. Proceedings..

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

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

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

Fabian J. Theis, Andreas Kowarsch, Florian Blöchl, 2010, LVA/ICA.

Exploiting Blind Matrix Decomposition Techniques to Identify Diagnostic Marker Genes

Fabian J. Theis, Dominik Lutter, Elmar Wolfgang Lang, 2007, ICANN.

3D Spatial Analysis of fMRI Data on a Word Perception Task

Fabian J. Theis, Peter Gruber, Elmar Wolfgang Lang, 2004, ICA.

Geometric ICA in overcomplete and high-dimensional settings

Fabian J. Theis, 2002 .

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

Fabian J. Theis, Christiane Fuchs, Fabian J Theis, 2017, Comput. Math. Methods Medicine.

Hypergraphs and Cellular Networks

Steffen Klamt, Fabian J. Theis, Fabian J Theis, 2009, PLoS Comput. Biol..

Munich School for Data Science (MUDS) – Eine Graduiertenschule für Data Science in München

Fabian J. Theis, Thomas Ludwig, 2019, Informatik Spektrum.

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

Fabian J. Theis, Jan Hasenauer, Fabian Fröhlich, 2014, CMSB.

MIPS: curated databases and comprehensive secondary data resources in 2010

Fabian J. Theis, Dmitrij Frishman, Thomas Rattei, 2010, Nucleic Acids Res..

Colored Subspace Analysis

Motoaki Kawanabe, Fabian J. Theis, 2007, ICA.

Hybridizing sparse component analysis with genetic algorithms for microarray analysis

Fabian J. Theis, Juan Manuel Górriz, Kurt Stadlthanner, 2008, Neurocomputing.

Sparseness by Iterative Projections Onto Spheres

Toshihisa Tanaka, Fabian J. Theis, 2006, 2006 IEEE International Conference on Acoustics Speech and Signal Processing Proceedings.

MATLAB code; Supplemental notes from Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

Fabian J. Theis, Jan Hasenauer, Sabrina Hross, 2018 .

Supplementary material from "Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data"

Fabian J. Theis, Jan Hasenauer, Sabrina Hross, 2018 .

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

Fabian J. Theis, Barbara Kaltenbacher, Jan Hasenauer, 2016, bioRxiv.

Spatial ICA of fMRI data in time windows

Fabian J. Theis, Juha Karvanen, Fabian J Theis, 2004 .

New Riemannian metrics for speeding-up the convergence of over- and underdetermined ICA

Francesco Piazza, Fabian J. Theis, Stefano Squartini, 2006, 2006 IEEE International Symposium on Circuits and Systems.

Linear Geometric ICA: Fundamentals and Algorithms

Fabian J. Theis, Elmar Wolfgang Lang, Carlos García Puntonet, 2003, Neural Computation.

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

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

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

Christian Böhm, Fabian J. Theis, Nikola S. Müller, 2010, LVA/ICA.

On the use of simulated annealing to automatically assign independent components

Fabian J. Theis, Ana Maria Tomé, Elmar Lang, 2005 .

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.

Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells

Anke Meyer-Bäse, Fabian J. Theis, Fabian J Theis, 2011, Defense + Commercial Sensing.

ICA over finite fields - Separability and algorithms

Arie Yeredor, Harold W. Gutch, Fabian J. Theis, 2012, Signal Process..

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

Anke Meyer-Bäse, Fabian J. Theis, Fabian J Theis, 2009, Eng. Appl. Artif. Intell..

The signal separation evaluation campaign (2007-2010): Achievements and remaining challenges

Fabian J. Theis, Emmanuel Vincent, Hiroshi Sawada, 2012, Signal Process..

Pattern Repulsion Revisited

Fabian J. Theis, Elmar Wolfgang Lang, Carlos García Puntonet, 2001, IWANN.

Sparse Nonnegative Matrix Factorization Applied to Microarray Data Sets

Fabian J. Theis, Pedro Gómez Vilda, Kurt Stadlthanner, 2006, ICA.

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

Fabian J. Theis, Claudia Langenberg, Sophie Molnos, 2018 .

Classification of immunological data using independent component analysis and neural networks

Fabian J. Theis, Elmar Lang, Susanne Krauss-Etschmann, 2003 .

Blind source separation and sparse component analysis of overcomplete mixtures

Fabian J. Theis, Andrzej Cichocki, Fabian J Theis, 2004, 2004 IEEE International Conference on Acoustics, Speech, and Signal Processing.

Author's Personal Copy Theoretical Computer Science Reconstruction of Graphs Based on Random Walks

Fabian J. Theis, Florian Blöchl, Dominik M. Wittmann, 2022 .

Separation of water artifacts in 2D NOESY protein spectra using congruent matrix pencils

Fabian J. Theis, Kurt Stadlthanner, Elmar Wolfgang Lang, 2006, Neurocomputing.

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

Fabian J. Theis, Juan C. Caicedo, Shantanu Singh, 2019, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

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

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

Automated counting of labelled cells in rodent brain section images

Fabian J. Theis, Elmar Lang, Fabian J Theis, 2004 .

Foundations of medical imaging and signal recording

Anke Meyer-Bäse, Fabian J. Theis, Fabian J Theis, 2010 .

Stability analysis of hybrid stochastic gene regulatory networks

Anke Meyer-Bäse, Fabian J. Theis, Claudia Plant, 2011 .

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints

Fabian J. Theis, Jan Hasenauer, Anna Fiedler, 2016, BMC Systems Biology.

Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary

Fabian J. Theis, Florian Blöchl, Dominik M. Wittmann, 2009, PLoS Comput. Biol..

Blind source recovery: algorithm comparison and fusion

Fabian J. Theis, Andrzej Cichocki, Pando Georgiev, 2004 .

Multiscale Optimization Methods and Applications

Fabian J. Theis, Andrzej Cichocki, Pando Georgiev, 2006 .

Blind Source Separation of Linear Mixtures with Singular Matrices

Fabian J. Theis, Fabian J Theis, Pando G. Georgiev, 2004, ICA.

How to generalize geometric ICA to higher dimensions

Fabian J. Theis, Elmar Wolfgang Lang, Fabian J Theis, 2002, ESANN.

Deep learning does not outperform classical machine learning for cell-type annotation

Fabian J. Theis, Fabian J Theis, Maren Büttner, 2019, bioRxiv.

TREVOR HASTIE, ROBERT TIBSHIRANI, AND MARTIN WAINWRIGHT. Statistical Learning with Sparsity: The Lasso and Generalizations. Boca Raton: CRC Press.

Fabian J. Theis, Ivan Kondofersky, 2018, Biometrics.

Learning interpretable latent autoencoder representations with annotations of feature sets

Fabian J. Theis, Mohammad Lotfollahi, Fabian J Theis, 2020, bioRxiv.

To Infinity and Beyond: On ICA over Hilbert Spaces

Harold W. Gutch, Fabian J. Theis, Fabian J Theis, 2012, LVA/ICA.

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

Fabian J. Theis, Peter Gruber, Kurt Stadlthanner, 2006, IEEE Transactions on Biomedical Engineering.

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

Fabian J. Theis, Fabian J Theis, Jerzy Adamski, 2011, BMC Systems Biology.

Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More

Fabian J. Theis, Jan Hasenauer, Fabian Fröhlich, 2014, CMSB.

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics

Fabian J. Theis, Jan Hasenauer, Fabian J Theis, 2014, PLoS Comput. Biol..

Grassmann clustering

Fabian J. Theis, Peter Gruber, Fabian J Theis, 2006, 2006 14th European Signal Processing Conference.

Joint low-rank approximation for extracting non-Gaussian subspaces

Motoaki Kawanabe, Fabian J. Theis, Fabian J Theis, 2007, Signal Process..

Classification of skin lesions by fluorscence diagnosis and independent component analysis

Fabian J. Theis, Elmar Lang, Carlos G. Puntonet, 2004 .

Model-based outliers treatment in image-based systems biology: filtering vs. noise model

Fabian J. Theis, Jan Hasenauer, Sabrina Hross, 2014 .

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

Fabian J. Theis, Fabian J Theis, Gonzalo A. García, 2006, Signal Process..

Centroid Clustering of Cellular Lineage Trees

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

Identifiability Conditions and Subspace Clustering in Sparse BSS

Fabian J. Theis, Anca L. Ralescu, Fabian J Theis, 2007, ICA.

An Adaptive Approach to Blind Source Separation Using a Self-Organzing Map and a Neural Gas

Fabian J. Theis, Elmar Wolfgang Lang, Carlos García Puntonet, 2009, IWANN.

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems

Fabian J. Theis, Jan Hasenauer, Sabine Hug, 2017, BMC Systems Biology.

Overcomplete ICA with a Geometric Algorithm

Fabian J. Theis, Elmar Wolfgang Lang, Carlos García Puntonet, 2002, ICANN.

iVUN: interactive Visualization of Uncertain biochemical reaction Networks

Fabian J. Theis, Daniel Weiskopf, Jens Timmer, 2013, BMC Bioinformatics.

Bayesian Blind Source Separation for Data with Network Structure

Fabian J. Theis, Katrin Illner, Christiane Fuchs, 2014, J. Comput. Biol..

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

Christian Gieger, Fabian J. Theis, Fabian J Theis, 2012, BMC Bioinformatics.

Uniqueness of complex and multidimensional independent component analysis

Fabian J. Theis, Fabian J Theis, 2004, Signal Process..

Second Order Subspace Analysis and Simple Decompositions

Harold W. Gutch, Fabian J. Theis, Takanori Maehara, 2010, LVA/ICA.

Robust overcomplete matrix recovery for sparse sources using a generalized Hough transform

Fabian J. Theis, Andrzej Cichocki, Fabian J Theis, 2004, ESANN.

Model-free identification of brain activity in functional MRI

Fabian J. Theis, Fabian J Theis, 2006 .

Reconstructing cell cycle and disease progression using deep learning

Fabian J. Theis, Anne E. Carpenter, F. Alexander Wolf, 2017 .

Information-Theoretic Model Selection for Independent Components

Christian Böhm, Anke Meyer-Bäse, Fabian J. Theis, 2010, LVA/ICA.

Blind source separation based on self-organizing neural network

Anke Meyer-Bäse, Fabian J. Theis, Fabian J Theis, 2006, Eng. Appl. Artif. Intell..

Spatiotemporal blind source separation using double-sided approximate joint diagonalization

Anke Meyer-Bäse, Fabian J. Theis, Peter Gruber, 2005, 2005 13th European Signal Processing Conference.

Towards a general independent subspace analysis

Fabian J. Theis, Fabian J Theis, 2006, NIPS.

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

Fabian J. Theis, Jan Hasenauer, Anita Reiser, 2018 .

12 Grand Challenges in Single-Cell Data Science

Alexander Zelikovsky, Fabian J. Theis, Marcel J. T. Reinders, 2019, PeerJ Prepr..

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

Fabian J. Theis, Lukas M. Simon, Philipp Angerer, 2018 .

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

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

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

Fabian J. Theis, Fabian J Theis, Andre Zeug, 2009, ICA.

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

Fabian J. Theis, Jan Hasenauer, Fabian J Theis, 2018, Bioinform..

Stability Analysis of an Unsupervised Competitive Neural Network

Anke Meyer-Bäse, Fabian J. Theis, Vera Thümmler, 2006, IJCNN.

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

Fabian J. Theis, Nikola S. Müller, Fabian J Theis, 2015, Bioinform..

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.

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

Fabian J. Theis, Jan Hasenauer, Fabian J Theis, 2017, Bioinform..

Are We to Integrate Previous Information into Microarray Analyses? Interpretation of a Lmx1b-Knockout Experiment

Fabian J. Theis, Florian Blöchl, Ralph Witzgall, 2011 .

Proceedings of the 10th international conference on Latent Variable Analysis and Signal Separation

Arie Yeredor, Fabian J. Theis, Andrzej Cichocki, 2012 .

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

Vasilis Ntziachristos, Fabian J. Theis, Carsten Marr, 2020, Photoacoustics.

The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Audio Source Separation

Fabian J. Theis, Hiroshi Sawada, Shoko Araki, 2010, LVA/ICA.

Learning Tn5 Sequence Bias from ATAC-seq on Naked Chromatin

Fabian J. Theis, Fabian J Theis, David S. Fischer, 2020, ICANN.

Odefy -- From discrete to continuous models

Fabian J. Theis, Dominik M. Wittmann, Fabian J Theis, 2010, BMC Bioinformatics.

MPRAnalyze: statistical framework for massively parallel reporter assays

Fabian J. Theis, Nir Yosef, Fabian J Theis, 2019, bioRxiv.

A Fast Predictive Lossless Coder for fMRI Data Sets

Toshihisa Tanaka, Fabian J. Theis, Yumi Murakami, 2006, 2006 International Conference on Image Processing.

Orthonormal approximate joint block-diagonalization Bloc-diagonalisation simultanée approchée avec contrainte orthonormale

Fabian J. Theis, Cédric Févotte, 2007 .

Blind Matrix Decomposition Via Genetic Optimization of Sparseness and Nonnegativity Constraints

Fabian J. Theis, Kurt Stadlthanner, Elmar Wolfgang Lang, 2007, ICANN.

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

Fabian J. Theis, Dominik Lutter, Jan Hasenauer, 2013, BMC Systems Biology.

The nature and perception of human musical rhythms

Fabian J. Theis, Annette Witt, Theo Geisel, 2012 .

Uniqueness of real and complex linear independent component analysis revisited

Fabian J. Theis, Fabian J Theis, 2004, 2004 12th European Signal Processing Conference.

Statistical Analysis of Sample-Size Effects in ICA

Fabian J. Theis, J. Michael Herrmann, Fabian J Theis, 2007, IDEAL.

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

Fabian J. Theis, Fabian J Theis, 2010, IEEE Transactions on Circuits and Systems I: Regular Papers.

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..

Median-based clustering for underdetermined blind signal processing

Fabian J. Theis, Elmar Wolfgang Lang, Carlos García Puntonet, 2006, IEEE Signal Processing Letters.

Data-driven modelling of biological multi-scale processes

Fabian J. Theis, Jan Hasenauer, Nick Jagiella, 2015, 1506.06392.

The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Biomedical Source Separation

Fabian J. Theis, Hiroshi Sawada, Shoko Araki, 2010, LVA/ICA.

Blind signal separation into groups of dependent signals using joint block diagonalization

Fabian J. Theis, Fabian J Theis, 2005, 2005 IEEE International Symposium on Circuits and Systems.

A bilinear algorithm for sparse representations

Panos M. Pardalos, Fabian J. Theis, Fabian J Theis, 2007, Comput. Optim. Appl..

Geometric source separation: algorithms and applications

Fabian J. Theis, Fabian J Theis, 2003 .

New Geometric ICA Approach for Blind Source Separation

Fabian J. Theis, Elmar Lang, Carlos G. Puntonet, 2003 .

Tree-Dependent and Topographic Independent Component Analysis for fMRI Analysis

Anke Meyer-Bäse, Fabian J. Theis, Carlos García Puntonet, 2004, ICA.

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

Fabian J. Theis, Fabian J Theis, Lukas M. Simon, 2018, Nature Communications.

A robust model for spatiotemporal dependencies

Fabian J. Theis, Peter Gruber, Elmar Wolfgang Lang, 2008, Neurocomputing.

From Binary to Multivalued to Continuous Models: The Lac Operon as a Case Study

Steffen Klamt, Fabian J. Theis, Raimo Franke, 2010, J. Integr. Bioinform..

Geometric overcomplete ICA

Fabian J. Theis, Elmar Wolfgang Lang, 2002, ESANN.

Estimating Non-Gaussian Subspaces by Characteristic Functions

Motoaki Kawanabe, Fabian J. Theis, Fabian J Theis, 2006, ICA.

A spatiotemporal second-order algorithm for fMRI data analysis

Fabian J. Theis, Peter Gruber, Ana Maria Tomé, 2005 .

Beyond Predictions in Neural ODEs: Identification and Interventions pdf

Fabian J. Theis, Hananeh Aliee, Fabian J Theis, 2021, ArXiv.

An ISA algorithm with unknown group sizes successfully identifies biologically meaningful clusters in metabolomics data

Harold W. Gutch, Fabian J. Theis, Jan Krumsiek, 2011 .

Optimization Algorithms for Sparse Representations and Applications

Fabian J. Theis, Andrzej Cichocki, Fabian J Theis, 2006 .

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Masahiro Yoshida, Fabian J. Theis, Oliver Eickelberg, 2020, Nature Medicine.

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

Fabian J. Theis, Anagha Joshi, Berthold Göttgens, 2013, Nature Cell Biology.

The Heckscher-Ohlin Model and the Network Structure of International Trade

Fabian J. Theis, Florian Blöchl, Fabian J Theis, 2011 .

A Geometric ICA Procedure Based on a Lattice of the Observation Space

Fabian J. Theis, Julio Ortega, Elmar Lang, 2003 .

Quadratic Independent Component Analysis

Fabian J. Theis, Fabian J Theis, Wakako Nakamura, 2004 .

The Human Lung Cell Atlas - A high-resolution reference map of the human lung in health and disease.

Fabian J. Theis, Kerstin B. Meyer, Sarah A. Teichmann, 2019, American journal of respiratory cell and molecular biology.

Analyzing gene expression profiles with ICA

Fabian J. Theis, Ana Maria Tomé, Elmar Lang, 2006 .

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

Fabian J. Theis, Jan Hasenauer, Anna Fiedler, 2017, bioRxiv.

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

Fabian J. Theis, Sebastian Bohl, Ursula Klingmüller, 2017, Front. Physiol..

A modular framework for gene set analysis integrating multilevel omics data

Fabian J. Theis, Fabian J Theis, Florian Buettner, 2013, Nucleic acids research.

Uncertain gene regulatory networks simplified by gramian-based approach

Anke Meyer-Bäse, Fabian J. Theis, Susanne L.T. Cappendijk, 2012 .

A new geometrical method of BSS on a lattice of the space of observations

Fabian J. Theis, Julio Ortega, Elmar Lang, 2003 .

Network plasticity of pluripotency transcription factors in embryonic stem cells

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

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

Fabian J. Theis, Zhongming Zhao, Fabian J Theis, 2020, Nature Communications.

A Theoretical Framework for Overcomplete Geometric BMMR

Fabian J. Theis, Elmar Lang, Carlos G. Puntonet, 2002 .

Blind Source Separation of Water Artefacts in NMR Spectra using a Matrix Pencil

Fabian J. Theis, Ana Maria Tomé, Elmar Lang, 2003 .

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

Fabian J. Theis, Fabian J Theis, Heiko Lickert, 2019, Development.

Maximum Entropy and Minimal Mutual Information in a Nonlinear Model

Fabian J. Theis, Elmar Lang, Fabian J Theis, 2001 .

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

Fabian J. Theis, Jan Hasenauer, Fabian J Theis, 2014 .

Concepts and limitations for learning developmental trajectories from single cell genomics

Fabian J. Theis, Fabian J Theis, David S. Fischer, 2019, Development.

Biomedical Signal Analysis

Anke Meyer-Bäse, Fabian J. Theis, 2010 .

DeepWAS : Directly integrating regulatory information into GWAS using 1 deep learning supports master regulator MEF 2 C as risk factor for major 2 depressive disorder 3 4

Fabian J. Theis, Fabian J Theis, Gökcen Eraslan, 2016 .

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

Fabian J. Theis, Oliver Eickelberg, Fabian J Theis, 2017, Scientific Reports.

A Single Cell Haematopoietic Landscape Resolves Eight Lineage Trajectories and Defects in Kit Mutant Mice

Fabian J. Theis, Berthold Göttgens, Fabian J Theis, 2018, Experimental Hematology.

A Theoretic Model for Linear Geometric ICA

Fabian J. Theis, Elmar Lang, Carlos G. Puntonet, 2001 .

The Human Blood Metabolome-Transcriptome Interface

Christian Gieger, Fabian J. Theis, Gabi Kastenmüller, 2015, PLoS genetics.

Diffusion pseudotime robustly reconstructs lineage branching

Fabian J. Theis, F. Alexander Wolf, Laleh Haghverdi, 2016 .

FastGeo - A Histogram Based Approach to Linear Geometric ICA

Fabian J. Theis, Elmar Lang, Carlos G. Puntonet, 2001 .

Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information

Christian Gieger, Fabian J. Theis, Gabi Kastenmüller, 2012, PLoS genetics.

SOMICA - an application of self-organizing maps to geometric independent component analysis

Fabian J. Theis, Elmar Lang, Carlos G. Puntonet, 2003, Proceedings of the International Joint Conference on Neural Networks, 2003..

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

Fabian J. Theis, Berthold Göttgens, Chris P. Ponting, 2015, Cell stem cell.

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

Fabian J. Theis, Fabian J Theis, Michael W. Pfaffl, 2016, Biomolecular detection and quantification.

Quantitative comparison of competing PDE models for Pomlp dynamics in fission yeast

Fabian J. Theis, Jan Hasenauer, Anna Fiedler, 2016 .

Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas

Fabian J. Theis, Fabian J Theis, Heiko Lickert, 2017, Molecular metabolism.

Nonlinear Geometric ICA

Fabian J. Theis, Elmar Lang, Carlos G. Puntonet, 2003 .

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

Fabian J. Theis, Jens Timmer, Clemens Kreutz, 2013 .

AUTOMATIC DENOISING USING LOCAL INDEPENDENT COMPONENT ANALYSIS

Fabian J. Theis, Peter Gruber, Ana Maria Tomé, 2004 .

MPRAnalyze: statistical framework for massively parallel reporter assays

Fabian J. Theis, Nir Yosef, Anat Kreimer, 2019, Genome Biology.

MicroRNA Loss Enhances Learning and Memory in Mice

Fabian J. Theis, Andreas Kowarsch, Fabian J Theis, 2010, The Journal of Neuroscience.

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

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

Deep Learning for Imaging Flow Cytometry: Cell Cycle Analysis of Jurkat Cells

Fabian J. Theis, Anne E Carpenter, Anne E. Carpenter, 2016 .

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

Fabian J. Theis, Carsten Marr, Michael Strasser, 2012 .

Parameter estimation for stochastic biochemical processes: A comparison of moment equation and fintie state projection

Fabian J. Theis, Jan Hasenauer, Atefeh Kazeroonian, 2013 .

SOMICA and geometric ICA

Fabian J. Theis, Elmar Lang, Carlos G. Puntonet, 2003, Sixth International Conference of Information Fusion, 2003. Proceedings of the.

The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance

Fabian J. Theis, Fabian J Theis, Heiko Lickert, 2013, RNA biology.