Pattern Repulsion Revisited. - Fabian J. Theis; Christoph Bauer; Carlos García Puntonet; Elmar Wolfgang Lang (IWANN (2), 2001)

How to generalize geometric ICA to higher dimensions. - Fabian J. Theis; Elmar Wolfgang Lang (ESANN, 2002)

Geometric overcomplete ICA. - Fabian J. Theis; Elmar Wolfgang Lang (ESANN, 2002)

Overcomplete ICA with a Geometric Algorithm. - Fabian J. Theis; Elmar Wolfgang Lang; Tobias Westenhuber; Carlos García Puntonet (ICANN, 2002)

Comparison of maximum entropy and minimal mutual information in a nonlinear setting. - Fabian J. Theis; Christoph Bauer; Elmar Wolfgang Lang (Signal Process., 2002)

Local features in biomedical image clusters extracted with independent component analysis. - Christoph Bauer; Fabian J. Theis; Wolfgang Bäumler; Elmar Wolfgang Lang (IJCNN, 2003)

SOMICA - an application of self-organizing maps to geometric independent component analysis. - Fabian J. Theis; Carlos García Puntonet; Elmar Wolfgang Lang (IJCNN, 2003)

Removing water artefacts from 2D protein NMR spectra using GEVD with congruent matrix pencils. - Kurt Stadlthanner; Ana Maria Tomé; Fabian J. Theis; Wolfram Gronwald; Hans Robert Kalbitzer; Elmar Wolfgang Lang (ISSPA (2), 2003)

Mathematics in independent component analysis. - Fabian J. Theis (ISSPA (2), 2003)

Neural network signal analysis in immunology. - Fabian J. Theis; Dominik Hartl; Susanne Krauss-Etschmann; Elmar Wolfgang Lang (ISSPA (2), 2003)

A Generalized Eigendecomposition Approach Using Matrix Pencils to Remove Artefacts from 2D NMR Spectra. - Kurt Stadlthanner; Ana Maria Tomé; Fabian J. Theis; Elmar Wolfgang Lang (IWANN (2), 2003)

An Adaptive Approach to Blind Source Separation Using a Self-Organzing Map and a Neural Gas. - Fabian J. Theis; Manuel Rodríguez Álvarez; Carlos García Puntonet; Elmar Wolfgang Lang (IWANN (2), 2003)

An Improved Geometric Overcomplete Blind Source Separation Algorithm. - Fabian J. Theis; Carlos García Puntonet; Elmar Wolfgang Lang (IWANN (2), 2003)

Generalizing Geometric ICA to Nonlinear Settings. - Fabian J. Theis; Carlos García Puntonet; Elmar Wolfgang Lang (IWANN (2), 2003)

Linear Geometric ICA: Fundamentals and Algorithms. - Fabian J. Theis; Andreas Jung; Carlos García Puntonet; Elmar Wolfgang Lang (Neural Comput., 2003)

Mathematics in independent component analysis. - Fabian J. Theis (Logos-Verlag, 2003)

Geometric source separation: algorithms and applications. - Fabian J. Theis (2003)

Separability of analytic postnonlinear blind source separation with bounded sources. - Fabian J. Theis; Peter Gruber 002 (ESANN, 2004)

Robust overcomplete matrix recovery for sparse sources using a generalized Hough transform. - Fabian J. Theis; Pando G. Georgiev; Andrzej Cichocki (ESANN, 2004)

Linearization identification and an application to BSS using a SOM. - Fabian J. Theis; Elmar Wolfgang Lang (ESANN, 2004)

Uniqueness of real and complex linear independent component analysis revisited. - Fabian J. Theis (EUSIPCO, 2004)

Blind Source Separation of Linear Mixtures with Singular Matrices. - Pando G. Georgiev; Fabian J. Theis (ICA, 2004)

Denoising Using Local ICA and a Generalized Eigendecomposition with Time-Delayed Signals. - Peter Gruber 002; Kurt Stadlthanner; Ana Maria Tomé; Ana R. Teixeira; Fabian J. Theis; Carlos García Puntonet; Elmar Wolfgang Lang (ICA, 2004)

3D Spatial Analysis of fMRI Data on a Word Perception Task. - Ingo R. Keck; Fabian J. Theis; Peter Gruber 002; Elmar Wolfgang Lang; Karsten Specht; Carlos García Puntonet (ICA, 2004)

Tree-Dependent and Topographic Independent Component Analysis for fMRI Analysis. - Anke Meyer-Bäse; Fabian J. Theis; Oliver Lange; Carlos García Puntonet (ICA, 2004)

Postnonlinear Overcomplete Blind Source Separation Using Sparse Sources. - Fabian J. Theis; Shun-ichi Amari (ICA, 2004)

Second-Order Blind Source Separation Based on Multi-dimensional Autocovariances. - Fabian J. Theis; Anke Meyer-Bäse; Elmar Wolfgang Lang (ICA, 2004)

Blind source separation and sparse component analysis of overcomplete mixtures. - Pando G. Georgiev; Fabian J. Theis; Andrzej Cichocki (ICASSP (5), 2004)

Denoising using local ICA and kernel-PCA. - Peter Gruber 002; Fabian J. Theis; Kurt Stadlthanner; Elmar Wolfgang Lang; Ana Maria Tomé; Ana Rita Teixeira (IJCNN, 2004)

3D spatial analysis of fMRI data: a comparison of ICA and GLM analysis on a word perception task. - Ingo R. Keck; Fabian J. Theis; Peter Gruber 002; Elmar Wolfgang Lang; Karsten Specht; Carlos García Puntonet (IJCNN, 2004)

Clustering of dependent components: a new paradigm for fMRI signal detection. - Anke Meyer-Bäse; Fabian J. Theis; Oliver Lange; Axel Wismüller (IJCNN, 2004)

Kernel-PCA denoising of artifact-free protein NMR spectra. - Kurt Stadlthanner; Elmar Wolfgang Lang; Peter Gruber 002; Fabian J. Theis; Ana Maria Tomé; Ana Rita Teixeira; Carlos García Puntonet (IJCNN, 2004)

Postnonlinear blind source separation via linearization identification. - Fabian J. Theis; Elmar Wolfgang Lang (IJCNN, 2004)

Mobile decision support for transplantation patient data. - Andreas Krause 001; Dominik Hartl; Fabian J. Theis; Manfred Stangl; Klaus-E. Gerauer; Alexander T. Mehlhorn (Int. J. Medical Informatics, 2004)

A geometric algorithm for overcomplete linear ICA. - Fabian J. Theis; Elmar Wolfgang Lang; Carlos García Puntonet (Neurocomputing, 2004)

A New Concept for Separability Problems in Blind Source Separation. - Fabian J. Theis (Neural Comput., 2004)

Uniqueness of complex and multidimensional independent component analysis. - Fabian J. Theis (Signal Process., 2004)

Multidimensional independent component analysis using characteristic functions. - Fabian J. Theis (EUSIPCO, 2005)

Spatiotemporal blind source separation using double-sided approximate joint diagonalization. - Fabian J. Theis; Peter Gruber 002; Ingo R. Keck; Anke Meyer-Bäse; Elmar Wolfgang Lang (EUSIPCO, 2005)

First results on uniqueness of sparse non-negative matrix factorization. - Fabian J. Theis; Kurt Stadlthanner; Toshihisa Tanaka 001 (EUSIPCO, 2005)

AutoAssign - An Automatic Assignment Tool for Independent Components. - Matthias Böhm 002; Kurt Stadlthanner; Ana Maria Tomé; Peter Gruber 002; Ana R. Teixeira; Fabian J. Theis; Carlos García Puntonet; Elmar Wolfgang Lang (IbPRIA (2), 2005)

Bispectrum-Based Statistical Tests for VAD. - Juan Manuel Górriz Sáez; Javier Ramírez 001; Carlos García Puntonet; Fabian J. Theis; Elmar Wolfgang Lang (ICANN (2), 2005)

Functional MRI Analysis by a Novel Spatiotemporal ICA Algorithm. - Fabian J. Theis; Peter Gruber 002; Ingo R. Keck; Elmar Wolfgang Lang (ICANN (1), 2005)

A Fast and Efficient Method for Compressing fMRI Data Sets. - Fabian J. Theis; Toshihisa Tanaka 001 (ICANN (2), 2005)

An algorithm for automatic assignment of artifact-related independent components in biomedical signal analysis. - Matthias Böhm 002; Kurt Stadlthanner; Elmar Wolfgang Lang; Fabian J. Theis; Peter Gruber 002; Ana Maria Tomé; Ana Rita Teixeira; Carlos García Puntonet (IJCNN, 2005)

Blind signal separation into groups of dependent signals using joint block diagonalization. - Fabian J. Theis (ISCAS (6), 2005)

Hybridizing Sparse Component Analysis with Genetic Algorithms for Blind Source Separation. - Kurt Stadlthanner; Fabian J. Theis; Carlos García Puntonet; Juan Manuel Górriz; Ana Maria Tomé; Elmar Wolfgang Lang (ISBMDA, 2005)

A Hybridization of Simulated Annealing and Local PCA for Automatic Component Assignment Within ICA. - Matthias Böhm 002; Kurt Stadlthanner; Elmar Wolfgang Lang; Ana Maria Tomé; Ana R. Teixeira; Fabian J. Theis; Carlos García Puntonet (IWANN, 2005)

Extended Sparse Nonnegative Matrix Factorization. - Kurt Stadlthanner; Fabian J. Theis; Carlos García Puntonet; Elmar Wolfgang Lang (IWANN, 2005)

On model identifiability in analytic postnonlinear ICA. - Fabian J. Theis; Peter Gruber 002 (Neurocomputing, 2005)

Sparse component analysis and blind source separation of underdetermined mixtures. - Pando G. Georgiev; Fabian J. Theis; Andrzej Cichocki (IEEE Trans. Neural Networks, 2005)

Grassmann clustering. - Peter Gruber 002; Fabian J. Theis (EUSIPCO, 2006)

Estimating Non-Gaussian Subspaces by Characteristic Functions. - Motoaki Kawanabe; Fabian J. Theis (ICA, 2006)

Sparse Nonnegative Matrix Factorization Applied to Microarray Data Sets. - Kurt Stadlthanner; Fabian J. Theis; Elmar Wolfgang Lang; Ana Maria Tomé; Carlos García Puntonet; Pedro Gómez-Vilda; Thomas Langmann; Gerd Schmitz 001 (ICA, 2006)

Uniqueness of Non-Gaussian Subspace Analysis. - Fabian J. Theis; Motoaki Kawanabe (ICA, 2006)

Sparseness by Iterative Projections Onto Spheres. - Fabian J. Theis; Toshihisa Tanaka 001 (ICASSP (5), 2006)

A Fast Predictive Lossless Coder for fMRI Data Sets. - Toshihisa Tanaka 001; Yumi Murakami; Fabian J. Theis (ICIP, 2006)

Region of Interest Based Independent Component Analysis. - Ingo R. Keck; Jan Churan; Fabian J. Theis; Peter Gruber 002; Elmar Wolfgang Lang; Carlos García Puntonet (ICONIP (1), 2006)

Stability Analysis of an Unsupervised Competitive Neural Network. - Anke Meyer-Bäse; Vera Thümmler; Fabian J. Theis (IJCNN, 2006)

New Riemannian metrics for speeding-up the convergence of over- and underdetermined ICA. - Stefano Squartini; Francesco Piazza; Fabian J. Theis (ISCAS, 2006)

On the use of joint diagonalization in blind signal processing. - Fabian J. Theis; Yujiro Inouye (ISCAS, 2006)

Towards a general independent subspace analysis. - Fabian J. Theis (NIPS, 2006)

Blind source separation based on self-organizing neural network. - Anke Meyer-Bäse; Peter Gruber 002; Fabian J. Theis; Simon Y. Foo (Eng. Appl. Artif. Intell., 2006)

Denoising using local projective subspace methods. - Peter Gruber 002; Kurt Stadlthanner; Matthias Böhm 002; Fabian J. Theis; Elmar Wolfgang Lang; Ana Maria Tomé; Ana R. Teixeira; Carlos García Puntonet; Juan Manuel Górriz Sáez (Neurocomputing, 2006)

Separation of water artifacts in 2D NOESY protein spectra using congruent matrix pencils. - Kurt Stadlthanner; Ana Maria Tomé; Fabian J. Theis; Elmar Wolfgang Lang; Wolfram Gronwald; Hans Robert Kalbitzer (Neurocomputing, 2006)

On the use of sparse signal decomposition in the analysis of multi-channel surface electromyograms. - Fabian J. Theis; Gonzalo A. García (Signal Process., 2006)

Median-based clustering for underdetermined blind signal processing. - Fabian J. Theis; Carlos García Puntonet; Elmar Wolfgang Lang (IEEE Signal Process. Lett., 2006)

On the use of simulated annealing to automatically assign decorrelated components in second-order blind source separation. - Matthias Böhm 002; Kurt Stadlthanner; Peter Gruber 002; Fabian J. Theis; Elmar Wolfgang Lang; Ana Maria Tomé; Ana R. Teixeira; Wolfram Gronwald; Hans Robert Kalbitzer (IEEE Trans. Biomed. Eng., 2006)

Pivot Selection Strategies in Jacobi Joint Block-Diagonalization. - Cédric Févotte; Fabian J. Theis (ICA, 2007)

Identifiability Conditions and Subspace Clustering in Sparse BSS. - Pando G. Georgiev; Fabian J. Theis; Anca L. Ralescu (ICA, 2007)

A Toolbox for Model-Free Analysis of fMRI Data. - Peter Gruber 002; C. Kohler; Fabian J. Theis (ICA, 2007)

Independent Subspace Analysis Is Unique, Given Irreducibility. - Harold W. Gutch; Fabian J. Theis (ICA, 2007)

Blind Matrix Decomposition Techniques to Identify Marker Genes from Microarrays. - Reinhard Schachtner; Dominik Lutter; Fabian J. Theis; Elmar Wolfgang Lang; Ana Maria Tomé; Juan Manuel Górriz Sáez; Carlos García Puntonet (ICA, 2007)

Colored Subspace Analysis. - Fabian J. Theis; Motoaki Kawanabe (ICA, 2007)

Exploiting Blind Matrix Decomposition Techniques to Identify Diagnostic Marker Genes. - Reinhard Schachtner; Dominik Lutter; Fabian J. Theis; Elmar Wolfgang Lang; Ana Maria Tomé; Gerd Schmitz 001 (ICANN (2), 2007)

Blind Matrix Decomposition Via Genetic Optimization of Sparseness and Nonnegativity Constraints. - Kurt Stadlthanner; Fabian J. Theis; Elmar Wolfgang Lang; Ana Maria Tomé; Carlos García Puntonet (ICANN (1), 2007)

Statistical Analysis of Sample-Size Effects in ICA. - J. Michael Herrmann; Fabian J. Theis (IDEAL, 2007)

Sparse Nonnegative Matrix Factorization with Genetic Algorithms for Microarray Analysis. - Kurt Stadlthanner; Dominik Lutter; Fabian J. Theis; Elmar Wolfgang Lang; Ana Maria Tomé; Petia Georgieva; Carlos García Puntonet (IJCNN, 2007)

A bilinear algorithm for sparse representations. - Pando G. Georgiev; Panos M. Pardalos; Fabian J. Theis (Comput. Optim. Appl., 2007)

Robust Sparse Component Analysis Based on a Generalized Hough Transform. - Fabian J. Theis; Pando G. Georgiev; Andrzej Cichocki (EURASIP J. Adv. Signal Process., 2007)

Joint low-rank approximation for extracting non-Gaussian subspaces. - Motoaki Kawanabe; Fabian J. Theis (Signal Process., 2007)

Stochastic Stability Analysis of the Heat Shock Response in E. Coli. - Anke Meyer-Bäse; Fabian J. Theis (BIOCOMP, 2008)

Effective Emission Tomography Image Reconstruction Algorithms for SPECT Data. - Javier Ramírez 001; Juan Manuel Górriz; Manuel Gómez-Río; Alejandro Romero; Rosa Chaves; A. Lassl; A. Rodríguez; Carlos García Puntonet; Fabian J. Theis; Elmar Wolfgang Lang (ICCS (1), 2008)

Knowledge-based gene expression classification via matrix factorization. - Reinhard Schachtner; Dominik Lutter; P. Knollmüller; Ana Maria Tomé; Fabian J. Theis; Gerd Schmitz 001; Martin Stetter; Pedro Gómez-Vilda; Elmar Wolfgang Lang (Bioinform., 2008)

Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis. - Dominik Lutter; Peter Ugocsai; Margot Grandl; Evelyn Orso; Fabian J. Theis; Elmar Wolfgang Lang; Gerd Schmitz 001 (BMC Bioinform., 2008)

Hybridizing sparse component analysis with genetic algorithms for microarray analysis. - Kurt Stadlthanner; Fabian J. Theis; Elmar Wolfgang Lang; Ana Maria Tomé; Carlos García Puntonet; Juan Manuel Górriz (Neurocomputing, 2008)

A robust model for spatiotemporal dependencies. - Fabian J. Theis; Peter Gruber 002; Ingo R. Keck; Elmar Wolfgang Lang (Neurocomputing, 2008)

Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns. - Dirk Brockmann; Fabian J. Theis (IEEE Pervasive Comput., 2008)

Estimating Hidden Influences in Metabolic and Gene Regulatory Networks. - Florian Blöchl; Fabian J. Theis (ICA, 2009)

Hierarchical Extraction of Independent Subspaces of Unknown Dimensions. - Peter Gruber 002; Harold W. Gutch; Fabian J. Theis (ICA, 2009)

Soft Dimension Reduction for ICA by Joint Diagonalization on the Stiefel Manifold. - Fabian J. Theis; Thomas P. Cason; Pierre-Antoine Absil (ICA, 2009)

Blind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data. - Fabian J. Theis; Richard A. Neher; Andre Zeug (ICA, 2009)

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. - Dominik M. Wittmann; Jan Krumsiek; Julio Saez-Rodriguez; Douglas A. Lauffenburger; Steffen Klamt; Fabian J. Theis (BMC Syst. Biol., 2009)

ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data. - Peter Gruber 002; Anke Meyer-Bäse; Simon Y. Foo; Fabian J. Theis (Eng. Appl. Artif. Intell., 2009)

Hypergraphs and Cellular Networks. - Steffen Klamt; Utz-Uwe Haus; Fabian J. Theis (PLoS Comput. Biol., 2009)

Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary. - Dominik M. Wittmann; Florian Blöchl; Dietrich Trümbach; Wolfgang Wurst; Nilima Prakash; Fabian J. Theis (PLoS Comput. Biol., 2009)

Reconstruction of graphs based on random walks. - Dominik M. Wittmann; Daniel Schmidl; Florian Blöchl; Fabian J. Theis (Theor. Comput. Sci., 2009)

Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops in the Tryptophan Regulatory Network of E. coli. - Anke Meyer-Bäse; Fabian J. Theis (BIOCOMP, 2010)

Robust Stability Analysis of Multi-Time Scale Genetic Regulatory Networks under Parametric Uncertainties. - Anke Meyer-Bäse; Claudia Plant; Susanne Cappendijk; Fabian J. Theis (BIOCOMP, 2010)

Uncovering the Structure of Heterogenous Biological Data: Fuzzy Graph Partitioning in the k-partite Setting. - Florian Blöchl; Mara L. Hartsperger; Volker Stümpflen; Fabian J. Theis (GCB, 2010)

The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Audio Source Separation. - Shoko Araki; Alexey Ozerov; Vikrham Gowreesunker; Hiroshi Sawada; Fabian J. Theis; Guido Nolte; Dominik Lutter; Ngoc Q. K. Duong (LVA/ICA, 2010)

The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Biomedical Source Separation. - Shoko Araki; Fabian J. Theis; Guido Nolte; Dominik Lutter; Alexey Ozerov; Vikrham Gowreesunker; Hiroshi Sawada; Ngoc Q. K. Duong (LVA/ICA, 2010)

Second-Order Source Separation Based on Prior Knowledge Realized in a Graph Model. - Florian Blöchl; Andreas Kowarsch; Fabian J. Theis (LVA/ICA, 2010)

ICA over Finite Fields. - Harold W. Gutch; Peter Gruber 002; Fabian J. Theis (LVA/ICA, 2010)

Second Order Subspace Analysis and Simple Decompositions. - Harold W. Gutch; Takanori Maehara; Fabian J. Theis (LVA/ICA, 2010)

Information-Theoretic Model Selection for Independent Components. - Claudia Plant; Fabian J. Theis; Anke Meyer-Bäse; Christian Böhm 001 (LVA/ICA, 2010)

Robust Second-Order Source Separation Identifies Experimental Responses in Biomedical Imaging. - Fabian J. Theis; Nikola S. Müller; Claudia Plant; Christian Böhm 001 (LVA/ICA, 2010)

Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. - Mara L. Hartsperger; Florian Blöchl; Volker Stümpflen; Fabian J. Theis (BMC Bioinform., 2010)

Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation. - Andreas Kowarsch; Florian Blöchl; Sebastian Bohl; Maria Saile; Norbert Gretz; Ursula Klingmüller; Fabian J. Theis (BMC Bioinform., 2010)

Odefy – From discrete to continuous models. - Jan Krumsiek; Sebastian Pölsterl; Dominik M. Wittmann; Fabian J. Theis (BMC Bioinform., 2010)

From Binary to Multivalued to Continuous Models: The Lac Operon as a Case Study. - Raimo Franke; Fabian J. Theis; Steffen Klamt (J. Integr. Bioinform., 2010)

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

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

An ISA algorithm with unknown group sizes identifies meaningful clusters in metabolomics data. - Harold W. Gutch; Jan Krumsiek; Fabian J. Theis (EUSIPCO, 2011)

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. - Jan Krumsiek; Karsten Suhre; Thomas Illig; Jerzy Adamski; Fabian J. Theis (BMC Syst. Biol., 2011)

MicroRNAs coordinately regulate protein complexes. - Steffen Sass; Sabine Dietmann; Ulrike C. Burk; Simone Brabletz; Dominik Lutter; Andreas Kowarsch; Klaus F. X. Mayer; Thomas Brabletz; Andreas Ruepp; Fabian J. Theis; Yu Wang 008 (BMC Syst. Biol., 2011)

Modularity maximization and tree clustering: Novel ways to determine effective geographic borders - Daniel Grady; Rafael Brune; Christian Thiemann; Fabian J. Theis; Dirk Brockmann (CoRR, 2011)

MIPS: curated databases and comprehensive secondary data resources in 2010. - Hans-Werner Mewes; Andreas Ruepp; Fabian J. Theis; Thomas Rattei; Mathias C. Walter; Dmitrij Frishman; Karsten Suhre; Manuel Spannagl; Klaus F. X. Mayer; Volker Stümpflen; Alexey V. Antonov (Nucleic Acids Res., 2011)

Uniqueness of Non-Gaussianity-Based Dimension Reduction. - Fabian J. Theis; Motoaki Kawanabe; Klaus-Robert Müller (IEEE Trans. Signal Process., 2011)

To Infinity and Beyond: On ICA over Hilbert Spaces. - Harold W. Gutch; Fabian J. Theis (LVA/ICA, 2012)

Bayesian Inference of Latent Causes in Gene Regulatory Dynamics. - Sabine Hug; Fabian J. Theis (LVA/ICA, 2012)

Joint Diagonalization of Several Scatter Matrices for ICA. - Klaus Nordhausen; Harold W. Gutch; Hannu Oja; Fabian J. Theis (LVA/ICA, 2012)

Bayesian Fuzzy Clustering of Colored Graphs. - Fabian J. Theis (LVA/ICA, 2012)

Measuring Non-Gaussianity by Phi-Transformed and Fuzzy Histograms. - Claudia Plant; Son Thai Mai; Junming Shao; Fabian J. Theis; Anke Meyer-Baese; Christian Böhm 001 (Adv. Artif. Neural Syst., 2012)

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. - Florian Buettner 002; Fabian J. Theis (Bioinform., 2012)

On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. - Ann-Kristin Petersen; Jan Krumsiek; Brigitte Wägele; Fabian J. Theis; Heinz-Erich Wichmann; Christian Gieger; Karsten Suhre (BMC Bioinform., 2012)

Bayesian model selection validates a biokinetic model for zirconium processing in humans. - Daniel Schmidl; Sabine Hug; Wei Li; Matthias B. Greiter; Fabian J. Theis (BMC Syst. Biol., 2012)

Uniqueness of linear factorizations into independent subspaces. - Harold W. Gutch; Fabian J. Theis (J. Multivar. Anal., 2012)

ICA over finite fields - Separability and algorithms. - Harold W. Gutch; Peter Gruber 002; Arie Yeredor; Fabian J. Theis (Signal Process., 2012)

The signal separation evaluation campaign (2007-2010): Achievements and remaining challenges. - Emmanuel Vincent 001; Shoko Araki; Fabian J. Theis; Guido Nolte; Pau Bofill; Hiroshi Sawada; Alexey Ozerov; Vikrham Gowreesunker; Dominik Lutter; Ngoc Q. K. Duong (Signal Process., 2012)

Visualizing edge-edge relations in graphs. - Corinna Vehlow; Jan Hasenauer; Fabian J. Theis; Daniel Weiskopf (PacificVis, 2013)

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

Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis. - Sabrina Hock; Jan Hasenauer; Fabian J. Theis (BMC Bioinform., 2013)

iVUN: interactive Visualization of Uncertain biochemical reaction Networks. - Corinna Vehlow; Jan Hasenauer; Andrei Kramer; Andreas Raue; Sabine Hug; Jens Timmer; Nicole Radde; Fabian J. Theis; Daniel Weiskopf (BMC Bioinform., 2013)

Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation. - Sabrina Hock; Yen-Kar Ng; Jan Hasenauer; Dominik M. Wittmann; Dominik Lutter; Dietrich Trümbach; Wolfgang Wurst; Nilima Prakash; Fabian J. Theis (BMC Syst. Biol., 2013)

Dependent component analysis. - Ercan E. Kuruoglu; Fabian J. Theis (EURASIP J. Adv. Signal Process., 2013)

Truth-Content and Phase Transitions of Random Boolean Networks with Generic Logics. - Dominik M. Wittmann; Sabrina Hock; Fabian J. Theis (SIAM J. Appl. Dyn. Syst., 2013)

Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis. - Fabian Fröhlich; Sabrina Hross; Fabian J. Theis; Jan Hasenauer (CMSB, 2014)

Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More. - Fabian Fröhlich; Fabian J. Theis; Jan Hasenauer (CMSB, 2014)

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

Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain. - Michaela Matthes; Martin Preusse; Jingzhong Zhang; Julia Schechter; Daniela Mayer; Bernd Lentes; Fabian J. Theis; Nilima Prakash; Wolfgang Wurst; Dietrich Trümbach (Database J. Biol. Databases Curation, 2014)

Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. - Florian Buettner 002; Victoria Moignard; Berthold Göttgens; Fabian J. Theis (Bioinform., 2014)

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

Bayesian Blind Source Separation for Data with Network Structure. - Katrin Illner; Christiane Fuchs; Fabian J. Theis (J. Comput. Biol., 2014)

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics. - Jan Hasenauer; Christine Hasenauer; Tim Hucho; Fabian J. Theis (PLoS Comput. Biol., 2014)

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

An Affine Equivariant Robust Second-Order BSS Method. - Pauliina Ilmonen; Klaus Nordhausen; Hannu Oja; Fabian J. Theis (LVA/ICA, 2015)

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

Diffusion maps for high-dimensional single-cell analysis of differentiation data. - Laleh Haghverdi; Florian Buettner 002; Fabian J. Theis (Bioinform., 2015)

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. - Andrea Ocone; Laleh Haghverdi; Nikola S. Müller; Fabian J. Theis (Bioinform., 2015)

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. - Andreas Raue; Bernhard Steiert; Max Schelker; Clemens Kreutz; Tim Maiwald; Helge Hass; Joep Vanlier; Christian Tönsing; Lorenz Adlung; Raphael Engesser; Wolfgang Mader 002; Tim Heinemann; et al. (Bioinform., 2015)

RAMONA: a Web application for gene set analysis on multilevel omics data. - Steffen Sass; Florian Buettner 002; Nikola S. Müller; Fabian J. Theis (Bioinform., 2015)

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

Model selection using limiting distributions of second-order blind source separation algorithms. - Katrin Illner; Jari Miettinen; Christiane Fuchs; Sara Taskinen; Klaus Nordhausen; Hannu Oja; Fabian J. Theis (Signal Process., 2015)

Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields. - Gerda Bortsova; Michael Sterr; Lichao Wang; Fausto Milletari; Nassir Navab; Anika Böttcher; Heiko Lickert; Fabian J. Theis; Tingying Peng (MLMI@MICCAI, 2016)

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

MEMO: multi-experiment mixture model analysis of censored data. - Eva-Maria Geissen; Jan Hasenauer; Stephanie Heinrich; Silke Hauf; Fabian J. Theis; Nicole Radde (Bioinform., 2016)

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints. - Anna Fiedler; Sebastian Raeth; Fabian J. Theis; Angelika Hausser; Jan Hasenauer (BMC Syst. Biol., 2016)

Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression. - Michael Laimighofer; Jan Krumsiek; Florian A. Büttner; Fabian J. Theis (J. Comput. Biol., 2016)

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. - Fabian Fröhlich; Philipp Thomas; Atefeh Kazeroonian; Fabian J. Theis; Ramon Grima; Jan Hasenauer (PLoS Comput. Biol., 2016)

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

Model-based branching point detection in single-cell data by K-branches clustering. - Nikolaos-Kosmas Chlis; F. Alexander Wolf; Fabian J. Theis (Bioinform., 2017)

Parameter estimation for dynamical systems with discrete events and logical operations. - Fabian Fröhlich; Fabian J. Theis; Joachim O. Rädler; Jan Hasenauer (Bioinform., 2017)

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

A scalable moment-closure approximation for large-scale biochemical reaction networks. - Atefeh Kazeroonian; Fabian J. Theis; Jan Hasenauer (Bioinform., 2017)

pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. - Sophie Molnos; Clemens Baumbach; Simone Wahl; Martina Müller-Nurasyid; Konstantin Strauch; Rui Wang-Sattler; Melanie Waldenberger; Thomas Meitinger; Jerzy Adamski; Gabi Kastenmüller; Karsten Suhre; Annette Peters; et al. (BMC Bioinform., 2017)

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems. - Benjamin Ballnus; Sabine Hug; Kathrin Hatz; Linus Görlitz; Jan Hasenauer; Fabian J. Theis (BMC Syst. Biol., 2017)

Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies. - Norbert Krautenbacher; Fabian J. Theis; Christiane Fuchs (Comput. Math. Methods Medicine, 2017)

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. - Fabian Fröhlich; Barbara Kaltenbacher; Fabian J. Theis; Jan Hasenauer (PLoS Comput. Biol., 2017)

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

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering. - Benjamin Ballnus; Steffen Schaper; Fabian J. Theis; Jan Hasenauer (Bioinform., 2018)

netReg: network-regularized linear models for biological association studies. - Simon Dirmeier; Christiane Fuchs; Nikola S. Müller; Fabian J. Theis (Bioinform., 2018)

Supplementary Code to Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection. - Fabian Fröhlich; Anita Reiser; Laura Fink; Daniel Woschée; Thomas S. Ligon; Fabian J. Theis; Joachim O. Rädler; Jan Hasenauer (Zenodo, 2018)

Conditional out-of-sample generation for unpaired data using trVAE. - Mohammad Lotfollahi; Mohsen Naghipourfar; Fabian J. Theis; F. Alexander Wolf (CoRR, 2019)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

Learning Tn5 Sequence Bias from ATAC-seq on Naked Chromatin. - Meshal Ansari; David S. Fischer; Fabian J. Theis (ICANN (1), 2020)

Copy number aberrations from Affymetrix SNP 6.0 genotyping data - how accurate are commonly used prediction approaches? - Adriana Pitea; Ivan Kondofersky; Steffen Sass; Fabian J. Theis; Nikola S. Müller; Kristian Unger (Briefings Bioinform., 2020)

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

Conditional out-of-distribution generation for unpaired data using transfer VAE. - Mohammad Lotfollahi; Mohsen Naghipourfar; Fabian J. Theis; F. Alexander Wolf (Bioinform., 2020)

Munich School for Data Science (MUDS) - Eine Graduiertenschule für Data Science in München. - Fabian J. Theis; Thomas Ludwig 002 (Inform. Spektrum, 2020)

Self-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy. - Olle G. Holmberg; Niklas D. Köhler; Thiago Martins; Jakob Siedlecki; Tina Herold; Leonie Keidel; Ben Asani; Johannes Schiefelbein; Siegfried Priglinger; Karsten U. Kortuem; Fabian J. Theis (Nat. Mach. Intell., 2020)

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning. - Janine Arloth; Gökcen Eraslan; Till F. M. Andlauer; Jade Martins; Stella Iurato; Brigitte Kühnel; Melanie Waldenberger; Josef Frank; Ralf Gold; Bernhard Hemmer; Felix Luessi; Sandra Nischwitz; et al. (PLoS Comput. Biol., 2020)

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines. - Elba Raimúndez-Álvarez; Simone Keller; Gwen Zwingenberger; Karolin Ebert; Sabine Hug; Fabian J. Theis; Dieter Maier; Birgit Luber; Jan Hasenauer (PLoS Comput. Biol., 2020)

EpiScanpy: integrated single-cell epigenomic analysis. - Anna Danese; Maria L. Richter; Kridsadakorn Chaichoompu; David S. Fischer; Fabian J. Theis; Maria Colomé-Tatché (Zenodo, 2020)

[DEPRECATED] Theislab sfaira Model Repository. - Leander Dony; David S. Fischer; Fabian J. Theis (Zenodo, 2020)

Multimodal single cell data integration challenge: Results and lessons learned. - Christopher Lance; Malte D. Lücken; Daniel B. Burkhardt; Robrecht Cannoodt; Pia Rautenstrauch; Anna Laddach; Aidyn Ubingazhibov; Zhi-Jie Cao; Kaiwen Deng; Sumeer Khan; Qiao Liu 008; Nikolay Russkikh; et al. (NeurIPS (Competition and Demos), 2021)

A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. - Malte Lücken; Daniel Burkhardt; Robrecht Cannoodt; Christopher Lance; Aditi Agrawal; Hananeh Aliee; Ann Chen; Louise Deconinck; Angela Detweiler; Alejandro Granados; Shelly Huynh; Laura Isacco; et al. (NeurIPS Datasets and Benchmarks, 2021)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

Beyond Predictions in Neural ODEs: Identification and Interventions. - Hananeh Aliee; Fabian J. Theis; Niki Kilbertus (CoRR, 2021)

Theislab sfaira Model Repository. - Leander Dony; David S. Fischer; Fabian J. Theis (Zenodo, 2021)

1000 tools paper. - Luke Zappia; Fabian J. Theis (Zenodo, 2021)

1000 tools paper. - Luke Zappia; Fabian J. Theis (Zenodo, 2021)

Noise Transfer for Unsupervised Domain Adaptation of Retinal OCT Images. - Valentin Koch; Olle G. Holmberg; Hannah Spitzer; Johannes Schiefelbein; Ben Asani; Michael Hafner; Fabian J. Theis (MICCAI (2), 2022)

Sparsity in Continuous-Depth Neural Networks. - Hananeh Aliee; Till Richter; Mikhail Solonin; Ignacio Ibarra; Fabian J. Theis; Niki Kilbertus (NeurIPS, 2022)

Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution. - Leon Hetzel; Simon Böhm; Niki Kilbertus; Stephan Günnemann; Mohammad Lotfollahi; Fabian J. Theis (NeurIPS, 2022)

Predicting single-cell perturbation responses for unseen drugs. - Leon Hetzel; Simon Böhm; Niki Kilbertus; Stephan Günnemann; Mohammad Lotfollahi; Fabian J. Theis (CoRR, 2022)

SystemMatch: optimizing preclinical drug models to human clinical outcomes via generative latent-space matching. - Scott Gigante; Varsha G. Raghavan; Amanda M. Robinson; Robert A. Barton; Adeeb H. Rahman; Drausin F. Wulsin; Jacques Banchereau; Noam Solomon; Luis F. Voloch; Fabian J. Theis (CoRR, 2022)

FedNorm: Modality-Based Normalization in Federated Learning for Multi-Modal Liver Segmentation. - Tobias Bernecker; Annette Peters; Christopher L. Schlett; Fabian Bamberg; Fabian J. Theis; Daniel Rueckert; Jakob Weiß; Shadi Albarqouni (CoRR, 2022)

Uncertainty Quantification for Atlas-Level Cell Type Transfer. - Jan P. Engelmann; Leon Hetzel; Giovanni Palla; Lisa Sikkema; Malte Lücken; Fabian J. Theis (CoRR, 2022)

4i dataset for "Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps". - Hannah Spitzer; Scott D. Berry; Lucas Pelkmans; Fabian J. Theis (Zenodo, 2022)

Analysis results reported in "Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps". - Hannah Spitzer; Scott D. Berry; Lucas Pelkmans; Fabian J. Theis (Zenodo, 2022)

B-Cos Aligned Transformers Learn Human-Interpretable Features. - Manuel Tran; Amal Lahiani; Yashin Dicente Cid; Melanie Boxberg; Peter Lienemann; Christian Matek; Sophia J. Wagner; Fabian J. Theis; Eldad Klaiman; Tingying Peng (MICCAI (8), 2023)

Training Transitive and Commutative Multimodal Transformers with LoReTTa. - Manuel Tran; Yashin Dicente Cid; Amal Lahiani; Fabian J. Theis; Tingying Peng; Eldad Klaiman (NeurIPS, 2023)

MAGNet: Motif-Agnostic Generation of Molecules from Shapes. - Leon Hetzel; Johanna Sommer; Bastian Rieck; Fabian J. Theis; Stephan Günnemann (CoRR, 2023)

The power of motifs as inductive bias for learning molecular distributions. - Johanna Sommer; Leon Hetzel; David Lüdke; Fabian J. Theis; Stephan Günnemann (CoRR, 2023)

Conditionally Invariant Representation Learning for Disentangling Cellular Heterogeneity. - Hananeh Aliee; Ferdinand Kapl; Soroor Hediyeh-Zadeh; Fabian J. Theis (CoRR, 2023)

Generative Entropic Neural Optimal Transport To Map Within and Across Spaces. - Dominik Klein 005; Théo Uscidda; Fabian J. Theis; Marco Cuturi (CoRR, 2023)

Causal machine learning for single-cell genomics. - Alejandro Tejada-Lapuerta; Paul Bertin; Stefan Bauer; Hananeh Aliee; Yoshua Bengio; Fabian J. Theis (CoRR, 2023)

Attention-based Multi-instance Mixed Models. - Jan P. Engelmann; Alessandro Palma; Jakub M. Tomczak; Fabian J. Theis; Francesco Paolo Casale (CoRR, 2023)

To Transformers and Beyond: Large Language Models for the Genome. - Micaela E. Consens; Cameron Dufault; Michael Wainberg; Duncan Forster; Mehran Karimzadeh; Hani Goodarzi; Fabian J. Theis; Alan Moses; Bo Wang 044 (CoRR, 2023)

Modeling fragment counts improves single-cell ATAC-seq analysis. - Laura D. Martens; David S. Fischer; Vicente A. Yépez; Fabian J. Theis; Julien Gagneur (Zenodo, 2023)

Multi-omics regulatory network inference in the presence of missing data. - Juan D. Henao; Michael Lauber; Manuel Azevedo; Anastasiia Grekova; Fabian J. Theis; Markus List; Christoph Ogris; Benjamin Schubert (Briefings Bioinform., 2023)

Reporting electricity consumption is essential for sustainable AI. - Charlotte Debus; Marie Piraud; Achim Streit; Fabian J. Theis; Markus Götz (Nat. Mac. Intell., 2023)

Mixed Models with Multiple Instance Learning. - Jan P. Engelmann; Alessandro Palma; Jakub M. Tomczak; Fabian J. Theis; Francesco Paolo Casale (AISTATS, 2024)

Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation. - Luca Eyring; Dominik Klein 005; Théo Uscidda; Giovanni Palla; Niki Kilbertus; Zeynep Akata; Fabian J. Theis (ICLR, 2024)

Unified Guidance for Geometry-Conditioned Molecular Generation. - Sirine Ayadi; Leon Hetzel; Johanna Sommer; Fabian J. Theis; Stephan Günnemann (NeurIPS, 2024)

GENOT: Entropic (Gromov) Wasserstein Flow Matching with Applications to Single-Cell Genomics. - Dominik Klein 005; Théo Uscidda; Fabian J. Theis; Marco Cuturi (NeurIPS, 2024)

A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types. - Artur Szalata; Andrew Benz; Robrecht Cannoodt; Mauricio Cortes; Jason Fong; Sunil Kuppasani; Richard Lieberman; Tianyu Liu; Javier Mas-Rosario; Rico Meinl; Jalil Nourisa; Jared Tumiel; et al. (NeurIPS, 2024)

Single cell transcriptomic analysis of epithelial and mesenchymal tumour cells. - Aristeidis Papargyriou; Till Richter; Malte Luecken; Fabian J. Theis; Maximilian Reichert (Zenodo, 2024)

GraphCompass: spatial metrics for differential analyses of cell organization across conditions. - Mayar Ali; Merel Kuijs; Soroor Hediyeh-Zadeh; Tim Treis; Karin Hrovatin; Giovanni Palla; Anna C. Schaar; Fabian J. Theis (Bioinform., 2024)

Disentangled Representation Learning through Geometry Preservation with the Gromov-Monge Gap. - Théo Uscidda; Luca Eyring; Karsten Roth; Fabian J. Theis; Zeynep Akata; Marco Cuturi (CoRR, 2024)

Generating Multi-Modal and Multi-Attribute Single-Cell Counts with CFGen. - Alessandro Palma; Till Richter; Hanyi Zhang; Manuel Lubetzki; Alexander Tong 001; Andrea Dittadi; Fabian J. Theis (CoRR, 2024)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)

Centaur: a foundation model of human cognition. - Marcel Binz; Elif Akata; Matthias Bethge; Franziska Brändle; Fred Callaway; Julian Coda-Forno; Peter Dayan; Can Demircan; Maria K. Eckstein; Noémi Élteto; Thomas L. Griffiths 001; Susanne Haridi; et al. (CoRR, 2024)

anndata: Access and store annotated data matrices. - Isaac Virshup; Sergei Rybakov; Fabian J. Theis; Philipp Angerer; F. Alexander Wolf (J. Open Source Softw., 2024)

Single cell transcriptomic analysis of epithelial and mesenchymal tumour cells. - Aristeidis Papargyriou; Till Richter; Malte Luecken; Fabian J. Theis; Maximilian Reichert (Zenodo, 2024)

MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery. - Till Siebenmorgen; Filipe Menezes; Sabrina Benassou; Erinc Merdivan; Kieran Didi; André Santos Dias Mourão; Radoslaw Kitel; Pietro Liò; Stefan Kesselheim; Marie Piraud; Fabian J. Theis; Michael Sattler; et al. (Nat. Comput. Sci., 2024)

Code for "Feature selection methods affect the performance of scRNA-seq data integration and querying". - Luke Zappia; Sabrina Richter; Ciro Ramírez-Suástegui; Raphael Kfuri-Rubens; Weixu Wang; Oliver Dietrich; Amit Frishberg; Malte D. Lücken; Fabian J. Theis (Zenodo, 2024)

MAGNet: Motif-Agnostic Generation of Molecules from Scaffolds. - Leon Hetzel; Johanna Sommer; Bastian Rieck; Fabian J. Theis; Stephan Günnemann (ICLR, 2025)

Multi-Modal and Multi-Attribute Generation of Single Cells with CFGen. - Alessandro Palma; Till Richter; Hanyi Zhang; Manuel Lubetzki; Alexander Tong 001; Andrea Dittadi; Fabian J. Theis (ICLR, 2025)

Disentangled Representation Learning with the Gromov-Monge Gap. - Théo Uscidda; Luca Eyring; Karsten Roth; Fabian J. Theis; Zeynep Akata; Marco Cuturi (ICLR, 2025)

TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates. - Kemal Inecik; Aleyna Kara; Antony Rose; Muzlifah Haniffa; Fabian J. Theis (RECOMB, 2025)

Integration and Querying of Multimodal Single-Cell Data with PoE-VAE. - Anastasia Litinetskaya; Maiia Schulman; Fabiola Curion; Artur Szalata; Alireza Omidi; Mohammad Lotfollahi; Fabian J. Theis (RECOMB, 2025)

Transformers and genome language models. - Micaela E. Consens; Cameron Dufault; Michael Wainberg; Duncan Forster; Mehran Karimzadeh; Hani Goodarzi; Fabian J. Theis; Alan Moses; Bo Wang 044 (Nat. Mac. Intell., 2025)

Delineating the effective use of self-supervised learning in single-cell genomics. - Till Richter; Mojtaba Bahrami; Yufan Xia; David S. Fischer; Fabian J. Theis (Nat. Mac. Intell., 2025)

UniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions. - Aayush Grover; Lin Zhang 031; Till Muser; Simeon Haefliger; Minjia Wang; Josephine Yates; Eliezer M. Van Allen; Fabian J. Theis; Ignacio Ibarra; Ekaterina A. Krymova; Valentina Boeva (Zenodo, 2025)

Spatial profiling of human pancreas during type 1 diabetes progression. - Sara Jiménez; Maike Sander; Fabian J. Theis; Kyle Gaulton (Zenodo, 2025)

Embedding computational neurorehabilitation in clinical practice using a modular intelligent health system. - Thomas Weikert; Eljas Roellin; Monica Pérez-Serrano; Elisa Du; Lukas Heumos; Fabian J. Theis; Diego Paez-Granados; Christopher Awai Easthope (CoRR, 2025)

A scalable gene network model of regulatory dynamics in single cells. - Paul Bertin; Joseph D. Viviano; Alejandro Tejada-Lapuerta; Weixu Wang; Stefan Bauer; Fabian J. Theis; Yoshua Bengio (CoRR, 2025)

Targeted AMP generation through controlled diffusion with efficient embeddings. - Diogo Soares; Leon Hetzel; Paulina Szymczak; Fabian J. Theis; Stephan Günnemann; Ewa Szczurek (CoRR, 2025)

A Foundation Model for Spatial Proteomics. - Muhammad Shaban; Yuzhou Chang; Huaying Qiu; Yao Yu Yeo; Andrew H. Song; Guillaume Jaume; Yuchen Wang; Luca L. Weishaupt; Tong Ding; Anurag Vaidya; Abdallah Lamane; Daniel Shao; et al. (CoRR, 2025)

cp_measure: API-first feature extraction for image-based profiling workflows. - Alán F. Muñoz; Tim Treis; Alexandr A. Kalinin; Shatavisha Dasgupta; Fabian J. Theis; Anne E. Carpenter; Shantanu Singh (CoRR, 2025)

Enforcing Latent Euclidean Geometry in Single-Cell VAEs for Manifold Interpolation. - Alessandro Palma; Sergei Rybakov; Leon Hetzel; Stephan Günnemann; Fabian J. Theis (CoRR, 2025)

CellForge: Agentic Design of Virtual Cell Models. - Xiangru Tang; Zhuoyun Yu; Jiapeng Chen; Yan Cui; Daniel Shao; Weixu Wang; Fang Wu; Yuchen Zhuang; Wenqi Shi; Zhi Huang; Arman Cohan; Xihong Lin; et al. (CoRR, 2025)