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ORCIDFabian J. Theis
Person information
- affiliation: Helmholtz Munich, Institute for Computational Biology, Germany
- affiliation: Technical University Munich, Germany
- affiliation (PhD 2002): University of Regensburg, Germany
- affiliation (PhD 2003): University of Granada, Spain
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2020 – today
- 2024
[j86]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, Grzegorz M. Popowicz:
MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery. Nat. Comput. Sci. 4(5): 367-378 (2024)- [c94]Jan P. Engelmann, Alessandro Palma, Jakub M. Tomczak, Fabian J. Theis, Francesco Paolo Casale:
Mixed Models with Multiple Instance Learning. AISTATS 2024: 3664-3672 - [c93]Luca Eyring, Dominik Klein, Théo Uscidda, Giovanni Palla, Niki Kilbertus, Zeynep Akata, Fabian J. Theis:
Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation. ICLR 2024 - [i24]Manuel Tran, Amal Lahiani, Yashin Dicente Cid, Melanie Boxberg, Peter Lienemann, Christian Matek, Sophia J. Wagner, Fabian J. Theis, Eldad Klaiman, Tingying Peng:
B-Cos Aligned Transformers Learn Human-Interpretable Features. CoRR abs/2401.08868 (2024) - [i23]Théo Uscidda, Luca Eyring, Karsten Roth, Fabian J. Theis, Zeynep Akata, Marco Cuturi:
Disentangled Representation Learning through Geometry Preservation with the Gromov-Monge Gap. CoRR abs/2407.07829 (2024) - [i22]Alessandro Palma, Till Richter, Hanyi Zhang, Manuel Lubetzki, Alexander Tong, Andrea Dittadi, Fabian J. Theis:
Generating Multi-Modal and Multi-Attribute Single-Cell Counts with CFGen. CoRR abs/2407.11734 (2024) - 2023
- [j85]Juan D. Henao, Michael Lauber, Manuel Azevedo, Anastasiia Grekova, Fabian J. Theis, Markus List, Christoph Ogris, Benjamin Schubert:
Multi-omics regulatory network inference in the presence of missing data. Briefings Bioinform. 24(5) (2023) - [j84]Charlotte Debus, Marie Piraud, Achim Streit, Fabian J. Theis, Markus Götz:
Reporting electricity consumption is essential for sustainable AI. Nat. Mac. Intell. 5(11): 1176-1178 (2023) - [c92]Manuel Tran, Amal Lahiani, Yashin Dicente Cid, Melanie Boxberg, Peter Lienemann, Christian Matek, Sophia J. Wagner, Fabian J. Theis, Eldad Klaiman, Tingying Peng:
B-Cos Aligned Transformers Learn Human-Interpretable Features. MICCAI (8) 2023: 514-524 - [c91]Manuel Tran, Yashin Dicente Cid, Amal Lahiani, Fabian J. Theis, Tingying Peng, Eldad Klaiman:
Training Transitive and Commutative Multimodal Transformers with LoReTTa. NeurIPS 2023 - [i21]Leon Hetzel, Johanna Sommer, Bastian Rieck, Fabian J. Theis, Stephan Günnemann:
MAGNet: Motif-Agnostic Generation of Molecules from Shapes. CoRR abs/2305.19303 (2023) - [i20]Johanna Sommer, Leon Hetzel, David Lüdke, Fabian J. Theis, Stephan Günnemann:
The power of motifs as inductive bias for learning molecular distributions. CoRR abs/2306.17246 (2023) - [i19]Hananeh Aliee, Ferdinand Kapl, Soroor Hediyeh-Zadeh, Fabian J. Theis:
Conditionally Invariant Representation Learning for Disentangling Cellular Heterogeneity. CoRR abs/2307.00558 (2023) - [i18]Dominik Klein, Théo Uscidda, Fabian J. Theis, Marco Cuturi:
Generative Entropic Neural Optimal Transport To Map Within and Across Spaces. CoRR abs/2310.09254 (2023) - [i17]Alejandro Tejada-Lapuerta, Paul Bertin, Stefan Bauer, Hananeh Aliee, Yoshua Bengio, Fabian J. Theis:
Causal machine learning for single-cell genomics. CoRR abs/2310.14935 (2023) - [i16]Jan P. Engelmann, Alessandro Palma, Jakub M. Tomczak, Fabian J. Theis, Francesco Paolo Casale:
Attention-based Multi-instance Mixed Models. CoRR abs/2311.02455 (2023) - [i15]Micaela E. Consens, Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi, Fabian J. Theis, Alan Moses, Bo Wang:
To Transformers and Beyond: Large Language Models for the Genome. CoRR abs/2311.07621 (2023) - [i14]Luca Eyring, Dominik Klein, Théo Uscidda, Giovanni Palla, Niki Kilbertus, Zeynep Akata, Fabian J. Theis:
Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation. CoRR abs/2311.15100 (2023) - 2022
- [c90]Valentin Koch, Olle G. Holmberg, Hannah Spitzer, Johannes Schiefelbein, Ben Asani, Michael Hafner, Fabian J. Theis:
Noise Transfer for Unsupervised Domain Adaptation of Retinal OCT Images. MICCAI (2) 2022: 699-708 - [c89]Hananeh Aliee, Till Richter, Mikhail Solonin, Ignacio Ibarra, Fabian J. Theis, Niki Kilbertus:
Sparsity in Continuous-Depth Neural Networks. NeurIPS 2022 - [c88]Leon Hetzel, Simon Böhm, Niki Kilbertus, Stephan Günnemann, Mohammad Lotfollahi, Fabian J. Theis:
Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution. NeurIPS 2022 - [i13]Leon Hetzel, Simon Böhm, Niki Kilbertus, Stephan Günnemann, Mohammad Lotfollahi, Fabian J. Theis:
Predicting single-cell perturbation responses for unseen drugs. CoRR abs/2204.13545 (2022) - [i12]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:
SystemMatch: optimizing preclinical drug models to human clinical outcomes via generative latent-space matching. CoRR abs/2205.07110 (2022) - [i11]Tobias Bernecker, Annette Peters, Christopher L. Schlett, Fabian Bamberg, Fabian J. Theis, Daniel Rueckert, Jakob Weiß, Shadi Albarqouni:
FedNorm: Modality-Based Normalization in Federated Learning for Multi-Modal Liver Segmentation. CoRR abs/2205.11096 (2022) - [i10]Valentin Koch, Olle G. Holmberg, Hannah Spitzer, Johannes Schiefelbein, Ben Asani, Michael Hafner, Fabian J. Theis:
Noise transfer for unsupervised domain adaptation of retinal OCT images. CoRR abs/2209.08097 (2022) - [i9]Hananeh Aliee, Till Richter, Mikhail Solonin, Ignacio Ibarra, Fabian J. Theis, Niki Kilbertus:
Sparsity in Continuous-Depth Neural Networks. CoRR abs/2210.14672 (2022) - [i8]Jan P. Engelmann, Leon Hetzel, Giovanni Palla, Lisa Sikkema, Malte Lücken, Fabian J. Theis:
Uncertainty Quantification for Atlas-Level Cell Type Transfer. CoRR abs/2211.03793 (2022) - 2021
- [c87]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, Nikolay Russkikh, Gleb Ryazantsev, Uwe Ohler, Angela Oliveira Pisco, Jonathan Bloom, Smita Krishnaswamy, Fabian J. Theis:
Multimodal single cell data integration challenge: Results and lessons learned. NeurIPS (Competition and Demos) 2021: 162-176 - [c86]Malte Lücken, Daniel Burkhardt, Robrecht Cannoodt, Christopher Lance, Aditi Agrawal, Hananeh Aliee, Ann Chen, Louise Deconinck, Angela Detweiler, Alejandro Granados, Shelly Huynh, Laura Isacco, Yang Kim, Dominik Klein, Bony de Kumar, Sunil Kuppasani, Heiko Lickert, Aaron McGeever, Joaquin Melgarejo, Honey Mekonen, Maurizio Morri, Michaela Müller, Norma Neff, Sheryl Paul, Bastian Rieck, Kaylie Schneider, Scott Steelman, Michael Sterr, Daniel Treacy, Alexander Tong, Alexandra-Chloé Villani, Guilin Wang, Jia Yan, Ce Zhang, Angela Pisco, Smita Krishnaswamy, Fabian J. Theis, Jonathan M. Bloom:
A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. NeurIPS Datasets and Benchmarks 2021 - [i7]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, Jean Y. H. Yang, Elana J. Fertig:
A field guide to cultivating computational biology. CoRR abs/2104.11364 (2021) - [i6]Hananeh Aliee, Fabian J. Theis, Niki Kilbertus:
Beyond Predictions in Neural ODEs: Identification and Interventions. CoRR abs/2106.12430 (2021) - 2020
- [j83]Adriana Pitea, Ivan Kondofersky, Steffen Sass, Fabian J. Theis, Nikola S. Müller, Kristian Unger:
Copy number aberrations from Affymetrix SNP 6.0 genotyping data - how accurate are commonly used prediction approaches? Briefings Bioinform. 21(1): 272-281 (2020) - [j82]Philipp Angerer, David S. Fischer, Fabian J. Theis, Antonio Scialdone, Carsten Marr:
Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data. Bioinform. 36(15): 4291-4295 (2020) - [j81]Fabian J. Theis, Thomas Ludwig:
Munich School for Data Science (MUDS) - Eine Graduiertenschule für Data Science in München. Inform. Spektrum 42(6): 429-431 (2020) - [j80]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:
Self-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy. Nat. Mach. Intell. 2(11): 719-726 (2020) - [j79]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, Friedemann Paul, Heinz Wiendl, Christian Gieger, Stefanie Heilmann-Heimbach, Tim Kacprowski, Matthias Laudes, Thomas Meitinger, Annette Peters, Rajesh Rawal, Konstantin Strauch, Susanne Lucae, Bertram Müller-Myhsok, Marcella Rietschel, Fabian J. Theis, Elisabeth B. Binder, Nikola S. Müller:
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning. PLoS Comput. Biol. 16(2) (2020) - [j78]Elba Raimúndez-Álvarez, Simone Keller, Gwen Zwingenberger, Karolin Ebert, Sabine Hug, Fabian J. Theis, Dieter Maier, Birgit Luber, Jan Hasenauer:
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines. PLoS Comput. Biol. 16(3) (2020) - [c85]Meshal Ansari, David S. Fischer, Fabian J. Theis:
Learning Tn5 Sequence Bias from ATAC-seq on Naked Chromatin. ICANN (1) 2020: 105-114
2010 – 2019
- 2019
- [e6]Igor V. Tetko, Vera Kurková, Pavel Karpov, Fabian J. Theis:
Artificial Neural Networks and Machine Learning - ICANN 2019: Theoretical Neural Computation - 28th International Conference on Artificial Neural Networks, Munich, Germany, September 17-19, 2019, Proceedings, Part I. Lecture Notes in Computer Science 11727, Springer 2019, ISBN 978-3-030-30486-7 [contents] - [e5]Igor V. Tetko, Vera Kurková, Pavel Karpov, Fabian J. Theis:
Artificial Neural Networks and Machine Learning - ICANN 2019: Deep Learning - 28th International Conference on Artificial Neural Networks, Munich, Germany, September 17-19, 2019, Proceedings, Part II. Lecture Notes in Computer Science 11728, Springer 2019, ISBN 978-3-030-30483-6 [contents] - [e4]Igor V. Tetko, Vera Kurková, Pavel Karpov, Fabian J. Theis:
Artificial Neural Networks and Machine Learning - ICANN 2019: Image Processing - 28th International Conference on Artificial Neural Networks, Munich, Germany, September 17-19, 2019, Proceedings, Part III. Lecture Notes in Computer Science 11729, Springer 2019, ISBN 978-3-030-30507-9 [contents] - [e3]Igor V. Tetko, Vera Kurková, Pavel Karpov, Fabian J. Theis:
Artificial Neural Networks and Machine Learning - ICANN 2019: Text and Time Series - 28th International Conference on Artificial Neural Networks, Munich, Germany, September 17-19, 2019, Proceedings, Part IV. Lecture Notes in Computer Science 11730, Springer 2019, ISBN 978-3-030-30489-8 [contents] - [e2]Igor V. Tetko, Vera Kurková, Pavel Karpov, Fabian J. Theis:
Artificial Neural Networks and Machine Learning - ICANN 2019 - 28th International Conference on Artificial Neural Networks, Munich, Germany, September 17-19, 2019, Proceedings - Workshop and Special Sessions. Lecture Notes in Computer Science 11731, Springer 2019, ISBN 978-3-030-30492-8 [contents] - [i5]Mohammad Lotfollahi, Mohsen Naghipourfar, Fabian J. Theis, F. Alexander Wolf:
Conditional out-of-sample generation for unpaired data using trVAE. CoRR abs/1910.01791 (2019) - [i4]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, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth:
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7: e27885 (2019) - 2018
- [j77]Simon Dirmeier, Christiane Fuchs, Nikola S. Müller, Fabian J. Theis:
netReg: network-regularized linear models for biological association studies. Bioinform. 34(5): 896-898 (2018) - [j76]Benjamin Ballnus, Steffen Schaper, Fabian J. Theis, Jan Hasenauer:
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering. Bioinform. 34(13): i494-i501 (2018) - [c84]Justin Feigelman, Daniel Weindl, Fabian J. Theis, Carsten Marr, Jan Hasenauer:
LNA++: Linear Noise Approximation with First and Second Order Sensitivities. CMSB 2018: 300-306 - [d1]Fabian Fröhlich, Anita Reiser, Laura Fink, Daniel Woschée, Thomas S. Ligon, Fabian J. Theis, Joachim O. Rädler, Jan Hasenauer:
Supplementary Code to Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection. Zenodo, 2018
- 2017
- [j75]Fabian Fröhlich, Fabian J. Theis, Joachim O. Rädler, Jan Hasenauer:
Parameter estimation for dynamical systems with discrete events and logical operations. Bioinform. 33(7): 1049-1056 (2017) - [j74]Oliver Hilsenbeck, Michael Schwarzfischer, Dirk Loeffler, Sotiris Dimopoulos, Simon Hastreiter, Carsten Marr, Fabian J. Theis, Timm Schroeder:
fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy. Bioinform. 33(13): 2020-2028 (2017) - [j73]Atefeh Kazeroonian, Fabian J. Theis, Jan Hasenauer:
A scalable moment-closure approximation for large-scale biochemical reaction networks. Bioinform. 33(14): i293-i300 (2017) - [j72]Nikolaos-Kosmas Chlis, F. Alexander Wolf, Fabian J. Theis:
Model-based branching point detection in single-cell data by K-branches clustering. Bioinform. 33(20): 3211-3219 (2017) - [j71]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, Harald Grallert, Fabian J. Theis, Christian Gieger:
pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. BMC Bioinform. 18(1): 429:1-429:8 (2017) - [j70]Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer, Fabian J. Theis:
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems. BMC Syst. Biol. 11(1): 63:1-63:18 (2017) - [j69]Norbert Krautenbacher, Fabian J. Theis, Christiane Fuchs:
Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies. Comput. Math. Methods Medicine 2017: 7847531:1-7847531:18 (2017) - [j68]Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer:
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput. Biol. 13(1) (2017) - 2016
- [j67]Philipp Angerer, Laleh Haghverdi, Maren Büttner, Fabian J. Theis, Carsten Marr, Florian A. Büttner:
destiny: diffusion maps for large-scale single-cell data in R. Bioinform. 32(8): 1241-1243 (2016) - [j66]Eva-Maria Geissen, Jan Hasenauer, Stephanie Heinrich, Silke Hauf, Fabian J. Theis, Nicole Radde:
MEMO: multi-experiment mixture model analysis of censored data. Bioinform. 32(16): 2464-2472 (2016) - [j65]Anna Fiedler, Sebastian Raeth, Fabian J. Theis, Angelika Hausser, Jan Hasenauer:
Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints. BMC Syst. Biol. 10: 80 (2016) - [j64]Michael Laimighofer, Jan Krumsiek, Florian A. Büttner, Fabian J. Theis:
Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression. J. Comput. Biol. 23(4): 279-290 (2016) - [j63]Fabian Fröhlich, Philipp Thomas, Atefeh Kazeroonian, Fabian J. Theis, Ramon Grima, Jan Hasenauer:
Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. PLoS Comput. Biol. 12(7) (2016) - [j62]Sabine Hug, Michael Schwarzfischer, Jan Hasenauer, Carsten Marr, Fabian J. Theis:
An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson's rule. Stat. Comput. 26(3): 663-677 (2016) - [c83]Gerda Bortsova, Michael Sterr, Lichao Wang, Fausto Milletari, Nassir Navab, Anika Böttcher, Heiko Lickert, Fabian J. Theis, Tingying Peng:
Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields. MLMI@MICCAI 2016: 287-295 - [i3]Gerda Bortsova, Michael Sterr, Lichao Wang, Fausto Milletari, Nassir Navab, Anika Böttcher, Heiko Lickert, Fabian J. Theis, Tingying Peng:
Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields. CoRR abs/1608.07616 (2016) - 2015
- [j61]Steffen Sass, Florian Buettner, Nikola S. Müller, Fabian J. Theis:
RAMONA: a Web application for gene set analysis on multilevel omics data. Bioinform. 31(1): 128-130 (2015) - [j60]Andrea Ocone, Laleh Haghverdi, Nikola S. Müller, Fabian J. Theis:
Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. Bioinform. 31(12): 89-96 (2015) - [j59]Laleh Haghverdi, Florian Buettner, Fabian J. Theis:
Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinform. 31(18): 2989-2998 (2015) - [j58]Andreas Raue, Bernhard Steiert, Max Schelker, Clemens Kreutz, Tim Maiwald, Helge Hass, Joep Vanlier, Christian Tönsing, Lorenz Adlung, Raphael Engesser, Wolfgang Mader, Tim Heinemann, Jan Hasenauer, Marcel Schilling, Thomas Höfer, Edda Klipp, Fabian J. Theis, Ursula Klingmüller, Birgit Schoeberl, Jens Timmer:
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinform. 31(21): 3558-3560 (2015) - [j57]Michael K. Strasser, Justin Feigelman, Fabian J. Theis, Carsten Marr:
Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy. BMC Syst. Biol. 9: 61 (2015) - [j56]Katrin Illner, Jari Miettinen, Christiane Fuchs, Sara Taskinen, Klaus Nordhausen, Hannu Oja, Fabian J. Theis:
Model selection using limiting distributions of second-order blind source separation algorithms. Signal Process. 113: 95-103 (2015) - [c82]Carolin Loos, Carsten Marr, Fabian J. Theis, Jan Hasenauer:
Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics. CMSB 2015: 52-63 - [c81]Pauliina Ilmonen, Klaus Nordhausen, Hannu Oja, Fabian J. Theis:
An Affine Equivariant Robust Second-Order BSS Method. LVA/ICA 2015: 328-335 - [c80]Lichao Wang, Vasileios Belagiannis, Carsten Marr, Fabian J. Theis, Guang-Zhong Yang, Nassir Navab:
Anatomic-landmark detection using graphical context modelling. ISBI 2015: 1304-1307 - 2014
- [j55]Michaela Matthes, Martin Preusse, Jingzhong Zhang, Julia Schechter, Daniela Mayer, Bernd Lentes, Fabian J. Theis, Nilima Prakash, Wolfgang Wurst, Dietrich Trümbach:
Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain. Database J. Biol. Databases Curation 2014 (2014) - [j54]Florian Buettner, Victoria Moignard, Berthold Göttgens, Fabian J. Theis:
Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. Bioinform. 30(13): 1867-1875 (2014) - [j53]Justin Feigelman, Fabian J. Theis, Carsten Marr:
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data. BMC Bioinform. 15: 240 (2014) - [j52]Katrin Illner, Christiane Fuchs, Fabian J. Theis:
Bayesian Blind Source Separation for Data with Network Structure. J. Comput. Biol. 21(11): 855-865 (2014) - [j51]Jan Hasenauer, Christine Hasenauer, Tim Hucho, Fabian J. Theis:
ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics. PLoS Comput. Biol. 10(7) (2014) - [c79]Fabian Fröhlich, Fabian J. Theis, Jan Hasenauer:
Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More. CMSB 2014: 61-72 - [c78]Fabian Fröhlich, Sabrina Hross, Fabian J. Theis, Jan Hasenauer:
Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis. CMSB 2014: 73-85 - [c77]Valeriy Khakhutskyy, Michael Schwarzfischer, Nina C. Hubig, Claudia Plant, Carsten Marr, Michael A. Rieger, Timm Schroeder, Fabian J. Theis:
Centroid Clustering of Cellular Lineage Trees. ITBAM 2014: 15-29 - [i2]Justin Feigelman, Fabian J. Theis, Carsten Marr:
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data. CoRR abs/1407.2112 (2014) - 2013
- [j50]Felix Buggenthin, Carsten Marr, Michael Schwarzfischer, Philipp S. Hoppe, Oliver Hilsenbeck, Timm Schroeder, Fabian J. Theis:
An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. BMC Bioinform. 14: 297 (2013) - [j49]Sabrina Hock, Jan Hasenauer, Fabian J. Theis:
Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis. BMC Bioinform. 14(S-10): S7 (2013) - [j48]Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Andreas Raue, Sabine Hug, Jens Timmer, Nicole Radde, Fabian J. Theis, Daniel Weiskopf:
iVUN: interactive Visualization of Uncertain biochemical reaction Networks. BMC Bioinform. 14(S-19): S2 (2013) - [j47]Sabrina Hock, Yen-Kar Ng, Jan Hasenauer, Dominik M. Wittmann, Dominik Lutter, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash, Fabian J. Theis:
Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation. BMC Syst. Biol. 7: 48 (2013) - [j46]Ercan E. Kuruoglu, Fabian J. Theis:
Dependent component analysis. EURASIP J. Adv. Signal Process. 2013: 185 (2013) - [j45]Dominik M. Wittmann, Sabrina Hock, Fabian J. Theis:
Truth-Content and Phase Transitions of Random Boolean Networks with Generic Logics. SIAM J. Appl. Dyn. Syst. 12(1): 315-351 (2013) - [c76]Corinna Vehlow, Jan Hasenauer, Fabian J. Theis, Daniel Weiskopf:
Visualizing edge-edge relations in graphs. PacificVis 2013: 201-208 - 2012
- [j44]Claudia Plant, Son Thai Mai, Junming Shao, Fabian J. Theis, Anke Meyer-Baese, Christian Böhm:
Measuring Non-Gaussianity by Phi-Transformed and Fuzzy Histograms. Adv. Artif. Neural Syst. 2012: 962105:1-962105:13 (2012) - [j43]Florian Buettner, Fabian J. Theis:
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Bioinform. 28(18): 626-632 (2012) - [j42]Ann-Kristin Petersen, Jan Krumsiek, Brigitte Wägele, Fabian J. Theis, Heinz-Erich Wichmann, Christian Gieger, Karsten Suhre:
On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. BMC Bioinform. 13: 120 (2012) - [j41]Daniel Schmidl, Sabine Hug, Wei Li, Matthias B. Greiter, Fabian J. Theis:
Bayesian model selection validates a biokinetic model for zirconium processing in humans. BMC Syst. Biol. 6: 95 (2012) - [j40]Harold W. Gutch, Fabian J. Theis:
Uniqueness of linear factorizations into independent subspaces. J. Multivar. Anal. 112: 48-62 (2012) - [j39]Harold W. Gutch, Peter Gruber, Arie Yeredor, Fabian J. Theis:
ICA over finite fields - Separability and algorithms. Signal Process. 92(8): 1796-1808 (2012) - [j38]Emmanuel Vincent, Shoko Araki, Fabian J. Theis, Guido Nolte, Pau Bofill, Hiroshi Sawada, Alexey Ozerov, Vikrham Gowreesunker, Dominik Lutter, Ngoc Q. K. Duong:
The signal separation evaluation campaign (2007-2010): Achievements and remaining challenges. Signal Process. 92(8): 1928-1936 (2012) - [c75]Klaus Nordhausen, Harold W. Gutch, Hannu Oja, Fabian J. Theis:
Joint Diagonalization of Several Scatter Matrices for ICA. LVA/ICA 2012: 172-179 - [c74]Harold W. Gutch, Fabian J. Theis:
To Infinity and Beyond: On ICA over Hilbert Spaces. LVA/ICA 2012: 180-187 - [c73]Sabine Hug, Fabian J. Theis:
Bayesian Inference of Latent Causes in Gene Regulatory Dynamics. LVA/ICA 2012: 520-527 - [c72]Fabian J. Theis:
Bayesian Fuzzy Clustering of Colored Graphs. LVA/ICA 2012: 528-535 - [e1]