Publications by authors named "Fabian J Theis"

100Publications

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

Mol Syst Biol 2020 Aug;16(8):e9416

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.

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http://dx.doi.org/10.15252/msb.20199416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418512PMC
August 2020

Generalizing RNA velocity to transient cell states through dynamical modeling.

Nat Biotechnol 2020 Aug 3. Epub 2020 Aug 3.

Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.

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http://dx.doi.org/10.1038/s41587-020-0591-3DOI Listing
August 2020

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

Nat Commun 2020 06 17;11(1):3068. Epub 2020 Jun 17.

Helmholtz Zentrum München, Institute of Lung Biology and Disease, Regenerative Biology and Medicine, Member of the German Center for Lung Research (DZL), Munich, Germany.

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http://dx.doi.org/10.1038/s41467-020-16893-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7299976PMC
June 2020

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

Cell 2020 05 27;181(5):1016-1035.e19. Epub 2020 Apr 27.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.04.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252096PMC
May 2020

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

Bioinformatics 2020 Aug;36(15):4291-4295

Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btaa198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520047PMC
August 2020

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

PLoS Comput Biol 2020 03 2;16(3):e1007147. Epub 2020 Mar 2.

Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1007147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067490PMC
March 2020

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

Curr Biol 2020 Mar 27;30(6):1142-1151.e6. Epub 2020 Feb 27.

Research Unit of Sensory Biology & Organogenesis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2020.01.027DOI Listing
March 2020

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

Mol Metab 2019 12 24;30:16-29. Epub 2019 Sep 24.

Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764, Neuherberg, Germany; German Center for Diabetes Research (DZD), D-85764, Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764, Neuherberg, Germany; Technical University of Munich, School of Medicine, Munich, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.molmet.2019.09.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6812400PMC
December 2019

MPRAnalyze: statistical framework for massively parallel reporter assays.

Genome Biol 2019 09 2;20(1):183. Epub 2019 Sep 2.

Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1186/s13059-019-1787-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717970PMC
September 2019

scGen predicts single-cell perturbation responses.

Nat Methods 2019 08 29;16(8):715-721. Epub 2019 Jul 29.

Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.

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http://dx.doi.org/10.1038/s41592-019-0494-8DOI Listing
August 2019

scSLAM-seq reveals core features of transcription dynamics in single cells.

Nature 2019 07 10;571(7765):419-423. Epub 2019 Jul 10.

Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1038/s41586-019-1369-yDOI Listing
July 2019

Inferring Interaction Networks From Multi-Omics Data.

Front Genet 2019 12;10:535. Epub 2019 Jun 12.

Institute of Computational Biology, HelmholtzZentrum München, Munich, Germany.

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http://dx.doi.org/10.3389/fgene.2019.00535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582773PMC
June 2019

Concepts and limitations for learning developmental trajectories from single cell genomics.

Development 2019 06 27;146(12). Epub 2019 Jun 27.

Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany

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http://dx.doi.org/10.1242/dev.170506DOI Listing
June 2019

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

Mol Syst Biol 2019 06 19;15(6):e8746. Epub 2019 Jun 19.

Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany

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http://dx.doi.org/10.15252/msb.20188746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582955PMC
June 2019

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

Development 2019 06 17;146(12). Epub 2019 Jun 17.

Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany

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http://dx.doi.org/10.1242/dev.173849DOI Listing
June 2019

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

PLoS One 2019 23;14(5):e0216110. Epub 2019 May 23.

Chair of Nutritional Medicine, Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216110PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532850PMC
January 2020

Deep learning: new computational modelling techniques for genomics.

Nat Rev Genet 2019 07;20(7):389-403

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.

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http://www.nature.com/articles/s41576-019-0122-6
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http://dx.doi.org/10.1038/s41576-019-0122-6DOI Listing
July 2019

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

J R Soc Interface 2018 12;15(149):20180600

1 Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health , München , Germany.

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http://dx.doi.org/10.1098/rsif.2018.0600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303801PMC
December 2018

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

Genome Biol 2019 03 19;20(1):59. Epub 2019 Mar 19.

Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany.

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http://dx.doi.org/10.1186/s13059-019-1663-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425583PMC
March 2019

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

Nat Commun 2019 01 23;10(1):390. Epub 2019 Jan 23.

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.

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http://www.nature.com/articles/s41467-018-07931-2
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http://dx.doi.org/10.1038/s41467-018-07931-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344535PMC
January 2019

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

Nat Methods 2019 01 20;16(1):43-49. Epub 2018 Dec 20.

Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.

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http://www.nature.com/articles/s41592-018-0254-1
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http://dx.doi.org/10.1038/s41592-018-0254-1DOI Listing
January 2019

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

Cell Rep 2018 12;25(12):3231-3240.e8

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.11.088DOI Listing
December 2018

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

Cell Syst 2018 12 28;7(6):567-579.e6. Epub 2018 Nov 28.

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany; Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching 85748, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.10.013DOI Listing
December 2018

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

Exp Clin Endocrinol Diabetes 2020 Jan 5;128(1):20-29. Epub 2018 Nov 5.

German Center for Diabetes Research (DZD), Neuherberg, Germany.

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http://www.thieme-connect.de/DOI/DOI?10.1055/a-0735-9533
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http://dx.doi.org/10.1055/a-0735-9533DOI Listing
January 2020

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

Brief Bioinform 2018 Oct 23. Epub 2018 Oct 23.

Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany.

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http://dx.doi.org/10.1093/bib/bby096DOI Listing
October 2018

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

Nucleic Acids Res 2018 11;46(20):e119

Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gky675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237758PMC
November 2018

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

Nat Commun 2018 07 12;9(1):2697. Epub 2018 Jul 12.

Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.

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http://dx.doi.org/10.1038/s41467-018-05037-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043612PMC
July 2018

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

Bioinformatics 2018 07;34(13):i494-i501

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022572PMC
July 2018

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

Stem Cell Reports 2018 07 17;11(1):58-69. Epub 2018 May 17.

Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; Research Unit Stem Cell Dynamics, Helmholtz Zentrum München, 85764 Neuherberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2018.04.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6066909PMC
July 2018

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

Science 2018 05 19;360(6391). Epub 2018 Apr 19.

Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.

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http://dx.doi.org/10.1126/science.aaq1723DOI Listing
May 2018

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

Genome Biol 2018 02 6;19(1):15. Epub 2018 Feb 6.

Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Munich, Neuherberg, Germany.

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http://dx.doi.org/10.1186/s13059-017-1382-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802054PMC
February 2018

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

Comput Math Methods Med 2017 24;2017:7847531. Epub 2017 Sep 24.

Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany.

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http://dx.doi.org/10.1155/2017/7847531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5632994PMC
September 2018

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

Bioinformatics 2018 03;34(5):896-898

Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030897PMC
March 2018

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

Mol Metab 2017 09 20;6(9):974-990. Epub 2017 Jul 20.

Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Am Parkring 11, 85748 Garching-Hochbrück, Germany.

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http://dx.doi.org/10.1016/j.molmet.2017.06.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605721PMC
September 2017

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

Bioinformatics 2017 Jul;33(14):i293-i300

Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.

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https://academic.oup.com/bioinformatics/article/33/14/i293/3
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http://dx.doi.org/10.1093/bioinformatics/btx249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870627PMC
July 2017

Reconstructing cell cycle and disease progression using deep learning.

Nat Commun 2017 09 6;8(1):463. Epub 2017 Sep 6.

Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany.

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http://dx.doi.org/10.1038/s41467-017-00623-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587733PMC
September 2017

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

Pediatr Diabetes 2018 03 11;19(2):277-283. Epub 2017 Jul 11.

Barbara Davis Center for Childhood Diabetes, School of Medicine, University of Colorado, Aurora, Colorado.

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http://dx.doi.org/10.1111/pedi.12543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764829PMC
March 2018

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems.

BMC Syst Biol 2017 Jun 24;11(1):63. Epub 2017 Jun 24.

Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.

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http://dx.doi.org/10.1186/s12918-017-0433-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482939PMC
June 2017

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

Nat Commun 2017 06 8;8:14836. Epub 2017 Jun 8.

Department of Computer Science, Chair of Computer Aided Medical Procedure, Technische Universität München, Boltzmannstr. 3, Garching 85748, Germany.

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http://dx.doi.org/10.1038/ncomms14836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472168PMC
June 2017

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

Bioinformatics 2017 Oct;33(20):3211-3219

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860029PMC
October 2017

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

Sci Rep 2017 04 6;7:46026. Epub 2017 Apr 6.

Early origins of chronic lung disease, Priority Area Asthma &Allergy, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany.

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http://dx.doi.org/10.1038/srep46026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5382551PMC
April 2017

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

Bioinformatics 2017 Jul;33(13):2020-2028

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btx107DOI Listing
July 2017

Prospective identification of hematopoietic lineage choice by deep learning.

Nat Methods 2017 Apr 20;14(4):403-406. Epub 2017 Feb 20.

Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.1038/nmeth.4182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376497PMC
April 2017

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

Phys Biol 2017 05 11;14(3):036001. Epub 2017 May 11.

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany. Department of Mathematics, Technische Universität München, Garching, Germany.

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http://dx.doi.org/10.1088/1478-3975/aa609aDOI Listing
May 2017

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.

PLoS Comput Biol 2017 01 23;13(1):e1005331. Epub 2017 Jan 23.

Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1005331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5256869PMC
January 2017

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

Cell Syst 2017 02 11;4(2):194-206.e9. Epub 2017 Jan 11.

Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Chair of Mathematical Modeling of Biological Systems, Center for Mathematics, Technische Universität München, Boltzmannstraße 3, 85748 Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.12.002DOI Listing
February 2017

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

Bioinformatics 2017 04;33(7):1049-1056

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw764DOI Listing
April 2017

Inferring catalysis in biological systems.

IET Syst Biol 2016 Dec;10(6):210-218

Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Boltzmannstr. 3, 85748 Garching, Germany.

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http://dx.doi.org/10.1049/iet-syb.2015.0087DOI Listing
December 2016

Peptide serum markers in islet autoantibody-positive children.

Diabetologia 2017 02 4;60(2):287-295. Epub 2016 Nov 4.

Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764, München, Germany.

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http://dx.doi.org/10.1007/s00125-016-4150-xDOI Listing
February 2017

Diffusion pseudotime robustly reconstructs lineage branching.

Nat Methods 2016 10 29;13(10):845-8. Epub 2016 Aug 29.

Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.

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http://www.nature.com/articles/nmeth.3971
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http://dx.doi.org/10.1038/nmeth.3971DOI Listing
October 2016

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

BMC Syst Biol 2016 08 22;10(1):80. Epub 2016 Aug 22.

Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918
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http://dx.doi.org/10.1186/s12918-016-0319-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4994295PMC
August 2016

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

PLoS Comput Biol 2016 07 22;12(7):e1005030. Epub 2016 Jul 22.

Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1005030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4957800PMC
July 2016

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

J Allergy Clin Immunol 2016 10 13;138(4):1207-1210.e2. Epub 2016 May 13.

ZAUM - Center of Allergy and Environment, Technische Universität and Helmholtz Center Munich, Member of the German Center for Lung Research (DZL), Munich, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2016.04.018DOI Listing
October 2016

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

Curr Opin Biotechnol 2016 06 9;39:iv-vi. Epub 2016 May 9.

Institute of Computational Biology, Helmholtz Zentrum, München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Computational, Biology Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Department of Mathematics Technical University of Munich Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85748 Garching bei München, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09581669163013
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http://dx.doi.org/10.1016/j.copbio.2016.04.025DOI Listing
June 2016

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

Bioinformatics 2016 08 19;32(16):2464-72. Epub 2016 Apr 19.

Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart 70550, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978932PMC
August 2016

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

Cell Syst 2016 01 27;2(1):49-58. Epub 2016 Jan 27.

Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.01.002DOI Listing
January 2016

Computational approaches for systems metabolomics.

Curr Opin Biotechnol 2016 06 30;39:198-206. Epub 2016 Apr 30.

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany; Department of Mathematics, Technische Universität München, Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2016.04.009DOI Listing
June 2016

miTALOS v2: Analyzing Tissue Specific microRNA Function.

PLoS One 2016 21;11(3):e0151771. Epub 2016 Mar 21.

Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801359PMC
August 2016

Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression.

J Comput Biol 2016 Apr 19;23(4):279-90. Epub 2016 Feb 19.

1 Institute of Computational Biology , Helmholtz-Zentrum München, Neuherberg, Germany .

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http://dx.doi.org/10.1089/cmb.2015.0192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827277PMC
April 2016

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

PLoS One 2016 25;11(1):e0146732. Epub 2016 Jan 25.

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4726759PMC
July 2016

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

Nat Commun 2016 Jan 7;7:10256. Epub 2016 Jan 7.

Imaging Platform at the Broad Institute of Harvard and MIT, 415 Main St, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/ncomms10256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729834PMC
January 2016

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

Biomol Detect Quantif 2017 Mar 21;11:31-44. Epub 2016 Nov 21.

Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.

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http://dx.doi.org/10.1016/j.bdq.2016.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348118PMC
March 2017

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

Int J Mol Sci 2015 Dec 18;16(12):30204-22. Epub 2015 Dec 18.

Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.

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December 2015