Publications of 2015

201537 publications

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

   Steffen Sass, Adriana Pitea, Kristian Unger, Julia Hess, Nikola Mueller, Fabian Theis

   International Journal of Molecular SciencesOpen accessDOIPDF
   Topic: Gene regulation

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

   Philipp Angerer, Laleh Haghverdi, Maren Büttner, Fabian J. Theis, Carsten Marr, Florian Buettner

   BioinformaticsOpen accessDOIPDF
   Topic: Open-source software

3. Bayesian Model Selection Methods and Their Application to Biological ODE Systems

   Sabine Hug, Daniel Schmidl, Wei Bo Li, Matthias B. Greiter, Fabian J. Theis

   Studies in Mechanobiology, Tissue Engineering and BiomaterialsBook chapterDOI
   Topic: Statistical inference

4. Identifying latent dynamic components in biological systems

   Ivan Kondofersky, Christiane Fuchs, Fabian J. Theis

   IET Systems BiologyOpen accessDOIPDF
   Topic: Mechanistic modelling

5. Network plasticity of pluripotency transcription factors in embryonic stem cells

   Adam Filipczyk, Carsten Marr, Simon Hastreiter, …, Fabian J. Theis, Timm Schroeder

   Nature Cell BiologyDOI
   Topic: Gene regulation

6. Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy

   Michael K. Strasser, Justin Feigelman, Fabian J. Theis, Carsten Marr

   BMC Systems BiologyOpen accessDOIPDF
   Topic: Statistical inference

7. Separation of Uncorrelated Stationary time series using Autocovariance Matrices

   Jari Miettinen, Katrin Illner, Klaus Nordhausen, Hannu Oja, Sara Taskinen, Fabian J. Theis

   Journal of Time Series AnalysisOpen accessDOI
   Topic: Component analysis and signal separation

8. SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins

   Martin Preusse, Carsten Marr, Sita Saunders, Daniel Maticzka, Heiko Lickert, Rolf Backofen, Fabian Theis

   RNA BiologyOpen accessDOIPDF
   Topic: Gene regulation

9. Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1

   Swanhild U. Meyer, Steffen Sass, Nikola S. Mueller, …, Fabian J. Theis, Michael W. Pfaffl

   PLOS ONEOpen accessDOIPDF
   Topic: Gene regulation

10. Gender-specific pathway differences in the human serum metabolome

    Jan Krumsiek, Kirstin Mittelstrass, Kieu Trinh Do, …, Fabian J. Theis, Gabi Kastenmüller

    MetabolomicsOpen accessDOIPDF
    Topic: Bulk omics and genetics

11. 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 ProcessingDOI
    Topic: Component analysis and signal separation

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

    A. Raue, B. Steiert, M. Schelker, …, F. Theis, …, J. Timmer

    BioinformaticsOpen accessDOIPDF
    Topic: Mechanistic modelling

13. Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes

    Giacomo Masserdotti, Sébastien Gillotin, Bernd Sutor, …, Fabian J. Theis, …, Magdalena Götz

    Cell Stem CellOpen accessDOIPDF
    Topic: Cell fate and dynamics

14. The Human Blood Metabolome-Transcriptome Interface

    Jörg Bartel, Jan Krumsiek, Katharina Schramm, …, Fabian J. Theis

    PLOS GeneticsOpen accessDOIPDF
    Topic: Bulk omics and genetics

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

    Andrea Ocone, Laleh Haghverdi, Nikola S. Mueller, Fabian J. Theis

    BioinformaticsOpen accessDOIPDF
    Topic: Cell fate and dynamics

16. Data-Driven Modelling of Biological Multi-Scale Processes

    Jan Hasenauer, Nick Jagiella, Sabrina Hross, Fabian J. Theis

    Journal of Coupled Systems and Multiscale DynamicsOpen accessDOI
    Topic: Mechanistic modelling

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

    Nicola K. Wilson, David G. Kent, Florian Buettner, …, Fabian J. Theis, Berthold Göttgens

    Cell Stem CellOpen accessDOIPDF
    Topic: Single-cell genomics

18. Opposing effects of allogrooming on disease transmission in ant societies

    Fabian J. Theis, Line V. Ugelvig, Carsten Marr, Sylvia Cremer

    Philosophical Transactions of the Royal Society B: Biological SciencesOpen accessDOIPDF
    Topic: Mechanistic modelling

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

    Laleh Haghverdi, Florian Buettner, Fabian J. Theis

    BioinformaticsOpen accessDOI
    Topic: Cell fate and dynamics

20. Atrx promotes heterochromatin formation at retrotransposons

    Dennis Sadic, Katharina Schmidt, Sophia Groh, Ivan Kondofersky, Joachim Ellwart, Christiane Fuchs, Fabian J Theis, Gunnar Schotta

    The EMBO ReportsOpen accessDOIPDF
    Topic: Gene regulation

21. Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain

    Joana S. Barbosa, Rosario Sanchez-Gonzalez, Rossella Di Giaimo, Emily Violette Baumgart, Fabian J. Theis, Magdalena Götz, Jovica Ninkovic

    ScienceDOI
    Topic: Cell fate and dynamics

22. Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer

    Sören Müller, Susanne Raulefs, Philipp Bruns, …, Fabian J Theis, …, Christoph W Michalski

    Molecular CancerOpen accessDOIPDF
    Topic: Bulk omics and genetics

23. Effects of High-Dose Oral Insulin on Immune Responses in Children at High Risk for Type 1 Diabetes

    Ezio Bonifacio, Anette-G. Ziegler, Georgeanna Klingensmith, …, Peter Achenbach

    JAMADOI
    Topic: Clinical and cohort data

24. A Critical Period for Postnatal Adaptive Plasticity in a Model of Motor Axon Miswiring

    Michaela S. Helmbrecht, Heidi Soellner, Maria A. Castiblanco-Urbina, Stefan Winzeck, Julia Sundermeier, Fabian J. Theis, Karim Fouad, Andrea B. Huber

    PLOS ONEOpen accessDOIPDF
    Topic: Brain and mental health

25. Anatomic-landmark detection using graphical context modelling

    Lichao Wang, Vasileios Belagiannis, Carsten Marr, Fabian Theis, Guang-Zhong Yang, Nassir Navab

    2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)Conference paperOpen accessDOI
    Topic: Imaging

26. Multi-omic signature of body weight change: results from a population-based cohort study

    Simone Wahl, Susanne Vogt, Ferdinand Stückler, …, Fabian J Theis, …, Harald Grallert

    BMC MedicineOpen accessDOIPDF
    Topic: Bulk omics and genetics

27. 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

    Statistics and ComputingDOI
    Topic: Statistical inference

28. Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone

    Filippo Calzolari, Julia Michel, Emily Violette Baumgart, Fabian Theis, Magdalena Götz, Jovica Ninkovic

    Nature NeuroscienceDOI
    Topic: Cell fate and dynamics

29. Decoding the regulatory network of early blood development from single-cell gene expression measurements

    Victoria Moignard, Steven Woodhouse, Laleh Haghverdi, …, Fabian J Theis, …, Berthold Göttgens

    Nature BiotechnologyOpen accessDOIPDF
    Topic: Gene regulation

30. Metabolism gene signatures and surgical site infections in abdominal surgery

    Bo Kong, Philipp Bruns, Susanne Raulefs, …, Fabian J. Theis, …, Jörg Kleeff

    International Journal of SurgeryOpen accessDOI
    Topic: Bulk omics and genetics

31. miR-23a-3p Causes Cellular Senescence by Targeting Hyaluronan Synthase 2: Possible Implication for Skin Aging

    Katharina Röck, Julia Tigges, Steffen Sass, …, Florian J. Theis, …, Jens W. Fischer

    Journal of Investigative DermatologyOpen accessDOI
    Topic: Gene regulation

32. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

    Florian Buettner, Kedar N Natarajan, F Paolo Casale, …, Fabian J Theis, …, Oliver Stegle

    Nature BiotechnologyOpen accessDOIPDF
    Topic: Single-cell genomics

33. A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling

    Bo Kong, Weiwei Wu, Tao Cheng, …, Fabian J Theis, …, Christoph W Michalski

    GutDOI
    Topic: Perturbation responses

34. Quantification of regenerative potential in primary human mammary epithelial cells

    Jelena R. Linnemann, Haruko Miura, Lisa K. Meixner, …, Fabian J. Theis, …, Christina H. Scheel

    DevelopmentOpen accessDOI
    Topic: Cell fate and dynamics

35. Stem-Cell-like Properties and Epithelial Plasticity Arise as Stable Traits after Transient Twist1 Activation

    Johanna M. Schmidt, Elena Panzilius, Harald S. Bartsch, …, Fabian Theis, …, Christina H. Scheel

    Cell ReportsOpen accessDOI
    Topic: Cell fate and dynamics

36. An Affine Equivariant Robust Second-Order BSS Method

    Pauliina Ilmonen, Klaus Nordhausen, Hannu Oja, Fabian Theis

    Lecture Notes in Computer ScienceBook chapterDOI
    Topic: Component analysis and signal separation

37. Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics

    Carolin Loos, Carsten Marr, Fabian J. Theis, Jan Hasenauer

    Lecture Notes in Computer ScienceBook chapterDOI
    Topic: Statistical inference