Publications of 2017

201734 publications

1. The Human Cell Atlas

   Aviv Regev, Sarah A Teichmann, Eric S Lander, …, Fabian J Theis, …, Human Cell Atlas Meeting Participants

   eLifeOpen accessDOIPDF
   Topic: Cell atlases

2. Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway

   Elisa Benedetti, Maja Pučić-Baković, Toma Keser, …, Fabian J. Theis, …, Jan Krumsiek

   Nature CommunicationsOpen accessDOIPDF
   Topic: Networks and graphs

3. GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency

   Christian Krendl, Dmitry Shaposhnikov, Valentyna Rishko, …, Fabian J. Theis, Micha Drukker

   Proceedings of the National Academy of SciencesOpen accessDOIPDF
   Topic: Cell fate and dynamics

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

   Simon Dirmeier, Christiane Fuchs, Nikola S Mueller, Fabian J Theis

   BioinformaticsOpen accessDOIPDF
   Topic: Open-source software

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

   Svantje Sobotta, Andreas Raue, Xiaoyun Huang, …, Fabian J. Theis, …, Ursula Klingmüller

   Frontiers in PhysiologyOpen accessDOIPDF
   Topic: Mechanistic modelling

6. 360 Interface Dermatitis is characterized by a type I immune response and an epidermal reaction to IFN-γ and TNF-α

   F. Lauffer, M. Jargosch, L. Krause, …, F. Theis, …, K. Eyerich

   Journal of Investigative DermatologyOpen accessDOI
   Topic: Immunity and inflammation

7. 489 TLR7/8 agonists stimulate plasmacytoid dendritic cells to initiate a Th17-deviated acute contact dermatitis in humans

   N. Garzorz-Stark, F. Lauffer, L. Krause, …, F. Theis, …, K. Eyerich

   Journal of Investigative DermatologyOpen accessDOI
   Topic: Immunity and inflammation

8. pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms

   Sophie Molnos, Clemens Baumbach, Simone Wahl, …, Fabian J. Theis, Christian Gieger

   BMC BioinformaticsOpen accessDOIPDF
   Topic: Open-source software

9. Reconstructing cell cycle and disease progression using deep learning

   Philipp Eulenberg, Niklas Köhler, Thomas Blasi, Andrew Filby, Anne E. Carpenter, Paul Rees, Fabian J. Theis, F. Alexander Wolf

   Nature CommunicationsOpen accessDOIPDF
   Topic: Deep learning and generative models

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

    Sophie Tritschler, Fabian J. Theis, Heiko Lickert, Anika Böttcher

    Molecular MetabolismReviewOpen accessDOIPDF
    Topic: Metabolism and diabetes

11. 2D cross-omics integrated enrichment analysis reveals insights into COPD pathogenesis

    Julian Dorer, Thomas M Conlon, Jörg Bartel, Martina Häckl, Fabian J. Theis, Oliver Eickelberg, Ali Önder Yildirim, Jan Krumsiek

    Airway Cell Biology and ImmunopathologyConference paperDOI
    Topic: Immunity and inflammation

12. MicroRNA as an Integral Part of Cell Communication: Regularized Target Prediction and Network Prediction

    Rolf Backofen, Fabrizio Costa, Fabian Theis, …, Oleksandr Dovzhenko

    Lecture Notes in BioengineeringBook chapterDOI
    Topic: Gene regulation

13. Information Theoretic Concepts to Unravel Cell–Cell Communication

    Nikola Müller, Steffen Sass, Barbara Offermann, …, Fabian Theis, …, Melanie Boerries

    Lecture Notes in BioengineeringBook chapterDOI

14. Single cells make big data: New challenges and opportunities in transcriptomics

    Philipp Angerer, Lukas Simon, Sophie Tritschler, F. Alexander Wolf, David Fischer, Fabian J. Theis

    Current Opinion in Systems BiologyOpen accessDOI
    Topic: Single-cell genomics

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

    Atefeh Kazeroonian, Fabian J Theis, Jan Hasenauer

    BioinformaticsOpen accessDOIPDF
    Topic: Mechanistic modelling

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

    Brigitte I Frohnert, Michael Laimighofer, Jan Krumsiek, Fabian J Theis, …, Andrea K Steck

    Pediatric DiabetesOpen accessDOIPDF
    Topic: Metabolism and diabetes

17. 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 Systems BiologyOpen accessDOIPDF
    Topic: Benchmarks and best practices

18. Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach

    K. Milger, J. Götschke, L. Krause, …, F. J. Theis, …, S. Krauss‐Etschmann

    AllergyOpen accessDOI
    Topic: Immunity and inflammation

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

    Tingying Peng, Kurt Thorn, Timm Schroeder, Lichao Wang, Fabian J. Theis, Carsten Marr, Nassir Navab

    Nature CommunicationsOpen accessDOIPDF
    Topic: Imaging

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

    Nikolaos K Chlis, F Alexander Wolf, Fabian J Theis

    BioinformaticsOpen accessDOIPDF
    Topic: Cell fate and dynamics

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

    Thomas Blasi, Florian Buettner, Michael K Strasser, Carsten Marr, Fabian J Theis

    Physical BiologyOpen accessDOIPDF
    Topic: Single-cell genomics

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

    Sabine Bartel, Nikola Schulz, Francesca Alessandrini, …, Fabian J. Theis, …, Susanne Krauss-Etschmann

    Scientific ReportsOpen accessDOIPDF
    Topic: Immunity and inflammation

23. 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

    BioinformaticsOpen accessDOI
    Topic: Imaging

24. Prospective identification of hematopoietic lineage choice by deep learning

    Felix Buggenthin, Florian Buettner, Philipp S Hoppe, …, Fabian J Theis, Carsten Marr

    Nature MethodsOpen accessDOIPDF
    Topic: Cell fate and dynamics

25. Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma

    Ana-Maria Florea, Elizabeth Varghese, Jennifer E. McCallum, …, Fabian J. Theis, …, Dietrich Büsselberg

    OncotargetOpen accessDOIPDF
    Topic: Perturbation responses

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

    Nick Jagiella, Dennis Rickert, Fabian J. Theis, Jan Hasenauer

    Cell SystemsOpen accessDOI
    Topic: Mechanistic modelling

27. Label Free Identification of Peripheral Blood Eosinophils Using High-Throughput Imaging Flow Cytometry

    Justyna Piasecka, Holger Hennig, Fabian J. Theis, Paul Rees, Huw D. Summers, Catherine A. Thornton

    Journal of Allergy and Clinical ImmunologyDOI
    Topic: Imaging

28. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

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

    PLOS Computational BiologyOpen accessDOIPDF
    Topic: Mechanistic modelling

29. AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients

    Marc A. Schneider, Petros Christopoulos, Thomas Muley, …, Fabian Theis, Michael Meister

    International Journal of OncologyOpen accessDOIPDF
    Topic: Clinical and cohort data

30. Polygenic Burden Analysis of Longitudinal Clusters of Psychopathological Features In A Cross-Diagnostic Group of Individuals with Severe Mental Illness

    Eva Schulte, Ivan Kondofersky, Monika Budde, …, Fabian J. Theis, …, Thomas G. Schulze

    European NeuropsychopharmacologyDOI
    Topic: Brain and mental health

31. Integrating Polygenic Allele Burden Information And Phenomic Data To Characterize Complex Disease Trajectories In Severe Mental Illness

    Monika Budde, Ivan Kondofersky, Kristina Adorjan, …, Fabian J. Theis, …, Thomas G. Schulze

    European NeuropsychopharmacologyDOI
    Topic: Brain and mental health

32. POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF QUALITY OF LIFE AND FUNCTIONING IN PATIENTS WITH SEVERE MENTAL ILLNESS

    Ashley Comes, Fanny Aldinger, Ivan Kondofersky, …, Fabian J. Theis, …, Thomas Schulze

    European NeuropsychopharmacologyOpen accessDOI
    Topic: Clinical and cohort data

33. The Role Of Micrornas In The Course Of Severe Mental Disorders

    Urs Heilbronner, Gaurav Jain, Lalit Kaurani, …, Fabian J. Theis, …, Thomas G. Schulze

    European NeuropsychopharmacologyDOI
    Topic: Brain and mental health

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

    Norbert Krautenbacher, Fabian J. Theis, Christiane Fuchs

    Computational and Mathematical Methods in MedicineOpen accessDOIPDF
    Topic: Statistical inference