All Stories

  1. DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data

    Article • June 2026, openRxiv

    Dr Susanne Gerber

  2. Sex-specific regulation of angiogenin in Alzheimer’s disease

    Article • Molecular Psychiatry, June 2026, Springer Science + Business Media

    Dr Susanne Gerber

  3. Benchmarking ambient RNA removal across droplet and well-plate platforms reveals artificial count generation as a critical failure mode of scAR and CellClear

    Article • April 2026, openRxiv

    Dr Susanne Gerber

  4. Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read nanopore sequencing

    Article • Nature Communications, March 2026, Springer Science + Business Media

    Dr Susanne Gerber

  5. Real-time transcriptomic profiling in distinct experimental conditions

    Article • July 2025, eLife

    Dr Susanne Gerber

  6. Deep Learning Reaction Framework (DLRN) for kinetic modeling of time-resolved data

    Article • Communications Chemistry, May 2025, Springer Science + Business Media

    Dr Susanne Gerber

  7. Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications

    Article • March 2025, Springer Science + Business Media

    Dr Susanne Gerber

  8. ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing

    Article • March 2025, Springer Science + Business Media

    Dr Susanne Gerber

  9. Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read Nanopore sequencing

    Article • March 2025, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  10. Enhancing Detection of Polygenic Adaptation: A Comparative Study of Machine Learning and Statistical Approaches Using Simulated Evolve-and-Resequence Data

    Article • November 2024, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  11. Pod5Viewer: a GUI for inspecting raw nanopore sequencing data

    Article • Bioinformatics, November 2024, Oxford University Press (OUP)

    Dr Susanne Gerber

  12. Selective RNA pseudouridinylation in situ by circular gRNAs in designer organelles

    Article • Nature Communications, October 2024, Springer Science + Business Media

    Dr Susanne Gerber

  13. Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex

    Article • Communications Biology, October 2024, Springer Science + Business Media

    Dr Susanne Gerber

  14. Deep Learning Reaction Network (DLRN): a deep learning kinetic model analysis for time-resolved data

    Article • August 2024, Springer Science + Business Media

    Dr Susanne Gerber

  15. Deep Learning Reaction Network: a machine learning framework for modeling time resolved data

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  16. Real-time transcriptomic profiling in distinct experimental conditions

    Article • July 2024, eLife

    Dr Susanne Gerber

  17. Neuroimage Denoiser for removing noise from transient fluorescent signals in functional imaging

    Article • June 2024, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  18. Chromatin Capture Upsampling Toolbox - CCUT: A Versatile and unified Framework to Train Your Chromatin Capture Deep Learning Models

    Article • June 2024, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  19. Long non-coding RNAs expression and regulation across different brain regions in primates

    Article • Scientific Data, May 2024, Springer Science + Business Media

    Dr Susanne Gerber

  20. Characterization of transcriptional profiles associated with stress-induced neuronal activation in Arc-GFP mice

    Article • Molecular Psychiatry, April 2024, Springer Science + Business Media

    Dr Susanne Gerber

  21. Cortexa – a comprehensive resource for studying gene expression and alternative splicing in the murine brain

    Article • April 2024, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  22. Real-time transcriptomic profiling in distinct experimental conditions

    Article • March 2024, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  23. Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  24. Freezing responses during prolonged threat memory retrieval reflect trait-like anxiety endophenotypes in female and male inbred mice

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  25. A mathematical model of the Alzheimer’s Disease biomarker cascade demonstrates statistical pitfalls in identifying neurobiological surrogates of cognitive reserve

    Article • October 2023, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  26. Characterization of transcriptional profiles associated with stress-induced neuronal activation in Arc-GFP mice

    Article • September 2023, Research Square

    Dr Susanne Gerber

  27. NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis

    Article • Bioinformatics, August 2023, Oxford University Press (OUP)

    Dr Susanne Gerber

  28. NAPE-PLD deletion in stress-TRAPed neurons results in an anxiogenic phenotype

    Article • Translational Psychiatry, May 2023, Springer Science + Business Media

    Dr Susanne Gerber

  29. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing

    Article • Cells, March 2023, MDPI AG

    Dr Susanne Gerber

  30. On cheap entropy-sparsified regression learning

    Article • Proceedings of the National Academy of Sciences, December 2022, Proceedings of the National Academy of Sciences

    Dr Susanne Gerber

  31. NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis

    Article • December 2022, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  32. A Resilience Related Glial-Neurovascular Network Is Transcriptionally Activated after Chronic Social Defeat in Male Mice

    Article • Cells, October 2022, MDPI AG

    Dr Susanne Gerber

  33. CollembolAI, a macrophotography and computer vision workflow to digitize and characterize samples of soil invertebrate communities preserved in fluid

    Article • Methods in Ecology and Evolution, October 2022, Wiley

    Dr Susanne Gerber

  34. Low-Cost Probabilistic 3D Denoising with Applications for Ultra-Low-Radiation Computed Tomography

    Article • Journal of Imaging, May 2022, MDPI AG

    Dr Susanne Gerber

  35. Selective targeting of chronic social stress-induced activated neurons identifies neurogenesis-related genes to be associated with resilience in female mice

    Article • Psychoneuroendocrinology, May 2022, Elsevier

    Dr Susanne Gerber

  36. Long‐term molecular differences between resilient and susceptible mice after a single traumatic exposure

    Article • British Journal of Pharmacology, February 2022, Wiley

    Dr Susanne Gerber

  37. Co-Inference of Data Mislabelings Reveals Improved Models in Genomics and Breast Cancer Diagnostics

    Article • Frontiers in Artificial Intelligence, January 2022, Frontiers

    Dr Susanne Gerber

  38. beeRapp: an R shiny app for automated high-throughput explorative analysis of multivariate behavioral data

    Article • Bioinformatics Advances, January 2022, Oxford University Press (OUP)

    Dr Susanne Gerber

  39. Photoperiod is an important seasonal selection factor in Chironomus riparius (Diptera: Chironomidae)

    Article • Biological Journal of the Linnean Society, December 2021, Oxford University Press (OUP)

    Dr Susanne Gerber

  40. IntelliPy: a GUI for analyzing IntelliCage data

    Article • Bioinformatics, October 2021, Oxford University Press (OUP)

    Dr Susanne Gerber

  41. The gut microbiota instructs the hepatic endothelial cell transcriptome

    Article • iScience, October 2021, Elsevier

    Dr Susanne Gerber

  42. N6 -Methyladenosine Modification in Chronic Stress Response Due to Social Hierarchy Positioning of Mice

    Article • Frontiers in Cell and Developmental Biology, August 2021, Frontiers

    Dr Susanne Gerber

  43. Quality-preserving low-cost probabilistic 3D denoising with applications to Computed Tomography

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  44. Genomic basis for drought resistance in European beech forests threatened by climate change

    Article • eLife, June 2021, eLife

    Dr Susanne Gerber

  45. mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex

    Article • International Journal of Molecular Sciences, June 2021, MDPI AG

    Dr Susanne Gerber

  46. INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison

    Article • International Journal of Molecular Sciences, May 2021, MDPI AG

    Dr Susanne Gerber

  47. Transcriptional signatures in prefrontal cortex confer vulnerability versus resilience to food and cocaine addiction-like behavior

    Article • Scientific Reports, April 2021, Springer Science + Business Media

    Dr Susanne Gerber

  48. Dichotomic Hippocampal Transcriptome After Glutamatergic vs. GABAergic Deletion of the Cannabinoid CB1 Receptor

    Article • Frontiers in Synaptic Neuroscience, April 2021, Frontiers

    Dr Susanne Gerber

  49. Voluntary Wheel Running Did Not Alter Gene Expression in 5xfad Mice, but in Wild-Type Animals Exclusively after One-Day of Physical Activity

    Article • Cells, March 2021, MDPI AG

    Dr Susanne Gerber

  50. tbg - a new file format for genomic data

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  51. A deeper look into natural sciences with physics-based and data-driven measures

    Article • iScience, March 2021, Elsevier

    Dr Susanne Gerber

  52. Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines

    Article • BMC Genomics, January 2021, Springer Science + Business Media

    Dr Susanne Gerber

  53. Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale

    Article • Cells, December 2020, MDPI AG

    Dr Susanne Gerber

  54. Genomic basis of drought resistance inFagus sylvatica

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  55. Isolation of nuclei and downstream processing of cell-type-specific nuclei from micro-dissected mouse brain regions – techniques and caveats

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  56. mTOR driven gene transcription is required for cholesterol production in neurons of the developing cerebral cortex

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  57. Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines

    Article • August 2020, Research Square

    Dr Susanne Gerber

  58. Dynamic longitudinal behavior in animals exposed to chronic social defeat stress

    Article • PLOS One, July 2020, PLOS

    Dr Susanne Gerber

  59. Germ-free housing conditions do not affect aortic root and aortic arch lesion size of late atherosclerotic low-density lipoprotein receptor-deficient mice

    Article • Gut Microbes, June 2020, Taylor & Francis

    Dr Susanne Gerber

  60. Prevention of age-associated neuronal hyperexcitability with improved learning and attention upon knockout or antagonism of LPAR2

    Article • Cellular and Molecular Life Sciences, May 2020, Springer Science + Business Media

    Dr Susanne Gerber

  61. Impact of Acute and Chronic Amyloid-β Peptide Exposure on Gut Microbial Commensals in the Mouse

    Article • Frontiers in Microbiology, May 2020, Frontiers

    Dr Susanne Gerber

  62. Applying univariate vs. multivariate statistics to investigate therapeutic efficacy in (pre)clinical trials: A Monte Carlo simulation study on the example of a controlled preclinical neurotrauma trial

    Article • PLOS One, March 2020, PLOS

    Dr Susanne Gerber

  63. α-Linolenic Acid-Rich Diet Influences Microbiota Composition and Villus Morphology of the Mouse Small Intestine

    Article • Nutrients, March 2020, MDPI AG

    Dr Susanne Gerber

  64. A specific prelimbic-nucleus accumbens pathway controls resilience versus vulnerability to food addiction

    Article • Nature Communications, February 2020, Springer Science + Business Media

    Dr Susanne Gerber

  65. Low-cost scalable discretization, prediction, and feature selection for complex systems

    Article • Science Advances, January 2020, American Association for the Advancement of Science

    Dr Susanne Gerber

  66. Dynamic longitudinal behavior in animals exposed to chronic social defeat stress

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  67. The Microbiota Promotes Arterial Thrombosis in Low-Density Lipoprotein Receptor-Deficient Mice

    Article • mBio, October 2019, ASM Journals

    Dr Susanne Gerber

  68. Low-cost scalable discretization, prediction and feature selection for complex systems

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  69. Common miRNA Patterns of Alzheimer’s Disease and Parkinson’s Disease and Their Putative Impact on Commensal Gut Microbiota

    Article • Frontiers in Neuroscience, March 2019, Frontiers

    Dr Susanne Gerber

  70. Imputation of posterior linkage probability relations reveals a significant influence of structural 3D constraints on linkage disequilibrium

    Article • January 2018, Cold Spring Harbor Laboratory Press

    Dr Susanne Gerber

  71. A scalable approach to the computation of invariant measures for high-dimensional Markovian systems

    Article • Scientific Reports, January 2018, Springer Science + Business Media

    Dr Susanne Gerber

  72. Toward a direct and scalable identification of reduced models for categorical processes

    Article • Proceedings of the National Academy of Sciences, April 2017, Proceedings of the National Academy of Sciences

    Dr Susanne Gerber

  73. A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae

    Article • PLoS Computational Biology, January 2016, PLOS

    Dr Susanne Gerber

  74. Improving clustering by imposing network information

    Article • Science Advances, August 2015, American Association for the Advancement of Science

    Dr Susanne Gerber, illia horenko

  75. On inference of causality for discrete state models in a multiscale context

    Article • Proceedings of the National Academy of Sciences, September 2014, Proceedings of the National Academy of Sciences

    Dr Susanne Gerber

  76. Impact of Acute Metal Stress in Saccharomyces cerevisiae

    Article • PLOS One, January 2014, PLOS

    Dr Susanne Gerber

  77. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology

    Article • BMC Bioinformatics, April 2011, Springer Science + Business Media

    Dr Susanne Gerber

  78. GRAPHICAL ANALYSIS AND EXPERIMENTAL EVALUATION OF SACCHAROMYCES CEREVISIAE P TRK 1|2 AND P BMH 1|2 PROMOTER REGION

    Article • January 2010, World Scientific Pub Co Pte Lt

    Dr Susanne Gerber

  79. Drug-efficacy depends on the inhibitor type and the target position in a metabolic network—A systematic study

    Article • Journal of Theoretical Biology, June 2008, Elsevier

    Dr Susanne Gerber

  80. On Inference and Validation of Causality Relations in Climate Teleconnections

    Article • Cambridge University Press

    Dr Susanne Gerber