Index of GitHub Repositories

Here you can explore GitHub repositories associated with SyNergy projects, and links to their related publications.

For more information on our research and publications, visit the SyNergy website.

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▶ Transcriptomics Projects

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Adult neural stem cell activation in mice is regulated by the day/night cycle and intracellular calcium dynamics

• Code for analysis of Ca2+ activity in neural stem cells

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CD8+ T cells induce interferon-responsive oligodendrocytes and microglia in white matter aging

• Transcriptomics characterization of oligodendrocytes and microglia in white matter aging

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Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons

• Astrocytes reprogramming analysis

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Phagocyte-mediated synapse removal in cortical neuroinflammation is promoted by local calcium accumulation

• • Code and sample data used for parts of the analysis in the paper Jafari et al., 2020
  • Re-analysis of snRNA-seq data from Schirmer et al., Nature, 2019

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Shared inflammatory glial cell signature after stab wound injury

• • Analysis pipeline for scRNA-seq/stRNA-seq
  • Microglia morphology quantification tool (MMQT)
  • Spatial gradient analysis

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Spatial Transcriptomics-correlated Electron Microscopy maps transcriptional and ultrastructural responses to brain injury

• Spatial Transcriptomics-correlated Electron Microscopy analysis

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T cell-mediated microglial activation triggers myelin pathology in a mouse model of amyloidosis

• scRNA-seq analysis

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T cells modulate the microglial response to brain ischemia

• scRNA-seq analysis

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CD74 is a functional MIF receptor on activated CD4+ T cells

• Re-analysis pipeline: BulkRNAseq

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Distinct molecular profiles of skull bone marrow in health and neurological disorders

• Analysis of transcriptomics and proteomics data

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High-calorie diets uncouple hypothalamic oxytocin neurons from a gut-to-brain satiation pathway via κ-opioid signaling

• RiboTag-mRNA-seq and snRNA-seq analysis

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Twin study identifies early immunological and metabolic dysregulation of CD8+ T cells in multiple sclerosis

• scRNA-seq and single-cell T-cell receptor (TCR) sequencing analysis

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▶ Proteomics Projects

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Defining the Adult Neural Stem Cell Niche Proteome Identifies Key Regulators of Adult Neurogenesis

• MATLAB scripts to analyze AFM data

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Mapping autophagosome contents identifies interleukin-7 receptor-alpha as a key cargo modulating CD4+ T cell proliferation

• Mass spectrometry data analysis

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Met/HGFR triggers detrimental reactive microglia in TBI

• PROTEAS: Protein microarray expression analysis

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Proteomic and lipidomic profiling of demyelinating lesions identifies fatty acids as modulators in lesion recovery

• Code for calculating the lesion volume

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Targeting the TCA cycle can ameliorate widespread axonal energy deficiency in neuroinflammatory lesions

• Python algorithm for the analysis of the EAE mitochondrial proteome

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▶ Multi-omics Projects

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Multiomic ALS signatures highlight subclusters and sex differences suggesting the MAPK pathway as therapeutic target

• Multi-omics analysis pipeline for the MAXOMOD project

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Multi-omic landscaping of human midbrains identifies disease-relevant molecular targets and pathways in advanced-stage Parkinson's disease

• DEx Multi-Omics in Parkinson Disease (PD)

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Diet triggers specific responses of hypothalamic astrocytes in time and region dependent manner

• Astrocytes Heterogenity (ARC)

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▶ Imaging Projects

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Amyloid-associated increases in soluble tau relate to tau aggregation rates and cognitive decline in early Alzheimer’s disease

• Sample R code from publication

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▶ Tutorials/Additional Resources

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Theis Lab (Helmholtz Munich)

• • Theis Lab GitHub page
  • Single-cell tutorial
  • Single-cell best practices

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MATLAB Tutorials

• • MATLAB Programs for Flow Cytometry
  • Western Blot Quantification in MATLAB

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PSMD (marker for cerebral small vessel disease)

• • PSMD (Peak width of Skeletonized Mean Diffusivity) Marker

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Nanoscale Hub: Analysis pipelines

• • Crop Electron Microscopy (EM) image to a bounding box (bbox)
  • Import Utility

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