SEEK ID: https://fairdomhub.org/people/577
Location:
Germany
ORCID:
https://orcid.org/0000-0002-1887-4772
Joined: 15th Sep 2015
Expertise: Bioinformatics, Transcriptomics, RNA-Seq, AI, Data Integration
Related items
- Programmes (1)
- Projects (2)
- Institutions (1)
- Investigations (1+5)
- Studies (5+9)
- Assays (6+12)
- Data files (11+13)
- Models (5)
- SOPs (4+3)
- Publications (1)
- Presentations (0+2)
- Events (0+1)
- Documents (3+2)
Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Endometriosis, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, Salmonella enterica relies on carbon metabolism for adaptation to agricultural environments, PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing
Web page: Not specified
The project addresses the generation and establishment of programmed pacemaker cells for an in vitro drug testing possibility to perform predictive tests. This may lead to an improved treatment of cardiac arrhythmias or an accurate identification of potential drug molecules at a very early stage of development. Important benefits will arise in verifying the safety of a wide variety of medicines while reducing animal testing. For more information you may visit our project website at ...
Programme: Independent Projects
Public web page: https://irhythmics.med.uni-rostock.de/
Organisms: Homo sapiens, Mus musculus
The gut–brain axis (GBA) provides a bidirectional homeostatic communication between the gastrointestinal tract and the central nervous system. The interdisciplinary collaboration is going to fully explore a first comprehensive GBA cross-disease map of genetic, expression and regulatory changes associated with ulcerative colitis and schizophrenia disease entities.
Dysfunction of this axis can have pathophysiological consequences. Genome-wide association studies (GWAS) have identified >300 ...
Programme: This Project is not associated with a Programme
Public web page: https://www.sbi.uni-rostock.de/research/projects/detail/49
Start date: 1st Feb 2019
End date: 12th Feb 2019
Organisms: Not specified
Aims: The immune response is important for mediating the benefit of cardiac cell therapies. The role of varied immune responses in influencing the outcome of cardiomyocyte cell transplantation after myocardial infarction was investigated. Methods and Results: Cardiac flow cytometric analysis of C57BL/6J and T- and B cell deficient Rag2del mice revealed varied CD11b, natural killer and dendritic cell responses following sham injection and a disparate macrophage response after myocardial infarction. ...
Submitter: Markus Wolfien
Studies: Single nuclei data analysis
Snapshots: No snapshots
This study contains the singele nuclei data analysis part of the Bl6 and Rag2del comparison. Here, we used Seurat, harmony, and monocle for an in-depth analysis.
Submitter: Markus Wolfien
Investigation: Disparate immune responses lead to varied outco...
Snapshots: No snapshots
Single-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all. All this refers to “low quality” potentially leading to data misinterpretation. Common standard quality control parameters involve the ...
Submitter: Markus Wolfien
Investigation: 1 hidden item
Assays: scRNA-Seq of in vitro "induced sinoatrial bodies" and ex vivo sinoatrial...
Snapshots: No snapshots
This study contains our snRNA-Seq based comparison of whole hearts from Fzt.DU and Bl6 mice published in Cardiovascular Research.
Submitter: Markus Wolfien
Investigation: 1 hidden item
Assays: Single nuclei RNA-Seq analysis of Fzt:DU and BL6 mice
Snapshots: Snapshot 1
This study includes the single snRNA-seq in whole adult murine hearts from an inbred (C57BL/6NRj) and an outbred (Fzt:DU) mouse strain in comparison to publicly available scRNA-seq data of the tabula muris project.
Submitter: Anne-Marie Galow
Investigation: 1 hidden item
Assays: integrative cluster analysis of single cell and single nuclei data
Snapshots: Snapshot 1
This study contains our single nuclei characterisation of whole hearts from Fzt.DU mice published in Cells.
Submitter: Markus Wolfien
Investigation: 1 hidden item
Snapshots: Snapshot 1
Submitter: Markus Wolfien
Biological problem addressed: Gene Expression
Investigation: 1 hidden item
Study: Single nuclei comparison
Organisms: No organisms
Models: No Models
SOPs: R script for single nuclei analysis, UNIX script for snRNA-Seq processing
Data files: Marker genes for single nuclei clusters, Nuclei characteristics for the single nuclei an...
Snapshots: Snapshot 1
Submitter: Markus Wolfien
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: Nuclei isolation for single nuclei RNA-seq
Data files: R script for snRNAseq analysis, Top 10 marker genes per nuclei, Top 100 marker genes for whole heart fzt:DU cel..., Top marker genes per nuclei, UNIX script for snRNAseq
Snapshots: No snapshots
Here, we conduct a proof of principle by comparing a 2D and 3D fluorescent image analysis based approach on unlabeled cardiomyocytes. Based on the CellProfiler software, we extracted high-dimensional features of individual cells and nuclei, which are subsequently down-sampled and clustered. These clusters are furthermore benchmarked via different machine learning classifiers (e.g., AdaBoost, Gradient Boosting, Random Forest) as the ground truth for our proposed approach.
Submitter: Markus Wolfien
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: 1 hidden item
Snapshots: No snapshots
Application of the LoRAS oversampling approach on single-cell/single-nuclei data to annotate/identify specific cell populations in new data based on previously, manually curated data.
Submitter: Markus Wolfien
Biological problem addressed: Annotation
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: No organisms
Models: Data and Jupyter notebooks for our analysis on ..., Data and Jupyter notebooks for our analysis on ..., R script for scSynO usage of the Allen Brain At..., R script to generate the preprocessing input fo..., Unix script for the kallisto bustools processin...
SOPs: No SOPs
Data files: Schematic overview of sc-SynO, sc-SynO use case 1: cardiac glial cell identifi..., sc-SynO use case 2: proliferative cardiomyocyte...
Snapshots: No snapshots
For scRNA-Seq, iSABs were dissociated using the Primary Cardiomyocyte Isolation Kit (Thermo Fisher Scientific) before library preparation was performed using the 10xGenomics system with subsequent sequencing on the HighSeq4000 (Illumina). The mouse-SAN scRNA-Seq protocol is described in Goodyer et al. Preprocessing of raw sequencing data from iSABs relied on tools of the Cell Ranger Software (v.6.1.0) as was the procedure in Goodyer et al. Downstream analyses were conducted similar for both ...
Submitter: Anne-Marie Galow
Biological problem addressed: Gene Expression
Investigation: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: Experimental protocol, R-script for scRNA-Seq analysis of in vivo "ind...
Data files: No Data files
Snapshots: No snapshots
Submitter: Markus Wolfien
Biological problem addressed: Gene Expression
Investigation: Disparate immune responses lead to varied outco...
Study: Single nuclei data analysis
Organisms: No organisms
Models: R script
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Visualization of the workflow demonstrating a step-by-step explanation for a sc-SynO analysis. a) Several or one snRNA-Seq or scRNA-Seq fastq datasets can be used as an input. Here, we identify our cell population of interest and provide raw or normalized read counts of this specific population to sc-SynO for training. b) Further information for cluster annotation and processed count data are serving as input for the core algorithm. c) Based on the data input, we utilize the LoRAS synthetic ...
Creators: Markus Wolfien, Saptarshi Bej
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: 1 hidden item
Validation of the sc-SynO model for the first use case of cardiac glial cell annotation. UMAP representation of the manually clustered Bl6 dataset of Wolfien et al. (2020) Precicted cells of sc-SynO are highlighted in blue, cells not chosen are grey. UMAP representation of the manually clustered dataset of Vidal (2019). Precicted cells of sc-SynO are highlighted in blue, cells not chosen are grey. Average expression of the respective top five cardiac glial cell marker genes for both validation ...
Creators: Markus Wolfien, Saptarshi Bej
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: 1 hidden item
Validation of the sc-SynO model for the second use case of proliferative cardiomyocytes annotation. a) UMAP representation of the manually clustered single-nuclei dataset of Linscheid et al. (2019) Precicted cells of sc-SynO are highlighted in blue (based on top 20 selected features in the training model), red (based on top 100 selected features in the training model) cells not chosen are grey. b) UMAP representation of the manually clustered dataset of Vidal et al. (2020). PPrecicted cells of ...
Creators: Markus Wolfien, Saptarshi Bej
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: 1 hidden item
This pdf file contains all figures of the article "Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice" in high resolution.
Creators: Anne-Marie Galow, Markus Wolfien
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
File contains the detailed cluster names for each data set, number of nuclei per cluster, average reads per nucleus, and average reads per cluster.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison
This dot-plot represents only the most significant genes per identified cell type cluster.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
This file contains the top markers for the identified cell types.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
This pdf contains the top 10 markers for each identified cell type as a dot-plot.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
This file contains the R-script to analyse single nuclei data previously processed with kallisto and bustools. The analyses utilizes the Seurat, harmony and RNAvelocity package.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
This file contains the detailed UNIX commands for mm10 index file creation (suitable for RNAvelocity) for kallisto as well as the commands used for the alignment with kallisto and the subsequent quantification with bustools.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
This file contains the IDs, adj. p-values and official gene names of the top 100 marker genes (where applicable) for each of the identified cluster.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison
Underlying R script for the investigation of immune cells. Script contains basic data processing, as well as a DE and monocle analysis.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Mus musculus
Investigations: Disparate immune responses lead to varied outco...
Studies: Single nuclei data analysis
Here, we describe the index file generation of the mm10 genome, the genome alignment with kallisto, and quantification with bustools to obtain the used spliced / unspliced transcript input.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Here is the detailed R script to generate the input needed by scSynO for synthetic cell generation and classification model training.
The code that can be embedded into any other Seurat data processing workflow is:
cell_expression_target_cluster <- as.matrix(GetAssayData(seuratobject, slot = "data")[, WhichCells(seuratobject, ident = "target_cluster_number")]) cell_expression_all_other_clusters <- as.matrix(GetAssayData(seuratobject, slot = "data")[, WhichCells(seuratobject, ident = ...
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Single nuclei transcriptomics data as .csv files from the Allen Brain atlas data set of mus musculus (https://celltypes.brain-map.org/) have been utilized as an input for scSynO. The underlying analysis is part of the manuscript entitled "Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling". Data anaylsis and visalizations were mainly generated with the Seurat R package (https://satijalab.org/seurat/archive/v3.2/spatial_vignette.html)
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Saptarshi Bej
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
This file contains the detailed experimental protocol for the cultivation of "induced sinoatrial bodies (iSABs), the scRNA-Seq procedure as well as the general computational workflow for data processing. The R-script is provided separately.
Creators: Anne-Marie Galow, Sophie Kussauer, Markus Wolfien
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison
This file contains the detailed experimental protocol to isolate nuclei from murine hearts.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei characterisation of adult mammali..., integrative cluster analysis - proliferative ca...
Assays: Single nuclei RNA-Seq analysis of Fzt:DU mice, integrative cluster analysis of single cell and...
This R-script contains the single nuclei analysis for our Fzt:DU and BL6 data, namely bustools file integration, preprocessing, scaling, clustering, marker indentification and annotation of markers and RNAvelocity computation.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison
Abstract (Expand)
Authors: A. M. Galow, S. Kussauer, M. Wolfien, R. M. Brunner, T. Goldammer, R. David, A. Hoeflich
Date Published: 24th Aug 2021
Publication Type: Manual
PubMed ID: 34427691
Citation: Cell Mol Life Sci. 2021 Aug 24. pii: 10.1007/s00018-021-03916-5. doi: 10.1007/s00018-021-03916-5.
Sehr geehrte Damen und Herren,
mit diesem Informationsflyer erfahren Sie mehr über das iRhythmics Projekt unseres Konsortiums.
Mit freundlichen Grüßen
Anna Skorska Projektmanagerin iRhythmics
Creator: Anna Skorska
Submitter: Markus Wolfien
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This file contains a detailed description of the underlying experimental procedure and the computational analysis.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison
This PDF contains a dotplot indicating the gene expression of the top 100 markers (where applicable) for each of the identified 23 clusters.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison