A5014496106- Single-cell and spatial transcriptomics
- Machine Learning in Bioinformatics
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Advanced Proteomics Techniques and Applications
- Cancer Genomics and Diagnostics
- Gene Regulatory Network Analysis
- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- RNA modifications and cancer
- Immune cells in cancer
- Cancer-related molecular mechanisms research
- Acute Myeloid Leukemia Research
- Extracellular vesicles in disease
- Gene expression and cancer classification
- Immune responses and vaccinations
- Acute Lymphoblastic Leukemia research
Max Delbrück Center
2022-2024
Humboldt-Universität zu Berlin
2022-2024
Charité - Universitätsmedizin Berlin
2022-2024
Freie Universität Berlin
2022-2024
Technical University of Munich
2018-2021
A few years ago, it was proposed to use the simultaneous quantification of unspliced and spliced messenger RNA (mRNA) add a temporal dimension high-throughput snapshots single cell sequencing data. This concept can yield additional insight into transcriptional dynamics biological systems under study. However, current methods for inferring state velocities from such data (known as velocities) are afflicted by several theoretical computational problems, hindering realistic reliable velocity...
Hematopoietic stem and progenitor cells (HSPCs) are known to respond acute inflammation; however, little is understood about the dynamics heterogeneity of these stress responses in HSPCs. Here, we performed single-cell sequencing during sensing, response, recovery phases inflammatory response HSPCs treatment (a total 10,046 from four time points spanning first 72 h response) with pro-inflammatory cytokine IFNα investigate HSPCs' dynamic changes inflammation. We developed essential novel...
Abstract Single cell RNA sequencing (scRNA-seq) data is widely used to study cancer states and their heterogeneity. However, the tumour microenvironment usually a mixture of healthy cancerous cells it can be difficult fully separate these two populations based on transcriptomics alone. If available, somatic single nucleotide variants (SNVs) observed in scRNA-seq could identify population. calling SNVs challenging task, as most seen short read are not somatic, but instead germline variants,...
Abstract Motivation Single-cell RNA sequencing (scRNA-seq) data are widely used to study cancer cell states and their heterogeneity. However, the tumour microenvironment is usually a mixture of healthy cancerous cells it can be difficult fully separate these two populations based on transcriptomics alone. If available, somatic single-nucleotide variants (SNVs) observed in scRNA-seq could identify population match that information with single cells’ expression profile. calling SNVs...
Many applications monitor predictions of a whole range features for biological datasets, e.g. the fraction secreted human proteins in proteome. Results and error estimates are typically derived from publications.Here, we present simple, alternative approximation that uses performance methods to error-correct predicted distributions. This confusion matrix (TP true positives, TN negatives, FP false positives FN negatives) describing prediction tool correction. As proof-of-principle, correction...
Abstract A few years ago, it was proposed to use the simultaneous quantification of unspliced and spliced messenger RNA (mRNA) add a temporal dimension high-throughput snapshots single cell sequencing data. This concept can yield additional insight into transcriptional dynamics biological systems under study. However, current methods for inferring state velocities from such data (known as velocities) are afflicted by several theoretical computational problems, hindering realistic reliable...
Abstract The native subcellular location (also referred to as localization or cellular compartment) of a protein is the one in which it acts most frequently; aspect function. Do ten eukaryotic model organisms differ their spectrum , i.e., fraction its proteome each seven major compartments? As experimental annotations locations remain biased and incomplete, we need prediction methods answer this question. After systematic bias corrections, complete but faulty appeared be more appropriate...
Background: Despite improvements of therapy regimens for acute lymphoblastic leukemia (ALL), a significant number patients experience relapse or do not respond to treatment, highlighting the need continued research into underlying mechanisms and development new treatments. It has been suggested that metabolic alterations are key drivers resistance. While most current understanding ALL is based upon assays investigate characteristics bulk samples, it important characterize disease at single...
Abstract The native subcellular localization or cellular compartment of a protein is the one in which it acts most often; aspect function. Do ten eukaryotic model organisms differ their location spectrum , i.e. fraction its proteome each seven major compartments? As experimental annotations locations remain biased and incomplete, we need prediction methods to answer this question. To gauge bias methods, merged all available for human proteome. In doing so, found important values both...