Biomedical subjects

Stephan Preibisch

Publications and source records attributed to Stephan Preibisch.

3 recordsLinked to original sources

PubMed2025

PEELing: an integrated and user-centric platform for spatially resolved proteomics data analysis.

SUMMARY: Molecular compartmentalization is vital for cellular physiology. Spatially resolved proteomics allows biologists to survey protein composition and dynamics with subcellular resolution. Here, we present PEELing, an integrated package and user-friendly web service for analyzing spatially resolved proteomics data. PEELing assesses data quality using curated or user-defined references, performs cutoff analysis to remove contaminants, connects to databases for functional annotation, and generates data visualizations-providing a streamlined and reproducible workflow to explore spatially resolved proteomics data. AVAILABILITY AND IMPLEMENTATION: PEELing and its tutorial are publicly available at https://peeling.janelia.org/ (Zenodo DOI: 10.5281/zenodo.15692517). A Python package of PEELing is available at https://github.com/JaneliaSciComp/peeling/ (Zenodo DOI: 10.5281/zenodo.15692434).

Proteomics↗

PubMed2005

Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays.

The microarray technology enables the expression degree of thousands of genes to be estimated at once by the measurement of the abundance of the respective messenger RNA. This method is based on the sequence specific binding of RNA to DNA probes and its detection using fluorescent labels. The raw intensity data are affected by the sequence-specific affinity of probe and RNA for duplex formation, by the background intensity due to nonspecific hybridization at small transcript concentrations and by the saturation of the probes at high transcript concentration owing to surface adsorption. We address these issues using a binding model which describes specific and nonspecific hybridization in terms of a competitive two-species Langmuir isotherm and DNA/RNA duplex formation in terms of sequence-specific, single-base related interactions. The GeneChip microarrays technology uses pairs of so-called perfect match (PM) and mismatch (MM) oligonucleotide probes to estimate the amount of nonspecific hybridization. The mean affinity of the probes decrease according to PM(specific) > MM(specific) >> PM(nonspecific) approximately MM(nonspecific). The stability of specific and nonspecific DNA/RNA duplexes is mainly determined by Watson Crick (WC) pairings. Mismatched self-complementary pairings in the middle of the MM sequence only weakly contribute to the duplex stability. The asymmetry of base pair interaction in the DNA/RNA hybrid duplexes gives rise to a duplet-like symmetry of the PM - MM intensity difference at dominating nonspecific hybridization and a triplet-like symmetry at specific hybridization. The signal intensities of the PM and MM probes and their difference are assessed in terms of sensitivity and specificity. The presented results imply the refinement of existing algorithms of probe level analysis to correct microarray data for nonspecific background intensities and saturation on the basis of the probe sequence.

Algorithms↗

PubMed2005

Specific and nonspecific hybridization of oligonucleotide probes on microarrays.

Gene expression analysis by means of microarrays is based on the sequence-specific binding of RNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving sequences other than the intended target is problematic because it adds a chemical background to the signal, which is not related to the expression degree of the target gene. The article presents a molecular signature of specific and nonspecific hybridization with potential consequences for gene expression analysis. We analyzed the signal intensities of perfect match (PM) and mismatch (MM) probes of GeneChip microarrays to specify the effect of specific and nonspecific hybridization. We found that these events give rise to different relations between the PM and MM intensities as function of the middle base of the PM, namely a triplet-like (C > G approximately T > A > 0) and a duplet-like (C approximately T > 0 > G approximately A) pattern of the PM-MM log-intensity difference upon binding of specific and nonspecific RNA fragments, respectively. The systematic behavior of the intensity difference can be rationalized on the level of basepairings of DNA/RNA oligonucleotide duplexes in the middle of the probe sequence. Nonspecific binding is characterized by the reversal of the central Watson-Crick (WC) pairing for each PM/MM probe pair, whereas specific binding refers to the combination of a WC and a self-complementary (SC) pairing in PM and MM probes, respectively. The Gibbs free energy contribution of WC pairs to duplex stability is asymmetric for purines and pyrimidines of the PM and decreases according to C > G approximately T > A. SC pairings on the average only weakly contribute to duplex stability. The intensity of complementary MM introduces a systematic source of variation which decreases the precision of expression measures based on the MM intensities.

Biophysics↗