Magdalena Gębala
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View article: Supplementary Figure S1 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence
Supplementary Figure S1 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence Open
Supplementary Figure S1) To assess the robustness and reproducibility of the CRC prediction models, we evaluated their performance on samples processed under varying conditions. This figure shows the performance of the final CRC model, aft…
View article: Supplementary Table S1 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence
Supplementary Table S1 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence Open
Supplementary Table S1. Training set sensitivity and specificity across confounders
View article: Supplementary Table S2 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence
Supplementary Table S2 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence Open
Supplementary Table S2. Validation set sensitivity and specificity across confounders
View article: Supplementary Methods S1 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence
Supplementary Methods S1 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence Open
supplementary methods
View article: Data from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence
Data from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence Open
Purpose:Colorectal cancer is the second leading cause of cancer-related deaths worldwide, and early detection significantly improves treatment outcomes, but existing blood-based tests often have limited sensitivity in early-stage disease. …
View article: Supplementary Figure S2 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence
Supplementary Figure S2 from Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence Open
Supplementary Figure S2. a) Model scores increase with overall stage (left panel), T stage (middle panel) and N stage (right panel). Statistical significance is determined using a one-sided Mann-Whitney U-test. b) Overall sensitivity and s…
View article: Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence
Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence Open
Purpose: Colorectal cancer is the second leading cause of cancer-related deaths worldwide, and early detection significantly improves treatment outcomes, but existing blood-based tests often have limited sensitivity in early-stage disease.…
View article: CENP-N promotes the compaction of centromeric chromatin
CENP-N promotes the compaction of centromeric chromatin Open
The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange int…
View article: CENP-N promotes the compaction of centromeric chromatin
CENP-N promotes the compaction of centromeric chromatin Open
The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange int…
View article: Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking
Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking Open
To better understand the forces that mediate nucleic acid compaction in biology, we developed the disulfide cross-linking approach xHEED (X-linking of Helices to measure Electrostatic Effects at Distance) to measure the distance-dependent …
View article: CENP-N promotes the compaction of centromeric chromatin
CENP-N promotes the compaction of centromeric chromatin Open
The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. The arrangement of nucleosomes at the centrom…
View article: Cation enrichment in the ion atmosphere is promoted by local hydration of DNA
Cation enrichment in the ion atmosphere is promoted by local hydration of DNA Open
Electrostatic interaction in the ion atmosphere goes beyond continuum models. Instead, the contribution of hydration of both ions and DNA is crucial for the composition of the atmosphere and the free energy.
View article: Ion counting demonstrates a high electrostatic field generated by the nucleosome
Ion counting demonstrates a high electrostatic field generated by the nucleosome Open
In eukaryotes, a first step towards the nuclear DNA compaction process is the formation of a nucleosome, which is comprised of negatively charged DNA wrapped around a positively charged histone protein octamer. Often, it is assumed that th…
View article: Quantitative studies of an RNA duplex electrostatics by ion counting
Quantitative studies of an RNA duplex electrostatics by ion counting Open
Ribonucleic acids are one of the most charged polyelectrolytes in nature, and understanding of their electrostatics is fundamental to their structure and biological functions. An effective way to characterize the electrostatic field genera…
View article: Ion counting demonstrates a high electrostatic potential of the nucleosome
Ion counting demonstrates a high electrostatic potential of the nucleosome Open
The fundamental unit of chromatin is the nucleosome, which comprises of DNA wrapped around a histone protein octamer. The association of positively charged histone proteins with negatively charged DNA is intuitively thought to attenuate th…
View article: Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and <i>in Vitro</i> -Selected RNA Tertiary Motifs in a Multistep Folding Pathway
Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and <i>in Vitro</i> -Selected RNA Tertiary Motifs in a Multistep Folding Pathway Open
Decades of study of the RNA folding problem have revealed that diverse and complex structured RNAs are built from a common set of recurring structural motifs, leading to the perspective that a generalizable model of RNA folding may be deve…
View article: Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH<sup>+</sup>·C Wobble Formation in Double-Stranded DNA
Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH<sup>+</sup>·C Wobble Formation in Double-Stranded DNA Open
The high charge density of nucleic acids and resulting ion atmosphere profoundly influence the conformational landscape of RNA and DNA and their association with small molecules and proteins. Electrostatic theories have been applied to qua…
View article: Electric Field Modulation of Silicon upon Tethering of Highly Charged Nucleic Acids. Capacitive Studies on DNA‐modified Silicon (111)
Electric Field Modulation of Silicon upon Tethering of Highly Charged Nucleic Acids. Capacitive Studies on DNA‐modified Silicon (111) Open
We provide complex capacitance studies which show that the tethering of negatively‐charged DNA molecules to p‐doped silicon (111), without intervening oxide layer, leads to changes of the electric field in the underlying silicon. We propos…
View article: Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?
Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? Open
Electrostatics are central to all aspects of nucleic acid behavior, including their folding, condensation, and binding to other molecules, and the energetics of these processes are profoundly influenced by the ion atmosphere that surrounds…