Related papers: Path Signatures Enable Model-Free Mapping of RNA M…
Nonsense-mediated mRNA decay (NMD) is a critical post-transcriptional surveillance mechanism that degrades transcripts with premature termination codons, safeguarding transcriptome integrity and shaping disease phenotypes. However,…
Image-based sequencing of mRNA makes it possible to see where in a tissue sample a given gene is active, and thus discern large numbers of different cell types in parallel. This is crucial for gaining a better understanding of tissue…
Motivation: The mapping of RNA-seq reads to their transcripts of origin is a fundamental task in transcript expression estimation and differential expression scoring. Where ambiguities in mapping exist due to transcripts sharing sequence,…
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce…
Deep neural networks are vulnerable to adversarial examples, which dramatically alter model output using small input changes. We propose Neural Fingerprinting, a simple, yet effective method to detect adversarial examples by verifying…
DNA shape readout is an important mechanism of target site recognition by transcription factors, in addition to the sequence readout. Several models of transcription factor-DNA binding which consider DNA shape have been developed in recent…
When recording the movement of individual animals, cells or molecules one will often observe changes in their diffusive behaviour at certain points in time along their trajectory. In order to capture the different diffusive modes assembled…
Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to…
Gene and RNA editing methods, technologies, and applications are emerging as innovative forms of therapy and medicine, offering more efficient implementation compared to traditional pharmaceutical treatments. Current trends emphasize the…
Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Background: Magnetic resonance spectroscopy (MRS) enables non-invasive detection and measurement of biochemicals and metabolites. However, MRS has low signal-to-noise ratio (SNR) when concentrations of metabolites are in the range of the…
Nanopore protein sequencing produces long, noisy ionic current traces in which key molecular phases, such as protein capture and translocation, are embedded. Capture phases mark the successful entry of a protein into the pore and serve as…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
We show that unsupervised machine learning can be used to learn physical and chemical transformation pathways from the observational microscopic data, as demonstrated for atomically resolved images in Scanning Transmission Electron…
Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of…
Raman spectroscopy can provide insight into the molecular composition of cells and tissue. Consequently, it can be used as a powerful diagnostic tool, e.g. to help identify changes in molecular contents with the onset of disease. But robust…
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…