Related papers: A minimum principle in mRNA editing ?
When constructing models of the world, we aim for optimal compressions: models that include as few details as possible while remaining as accurate as possible. But which details -- or features measured in data -- should we choose to include…
State-of-the-art neural networks can be trained to become remarkable solutions to many problems. But while these architectures can express symbolic, perfect solutions, trained models often arrive at approximations instead. We show that the…
In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Short peptides with antimicrobial activity have therapeutic potential for treating bacterial infections. Mechanisms of actions for antimicrobial peptides require binding the biological membrane of their target, which often represents a key…
Grounded dialogue models generate responses that are grounded on certain concepts. Limited by the distribution of grounded dialogue data, models trained on such data face the transferability challenges in terms of the data distribution and…
Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks. Experimental evidences of phenotypic differentiation are given by the presence of bimodal distributions…
We call change-point problem (CPP) the identification of changes in the probabilistic behavior of a sequence of observations. Solving the CPP involves detecting the number and position of such changes. In genetics the study of how and what…
We introduce a random bit-string model of post-transcriptional genetic regulation based on sequence matching. The model spontaneously yields a scale free network with power law scaling with $ \gamma=-1$ and also exhibits log-periodic…
The present paper is devoted to foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids, and proteins as information systems, we have formulated the corresponding p-adic formalisms…
Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short…
Constructing a quantum description of crystals from scattering experiments is of paramount importance to explain their macroscopic properties and to evaluate the pertinence of theoretical ab-initio models. While reconstruction methods of…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
For two decades, reproducing kernels and their associated discrepancies have facilitated elegant theoretical analyses in the setting of quasi Monte Carlo. These same tools are now receiving interest in statistics and related fields, as…
Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…
Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biological processes. Accurately predicting PTM sites and their…
The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…