相关论文: A minimum principle in mRNA editing ?
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
The classical attenuation regulation of gene expression in bacteria is considered. We propose to represent the secondary RNA structure in the leader region of a gene or an operon by a term, and we give a probabilistic term rewriting system…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Minimizers and convolutional neural networks (CNNs) are two quite distinct popular techniques that have both been employed to analyze categorical biological sequences. At face value, the methods seem entirely dissimilar. Minimizers use…
Fine-tuning criteria are frequently used to place upper limits on the masses of superpartners in supersymmetric extensions of the standard model. However, commonly used prescriptions for quantifying naturalness have some important…
Network embedding is a general-purpose machine learning technique that encodes network structure in vector spaces with tunable dimension. Choosing an appropriate embedding dimension -- small enough to be efficient and large enough to be…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
A fingerprint matching is a very difficult problem. Minutiae based matching is the most popular and widely used technique for fingerprint matching. The minutiae points considered in automatic identification systems are based normally on…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Starting with the Brezis-Browder principle, we give stronger versions of many variational principles and minimal element theorems which appeared in the recent literature. Relationships among the elements of different sets of assumptions are…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
We introduce genetic algorithms as a means to estimate the accuracy required to discriminate among different models using experimental observables. We exemplify the technique in the context of the minimal supersymmetric standard model. If…
Model editing aims at selectively updating a small subset of a neural model's parameters with an interpretable strategy to achieve desired modifications. It can significantly reduce computational costs to adapt to large language models…
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This…
We study the critical behavior of low-frequency vibrations of packings with pinned particles near the jamming point. Soft modes form a plateau in the density of states and its frequency is controlled by the contact number as the ordinary…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…