Related papers: Complete Human Mitochondrial Genome Construction U…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
We propose a general method for optimally approximating an arbitrary matrix $\mathbf{M}$ by a structured matrix $\mathbf{T}$ (circulant, Toeplitz/Hankel, etc.) and examine its use for estimating the spectra of genomic linkage disequilibrium…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…
Large language models (LLMs) show strong potential for neural architecture generation, yet existing approaches produce complete model implementations from scratch -- computationally expensive and yielding verbose code. We propose Delta-Code…
Lindenmayer systems (L-systems) are a formal grammar system, where the most notable feature is a set of rewriting rules that are used to replace every symbol in a string in parallel; by repeating this process, a sequence of strings is…
We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…
Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is…
Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
The advancement in generative AI could be boosted with more accessible mathematics. Beyond human-AI chat, large language models (LLMs) are emerging in programming, algorithm discovery, and theorem proving, yet their genomics application is…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
Molecular clock (MC) is a central concept of molecular evolution according to which each gene evolves at a characteristic, near constant rate. Numerous evolutionary studies have demonstrated the validity of MC but also have shown that MC is…
Mitochondrial diseases are currently untreatable due to our limited understanding of their pathology. We study the expression of various mitochondrial proteins in skeletal myofibres (SM) in order to discover processes involved in…
Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast…
Large language models (LLMs) are changing the way researchers interact with code and data in scientific computing. While their ability to generate general-purpose code is well established, their effectiveness in producing scientifically…
Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing. As genomes represent the entirety of an organism's hereditary…
Generating protein sequences conditioned on protein structures is an impactful technique for protein engineering. When synthesizing engineered proteins, they are commonly translated into DNA and expressed in an organism such as yeast. One…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…