Related papers: Algorithm for Optimized mRNA Design Improves Stabi…
In high-dimensional genomic data, the curse of dimensionality (d >> n) and limited sampling make feature selection inherently unstable - a critical barrier to biomarker discovery. We introduce StackFeat, an iterative algorithm that…
While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains…
This paper explores the application of spiking neural networks (SNNs), known for their low-power binary spikes, to bearing fault diagnosis, bridging the gap between high-performance AI algorithms and real-world industrial scenarios. In…
The traditional more-is-better dose selection paradigm, developed based on cytotoxic chemotherapeutics, is often problematic When applied to the development of novel molecularly targeted agents (e.g., kinase inhibitors, monoclonal…
RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of…
Each and every biological function in living organism happens as a result of protein-protein interactions.The diseases are no exception to this. Identifying one or more proteins for a particular disease and then designing a suitable…
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…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
Vaccination against COVID-19 with the recently approved mRNA vaccines BNT162b2 (BioNTech/Pfizer) and mRNA-1273 (Moderna) is currently underway in a large number of countries. However, high incidence rates and rapidly spreading SARS-CoV-2…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…
Predicting the future evolutionary trajectory of SARS-CoV-2 remains a critical challenge, particularly due to the pivotal role of spike protein mutations. It is therefore essential to develop evolutionary models capable of continuously…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
Imperfect measurement can degrade a quantum error correction scheme. A solution that restores fault tolerance is to add redundancy to the process of syndrome extraction. In this work, we show how to optimize this process for an arbitrary…
Optimizing combinatorial structures is core to many real-world problems, such as those encountered in life sciences. For example, one of the crucial steps involved in antibody design is to find an arrangement of amino acids in a protein…
Protein design using structure prediction models such as AlphaFold2 has shown remarkable success, but existing approaches like relaxed sequence optimization (RSO) rely on single-path gradient descent and ignore sequence-space constraints,…
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the major techniques in structural biology with over 11,800 protein structures deposited in the Protein Data Bank. NMR can elucidate structures and dynamics of small and medium size…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA…