Related papers: Automated DNA Motif Discovery
A natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are $k$ background sequences, and each character in a background sequence is a random…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
Large language models (LLMs) can learn to perform a wide range of natural language tasks from just a handful of in-context examples. However, for generating strings from highly structured languages (e.g., semantic parsing to complex…
Motif finding in DNA, RNA and proteins plays an important role in life science research. Recent patents concerning motif finding in the biomolecular data are recorded in the DNA Patent Database which serves as a resource for policy makers…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
Network motifs, the recurring regulatory structural patterns in networks, are able to self-organize to produce networks. Three major motifs, feedforward loop, single input modules and bi-fan are found in gene regulatory networks. The large…
Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site…
DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…
We develop a symbolic regression framework for extracting the governing mathematical expressions from observed data. The evolutionary approach, faiGP, is designed to leverage the properties of a function algebra that have been encoded into…
Motif discovery is one of the most challenging problems in bioinformatics today. DNA sequence motifs are becoming increasingly important in analysis of gene regulation. Motifs are short, recurring patterns in DNA that have a biological…
Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers…
RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these patterns is of fundamental importance for assessing the statistical significance of matches…
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…
A default theory can be characterized by its sets of plausible conclusions, called its extensions. But, due to the theoretical complexity of Default Logic (Sigma_2p-complete), the problem of finding such an extension is very difficult if…
The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…