Related papers: Long non-coding RNAs as a source of new peptides
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
Recent advances in Multimodal Large Language Models (MLLMs) have shown remarkable capabilities in understanding both images and 3D data, yet these modalities face inherent limitations in comprehensively representing object geometry and…
Both genomic stability and sustenance of day-to-day life rely on efficient and accurate readout of the genetic code. Single-molecule experiments show that transcription and replication are highly stochastic and irregular processes, with the…
While RNA has recently been recognized as an interesting small-molecule drug target, many challenges remain to be addressed before we take full advantage of it. This emphasizes the necessity to improve our understanding of its structures…
Ultra-long-chain fatty acids (ULCFAs) are biosynthesized in the restricted tissues such as retina, testis, and skin. The conformation of a single ULCFA, in which the sn-1 unsaturated chain has 32 carbons, in three types of tensionless…
The explosive growth of large language models (LLMs) has created a vast but opaque landscape: millions of models exist, yet their evolutionary relationships through fine-tuning, distillation, or adaptation are often undocumented or unclear,…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…
Prokaryotic gene prediction plays an important role in understanding the biology of organisms and their function with applications in medicine and biotechnology. Although the current gene finders are highly sensitive in finding long genes,…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
While protein language models (PLMs) are one of the most promising avenues of research for future de novo protein design, the way in which they transform sequences to hidden representations, as well as the information encoded in such…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…
Large language models (LLMs) have shown remarkable capabilities across various tasks, that are learned from massive amounts of text-based data. Although LLMs can control output sequence length, particularly in instruction-based settings,…
MicroRNAs (miRNAs) are a class of small noncoding RNAs that can regulate many genes by base pairing to sites in mRNAs. The functionality of miRNAs overlaps that of short interfering RNAs (siRNAs), and many features of miRNA targeting have…
Delineating how animal behavior arises from neural activity is a foundational goal of neuroscience. However, as the computations underlying behavior unfold in networks of thousands of individual neurons across the entire brain, this…
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly…
Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent…
RNA molecules follow a succession of enzyme-mediated processing steps from transcription until maturation. The participating enzymes, for example the spliceosome for mRNAs and Drosha and Dicer for microRNAs, are also produced in the cell…