Related papers: Long non-coding RNAs as a source of new peptides
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Given usefulness of protein language models (LMs) in structure and functional inference, RNA LMs have received increased attentions in the last few years. However, these RNA models are often not compared against the same standard. Here, we…
The 5' UTR, a regulatory region at the beginning of an mRNA molecule, plays a crucial role in regulating the translation process and impacts the protein expression level. Language models have showcased their effectiveness in decoding the…
Genome-wide experiments to map the DNA-binding locations of transcription-associated factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of possible direct target genes. Distinguishing functional from…
Systematic characterization of biological effects to genetic perturbation is essential to the application of molecular biology and biomedicine. However, the experimental exhaustion of genetic perturbations on the genome-wide scale is…
While coding regions in the genome have a direct interpretation in terms of protein products, significant fractions are non-coding and yet control essential biological functions. Unlike the genetic code, there is no "lookup table" that…
DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing…
Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i)…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
Image hash codes are produced by binarizing the embeddings of convolutional neural networks (CNN) trained for either classification or retrieval. While proxy embeddings achieve good performance on both tasks, they are non-trivial to…
DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…
As high-throughput biological sequencing becomes faster and cheaper, the need to extract useful information from sequencing becomes ever more paramount, often limited by low-throughput experimental characterizations. For proteins, accurate…
Most animals have separate sexes. The differential expression of gene products, in particular that of gene regulators, is underlying sexual dimorphism. Analyses of sex-biased expression have focused mostly in protein coding genes. Several…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…
A k-noncrossing RNA pseudoknot structure is a graph over $\{1,...,n\}$ without 1-arcs, i.e. arcs of the form (i,i+1) and in which there exists no k-set of mutually intersecting arcs. In particular, RNA secondary structures are 2-noncrossing…
RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…
Transcription factors (TFs) regulate gene expression by binding to specific genomic loci determined by DNA sequence. Their sequence specificity is commonly summarized by a consensus binding motif. However, eukaryotic genomes contain…
Face detection methods have relied on face datasets for training. However, existing face datasets tend to be in small scales for face learning in both constrained and unconstrained environments. In this paper, we first introduce our…
Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is…