Related papers: Noncoding RNAs evolutionarily extend animal lifesp…
Long non-coding RNAs (lncRNAs) serve as crucial regulators in numerous biological processes. Although they share sequence similarities with messenger RNAs (mRNAs), lncRNAs perform entirely different roles, providing new avenues for…
The reward system is one of the fundamental drivers of animal behaviors and is critical for survival and reproduction. Despite its importance, the problem of how the reward system has evolved is underexplored. In this paper, we try to…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Long non-coding RNAs (lncRNAs) are important regulators to modulate gene expression and cell proliferation in the developing human brain. Previous methods mainly use bulk lncRNA and mRNA expression data to study lncRNA regulation. However,…
My analysis uses methods developed for data mining microarray experiments, adapted for ageing research. Methods bridge knowledge of statistical mechanics with data mining methods developed in statistical mathematics. Analyses can reveal how…
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this…
In order to understand the phenomenon of longevity in biological world, the relationship between the potential of longevity and the structural complexity of an organism is analyzed. I. The potential of longevity is the maximum lifespan of…
As cell proliferation is limited due to the loss of telomere repeats in DNA of normal somatic cells during division, telomere attrition can possibly play an important role in determining the maximum life span of organisms as well as…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Emerging evidence suggests that the introns and intergenic sequences of the genomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based, genetic regulatory network. It is believed that this network is responsible for the…
Transfer RNAs (tRNAs) are essential components of the translational machinery. Their abundance and diversity shape decoding capacity and protein synthesis efficiency and accuracy. Because tRNA abundance is encoded in the genome through tDNA…
Expansion Microscopy is a super-resolution technique in which physically enlarging samples in an isotropic manner increases inter-molecular distances such that nano-scale structures can be resolved using light microscopy. This is…
The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of…
MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
Despite tremendous advances in the field of genomics, the amount and function of the large non-coding part of the genome in higher organisms remains poorly understood. Here we report an observation, made for 37 fully sequenced eukaryotic…
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an…
The paper proposes to employ deep convolutional neural networks (CNNs) to classify noncoding RNA (ncRNA) sequences. To this end, we first propose an efficient approach to convert the RNA sequences into images characterizing their…
Deep phenotyping study has become an emerging field to understand the gene function and the structure of biological networks. For the living animal C. elegans, recent advances in genome-editing tools, microfluidic devices and phenotypic…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…