Related papers: TranspoGene and microTranspoGene: transposed eleme…
Chromosomal rearrangements, particularly those mediated by transposable elements (TEs), can drive adaptive evolution by creating chimeric genes, inducing de novo gene formation, or altering gene expression. Here, we investigate…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new…
A major challenge in biology is explaining how novel characters originate, however, the molecular mechanisms that underlie the emergence of evolutionary innovations are unclear. Here we show that while gene expression in the uterus evolves…
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying…
Transfer-RNA genes in archaea often have introns intervening between exon sequences. The structural motif at the boundary between exon and intron is the bulge-helix-bulge. Computational investigations of these boundary structures in H.…
Bioinformatics, as an emerging and rapidly developing interdisciplinary, has become a promising and popular research field in 21st century. Extracting and explaining useful biological information from huge amount of genetic data is an…
In euryarchaeal methanogen M.kandleri and in Nanoarchaea N. equitans some of the missing tRNA genes are embedded in others. We argue from bioinformatic evidence that position specific intron splicing is the key behind co-location of these…
Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the human transcriptome. Most of the editing…
Transposable elements are DNA sequences that can move around to different positions in the genome. During this process, they can cause mutations, and lead to an increase in genome size. Despite representing a large genomic fraction,…
Transposons are small, self-replicating DNA sequences found in every branch of life. Often, one transposon will parasitize another, forming a tiny intracellular ecosystem. In some species these ecosystems thrive, while in others they go…
This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…
Here we present Translocatome, the first dedicated database of human translocating proteins. The core of the Translocatome database is the manually curated data set of 213 human translocating proteins listing the source of their…
Elucidating principles that underlie computation in neural networks is currently a major research topic of interest in neuroscience. Transfer Entropy (TE) is increasingly used as a tool to bridge the gap between network structure, function,…
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational…
Several recent studies show that companion cells in flowering plant gametophytes relax epigenetic control of transposable elements (TEs) to promote production of small RNA that presumably assist nearby reproductive cells in management of…
This paper introduces a novel approach to position embeddings in transformer models, named "Exact Positional Embeddings" (ExPE). An absolute positional embedding method that can extrapolate to sequences of lengths longer than the ones it…
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes…