24 papers · ranked by Valyu relevance
Yuri I Wolf, Eugene V Koonin
A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the…
Alexander Manolov, Dmitry Konanov, Dmitry Fedorov, Ivan Osmolovsky + 3 more
'Rinat Vereshchagin' 'Elena Ilina' 'Morgan Langille'] Comparative genomics studies may be used to acquire new knowledge regarding genome architecture, which defines the rules for combining sets of genes in the genome of living organisms. Hundreds of thousands of prokaryotic genomes have been sequenced and assembled.…
Helen Piontkivska, Fabia Ursula Battistuzzi, Tzu-Chiao Chao, Nicole Hansmeier
Genome complexity is an umbrella term that reflects the existence of multiple structural levels of genome organization, from compositional biases and differential gene expression to higher-order genome architectures. This includes whole genome duplications, pan-genomes, and 3D-folding, as well as how these features are…
Alexander I Manolov, Dmitry N Konanov, Dmitry E Fedorov, Ivan S Osmolovsky + 1 more
Comparative genomics studies may be used to acquire new knowledge about chromosomal architecture - the rules to combine a set of genes in a genome of a living organism. Hundreds of thousands of prokaryote genomes were sequenced and assembled. Still, there is a lack of computational tools able to compare hundreds of…
Vinhthuy Phan, Shanshan Gao, Quang Tran, Nam S Vo
Background Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem…
Andrés Moya, José L. Oliver, Miguel Verdú, Luis Delaye + 9 more
Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and…
L. P. Karakatsanis, Evgenios Pavlos, George Tsoulouhas, George Stamokostas + 4 more
'George Stamokostas' 'Timothy L. Mosbruger' 'Jamie L. Duke' 'G. P. Pavlos' 'Dimitri Monos'] Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes.…
Francisco Javier Lobo-Cabrera
Complexity is often associated with increasing non-coding DNA (ncDNA). For example, the human genome is in its vast majority ncDNA. Here, it is hypothesized that normalized ncDNA (nncDNA) has in fact diminished in evolution. This definition of ncDNA content takes into consideration total proteomic content. It is shown…
R. Salgado-Garcı́a, Edgardo Ugalde
We introduce a method to estimate the complexity function of symbolic dynamical systems from a finite sequence of symbols. We test such complexity estimator on several symbolic dynamical systems whose complexity functions are known exactly. We use this technique to estimate the complexity function for genomes of…
Jorge Miguel Silva, Diogo Pratas, Tânia Caetano, Sérgio Matos
Viruses are a strong driving force of life and evolution. They are the shortest and most abundant life realm, estimated at around 1031 particles . Likewise, viruses occupy almost every ecosystem [] and infect all types of life forms . Viruses depend on the host’s cell for replication. This dependence has forced viruses…
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…
Eugene V. Koonin
Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct…
Parthasarathi Sahu, Sashikanta Barik, Koushik Ghosh, Hemachander Subramanian
Genome size varies widely among organisms, from compact genomes of bacteria to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome size. We use a parameter-free model to study genome size evolution under selection…
Dan Graur
Because genomes are products of natural processes rather than "intelligent design," all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called "rubbish DNA." Rubbish DNA consists of "junk DNA," i.e., the fraction of the genome on which selection does not…
Joseph Riolo, Andrew J. Steckl
When knowledge has advanced to a state that includes a predictive understanding of the relationship between genome sequence and organism phenotype it will be possible for future engineers to design and produce synthetic organisms. However, the possibility of synthetic biology does not necessarily guarantee its…
Sachithra Kalhari Yaddehige, Chiara Vischioni, Leonardo Alberghini, Michele Berselli + 1 more
Evolutionary studies require extensive examination of genomic information across all domains of life. Despite the availability of a large number of genomes through GenBank, the effective visualisation or comparison of the information they contain is challenging due to many reasons including their size. We introduce…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Donald G. Gilbert
Significant discrepancies in genome sizes measured by cytometric methods versus DNA sequence estimates are frequent, including recent long-read DNA assemblies of plant and animal genomes. A new DNA sequence measure using a baseline of unique conserved genes, Gnodes, finds the larger cytometric measures are often…
John Herrick, Bianca Sclavi
Evolutionary changes in karyotype have long been implicated in speciation events; however, the phylogenetic relationship between karyotype diversity and species richness in closely and distantly related mammalian lineages remains to be fully elucidated. Here we examine the association between genome diversity and…
Alexei A. Sharov, Richard Gordon
An extrapolation of the genetic complexity of organisms to earlier times suggests that life began before the Earth was formed. Life may have started from systems with single heritable elements that are functionally equivalent to a nucleotide. The genetic complexity, roughly measured by the number of non-redundant…
Cindy Ng, Anirban Samanta, Ole Aalund Mandrup, Emily Tsang + 3 more
The folding of double-stranded DNA around histones is a central mechanism in eukaryotic cells for compacting the genetic information into chromosomes. Very few artificial methods are available for controlling the shape of dsDNA at any level, whereas several artificial methods have been developed to efficiently organize…
Anna Matuszyńska, Oliver Ebenhöh, Matias D. Zurbriggen, Daniel C. Ducat + 1 more
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It…
HANIYEH ABDOLLAHZADEH, Tonya Peeples, Mohammad Shahcheraghi
DNA-based nanomaterials have shown great potential in numerous applications, thanks to their unique properties including DNA's various molecular interactions, programmability, and versatility with biological modules. Meanwhile, the DNA origami platforms have shown promise in the creation of drug carriers. This…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…