26 papers · ranked by Valyu relevance
Claus O. Wilke, Sergei L. Kosakovsky Pond
Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I…
Michael R Rose, Todd H Oakley
Background The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research during that century. The foundations of that "Modernist" biology had thus largely crumbled by the…
Florian Jacques, Paulina Bolivar, Kristian Pietras, Emma U. Hammarlund + 1 more
'Emma U. Hammarlund' 'Arndt von Haeseler'] Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases…
Kun Li, Lian Hu, Xiantao Cai, Jialin Wu + 1 more
Molecular evolution is the process of simulating the natural evolution of molecules in chemical space to explore potential molecular structures and properties. The relationships between similar molecules are often described through transformations such as adding, deleting, and modifying atoms and chemical bonds…
Joel Valdivia Ortega
Today we are able to describe genome evolution but, there are still several open questions on this area such as: Which is the probability that a mutation occurs at a nucleotide level? Is it possible to predict the evolution of a particular genome?, or talking about preservation, is there a way to simulate the genetic…
Denghui Luo, Shi Huang
The field of molecular evolution started with the alignment of a few protein sequences in the early 1960s. Among the first results found, the genetic equidistance result has turned out to be the most unexpected. It directly inspired the ad hoc universal molecular clock hypothesis that in turn inspired the neutral…
Dovydas Kičiatovas, Johannes Cairns, Veera Partanen, Julius Hoffmann + 3 more
Recent studies have revealed bacterial genome-wide evolution to be complex and dynamic even in a constant environment. The evolution is characterized by the emergence of new clades competing or temporarily coexisting as each clade undergoes evolutionary change. Previous studies on predator-prey dynamics tracking simple…
Joel Valdivia Ortega
Today we are able to describe genome evolution but, there are still several open questions on this area such as: Which is the probability that a mutation occurs at a nucleotide level? Is it possible to predict the evolution of a particular genome?, or talking about preservation, is there a way to simulate the genetic…
Bernadette Mathew, Abhishek Halder, Nancy Jaiswal, Smruti Panda + 8 more
DNA is essentially a collection of short nucleotide sequences with a myriad of functionalities. These oligonucleotides are often studied for their function as molecular binding sites, regulatory motifs or sequence probes. The field of Bioinformatics uses a similar concept under the term “k-mers,” which is central to…
James A. Shapiro, John S. Torday
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution…
Elizabeth HJ Robbins, Yi Liu, Steven Kelly
Identifying recurrent changes in biological sequences is important to multiple aspects of biological research -from understanding the molecular basis of convergent phenotypes, to pinpointing the causative sequence changes that give rise to antibiotic resistance and disease. Here, we present RECUR, a method for…
Adi Livnat
The theory of interaction-based evolution argues that, at the most basic level of analysis, there is a third alternative for how adaptive evolution works besides a) accidental mutation and natural selection and b) Lamarckism, namely, c) information provided by natural selection on the fit between the organism and its…
Shi Huang
The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic diversity by using MET. We here examine the two key experimental observations of…
Dmitry Sherbakov, Yuri Panchin, Ancha Baranova
According to much quoted Russian/American geneticist Theodosius Dobzhansky, “Nothing in biology makes sense except in the light of evolution” [1]. Coined in 1973, this famous phrase remains up to date. Fascinating variety of the phenotypes seen as either visible or subtle differences in species, populations, and…
Joshua Meyers, Nathan Brown
De novo molecular design is effective for optimizing compounds with desirable properties in drug discovery. In the realm of chemoinformatics, population-based evolutionary approaches have been known for over a decade including those that use retrosynthetically inspired fragment-based workflows to to balance the…
Alexey V. Melkikh, Alexey V. Melkikh, Andrei Khrennikov
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of…
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…
Dariia Yehorova, Rory Crean, Peter Kasson, Shina Caroline Lynn Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction…
Authors not listed
Organic molecular crystals offer a broad spectrum of potential applications. The vast number of possible molecules is both an opportunity and a challenge, because of the prohibitive expense of exhaustively searching chemical space to find novel molecules with promising solid-state properties. Computational methods can…
Luca Peliti
Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I discuss how differential reproduction rates work in producing an exceedingly high…
Brianna Greenstein, Danielle Elsey, Geoffrey Hutchison
Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this work, we examine the general effects of a number of hyperparameters, such as population…
Julian Z. Xue, Leonid Chindelevich, Frédéric Guichard
Many well-documented macro-evolutionary phenomena, such as increases in organization hierarchy, or sudden and episodic creation of new taxa, still challenge current evolutionary theories. Here we show a new mechanism that can explain them. We begin by showing how the order of mutations can alter evolutionary…
Benjamin King, Max Winokan, Paul Stevenson, Jim Al-Khalili + 2 more
The adenine-thymine tautomer (A-T) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A-T while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A-T as…
Pavel Kohout, Michal Vasina, Marika Majerova, Veronika Novakova + 5 more
Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among residues. Computational methodologies predominantly rely on evolutionary insights, leveraging homologous sequences to pinpoint conserved and functionally…
Camille Ameline, Yann Bourgeois, Felix Vögtli, Eevi Savola + 3 more
'Jason Andras' 'Jan Engelstädter' 'Dieter Ebert'] Mol. Biol. Evol. doi: 10.1093/molbev/msaa311 In the originally published version of this manuscript, amendments were inadvertently made without author approval prior to publishing, making key data incomprehensible to the reader. The errors have now been corrected.
Fangfei Li, Jason Tarkington, Gavin Sherlock
Correction to: Journal of Molecular Evolution (2023) 91:334-344 10.1007/s00239-023-10098-0 In this article the legend for Fig. 2 and Fig. 3 was inadvertently swapped. The original article has been corrected.