scholarly journals GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

2019 ◽  
Vol 36 (11) ◽  
pp. 2604-2619 ◽  
Author(s):  
Elodie Laine ◽  
Yasaman Karami ◽  
Alessandra Carbone
Keyword(s):  
Evolutionary History ◽  
Recent Progress ◽  
State Of The Art ◽  
Fast Method ◽  
Biological Sequences ◽  
Epistatic Model ◽  
Input Alignment ◽  
Wide Range ◽  
History Of ◽  
Better Than

Abstract The systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering, and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modeling intersite dependencies within biological sequences. However, state-of-the-art methods remain time consuming. Here, we present Global Epistatic Model for predicting Mutational Effects (GEMME) (www.lcqb.upmc.fr/GEMME), an original and fast method that predicts mutational outcomes by explicitly modeling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. GEMME uses only a few biologically meaningful and interpretable parameters. Assessed against 50 high- and low-throughput mutational experiments, it overall performs similarly or better than existing methods. It accurately predicts the mutational landscapes of a wide range of protein families, including viral ones and, more generally, of much conserved families. Given an input alignment, it generates the full mutational landscape of a protein in a matter of minutes. It is freely available as a package and a webserver at www.lcqb.upmc.fr/GEMME/.

scholarly journals GEMME: a simple and fast global epistatic model predicting mutational effects

2019 ◽  
Author(s):  
Elodie Laine ◽  
Yasaman Karami ◽  
Alessandra Carbone
Keyword(s):  
High Throughput ◽  
Evolutionary History ◽  
Recent Progress ◽  
State Of The Art ◽  
Genomic Data ◽  
Biological Sequences ◽  
Epistatic Model ◽  
History Of ◽  
Viral Sequences ◽  
Better Than

AbstractsThe systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modeling inter-site dependencies within biological sequences. However, state-of-the-art methods require numerous highly variable sequences and remain time consuming. Here, we present GEMME (www.lcqb.upmc.fr/GEMME), a method that overcomes these limitations by explicitly modeling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. Assessed against 41 experimental high-throughput mutational scans, GEMME overall performs similarly or better than existing methods and runs faster by several orders of magnitude. It greatly improves predictions for viral sequences and, more generally, for very conserved families. It uses only a few biologically meaningful and interpretable parameters, while existing methods work with hundreds of thousands of parameters.

Computers in Geology - 25 Years of Progress

1994 ◽  
Keyword(s):  
Computer Modeling ◽  
Quantitative Methods ◽  
State Of The Art ◽  
International Association ◽  
Mathematical Geology ◽  
25Th Anniversary ◽  
The Earth ◽  
Wide Range ◽  
History Of ◽  
Mapping Techniques

This volume vividly demonstrates the importance and increasing breadth of quantitative methods in the earth sciences. With contributions from an international cast of leading practitioners, chapters cover a wide range of state-of-the-art methods and applications, including computer modeling and mapping techniques. Many chapters also contain reviews and extensive bibliographies which serve to make this an invaluable introduction to the entire field. In addition to its detailed presentations, the book includes chapters on the history of geomathematics and on R.G.V. Eigen, the "father" of mathematical geology. Written to commemorate the 25th anniversary of the International Association for Mathematical Geology, the book will be sought after by both practitioners and researchers in all branches of geology.

scholarly journals Cache-efficient sweeping-based interval joins for extended Allen relation predicates

2021 ◽  
Author(s):  
Danila Piatov ◽  
Sven Helmer ◽  
Anton Dignös ◽  
Fabio Persia
Keyword(s):  
Data Structure ◽  
Experimental Evaluation ◽  
State Of The Art ◽  
Temporal Databases ◽  
Access Method ◽  
Wide Range ◽  
Interval Relation ◽  
Cache Efficient ◽  
Join Algorithms ◽  
Better Than

AbstractWe develop a family of efficient plane-sweeping interval join algorithms for evaluating a wide range of interval predicates such as Allen’s relationships and parameterized relationships. Our technique is based on a framework, components of which can be flexibly combined in different manners to support the required interval relation. In temporal databases, our algorithms can exploit a well-known and flexible access method, the Timeline Index, thus expanding the set of operations it supports even further. Additionally, employing a compact data structure, the gapless hash map, we utilize the CPU cache efficiently. In an experimental evaluation, we show that our approach is several times faster and scales better than state-of-the-art techniques, while being much better suited for real-time event processing.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

scholarly journals Haplotype threading: accurate polyploid phasing from long reads

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Sven D. Schrinner ◽  
Rebecca Serra Mari ◽  
Jana Ebler ◽  
Mikko Rautiainen ◽  
Lancelot Seillier ◽  
...  
Keyword(s):  
Open Source ◽  
Evolutionary History ◽  
State Of The Art ◽  
Regions Of Interest ◽  
Breeding Strategies ◽  
Polyploid Species ◽  
Two Stage ◽  
Long Reads ◽  
History Of ◽  
Genomic Regions

Abstract Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WhatsHap polyphase, a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing quality. Using a real tetraploid potato dataset, we demonstrate how to assemble local genomic regions of interest at the haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap.

Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

2020 ◽  
Vol 66 (3-4) ◽  
pp. 142-150
Author(s):  
Jessica Worthington Wilmer ◽  
Andrew P. Amey ◽  
Carmel McDougall ◽  
Melanie Venz ◽  
Stephen Peck ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
The West ◽  
European Settlement ◽  
Low Genetic Diversity ◽  
Eastern Australia ◽  
Wide Range ◽  
History Of ◽  
Open Forests ◽  
Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

scholarly journals Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 70 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
Nigel French
Keyword(s):  
Evolutionary History ◽  
State Of The Art ◽  
Molecular Techniques ◽  
Evolutionary Significance ◽  
Phylogenetic Structure ◽  
Bayesian Approaches ◽  
Phylogenetic Studies ◽  
Anchored Phylogenomics ◽  
History Of ◽  
Phylogenomic Analyses

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.

Prospects of Emerging Engineered oxide nanomaterials and their Applications

2016 ◽  
Vol 66 (4) ◽  
pp. 323 ◽  
Author(s):  
Jitendra Gangwar ◽  
Bipin Kumar Gupta ◽  
Avanish Kumar Srivastava
Keyword(s):  
Recent Progress ◽  
State Of The Art ◽  
Vanadium Oxides ◽  
Review Article ◽  
Synthesis And Characterization ◽  
Oxide Materials ◽  
Wide Range ◽  
Fundamental Understanding ◽  
Potential Applications

<p>This review article mainly focused on the recent progress on the synthesis and characterization of emerging artificially engineered nanostructures of oxide materials as well as their potential applications. A fundamental understanding about the state-of-the-art of the synthesis for different size, shape and morphology, which can be tuned to the desired properties of oxide nanomaterials have discussed in details in this review. The present review covers the a wide range of artificially engineered oxide nanomaterials such as cadmium-, cupric-, nickel-, magnesium-, zinc-, titanium-, tin-, aluminium-, and vanadium-oxides and their useful applications in sensors, optical displays, nanofluids and defence.</p>

scholarly journals Evolutionary History of LTR Retrotransposon Chromodomains in Plants

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Anton Novikov ◽  
Georgiy Smyshlyaev ◽  
Olga Novikova
Keyword(s):  
Evolutionary History ◽  
Higher Plants ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Moss Species ◽  
Plant Genomes ◽  
Group I ◽  
Wide Range ◽  
History Of ◽  
Computer Based

Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization.

Piotrowski-Altmann law: State of the art

Glottotheory ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kamil Stachowski
Keyword(s):  
State Of The Art ◽  
Paper Briefly ◽  
Lexical Borrowing ◽  
Morphological Form ◽  
Wide Range ◽  
History Of ◽  
The Law ◽  
Slow Fashion

AbstractThe term Piotrowski-Altmann law refers to a wide range of linguistic phenomena which proceed in the “slow-fast-slow” fashion, i.e. drawing a sigmoid on a graph. They include the replacement of an old morphological form with a new one, lexical borrowing between languages, the growth of a child’s vocabulary, and many others. The paper briefly discusses the history of the law, its current variants and their applications, and lastly science theoretical problems connected with it. It concludes that our law is in fact a group of psycho- and sociological models, whose application to linguistics requires further deliberation.

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