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Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation
Ancestral sequence reconstruction (ASR) is a phylogenetic method widely used to analyze the properties of ancient biomolecules and to elucidate...
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Methodologies for Microbial Ancestral Sequence Reconstruction
The reconstruction of genetic material of ancestral organisms constitutes a powerful application of evolutionary biology. A fundamental step in this...
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Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution
The complex and bioactive monoterpene indole alkaloids (MIAs) found in Catharanthus roseus and related species are the products of many millions of...
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Reducing the Impact of Domain Rearrangement on Sequence Alignment and Phylogeny Reconstruction
Existing computational approaches for studying gene family evolution generally do not account for domain rearrangement within gene families. However,...
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Resurrecting Enzymes by Ancestral Sequence Reconstruction
Ancestral Sequence Reconstruction (ASR) allows one to infer the sequences of extinct proteins using the phylogeny of extant proteins. It consists of...
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Y chromosome sequence and epigenomic reconstruction across human populations
Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the...
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Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs
Understanding the evolutionary adaptations that enable avian influenza viruses to transmit in mammalian hosts could allow better detection of...
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Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor
SARS-CoV-2 is a unique event, having emerged suddenly as a highly infectious viral pathogen for human populations. Previous phylogenetic analyses...
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Gapr for large-scale collaborative single-neuron reconstruction
Whole-brain analysis of single-neuron morphology is crucial for unraveling the complex structure of the brain. However, large-scale neuron...
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Ancestral Sequence Reconstruction and Alternate Amino Acid States Guide Protein Library Design for Directed Evolution
Engineered proteins possess nearly limitless possibilities in medical and industrial applications but finding a precise amino acid sequence for these...
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Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond
As both a computational and an experimental endeavor, ancestral sequence reconstruction remains a timely and important technique. Modern approaches...
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A 217-year precipitation reconstruction in the Habahe area, **njiang, Northeast China
Evaluating long-term changes in precipitation resources is important for accurate hydrological evaluation and forecasting, water security and...
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Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom
Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies and can trace small-scale sequence modifications through the...
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Ancestral Sequence Reconstruction of the Ribosomal Protein uS8 and Reduction of Amino Acid Usage to a Smaller Alphabet
Understanding the origin and early evolution of proteins is important for unveiling how the RNA world developed into an RNA–protein world. Because...
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AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders
Reconstructing ancestral gene orders from the genome data of extant species is an important problem in comparative and evolutionary genomics. In a...
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Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
Open-3DSIM is an open-source reconstruction platform for three-dimensional structured illumination microscopy. We demonstrate its superior...
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Reconstruction of private genomes through reference-based genotype imputation
BackgroundGenotype imputation is an essential step in genetic studies to improve data quality and statistical power. Public imputation servers are...
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PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction
BackgroundThe specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the...
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Quorum sensing in bacteria: in silico protein analysis, ecophysiology, and reconstruction of their evolutionary history
BackgroundQuorum sensing (QS) is a sophisticated cell-to-cell signalling mechanism that allows the coordination of important processes in microbial...
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SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
BackgroundSimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well...
