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Preprints

Filtering by Subject: Bioinformatics

otb: Creating a HiC/HiFi Pipeline to Assemble the Prosapia bicincta Genome

David Molik, Amanda R Stahlke, Sharu P Sharma, et al.

Published: 2023-12-05
Subjects: Agriculture, Bioinformatics, Computational Biology, Genomics, Other Animal Sciences

The implementation of a new genomic assembly pipeline named only the best [Genome Assembly Tools] (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The [...]

Towards causal relationships for modelling species distribution

Daniele Da Re, Enrico Tordoni, Jonathan Lenoir, et al.

Published: 2023-10-15
Subjects: Biodiversity, Bioinformatics, Life Sciences, Natural Resources and Conservation, Statistical Models

1. Understanding the processes underlying the distribution of species through space and time is fundamental in several research fields spanning from ecology to spatial epidemiology. Correlative species distribution models (SDMs) involve popular statistical tools to infer species geographical distribution thanks to spatiotemporally explicit observations of species occurrences coupled with a set of [...]

Best practices for genetic and genomic data archiving

Deborah M Leigh, Amy Vandergast, Maggie Hunter, et al.

Published: 2023-09-26
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences

Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of [...]

CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes

Benjamin A Adler, Marena I Trinidad, Daniel Bellieny-Rabelo, et al.

Published: 2023-08-17
Subjects: Biochemistry, Biophysics, and Structural Biology, Bioinformatics, Life Sciences

CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain [...]

STRyper: a macOS application for microsatellite genotyping and chromatogram management

Jean Peccoud

Published: 2023-07-30
Subjects: Biodiversity, Bioinformatics, Molecular Genetics, Other Ecology and Evolutionary Biology

Microsatellite markers analyzed by capillary sequencing remain useful tools for rapid genotyping and low-cost studies. This contrasts with the lack of a free application to analyze chromatograms for microsatellite genotyping that is not restricted to human genotyping. To fill this gap, I have developed STRyper, a macOS application whose source code is published under the General Public License. [...]

Understanding local plant extinctions before it’s too late: bridging evolutionary genomics with global ecology.

Moises Exposito-Alonso

Published: 2022-12-01
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Plant Sciences

Understanding evolutionary genomic and population processes within a species range is key to anticipating the extinction of plant species before it is too late. However, most models of biodiversity risk projections under global change do not account for the genetic variation and local adaptation of different populations. Population diversity is critical to understanding extinction because [...]

Best practices in designing, sequencing and identifying random DNA barcodes

Milo S. Johnson, Sandeep Venkataram, Sergey Kryazhimskiy

Published: 2022-09-29
Subjects: Bioinformatics, Biotechnology, Cell and Developmental Biology, Ecology and Evolutionary Biology, Evolution, Life Sciences

Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new optimal design that balances [...]

Maintenance and expansion of genetic and trait variation following domestication in a clonal crop

Oliver White, Manosh Biswas, Wendawek M. Abebe, et al.

Published: 2022-09-02
Subjects: Agriculture, Bioinformatics, Biosecurity, Genetics and Genomics, Genomics, Life Sciences, Plant Sciences

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic [...]

European light skin may have evolved as an adaptation to the Neolithic sedentary lifestyle

Manuel Ferrando-Bernal

Published: 2022-07-28
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Evolution, Life Sciences, Population Biology

Light skin facilitates the penetration of ultraviolet light (UV) radiation through the skin, increasing the synthesis of vitamin D that in turn stimulates bone formation. It has been suggested that light skin appeared in the ancestors of modern Europeans as an adaptation to the conditions of low UV radiation in high latitudes; however, paleogenetic studies have recently shown it did not evolve [...]

The coevolutionary mosaic of bat betacoronavirus emergence risk

Norma Forero, Renata L. Muylaert, Stephanie N. Seifert, et al.

Published: 2022-07-02
Subjects: Biodiversity, Bioinformatics, Biology, Biotechnology, Cell and Developmental Biology, Ecology and Evolutionary Biology, Immunology and Infectious Disease, Life Sciences, Other Ecology and Evolutionary Biology, Other Life Sciences

Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially-explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like SARS, MERS, and COVID-19, we examine the global [...]

An operational workflow for producing periodic estimates of species occupancy at large scales

Rob James Boyd, Tom August, Robert Cooke, et al.

Published: 2022-06-24
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Life Sciences

Policy makers require high-level summaries of biodiversity change. However, deriving such summaries from raw biodiversity data is a complex process involving several intermediary stages. In this paper, we describe a workflow for generating annual estimates of species’ occupancy at national scales from raw species occurrence data, which can be used to construct a range of policy-relevant [...]

A minimum data standard for vector competence experiments

Velen Yifei Wu, Binqi Chen, Rebecca Christofferson, et al.

Published: 2022-06-15
Subjects: Bioinformatics, Entomology, Life Sciences, Microbiology, Virology

The growing threat of vector-borne diseases, highlighted by recent epidemics, has prompted increased focus on the fundamental biology of vector-virus interactions. To this end, experiments are often the most reliable way to measure vector competence (the potential for arthropod vectors to transmit certain pathogens). Data from these experiments are critical to understand outbreak risk, but – [...]

EvoPhylo: an R package for pre- and postprocessing of morphological data from relaxed clock Bayesian phylogenetics

Tiago R. Simões, Noah Greifer, Joëlle Barido-Sottani, et al.

Published: 2022-06-07
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Evolution, Life Sciences

1. Relaxed clock Bayesian evolutionary inference (BEI) enables the co-estimation of phylogenetic trees and evolutionary parameters associated with models of character and lineage evolution. Fast advances in new model developments over the past decade have boosted BEI as a major macroevolutionary analytical framework using morphological and/or molecular data across vastly different study systems. [...]

Evolution and impact of socially transferred materials

Sanja Maria Hakala, Haruna Fujioka, Ornela De Gasperin, et al.

Published: 2022-05-28
Subjects: Animal Sciences, Biodiversity, Bioinformatics, Cell and Developmental Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Physiology, Systems Biology

Since the dawn of life, transfers of metabolized material between individuals have led to great innovations of evolution. When metabolized material is transferred from one individual’s body to another (as with sperm, eggs, milk, symbionts), secondary manipulative molecules that induce a physiological response in the receiver are often transferred along with the primary cargo. The bioactive and [...]

Towards a cohesive understanding of ecological complexity

Federico Riva, Caio Graco-Roza, Gergana N. Daskalova, et al.

Published: 2022-04-15
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Life Sciences, Systems Biology

Understanding phenomena typical of complex systems is key for progress in ecology and conservation amidst escalating global environmental change. However, myriad definitions of complexity hamper conceptual advancements and synthesis. Ecological complexity may be better understood by following the strong theoretical basis of complexity science. We conduct bibliometric and text-mining analyses to [...]

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