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View article: The Unified Phenotype Ontology : a framework for cross-species integrative phenomics
The Unified Phenotype Ontology : a framework for cross-species integrative phenomics Open
Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities o…
View article: An evolutionarily conserved Hox-Gbx segmentation code in the rice coral Montipora capitata
An evolutionarily conserved Hox-Gbx segmentation code in the rice coral Montipora capitata Open
Segmentation of the gastric cavity is a synapomorphic trait of cnidarians of the class Anthozoa (corals and sea anemones), with different clades forming distinct numbers of segments. In the starlet sea anemone Nematostella vectensis, for e…
View article: An evolutionarily conserved Hox-Gbx segmentation code in the rice coral Montipora capitata
An evolutionarily conserved Hox-Gbx segmentation code in the rice coral Montipora capitata Open
Segmentation of the gastric cavity is a synapomorphic trait of cnidarians of the class Anthozoa (corals and sea anemones), with different clades forming distinct numbers of segments. In the starlet sea anemone Nematostella vectensis, for e…
View article: Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI) Open
Background Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their constructio…
View article: An evolutionarily conserved Hox-Gbx segmentation code in the rice coral <i>Montipora capitata</i>
An evolutionarily conserved Hox-Gbx segmentation code in the rice coral <i>Montipora capitata</i> Open
Segmentation of the gastric cavity is a synapomorphic trait of cnidarians of the class Anthozoa (corals and sea anemones), with different clades forming distinct numbers of segments. In the starlet sea anemone Nematostella vectensis , for …
View article: The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics
The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics Open
Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities o…
View article: <i>Chamaeleo calyptratus</i>(veiled chameleon) chromosome-scale genome assembly and annotation provides insights into the evolution of reptiles and developmental mechanisms.
<i>Chamaeleo calyptratus</i>(veiled chameleon) chromosome-scale genome assembly and annotation provides insights into the evolution of reptiles and developmental mechanisms. Open
The family Chamaeleonidae comprises 228 species, boasting an extensive geographic spread and an array of evolutionary novelties and adaptations, but a paucity of genetic and molecular analyses. Veiled chameleon ( Chamaeleo calyptratus ) ha…
View article: Sugar assimilation underlying dietary evolution of Neotropical bats
Sugar assimilation underlying dietary evolution of Neotropical bats Open
Dietary specializations in animals lead to adaptations in morphology, anatomy and physiology. Neotropical bats, with their high taxonomic and trophic diversity, offer a unique perspective on diet-driven evolutionary adaptations. Here we as…
View article: Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI) Open
Background: Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their constructi…
View article: Topological structures and syntenic conservation in sea anemone genomes
Topological structures and syntenic conservation in sea anemone genomes Open
There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these g…
View article: Sugar assimilation underlying dietary evolution of Neotropical bats
Sugar assimilation underlying dietary evolution of Neotropical bats Open
Summary Specializations in animal diets drive selective demands on morphology, anatomy, and physiology. Studying adaptations linked to diet evolution benefits from examining Neotropical bats, a remarkable group with high taxonomic and trop…
View article: An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes
An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes Open
Programmed DNA loss is a gene silencing mechanism that is employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. Reconstructing the evolution of somatically eliminated (germline-s…
View article: Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies Open
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dependency management. To manage these processes, a diverse se…
View article: Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies Open
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set…
View article: Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms Open
As the planarian research community expands, the need for an interoperable data organization framework for tool building has become increasingly apparent. Such software would streamline data annotation and enhance cross-platform and cross-…
View article: INCATools/ontology-development-kit: May 6 2021 release
INCATools/ontology-development-kit: May 6 2021 release Open
v1.2.28 (6 May 2021) New DOSDP tools version 0.17 Major: we developed an Apple M1 compatible ODK image! Thanks to @gouttegd who did all the hard work. Super excited about this! The new image can be found here: https://hub.docker.com/r/obot…
View article: INCATools/ontology-development-kit: 2021-04-04 release
INCATools/ontology-development-kit: 2021-04-04 release Open
v1.2.27 (4 April 2021) revived odklite image with a minimum install (smaller in size than odkfull, with just robot and owltools!) revived robot image with just robot installed Added Jena 3.12.0 to odkfull image Added module configs (see do…
View article: Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny
Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny Open
Draft genome sequences of non-bilaterian species have provided important insights into the evolution of the metazoan gene repertoire. However, there is little information about the evolution of gene clusters, genome architectures and karyo…
View article: Genomic diversity generated by a transposable element burst in a rice recombinant inbred population
Genomic diversity generated by a transposable element burst in a rice recombinant inbred population Open
Significance Transposable elements (TEs) represent the largest component of the genomes of higher eukaryotes. Among this component are some TEs that have attained very high copy numbers, with hundreds, even thousands, of elements. By docum…
View article: Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates
Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates Open
Regulatory elements of fish regeneration Some animals regenerate extensively, whereas others, such as mammals, do not. The reason behind this difference is not clear. If the genetic mechanisms driving regeneration are evolutionarily conser…
View article: Genomic diversity generated by a transposable element burst in a rice recombinant inbred population
Genomic diversity generated by a transposable element burst in a rice recombinant inbred population Open
Genomes of all characterized higher eukaryotes harbor examples of transposable element (TE) bursts - the rapid amplification of TE copies throughout a genome. Despite their prevalence, understanding how bursts diversify genomes requires th…
View article: The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms
The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms Open
As the planarian Schmidtea mediterranea ( Smed ) gains popularity as a research organism, the need for standard anatomical nomenclature is increasingly apparent. A controlled vocabulary streamlines data annotation, improves data organizati…
View article: The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species Open
In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characteri…
View article: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species
Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species Open
Logical definitions, in particular those following the Entity-Quality approach, are increasingly used to drive automated classification of phenotypes and integrate phenotypes across species semantically. Over the years, the lack of consist…
View article: Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution Open
When published, this article did not initially appear open access. This error has been corrected, and the open access status of the paper is noted in all versions of the paper. Additionally, affiliation 16 denoting equal contribution was m…
View article: Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses
Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses Open
Research in evolutionary biology has been progressively influenced by big data such as massive genome and transcriptome sequencing data, scalar measurements of several phenotypes on tens to thousands of individuals, as well as from collect…
View article: Phylogenetic and Phylogenomic Definition of <i>Rhizopus</i> Species
Phylogenetic and Phylogenomic Definition of <i>Rhizopus</i> Species Open
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bi…
View article: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution Open
The sea lamprey ( Petromyzon marinus ) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementar…