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64 results for “Assembly Modeling”
Genome assemblies and gene models of of the zoantharians Palythoa mizigama and Palythoa umbrosa
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Revealing the drivers of parasite community assembly: using avian haemosporidians to model global dynamics of parasite species turnover
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Long read genome assembly of Automeris io (Lepidoptera: Saturniidae) an emerging model for the evolution of deimatic displays
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Data from: Abundance data applied to a novel model invertebrate host sheds new light on parasite community assembly in nature
<ol> <li>Understanding how environmental drivers influence the assembly of parasite communities, in addition to how parasites may interact at an infracommunity level, are fundamental requirements for the study of parasite ecology. Knowledge of how parasite communities are assembled will help to predict the risk of parasitism for hosts, and model how parasite communities may change under variable conditions. However, studies frequently rely on presence-absence data and examine multiple host species or sites, metrics which may be too coarse to characterise nuanced within-host patterns.</li> <li>We utilised a novel host system, the freshwater mussel <i>Anodonta anatina</i>, to investigate the drivers of community structure and explore parasite interactions. In addition, we aimed to highlight consistencies and inconsistencies between presence-absence and abundance data.</li> <li>Our analysis incorporated 14 parasite taxa and 720 replicate infracommunities. Using redundancy analysis, a joint species distribution model and a Markov random fields approach, we modelled the impact of both host-level and environment-level characteristics on parasite structure, as well as parasite-parasite correlations after accounting for all other factors. This approach was repeated for both the presence and abundance of all parasites.</li> <li>We demonstrated that the regional species pool, individual host characteristics (mussel length and gravidity) and predicted parasite-parasite interactions are all important but to varying degrees across parasite species, suggesting that applying generalities to parasite community construction is too simplistic. Further, we showed that presence-absence data fails to capture important density-dependent effects of parasite load for parasites with high abundance, and in general performs poorly for high-intensity parasites.</li> <li>Host and parasite traits, as well as broader environmental factors, all contribute to parasite community structure, emphasising that an integrated approach is required to study community assembly. However, care must be taken with the data used to infer patterns, as presence-absence data may lead to incorrect ecological inference.</li> </ol>
Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
We assembled a de novo transcriptome of short-read Illumina RNA-Seq data generated from telencephalon and diencephalon tissue samples from the Kentish plover, Charadrius alexandrinus. This is a species of considerable interest in behavioural ecology for its highly variable mating system and parental behaviour, but it lacks genomic resources and is evolutionarily distant from the few available avian draft genome sequences. We assembled and identified over 21 000 transcript contigs with significant expression in our samples, showing high homology to exonic sequences in avian draft genomes. From these, we identified >31 000 high-quality SNPs and > 2500 simple sequence repeats (SSRs). We also analysed expression patterns in our data to identify potential candidate genes related to differences in male and female behaviour, identifying over 200 nonoverlapping putative autosomal transcripts that show significant expression differences between males and females. Gene ontology analysis revealed that female-biased transcripts were significantly enriched for cerebral functions related to learning, cognition and memory, and male-biased transcripts were mostly enriched for terms related to neural function such as neuron projection and synapses. This data set provides one of the first de novo transcriptome assemblies from non-normalized short-read next-generation data and outlines an effective strategy for measuring sequence and expression variability simultaneously without the aid of a reference genome.
Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
The self-incompatible species Arabidopsis halleri is a close relative of the self-compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability make A. halleri a useful model for ecological genomics studies. We used long-insert mate-pair libraries to improve the genome assembly of the A. halleri ssp. gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high-quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold. The assembly will enhance the genomewide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri.
Data from: Using filter-based community assembly models to improve restoration outcomes
1. Ecological filter models derived from community assembly theory can inform restoration planning by highlighting management actions most likely to affect community composition. Despite growing interest in these models, many restoration studies solely manipulate a single filter—the biotic filter by altering interspecific competition in studies—while ignoring abiotic and dispersal filters that may also influence restoration success. 2. To examine how manipulating all three filters (biotic, abiotic, dispersal) affected restoration in an annual-type grassland, we seeded native forbs from the same functional group as a target invader to increase biotic resistance to invasion (biotic filter), cut standing biomass and either removed it or returned it to plots as litter to alter light conditions (abiotic filter), and added native forbs at different seeding rates to alter density of establishing native populations (dispersal filter). We measured restoration success by recording native species and invader cover in plots. 3. The addition of native species with phenological and morphological traits similar to the target invader reduced invasion and increased native populations, but only in litter-free plots when high-densities of native seed were added. 4. Seeding two species with functional traits similar to the invader was more effective at reaching restoration goals than seeding just one functionally similar species. As such, trait differences among restoration species, even species belonging to the same functional group, may increase biotic resistance to invasion in restored communities. 5. Litter removal altered native-invader interactions. When litter was kept, added natives did not reduce invader cover. However, when litter was removed, added natives led to declines in invader cover. 6. Increasing native seeding rates led to larger native populations and increased invasion resistance. 7. Synthesis and applications. In this study, simultaneously manipulating biotic, abiotic and dispersal filters was necessary to optimize restoration outcomes. In particular, the biotic filter only contributed to successful restoration outcomes under abiotic and dispersal conditions that were created through management actions specifically targeting these two additional filters. Restoration planning based on filter models should incorporate actions that target all three filters, rather than solely focusing on the biotic filter.
Dataset from "Employing hidden Markov models to assess the genetic content of genome assemblies"
<p>Dataset used to reach the conclusions in "Employing hidden Markov models to assess the genetic content of genome assemblies".</p>
Formation and Retrieval of Cell Assemblies in a Biologically Realistic Spiking Neural Network Model of Area CA3 in the Mouse Hippocampus
<p>Dataset accompanying the manuscript "Formation and Retrieval of Cell Assemblies in a Biologically Realistic Spiking Neural Network Model of Area CA3 in the Mouse Hippocampus". This dataset is used to re-create all figure panels with underlying data in the manuscript.</p>
Model outputs and observation data for "Implementation and evaluation of the unified stomatal optimization approach in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)"
<p>Model outputs and observation data for paper "Implementation and evaluation of the unified stomatal optimization approach in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)".</p>
MD simulation trajectories associated to the publication: Multi-eGO: model improvements towards the study of complex self-assembly processes
<p>The three tgz compressed files include the simulations data and resulting trajectories for the three systems discussed in the work. In particular: </p><ul><li>ab42.tgz includes a random_coil simulation, the multi-eGO simulation of the monomer performed in triplicate and the simulations performed with the original multi-eGO model.</li><li>ttr.tgz includes the randomcoil simulations for both the intramolecular as well as the intermolecular interactions at the three different concentrations, the simulation of the monomer performed in triplicate, and the aggregation kinetics performed in triplicate at the three reported concentrations</li><li>protein_g.tgz includes the reference GB1 simulation, a randomcoil simulation and the 200 multi-eGO folding simulations.</li></ul>
Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
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Microscale modelling of dielectrophoresis assembly processes
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Data from: Abundance data applied to a novel model invertebrate host sheds new light on parasite community assembly in nature
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Data from: Using filter-based community assembly models to improve restoration outcomes
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Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
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Data from: Recasting the dynamic equilibrium model through a functional lens: the interplay of trait-based community assembly and climate
1. According to the dynamic equilibrium hypothesis (DEH), plant species richness is locally controlled by productivity and disturbance. Given that regional conditions widely affect local environmental variables such as soil nutrient availability, the DEH predictions could be improved by considering how climate influences local controls of species richness. Further, a trait-based approach to community assembly has the potential to reveal a deeper, mechanistic understanding of species richness variation across environments. Here we bring together DEH and trait-based community assembly expectations to examine if and how local relationships between diversity, disturbance and productivity are affected by habitat filtering and regional climate. 2. We specifically tested how gradients of local nutrient availability and disturbance intensity interact with climatic conditions to drive the species richness of grassland communities. Further, we recast the DEH through a functional lens by exploring how disturbance-diversity and nutrient availability-diversity relationships are shaped by the functional space occupied by species in a community and species packing within this functional space. 3. The functional space occupied by co-occurring species and the way they are functionally packed are quantified using multi-trait indices calculated with five core plant functional traits. Working with grassland communities spread across differing regional climatic conditions, we used mixed models to test if the variation in taxonomic and functional metrics corresponded to the dynamic equilibrium model's predictions as well as to determine the relationship between those metrics. 4. Contrary to the expectations based on the relation between species richness and the functional components considered, taxonomic and functional metrics did not vary in accordance along environmental gradients. Climate strongly interacted with the local environment to modulate local diversity patterns, sometimes even inversing a given trend and falsifying the DEH predictions. 5. Synthesis. Our findings quantitatively highlight the interplay between regional and local environmental gradients in driving community assembly. We demonstrate that, depending on climatic conditions, observed patterns of both taxonomic and functional community composition can be opposite to expected productivity-diversity and disturbance-diversity relationships. This emphasizes the relevance of multi-faceted studies of biodiversity and the need for a more systematic quantification of regional controls in community assembly studies.
Data from: State-space reduction and equivalence class sampling for a molecular self-assembly model
Direct simulation of a model with a large state space will generate enormous volumes of data, much of which is not relevant to the questions under study. In this paper, we consider a molecular self-assembly model as a typical example of a large state-space model, and present a method for selectively retrieving 'target information' from this model. This method partitions the state space into equivalence classes, as identified by an appropriate equivalence relation. The set of equivalence classes H, which serves as a reduced state space, contains none of the superfluous information of the original model. After construction and characterization of a Markov chain with state space H, the target information is efficiently retrieved via Markov chain Monte Carlo sampling. This approach represents a new breed of simulation techniques which are highly optimized for studying molecular self-assembly and, moreover, serves as a valuable guideline for analysis of other large state-space models.
The application of filter based assembly model to develop best practices for Pannonian sand grassland restoration
<p>Data used for a manuscript sent to JAE in 2015.</p>
Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes
<p>The SIM2 testing set.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.