cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57907/mirri/mvez1i
title: MIRRI0074653

description: Organism type: Filamentous Fungi ; Taxon name: Neosartorya fischeri ; Collection: CBS 118456 ; Country: Morocco
DOI: 10.57907/mirri/o0n6ve/tix5vb
title: MIRRI0074451.json

description: Strain json file
DOI: 10.57907/mirri/onivxz
title: MIRRI0074623

description: Organism type: Filamentous Fungi ; Taxon name: Pseudocercospora arecacearum ; Collection: CBS 118406 ; Country: New Zealand
DOI: 10.57907/mirri/qciwwb
title: MIRRI0074596

description: Organism type: Filamentous Fungi ; Taxon name: Petrophila incerta ; Collection: CBS 118305 ; Country: Spain
DOI: 10.57907/mirri/rpeehr/gsst0v
title: MIRRI0074585.json

description: Strain json file
DOI: 10.57907/mirri/slm8nb/gvfxc9
title: MIRRI0074663.json

description: Strain json file
DOI: 10.57907/mirri/ts02im/waef7d
title: MIRRI0074373.json

description: Strain json file
DOI: 10.57907/mirri/tzozdr
title: MIRRI0074603

description: Organism type: Filamentous Fungi ; Taxon name: Pseudoteratosphaeria perpendicularis ; Collection: CBS 118367 ; Country: Colombia
DOI: 10.57907/mirri/wccqef/idbzkp
title: MIRRI0074658.json

description: Strain json file
DOI: 10.57907/mirri/wrevvt/oy92ar
title: MIRRI0074361.json

description: Strain json file
DOI: 10.3535/3g4-d06-b63
title: Cephalanthera rubra (L.) Rich.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/64m-pjr-2gm
title: Ammi majus L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/gyx-0fj-jfm
title: Phlomoides tuberosa (L.) Moench

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/pls-2kf-g2s
title: Stipa capillata L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/4pqq1u/l8lpqo
title: MIRRI0073924.json

description: Strain json file
DOI: 10.57907/mirri/ce5sjb
title: MIRRI0074012

description: Organism type: Filamentous Fungi ; Taxon name: Ceratocystis fimbriata ; Collection: CBS 117356
DOI: 10.57907/mirri/ferefy
title: MIRRI0073906

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria tropica ; Collection: CBS 117216 ; Country: United States of America
DOI: 10.57907/mirri/ijggei
title: MIRRI0074583

description: Organism type: Filamentous Fungi ; Taxon name: Phaeoacremonium parasiticum ; Collection: CBS 118241
DOI: 10.57907/mirri/iqofif
title: MIRRI0073923

description: Organism type: Filamentous Fungi ; Taxon name: Fonsecaea monophora ; Collection: CBS 117237 ; Country: United States of America
DOI: 10.57907/mirri/jabqih/g8u8li
title: MIRRI0073918.json

description: Strain json file
DOI: 10.57907/mirri/meetqb
title: MIRRI0074622

description: Organism type: Filamentous Fungi ; Taxon name: Cercospora apii ; Collection: CBS 118405 ; Country: New Zealand
DOI: 10.57907/mirri/ncgqu1/v2stky
title: MIRRI0074617.json

description: Strain json file
DOI: 10.57907/mirri/qidfmn
title: MIRRI0074641

description: Organism type: Filamentous Fungi ; Taxon name: Neosartorya fischeri ; Collection: CBS 118443 ; Country: Dominican Republic
DOI: 10.57907/mirri/rprf6j
title: MIRRI0074608

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria soliaridae ; Collection: CBS 118387 ; Country: United States of America
DOI: 10.57907/mirri/tesn9j
title: MIRRI0074602

description: Organism type: Filamentous Fungi ; Taxon name: Zalerion maritimum ; Collection: CBS 118363
DOI: 10.57907/mirri/tevt64
title: MIRRI0074650

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium corylophilum ; Collection: CBS 118453 ; Country: Germany
DOI: 10.5524/102260
title: Supporting data for "Discovery of Druggable Cancer-Specific Pathways with Application in Acute Myeloid Leukemia"

description: An individualized cancer therapy is ideally chosen to target the cancers driving biological pathways, but identifying such pathways is challenging because of their underlying heterogeneity and there is no guarantee that they are druggable. We hypothesize that a cancer with an activated druggable cancer-specific pathway (DCSP) is more likely to respond to the relevant drug. Here we develop and validate a systematic method to search for such DCSPs, by (i) introducing a pathway activation score (PAS) that integrates cancer-specific driver mutations and gene expression profile, and drug-specific gene targets; (ii) applying the method to identify DCSPs from pan-cancer datasets; (iii) analysing the correlation between PAS and the response to relevant drugs. In total, 4,794 DCSPs from 23 different cancers are discovered in the Genomics of Drug Sensitivity in Cancer database and validated in The Cancer Genome Atlas database. Supporting the hypothesis, for the DCSPs in acute myeloid leukemia, cancers with higher PASs are shown to have stronger drug response, and this is validated in the BeatAML cohort.
DOI: 10.5524/102263
title: Supporting data for "Best genome sequencing strategies for annotation of complex immune gene families in wildlife"

description: The biodiversity crisis and increasing impact of wildlife disease on animal and human health provides impetus for studying immune genes in wildlife. Despite the recent boom in genomes for wildlife species, immune genes are poorly annotated in non-model species owing to their high level of polymorphism and complex genomic organisation. Our research over the past decade and a half on Tasmanian devils and koalas highlights the importance of genomics and accurate immune annotations to investigate disease in wildlife. Given this, we have increasingly been asked the minimum levels of genome quality required to effectively annotate immune genes in order to study immunogenetic diversity. Here we set out to answer this question by manually annotating immune genes in five marsupial genomes and one monotreme genome to determine the impact of sequencing data type, assembly quality and automated annotation on accurate immune annotation. <br>Genome quality is directly linked to our ability to annotate complex immune gene families, with long reads and scaffolding technologies required to reassemble immune gene clusters and elucidate evolution, organisation and true gene content of the immune repertoire. Draft quality genomes generated from short-reads with HiC or 10x Chromium linked-reads were unable to achieve this. Despite mammalian BUSCOv5 scores of up to 94.1 % amongst the six genomes, automated annotation pipelines incorrectly annotated up to 59% of manually annotated immune genes regardless of assembly quality or method of automated annotation. <br>Our results demonstrate that long-reads and scaffolding technologies, alongside manual annotation, are required to accurately study the immune gene repertoire of wildlife species.
DOI: 10.5524/102266
title: Supporting data for "A phased, chromosome-scale genome of ‘Honeycrisp’ apple (<i>Malus domestica</i>) "

description: Honeycrisp is one of the most valuable apple cultivars grown in the United States and a popular breeding parent due to its superior fruit quality traits, high levels of cold hardiness, and disease resistance. However, it suffers from a number of physiological disorders and is susceptible to production and postharvest issues. Although several apple genomes have been sequenced in the last decade, there is still a substantial knowledge gap in understanding the genetic mechanisms underlying cultivar-specific traits. Here we present a fully phased, chromosome-level genome of Honeycrisp apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms. Our genome assembly is by far the most contiguous among all the apple genomes. The sizes of the two assembled haplomes are 674 Mb and 660 Mb, with contig N50s of 32.8 Mb and 31.6 Mb, respectively. In total, 47,563 and 48,655 protein coding genes were annotated from each haplome, capturing 96.8-97.4% complete BUSCOs in the eudicot database, the most complete among all <i>Malus</i> annotations. A gene family analysis using seven <i>Malus</i> genomes shows that a vast majority of Honeycrisp genes are assigned into orthogroups shared with other genomes, but it also reveals 121 Honeycrisp-specific orthogroups. We provide a valuable resource for understanding the genetic basis of horticulturally important traits in apples and other related tree fruit species, including at-harvest and postharvest fruit quality, abiotic stress tolerance, and disease resistance, all of which can enhance breeding efforts in Rosaceae.
DOI: 10.5524/102235
title: Supporting data for "A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications"

description: Metagenomics is a culture-independent method for studying the microbes inhabiting a particular environment. Comparing the composition of samples (functionally/taxonomically), either from a longitudinal study or cross-sectional studies can provide clues into how the microbiota has adapted to the environment. However, a recurring challenge, especially when comparing results between independent studies, is that key metadata about the sample and molecular methods used to extract and sequence the genetic material are often missing from sequence records, making it difficult to account for confounding factors. Nevertheless, this missing metadata may be found in the narrative of publications describing the research. Here, we describe a machine learning framework that automatically extracts essential metadata for a wide range of metagenomics studies from the literature contained in Europe PMC. This framework has enabled the extraction of metadata from 114,099 publications in Europe PMC, including 19,900 publications describing metagenomics studies in ENA and MGnify.
DOI: 10.5524/102242
title: Supporting data for "Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other non-standard architectures in genome assemblies"

description: Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, heterokaryosis or extreme compositional biases can challenge current standard assembly procedures and result in highly fragmented assemblies. Hence, we hypothesized that genome databases must contain a non-negligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors. Here we present Karyon, a Python-based toolkit that uses raw sequencing data and <i>de novo</i> genome assembly to assess several parameters and generate informative plots to assist in the identification of non-chanonical genomic traits. Karyon includes automated <i>de novo</i> genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species. Our results show that 10 (28.57%) of the assemblies presented signs of unusual genomic configurations, suggesting that these are common, at least for some lineages within the Fungi.
DOI: 10.5524/102243
title: Supporting data for "Comparative maternal protein profiling of mouse biparental and uniparental embryos"

description: Maternal proteins have important roles during early embryonic development. However, our understanding of maternal proteins is still very limited. The integrated analysis of mouse uniparental (parthenogenetic) and biparental (fertilised) embryos at the protein level creates a protein expression landscape that can be used to explore pre-implantation mouse development. Using label-free quantitative mass spectrometry (MS) analysis, we report on the maternal proteome of mouse parthenogenetic embryos at pronucleus, 2-cell, 4-cell, 8-cell, morula and blastocyst stages, and highlight dynamic changes in protein expression. In addition, comparison of proteomic profiles of parthenogenotes and fertilised embryos highlight the different fates of maternal proteins. Enrichment analysis uncovered a set of maternal proteins that are strongly correlated with the subcortical maternal complex (SCMC), and we report that in parthenogenotes some of these maternal proteins escape the fate of protein degradation. Moreover, we identified a new maternal factor - Fbxw24 - and highlight its importance in early embryonic development. We report that Fbxw24 interacts with Ddb1-Cul4b, and may regulate maternal protein degradation in mouse. Our study provides an invaluable resource for mechanistic analaysis of maternal proteins, and highlights the role of the novel maternal factor Fbw24 in regulating maternal protein degradation during pre-implantation embryo development.
DOI: 10.5524/102246
title: Supporting data for "Sex-specific genomic region identification in male and female Asian arowana genomes"

description: The Asian arowana, <i>Scleropages formosus</i>, is one of the most famous and expensive aquarium fish species worldwide. The sex of Asian arowana, however, cannot be distinguished clearly at any development stage, which impedes captive breeding and species protection for this endangered aquarium fish. <br>To discover the molecular clues of the sex of Asian arowana, we sequenced the genomes of male and female individuals <i>de novo</i> with 367.8 Gb of raw Illumina reads, 27.4 Gb of PacBio long reads and 80.7 Gb of HiC reads. The final male and female assemblies were approximately 789.1 Mb and 781.5 Mb in size and contained 25,244 and 25,328 protein-coding genes. We also resequenced the genomes of 15 male and 15 female individuals with approximately 709.2 Gb Illumina reads. Genome-wide association study (GWAS) has identified several remarkably divergent regions between male individuals and female individuals. In these regions, the <i>cd48</i> and <i>cfap52</i> genes could be candidate genes for the determination of Asian arowana sex. We also found some structural variations in chromosomes between male and female individuals. <br>We provided an improved reference genome assembly of female arowana and generated the first sequenced genome of male individuals. These large and valuable genome assemblies and resequencing data will improve global aquarium fish research.
DOI: 10.5524/102249
title: Supporting data for "CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis"

description: Many organizations face challenges in managing and analyzing data, especially when relevant datasets arise from multiple sources and methods. Analyzing heterogeneous datasets and additional derived data requires rigorous tracking of their interrelationships and provenance. This task has long been a Grand Challenge of data science, and has more recently been formalized in the FAIR principles: that all data objects be Findable, Accessible, Interoperable and Reusable, both for machines and for people. Adherence to these principles is necessary for proper stewardship of information, for testing regulatory compliance, for measuring the efficiency of processes, and for facilitating reuse of data analytical frameworks. <br>We present the Contextual Ontology-based Repository Analysis Library (CORAL), a platform that greatly facilitates adherence to all four of the FAIR principles, including the especially difficult challenge of making heterogeneous datasets Interoperable and Reusable across all parts of a large, long-lasting organization. To achieve this, CORAL's data model requires that data generators extensively document the context for all data, and our tools maintain that context throughout the entire analysis pipeline. CORAL also features a web interface for data generators to upload and explore data, and a Jupyter notebook interface for data analysts, both backed by a common API. <br>CORAL enables organizations to build FAIR data types on the fly as they are needed, avoiding the expense of bespoke data modeling. CORAL provides a uniquely powerful platform to enable integrative cross-dataset analyses, generating deeper insights than are possible using traditional analysis tools
DOI: 10.5524/102251
title: Supporting data for "d-StructMAn: containerized structural annotation on the scale from genetic variants to whole proteomes"

description: Structural annotation of genetic variants in the context of inter-molecular interactions and protein stability can shed light onto mechanisms of disease-related phenotypes. Three-dimensional structures of related proteins in complexes with other proteins, nucleic acids, or ligands enriches such functional interpretation, since inter-molecular interactions are well conserved in evolution. <br>We present d-StructMAn, a novel computational method that enables structural annotation of local genetic variants, such as single-nucleotide variants and in-frame indels, and implements it in a highly efficient and user-friendly tool provided as a Docker container. Using d-StructMAn, we annotated several very large sets of human genetic variants, including all variants from ClinVar and all amino acid positions in the human proteome. We were able to provide annotation for more than 46% of positions in the human proteome representing over 60% proteins. <br>d-StructMAn is the first of its kind and is a highly efficient tool for structural annotation of protein-coding genetic variation in the context of observed and potential inter-molecular interactions. d-StructMAn is readily applicable to proteome-scale datasets and can be instrumental building machine-learning tools for predicting genotype-to-phenotype relationships.
DOI: 10.5524/102256
title: Supporting data for "High Temporal-Resolution Nanopore Sequencing Dataset of SARS-CoV-2 and Host Cell RNAs"

description: Recent studies have disclosed the genome, transcriptome and epigenetic compositions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the effect of viral infection on gene expression of the host cells. It has been demonstrated that, besides the major canonical transcripts, the viral genome also codes for non-canonical RNA molecules. While the structural characterizations have revealed a detailed transcriptomic architecture of the virus, the kinetic studies provided poor and often misleading results on the dynamics of both the viral and host transcripts due to the low temporal resolution of the infection event and the low virus/cell ratio (MOI=0.1) applied for the infection. It has never been tested whether the alteration in the host gene expressions is caused by aging of the cells, or by the viral infection. <br>In this study, we used Oxford Nanopores direct cDNA and direct RNA sequencing methods for the generation of a high-coverage, high-temporal-resolution transcriptomic dataset of SARS-CoV-2 and of the primate host cells, using a high infection titer (MOI=5). Sixteen sampling time points ranging from 1 to 96 h with a varying time resolution and three biological replicates were used in the experiment. In addition, for each infected sample, corresponding non-infected samples were employed. The raw reads were mapped to the viral and to the host reference genomes, resulting in 49,661,499 mapped reads (54,62Gbs). The genome of the viral isolate was also sequenced and phylogenetically classified.<br>This dataset can serve as a valuable resource for profiling the SARS-CoV-2 transcriptome dynamics, the virus-host interactions and the RNA base modifications. Comparison of expression profiles of the host gene in the virally-infected and in non-infected cells at different time points allows to make a distinction between the effect of the aging of cells in culture and the viral infection. These data can provide useful information for potential novel gene annotations and can also be used for studying the currently available bioinformatics pipelines.
DOI: 10.5524/102267
title: Supporting data for "Alignstein: optimal transport for improved LC-MS retention time alignment"

description: Reproducibility of liquid chromatography separation is limited by retention time drift. As a result, measured signals lack the correspondence over replicates of the liquid chromatography-mass spectrometry (LC-MS) experiments. Correction of these errors is named retention time alignment and needs to be performed before further statistical analysis of LC-MS datasets. Despite the availability of numerous alignment algorithms, their accuracy is limited, e.g. for retention time drift that swaps analytes elution order. <br>We present the Alignstein, an algorithm for liquid chromatography-mass spectrometry retention time alignment. It correctly finds correspondence even for swapped signals. To achieve this, we implemented the generalization of the Wasserstein distance to compare multidimensional features without any reduction of the information or dimension of the analyzed data. Moreover, Alignstein by design requires neither a reference sample nor prior signal identification. We validate the algorithm on publicly available benchmark datasets obtaining competitive results. Finally, we show that it can detect the information contained in the tandem mass spectrum by the spatial properties of chromatograms. <br>We show that the use of optimal transport effectively overcome the limitations of existing algorithms for statistical analysis of mass spectrometry datasets. The source code of the algorithm is available at https://github.com/grzsko/Alignstein.
DOI: 10.5524/102273
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 02 Q25 Effect of an NMDA lesion of the BLA on the development of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.