cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102244
title: Supporting data for "Statistical quantification of confounding bias in machine learning models"

description: The lack of non-parametric statistical tests for confounding bias significantly hampers the development of robust, valid and generalizable predictive models in many fields of research. Here I propose the <i>partial confounder test</i>, which, for a given confounder variable, probes the null hypotheses of the model being <i>unconfounded.</i> <br>The test provides a strict control for Type I errors and high statistical power, even for non-normally and non-linearly dependent predictions, often seen in machine learning. Applying the proposed test on models trained on large-scale functional brain connectivity data (N=1865) (i) reveals previously unreported confounders and (ii) shows that state-of-the-art confound mitigation approaches may fail preventing confounder bias in several cases. <br>The proposed test (implemented in the package <i>mlconfound1</i>) can aid the assessment and improvement of the generalizability and neurobiological validity of predictive models and, thereby, foster the development of clinically useful machine learning biomarkers
DOI: 10.5524/102247
title: Supporting data for "A curated human cellular microRNAome based on 196 primary cell types"

description: An incomplete picture of the expression distribution of microRNAs (miRNAs) across human cell types has long hindered our understanding of this important regulatory class of RNA. With the continued increase in available public small RNA sequencing datasets, there is an opportunity to more fully understand the general distribution of miRNAs at the cell level. <br>From the NCBI Sequence Read Archive, we obtained 6,054 human primary cell datasets and processed 4,184 of them through the miRge3.0 small RNA-seq alignment software. This dataset was curated down, through shared miRNA expression patterns, to 2,077 samples from 196 unique cell types derived from 175 separate studies. Of 2,731 putative miRNAs listed in miRBase (v22.1), 2,452 (89.8%) were detected. Among reasonably expressed miRNAs, 108 were designated as cell specific/near specific, 59 as infrequent, 52 as frequent, 54 as near ubiquitous and 50 as ubiquitous. The complexity of cellular microRNA expression estimates recapitulates tissue expression patterns and informs on the miRNA composition of plasma. <br>This study represents the most complete reference, to date, of miRNA expression patterns by primary cell type. The data is available through the human cellular microRNAome track at the UCSC Genome Browser and an R/Bioconductor package.
DOI: 10.5524/102255
title: Supporting data for "SYNPRED: Prediction of Drug Combination Effects in Cancer using Different Synergy Metrics and Ensemble Learning"

description: In cancer research, high-throughput screening technologies produce large amounts of multiomics data from different populations and cell types. However, analysis of such data encounters difficulties due to disease heterogeneity, further exacerbated by human biological complexity and genomic variability. The specific profile of cancer as a disease (or, more realistically, a set of diseases) urges the development of approaches that maximize the effect while minimizing the dosage of drugs. Now is the time to redefine the approach to drug discovery, bringing an Artificial Intelligence (AI)-powered informational view that integrates the relevant scientific fields and explores new territories. <br>Here, we show SYNPRED, an interdisciplinary approach that leverages specifically designed ensembles of AI algorithms, links omics and biophysical traits to predict anticancer drug synergy. It uses four reference models (Bliss, Highest Single Agent, Loewe, and Zero Interaction Potency), which, coupled with AI algorithms, allowed us to attain the ones with the best predictive performance and pinpoint the most appropriate reference model for synergy prediction, often overlooked in similar studies. By using an independent test set, SYNPRED exhibits state-of-the-art performance metrics either in the classification (accuracy 0.80, precision 0.81, recall 0.81, AUROC 0.80, and F1-score - 0.81) or in the regression models, mainly when using the Zero Interaction Potency synergy reference model (RMSE 7.10, MSE 50.46, Pearson 0.80, R2 0.43, MAE 4.61, Spearman 0.73). Moreover, data interpretability was achieved by deploying the most current and robust feature importance approaches. A simple web-based application was constructed, allowing easy access by non-expert researchers. <br>The performance of SYNPRED rivals that of the existing methods that tackle the same problem, yielding unbiased results trained with one of the most comprehensive datasets available (NCI-ALMANAC). The leveraging of different reference models allowed deeper insights into which of them is the most appropriate one to use for synergy prediction. The Zero Interaction Potency clearly stood out with improved performance among the full scope of surveyed approaches and synergy reference models. Furthermore, SYNPRED takes a particular focus on data interpretability, which has been in the spotlight lately when using the most advanced AI techniques.
DOI: 10.5524/102262
title: Supporting data for "Disease classification for whole blood DNA methylation: meta-analysis, missing values imputation, and XAI"

description: DNA methylation has a significant effect on gene expression and can be associated with various diseases. Meta-analysis of available DNA methylation datasets requires development of a specific pipeline for joint data processing. <br>We propose a comprehensive approach of combined DNA methylation datasets to classify controls and patients. The solution includes data harmonization, construction of machine learning classification models, dimensionality reduction of models, imputation of missing values, and explanation of model predictions by explainable artificial intelligence (XAI) algorithms. We show that harmonization can improve classification accuracy by up to 20% when preprocessing methods of the training and test datasets are different. The best accuracy results were obtained with tree ensembles, reaching above 95% for Parkinsons disease. Dimensionality reduction can substantially decrease the number of features, without detriment to the classification accuracy. The best imputation methods achieve almost the same classification accuracy for data with missing values as for the original data. Explainable artificial intelligence approaches have allowed us to explain model predictions from both populational and individual perspectives. <br>We propose a methodologically valid and comprehensive approach to the classification of healthy individuals and patients with various diseases based on whole blood DNA methylation data using Parkinsons disease and schizophrenia as examples. The proposed algorithm works better for the former pathology, characterized by a complex set of symptoms. It allows to solve data harmonization problems for meta-analysis of many different datasets, impute missing values, and build classification models of small dimensionality.
DOI: 10.5524/102231
title: Chromosome-scale assembly of the Indianmeal moth <i>Plodia interpunctella</i>

description: Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (<i>Plodia interpunctella</i>). The (<i>Plodia interpunctella</i>) genome was highly contiguous (N50 = 9.7 Mbp, L50 = 13) and complete (BUSCO Complete = 99.3%), with complete and contiguous recovery of silk <i>heavy fibroin</i> gene sequences. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.
DOI: 10.5524/102188
title: Genomic data of the bignose unicornfish, <i>Naso vlamingii</i>

description: <i>Naso vlamingii</i> is a species of unicornfish in the surgeonfish family known by the common names bignose unicornfish, scibbled unicornfish, Vlaming's unicornfish, and zebra unicornfish. <i>N. vlamingii</i> is a relatively large member of the Acanthuridae, easily reaching 60 cm. The adult has tall dorsal and anal fins, vertical blue lines on its sides, and small blue spots dorsally and ventrally. A broad blue band extends from the eyes to the prominent snout. The coloration of the juvenile is a dingy green with blue spots and lips, later turning deeper blue with purple markings. The fish turns mud-brown while sleeping or when frightened, a form of camouflage. <br><i>N. vlamingii</i> is found in the Indo-Pacific oceans off the coasts of East Africa, on the islands of the Marquesas and Tuamotu, southern Japan and southern areas of the Great Barrier Reef. This fish is mostly herbivorous but will eat small crustaceans such as copepods. In captivity brine shrimp and mysid shrimp. <br>Most of its natural diet is algae. It is most often found in association with reefs and coastal lagoons, sometimes in small schools. <i>N. vlamingii</i> has very little to commercial fishers but is occasionally available in the marine aquarium industry, where it is a higher-priced, more uncommon tang. Here we present the genome, which has an estimated genome size of 961.4Mb, scaffold N50 5,736,754, contig N50 182,642
DOI: 10.5524/102219
title: Supporting data for "Chromosome-level genome assembly of <i>Plazaster borealis</i>: shed light on the morphogenesis of multi-armed starfish and its regenerative capacity"

description: <i>Plazaster borealis</i> has a unique morphology, multiple arms with clear distinction between disk and arms, that does not follow remarkable characteristic of Echinoderm, penta-radial symmetry. Though it seems to be related with accelerated evolutionary rate at the morphological level, the lack of a reference genome has limited further research in-depth. Herein we report the first chromosome-level reference genome of <i>P. borealis</i>. <br>High coverage of long and short read data was used to assemble <i>de novo</i> 561Mb reference genome of <i>P. borealis</i> and Hi-C sequencing data was used to scaffold into 22 chromosomal scaffolds comprising 92.38% of the genome. The genome showed the presence of 98.1% of complete eukaryote BUSCO and 97.1% of complete metazoan BUSCO, indicating high quality assembly. Through the comparative genome analysis, we identified evolutionary accelerated genes related with morphogenesis and regeneration, suggesting their potential role in shaping body pattern and capacity of regeneration. <br>This first chromosome-level genome assembly of <i>P. borealis</i> provides fundamental insights into echinoderm biology, as well as the genomic mechanism underlying its unique morphology and regeneration.
DOI: 10.5524/102222
title: Supporting data for "A chromosome-level genome of the booklouse, Liposcelis brunnea provides insight into lice evolution and environmental stress adaptation"

description: Booklice (psocids) in the genus <i>Liposcelis</i> (Psocoptera: Liposcelididae), are a group of important storage pests, found in libraries, grain storages and food processing facilities. Booklice are able to survive under heat treatment and typically possess high resistance to common fumigant insecticide, hence posing a threat to storage security worldwide. <br>We assembled the genome of the booklouse, <i>L. brunnea</i>, the first genome reported in Psocoptera, using PacBio long-read sequencing, Illumina sequencing and chromatin conformation capture (HiC) methods. After assembly, polishing, haplotype purging and HiC scaffolding, we obtained nine linkage groups (174.1 Mb in total) ranging from 12.1 Mb to 27.6 Mb (N50: 19.7 Mb), with the BUSCO completeness at 98.9%. In total 15,543 genes were predicted by the Maker pipeline. Gene family analyses indicated the sensing-related gene families (OBP and OR) and the resistance-related gene families (ABC, EST, GST, UGT and P450) expanded significantly in <i>L. brunnea</i> compared with those of their closest relatives (two parasitic lice). Based on transcriptomic analysis, we found that the CYP4 subfamily from the P450 gene family functioned during phosphine fumigation; HSP genes, particularly those from the HSP70 subfamily, were upregulated significantly under high temperatures.<br>We present a chromosome-level genome assembly of <i>L. brunnea</i>, the first genome reported for the order Psocoptera. Our analyses provide new insights into the gene family evolution of the louse clade and the transcriptomic responses of booklice to environmental stresses.
DOI: 10.5524/102226
title: Supporting data for "A chromosome-level genome assembly and intestinal transcriptome of <i>Trypoxylus dichotomus</i> (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability"

description: Lignocellulose, as the key structural component of plant biomass, is a recalcitrant structure, difficult to degrade. The traditional management of plant waste including landfill and incineration usually causes serious environmental pollution and health problems. Interestingly, the xylophagous beetle, <i>Trypoxylus dichotomus</i> can decompose lignocellulosic biomass. However, the genomics around the digestion mechanism of this beetle remain to be elucidated. Here, we assembled the genome of <i>T. dichotomus</i>, showing that the draft genome size to be 636.27 Mb, with 95.37% scaffolds anchored onto 10 chromosomes. Phylogenetic results indicated that a divergent evolution between the ancestors of <i>T. dichotomus</i> and the closely related scarabaeid species <i>Onthophagus taurus</i> occurred in the early Cretaceous (120 Mya). Through gene family evolution analysis, we found 67 rapidly evolving gene families, within which there were two digestive gene families (encoding Trypsin and Enoyl-(Acyl carrier protein) reductase) that have experienced significant expansion, indicating that they may contribute to the high degradation efficiency of lignocellulose in <i>T. dichotomus</i>. Additionally, events of chromosome breakage and rearrangement were observed by synteny analysis during the evolution of <i>T. dichotomus</i> due to chromosomes 6 and 8 of <i>T. dichotomus</i> being intersected with chromosomes 2 and 10 of <i>Tribolium castaneum</i>, respectively. Furthermore, the comparative transcriptome analyses of larval guts showed that the digestion-related genes were more commonly expressed in the midgut or mushroom-residue group than the hindgut or sawdust group. This study reports the well-assembled and annotated genome of <i>T. dichotomus</i>, providing genomic and transcriptomic bases for further understanding the functional and evolutionary mechanisms of lignocellulose digestion in <i>T. dichotomus</i>.
DOI: 10.5524/102227
title: Supporting data for "Sand fly (Diptera: Psychodidae: Phlebotominae) records in Acre, Brazil: a Dataset"

description: Amazonian phlebotomine fauna is considered one of the most diverse in the world. In addition, the region is the most prevalent for leishmaniasis in Brazil and South America. The state of Acre, which belongs to this region, also stands out in terms of the diversity of the sand fly fauna, as well as the occurrence of American tegumentary leishmaniasis. In this context, the present Dataset comprise a bibliographic review of sand fly species recorded in Acre State, Amazon region, Brazil. A total of 1,096 observations from Material Citation type (and two of preserved specimens) were presented using 33 variables according to Darwin Core terms. The bibliographic review was performed in PubMed, Google Scholar, SciELO, BVS (Biblioteca Virtual em Saúde) and bibliographic references cited in related scientific articles. Thus, the present study is a solid report for further studies on sand fly studies in Acre and other Amazon states.
DOI: 10.5524/102228
title: Supporting data for "SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data"

description: Survival analysis is a branch of statistics that deals with both, the tracking of time and of the survival status simultaneously as the dependent response. Current comparisons of survival model performance mostly center on clinical data with classic statistical survival models, with prediction accuracy often serving as the sole metric of model performance. Moreover, survival analysis approaches for censored omics data have not been thoroughly investigated. The common approach is to binarise the survival time and perform a classification analysis.<br>Here, we develop a benchmarking design, SurvBenchmark, that evaluates a diverse collection of survival models for both clinical and omics datasets. SurvBenchmark not only focuses on classical approaches such as the Cox model, but it also evaluates state-of-art machine learning survival models. All approaches were assessed using multiple performance metrics, these include model predictability, stability, flexibility and computational issues. Our systematic comparison design with 320 comparisons (20 methods over 16 datasets) shows that the performances of survival models vary in practice over real-world datasets and over the choice of the evaluation metric. In particular, we highlight that using multiple performance metrics is critical in providing a balanced assessment of various models. The results in our study will provide practical guidelines for translational scientists and clinicians, as well as define possible areas of investigation in both survival technique and benchmarking strategies.
DOI: 10.5524/102232
title: Supporting data for "Antibiotic resistance genes are differentially mobilized according to resistance mechanism"

description: Screening for antibiotic resistance genes (ARGs) in, especially environmental, samples with (meta)genomic sequencing is associated with false-positive predictions of phenotypic resistance. This stems from the fact that most acquired ARGs require being overexpressed before conferring resistance, which is often caused by decontextualisation of putative ARGs by mobile genetic elements (MGEs). Consequent overexpression of ARGs can be caused by strong promoters often present in insertion sequence (IS) elements and integrons and the copy number effect of plasmids which may contribute to high expression of accessory genes. <br>Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed which indicates how mobilized detected ARGs are in bacterial genomes. It is concluded that antibiotic efflux genes are rarely mobilized and even 80% of b-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons. <br>In this study, ARGs in all complete bacterial genomes are classified by their association with MGEs, using the proposed ARG-MOB scale. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health. An interactive table of all results is provided for future studies targeting highly mobilized ARGs.
DOI: 10.5524/102183
title: Genome data of the long-spine porcupinefish, Diodon holocanthus

description: The long-spine porcupinefish is pale in colour with large black blotches and smaller black spots; these spots becoming fewer in number with age. It has many long, two-rooted depressible spines particularly on its head. The teeth of the two jaws are fused into a parrot-like "beak". Adults may reach 50 cm (20 in) in length.<br>The long-spine porcupinefish is circumtropical in distribution, being found in the tropical zones of major seas and oceans. It is an omnivore that feeds on mollusks, sea urchins, hermit crabs, snails, and crabs during its active phase at night. They use their beak combined with plates on the roof of their mouths to crush their prey such as mollusks and sea urchins that would otherwise be indigestible.<br> They are found over the muddy sea bottom, in estuaries, in lagoons or on coral and rocky reefs around the world in tropical and subtropical seas.<br>The long-spine porcupinefish spawns at the surface at dawn or at dusk in pairs or in groups of males with a single female; the juveniles remain pelagic until they are at least 7 cm (3 in) long. Young and sub-adult fish sometimes occur in groups. This fish is used in Chinese medicine, and is captured at the surface with a hand net. It is poisonous if not prepared correctly. It is also found in the aquarium trade. Here we present the genome, which has an estimated genome size of 722.9Mb, scaffold N50 6,098,089, contig N50 2,149,931
DOI: 10.5524/102184
title: Genome data of the African bonytongue, Heterotis niloticus

description: The African arowana or Nile arowana (Heterotis niloticus) is a species of bonytongue. It is a long-bodied fish with large scales, long dorsal and anal fins set far back on the body, and a rounded caudal fin. Its height is 3.5 to 5.0 times standard length. It has been reported to reach up to 1 m (3.3 ft) long and weigh up to 10.2 kg (22 lb). <br>The fish is gray, brown, or bronze in color. Coloration is uniform in adults, but juveniles often have dark longitudinal bands. African arowanas have air-breathing organs on its branchiae, enabling them to survive in oxygen-depleted water. A suprabranchial organ allows it to concentrate small planktonic food particles and also has a sensory function. <br>This species is widespread throughout Africa, where it is native to all the watersheds in Sahelo-Sudanese region, Senegal, and Gambia, as well as parts of eastern Africa. This range includes the basins of the Corubal, Volta, Oueme, Niger, Benoue, and Nile Rivers, as well as those of Lake Chad and Lake Turkana. It has been successfully introduced to Cote d'Ivoire, the Cross River in Nigeria, the Sanaga and Nyong Rivers in Cameroon, and the Ogooue River in Gabon, as well as the lower and middle Congo River basin, including Ubangui and Kasai Rivers. It has also been introduced in Madagascar. In some cases, introduction is reported to have had a negative impact on the local ecology. <br>African arowana is used locally as a food and has been collected in the past for the aquarium trade, but behavior of it in captivity. It is not feral or aggressive like its relatives. Here we present the genome, which has an estimated genome size of 743.4Mb, scaffold N50 9,615,753, contig N50 2,307,881
DOI: 10.5524/102186
title: Genomic data of the Siamese tigerfish, Datnioides pulcher

description: The Siamese tigerfish (Datnioides pulcher) is a critically endangered Asian fish native to the Chao Phraya, Mae Klong and Mekong basins. It has vertical yellow and black stripes running the length of its body. The dorsal fin has a spiny appearance. Siamese tigerfish grow to 40 cm (16 in) in standard length. <br> D. pulcher is protected in Thailand, and is on the IUCN International Union for Conservation of Nature) Red List as critically endangered. Here we present the genome, which has an estimated genome size of 623.1Mb, scaffold N50 9,741,635, contig N50 2,175,996