cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100197
title: Resource for “Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite.”

description: The cestode <em>Schistocephalus solidus</em> has been the focus of extensive research in parasitology for over 200 years and has now become a powerful model for studying host-parasite interactions. <em>S. solidus</em> can be utilized to better understand the complex molecular mechanisms underlying functional changes associated with host transitions. We have sequenced and assembled (<em>de novo</em>) the transcriptome of <em>S. solidus</em> using whole organisms from three key developmental stages involved in host transitions: immature plerocercoid, mature plerocercoid and adult. Recent publications in parasitology, and more specifically on host-parasite interactions, have been strongly focused towards reviews and development of ideas and theoretical frameworks, but empirical data acquisition is still lagging behind. The main objective underlying the publication of this data is to increase the amount of publicly available resources for host-parasite systems. <br>
Our <em>de novo</em> assembly pipeline for the transcriptome of <em>Schistocephalus solidus</em> allowed us to reconstruct 24,765 high-confidence, non-redundant transcripts, associated with 10,285 unique genes. In total 7,323 unique genes (71%) were assigned at least one gene ontology (GO) term, and 4,270 (35%) were assigned at least one KEGG pathway ID. Phylogenetic relationships with other parasitic and non-parasitic worm species were investigated, allowing the identification of 1,977 genes that are specific to <em>S. solidus</em>, 3,425 core orthologs shared only among parasites and 6,892 putative orthologs shared among all worm species included in the analysis. <br>
Accessibility to high-quality genetic resources for a wide panel of host-parasite systems is fundamental not only to the advancement of knowledge on the mechanisms of host-parasite interactions, but also on the evolution of complex life cycles and parasitism itself. This is, to our knowledge, the first large-scale transcriptomic dataset for <em>Schistocephalus solidus</em>.
DOI: 10.5524/100198
title: The data for: Genomic resources and draft reference assemblies of the human and porcine scabies mites, Sarcoptes scabiei var. hominis and var. suis

description: The scabies mite, <em>Sarcoptes scabiei</em>, is a parasitic arachnid and cause of the infectious skin disease scabies in humans or mange in many animal species. We sequenced the genome of two samples of <em>S. scabiei</em> var. <em>hominis</em> obtained from unrelated patients with crusted scabies located in different parts of northern Australia using the Illumina HiSeq. We also sequenced samples of <em>S. scabiei</em> var. <em>suis</em> from a pig model. Due to the small size of scabies mite, these data are derived from pools of thousands of mites and are metagenomic, including host and microbiome DNA. We performed cleaning and de novo assembly and present <em>Sarcoptes scabiei</em> var. <em>hominis</em> and var. <em>suis</em> draft reference genomes. We have constructed a preliminary annotation of this reference comprising 13,226 putative coding sequences based on sequence similarity to known proteins.
DOI: 10.5524/100200
title: Supporting data for "A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay"

description: Large-scale image sets acquired by automated microscopy of perturbed samples enable a detailed comparison of cell states induced by each treatment. Highly multiplexed measurements of cellular morphology can be extracted from each image and subsequently mined for a number of applications.<br>
This microscopy dataset includes 919,874 five-channel fields of view representing 30,616 tested compounds. The images are available at The Cell Image Library repository. All additional data files are available from GigaDB, including; morphological features derived from each cell in each image, both at the single-cell level and population-averaged (i.e., the per-image level); the image analysis workflows that generated the morphological features are also provided. Quality-control metrics are provided as metadata, indicating fields of view that are out-of-focus (blurry) or containing highly fluorescent material or debris. Lastly, chemical annotations are supplied for the compound treatments applied.<br>
Because computational algorithms and methods for handling single-cell morphological measurements are not yet routine, the dataset serves as a useful resource for the wider scientific community applying morphological (image-based) profiling. The dataset can be mined for many purposes, including small-molecule library enrichment and chemical mechanism-of-action studies, including target identification. Integration with genetically-perturbed datasets could enable identification of small-molecule mimetics of particular disease- or gene-related phenotypes that could be useful as probes or potential starting points for development of future therapeutics.
DOI: 10.5524/100156
title: Supporting data for "Deep sequencing of human major histocompatibility complex region contributes to studies of complex disease".

description: The human major histocompatibility complex (MHC) has been shown to be associated with numerous diseases. However, it remains a challenge to pinpoint causal variants of these associations due to the ex-treme complexity of the region. We thus sequenced the entire 5 Mb MHC region in 20,635 individuals of Han Chinese ethnicity (10,689 controls and 9,946 psoriasis patients) and constructed a Han-MHC da-tabase which included both variants and HLA gene typing results with high accuracy. We further identi-fied multiple independent novel susceptibility loci in HLA-C, HLA-B, HLA-DPB1, BTNL2 and an inter-genic variant, rs118178193 for psoriasis and confirmed the well-established susceptibility locus HLA-C*06:02. These discovered psoriasis-associated loci in MHC region were markedly different from those described in Caucasian population in a recent analysis and highlights the importance of generating population-specific MHC databases for studies of complex disease. We anticipate that our Han-MHC reference panel built by deep sequencing of a large number of samples will serve as a useful tool for investigating the role of the MHC region in a variety of diseases and thus advance our understanding of the pathogenesis of these disorders.
DOI: 10.5524/100157
title: Bovine whole-genome sequence alignments from the Canadian Cattle Genome Project

description: The Canadian Cattle Genome Project is a large-scale international project that aims to develop genomics-based tools to enhance the efficiency and sustainability of beef and dairy production. Obtaining DNA sequence information is an important part of achieving this goal as it facilitates efforts to associate specific DNA differences with phenotypic variation. These associations can be used to guide breeding decisions and provide valuable insight into the molecular basis of traits. <br>We present a dataset of 379 whole-genome sequences, taken primarily from key historic Bos taurus animals, along with the analyses that were performed to assess data quality. The sequenced animals represent ten populations relevant to beef or dairy production.<br>The large number of whole-genome sequences generated as a result of this project will contribute to ongoing work aiming to catalogue the variation that exists in cattle as well as efforts to improve traits through genotype-guided selection. Studies of gene function, population structure, and sequence evolution are also likely to benefit from the availability of this resource.<br><br><br>PLEASE NOTE: The files associated with this dataset are hosted in cold storage, please contact us via email with the details of the dataset and any particular files you would like to download, and we will be happy to make those available to you.<br>
DOI: 10.5524/100160
title: Supporting data for "Full-length single cell RNA-seq applied to a viral human cancer: Applications to HPV expression and splicing analysis in HeLa S3 cells".

description: Viral infection causes multiple forms of human cancer, and human papillomavirus (HPV) infection is the primary factor in cervical carcinomas. Single-cell RNA-seq studies highlight the tumor heterogeneity of most cancers, but virally induced tumors have not been studied. HeLa is a well characterized HPV+ cervical cancer cell line.
We developed a new high-throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip. Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells, 40 of which were randomly selected to perform single-cell RNA sequencing. On the basis of this data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in terms of gene expression, alternative splicing, and gene fusions. Furthermore, by co-expression analysis we can identify a high diversity of HPV-18 gene expression and splicing at the single-cell level. 
In addition to providing a characterization of the transcriptome of HeLa S3 cells at the single-cell level, our study demonstrates the power of single-cell RNA-seq analysis of virally infected cells and cancers.
DOI: 10.5524/100161
title: Supporting data and materials for "The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches".

description: Functional annotation of novel proteins is one of the central problems in bioinformatics. With the ever-increasing development of genome sequencing technologies, more and more sequence information is becoming available to analyze and annotate. To achieve fast and automatic function annotation, many computational (automated) function prediction (AFP) methods have been developed. To objectively evaluate the performance of such methods on a large scale, community-wide assessment experiments have been conducted. The second round of the Critical Assessment of Function Annotation (CAFA) experiment was held in 2013-2014. Evaluation of participating groups was reported in a special interest group meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in Boston in 2014. Our group participated in both CAFA1 and CAFA2 using multiple, in-house AFP methods. Here, we report benchmark results of our methods obtained in the course of preparation for CAFA2 prior to submitting function predictions for CAFA2 targets.
<br>For CAFA2, we updated the annotation databases used by our methods, protein function prediction (PFP) and extended similarity group (ESG), and benchmarked their function prediction performances using the original (older) and updated databases. Performance evaluation for PFP with different settings and ESG are discussed. We also developed two ensemble methods that combine function predictions from six independent, sequence-based AFP methods. We further analyzed the performances of our prediction methods by enriching the predictions with prior distribution of gene ontology (GO) terms. Examples of predictions by the ensemble methods are discussed.
DOI: 10.5524/100163
title: Supporting materials for "Metabolome of Human gut microbiome is predictive of host dysbiosis".

description: Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem, called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer, a condition called dysbiosis. However, the community compositions of the human microbiomes also vary dramatically from individual to individual and over time, making it difficult to uncover the underlying mechanisms linking microbiome to human health. We propose that a microbiomes interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on the community metabolome of microbiome, an emergent property of microbiome.<br>Using data from a previously published, longitudinal study of human gut microbiome populations, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the microbiomes aggregate predicted community enzyme function profiles and modeled metabolomes are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles.
DOI: 10.5524/100183
title: Supporting data for "Scalable linkage disequilibrium-based selective sweep detection: a performance guide".

description: Linkage disequilibrium is defined as the non-random associations of alleles at different loci, and it occurs when genotypes at the two loci depend on each other. The model of genetic hitchhiking predicts that strong positive selection affects the patterns of linkage disequilibrium around the site of a beneficial allele, resulting in specific motifs of correlations between neutral polymorphisms that surround the fixed beneficial allele. Linkage disequilibrium is built upon each side of a beneficial allele and diminishes for sites that are across the selected allele. This specific pattern of linkage disequilibrium occurs more frequently when positive selection has acted on the population rather than under various neutral models. Thus, detecting such patterns could accurately reveal targets of positive selection along a recombining chromosome or a genome. Calculating linkage disequilibria in whole genomes is computationally expensive since correlations of alleles need to be evaluated for millions of pairs of sites. To analyze large datasets efficiently, algorithmic implementations employed in modern population genetics need to exploit multiple cores of current workstations in a scalable way. <br>
Population genomic datasets come in different types and shapes while typically exhibiting SNP density heterogeneity. Due to such peculiarities, the implementation of generally scalable parallel algorithms is a challenging task. In this work, we present a series of four parallelization strategies targeting shared-memory systems for the computationally intensive problem of detecting genomic regions that have contributed to the past adaptation of the species, also referred to as selective sweep, based on linkage disequilibrium (LD) patterns. We provide a thorough performance evaluation of the proposed parallel algorithms for computing LD and outline the benefits of each approach. Furthermore, we
compare our open-source software OmegaPlus to a variety of neutrality tests.<br>
The computational demands of selective sweep detection algorithms can vary significantly depending on a variety of attributes such as the SNP density heterogeneity, and the analysis of DNA or binary data due to the finite or infinite site models, respectively. Choosing the right parallel algorithm for the analysis can lead to significant processing time reduction as well as major energy savings. However, which parallel algorithm is going to execute more efficiently on a specific processor architecture and number of available cores for a particular dataset is not straightforward.
DOI: 10.5524/100165
title: Supporting software for OPTIMA, a tool for sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

description: Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome mapping technologies (e.g. optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kbp2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging due to the lack of efficient and sensitive map alignment algorithms for robustly aligning error-prone maps to sequences.<br>
We introduce a novel seed-and-extend glocal alignment method, called OPTIMA (and a sliding-window extension for overlap alignment, called OPTIMA-Overlap), that is the first to be able to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests.
DOI: 10.5524/100105
title: Validation of 21 differentially methylated regions in childhood pre-B cell acute lymphoblastic leukemia using amplicon bisulfite sequencing.

description: A large number of differentially methylated regions (DMRs) with a similar distribution pattern across different genomic elements were discovered by methylome analysis of five pairs of twins . The DMRs located in coding genes and known regulatory elements were identified and examined in a further cohort of 150 sibling pair acute lymphoblastic leukemia (ALL) patients. We validated SNPs and indels in these coding regions and upstream regulatory region of genes that potentially have functional effects. Additionally we applied high-throughput MiSeq amplicon sequencing on libraries constructed by a bisulfite sequencing PCR (BSP)-based procedure, we successfully amplified and sequenced 21 DMRs. The data presented here represent the 150 ALL sibling pairs only, the data used in the original investigation of the five pairs of twins is available from the SRA and GEO databases under the accesions SRP045691 and GSE59869 respectively.
DOI: 10.5524/100109
title: Supporting software and materials for: "GWATCH: a web platform for automated gene association discovery analysis".

description: As genome-wide sequence analyses for complex human disease 
determinants are expanding, it is increasingly necessary to develop strategies to promote 
discovery and validation of potential disease gene associations. <br>GWATCH (Genome-Wide Association Tracks Chromosome Highway) is a 
dynamic genome browser that automates and displays primary analysis results. GWATCH is suitable for both GWAS and whole genome sequence 
association datasets. <br> Here we present the platform as it was published in Oct 2014, for the most recent version please visit the GWATCH GitHub page.
DOI: 10.3535/803-bes-gfv
title: †Cycloclypeus (Katacycloclypeus) transiens Tan, 1932

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/drl-dpg-ws2
title: Cythere Mueller, 1785

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9yl-587-ej5
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k8s-nnl-k10
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ed6-xql-mv2
title: †Discocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kkw-stv-0gc
title: Amphistegina d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9g8-g70-yaw
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gwd-xlf-smm
title: †Orbitoides d'Orbigny, in Lyell, 1848

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zxc-nbr-lml
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c8q-kv9-ep8
title: Hydrobia W. Hartmann, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xas-s5v-ljc
title: Porifera Grant, 1836

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lfb-8yf-bh5
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ayd-9ry-80j
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/frp-82s-5l6
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4jz-wg4-8b1
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6rq-kpq-1r7
title: †Cytherellina Jones & Holl, 1869

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9an-74g-khj
title: †Gryphaea Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k79-3af-ewy
title: †Gryphaea Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lte-zhm-jh7
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1l6-eyf-gm4
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6yk-hng-2h6
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c6g-lf3-q5c
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j3k-hgh-n94
title: Nummulitidae Blainville, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/02a-16l-03l
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dqs-bhn-ml2
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pgt-gws-8wy
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rjy-yyv-1rd
title: †Nummulites planulatus (Lamarck, 1804)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w18-es8-g2a
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2r7-pf1-dh1
title: Aegoceras

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t4f-2ca-f8t
title: †Lepidocyclina epigona Schubert, 1911

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lwb-vy9-3pf
title: Globigerina d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wtr-srg-45g
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/njj-xec-jxe
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/68m-74p-k0w
title: Sphaeroidinella dehiscens (Parker & Jones, 1865)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h0s-8cx-q5w
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mek-v60-axj
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.