cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13551054.v1
title: Additional file 4 of Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

description: Additional file 4: Table S1. Summary of sequencing data. Table S2. List of additional cattle samples for analysis of genetic background in Jiaxian Red cattle. Table S3. Distribution of SNPs identified in cattle breeds within various genomic regions annotated by ANNOVAR. Table S4. GO enrichment results for the genes containing specific nsSNPs &gt; 5 in Jiaxian Red cattle. Table S5. GO enrichment results for the genes containing specific nsSNPs &gt; 5 in Qinchuan cattle. Table S6. A summary of genes from θπ in Jiaxian Red. Table S7. A summary of genes from CLR in Jiaxian Red. Table S8. KEGG pathway analysis of Jiaxian Red candidate genes overlapped by θπ and CLR methods. Table S9. GO enrichment of Jiaxian Red candidate genes overlapped by θπ and CLR methods. Table S10. A summary of genes from FST. Table S11. A summary of genes from XP-CLR in Jiaxian Red cattle. Table S12. A summary of genes from FST and XP-EHH in Jiaxian Red cattle. Table S13. Cross-validation (CV) errors for ADMIXTURE ancestry models with K ranging from 2 to 8.
DOI: 10.15468/z7xrxu
title: CDG Express - Reptiles - Inventaire non protocolé

description: Liste des reptiles observés dans le cadre des prospections de terrain réalisées au niveau des mesures compensatoires dans le cadre du Charles de Gaulle Express
DOI: 10.15468/egvupn
title: demande de dérogation aux interdictions porté aux espèces protégées présentes sur le site de projets 1 et 2 portée par la SNC FP DONZERE, Parc des Eoliennes sur la commune de Donzère ( 26) - Chiroptères - Points d'écoute.

description: Listes des chiroptères contactées grâce à des points d'écoute au niveau de l'aire d'étude du site des projets 1 et 2 portée par la SNC FP DONZERE, Parc des Eoliennes sur la commune de Donzère (26).
DOI: 10.15468/embgg4
title: CDG Express - Insectes - Inventaire non protocolé

description: Liste des insectes observés dans le cadre des prospections de terrain réalisées au niveau des mesures compensatoires dans le cadre du Charles de Gaulle Express
DOI: 10.15468/dkrsgk
title: Parc éolien du Plateau de La Perche - Insectes - Inventaire non protocolé

description: Liste des insectes observés dans le cadre des prospections de terrain au niveau de l'aire d'étude
DOI: 10.15468/6hzpxk
title: Parc éolien du Plateau de La Perche - Reptiles - Inventaire non protocolé

description: Liste des reptiles observés dans le cadre des prospections de terrain au niveau de l'aire d'étude
DOI: 10.6084/m9.figshare.12502496
title: Additional file 2 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 2. Table S1. Full listing of the 272 transcript-deleterious variants identified in our cohort. * indicates genes that required more amplification cycles to detect expression.
DOI: 10.6084/m9.figshare.12502496.v1
title: Additional file 2 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 2. Table S1. Full listing of the 272 transcript-deleterious variants identified in our cohort. * indicates genes that required more amplification cycles to detect expression.
DOI: 10.6084/m9.figshare.13551078
title: Additional file 4 of The EGFR-HSF1 axis accelerates the tumorigenesis of pancreatic cancer

description: Additional file 4: Table S3. Source files of bioinformatics analysis on EGFR pathway (GEO GSE98399 datasets).
DOI: 10.6084/m9.figshare.12502520
title: Additional file 4 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 4. Table S3. List of families that map to a single locus and the outcome of their investigation.
DOI: 10.6084/m9.figshare.12502520.v1
title: Additional file 4 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 4. Table S3. List of families that map to a single locus and the outcome of their investigation.
DOI: 10.6084/m9.figshare.8832509
title: Data and R code for "The paleoclimatic footprint in the soil carbon stock of the Tibetan permafrost region"

description: A new estimate of Tibetan soil carbon pool, at a 0.1° spatial resolution, obtained by including paleoclimate, modern climate and landform, soil geochemical properties in multiple machine learning algorithms.
DOI: 10.6084/m9.figshare.12502529
title: Additional file 5 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 5. Table S4. Full list of negative clinical WES cases and the outcome of their analysis by RNA studies and other tools. ‘A’ indicates a novel gene/novel gene for the condition.
DOI: 10.6084/m9.figshare.12502529.v1
title: Additional file 5 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 5. Table S4. Full list of negative clinical WES cases and the outcome of their analysis by RNA studies and other tools. ‘A’ indicates a novel gene/novel gene for the condition.
DOI: 10.6084/m9.figshare.13551072
title: Additional file 2 of The EGFR-HSF1 axis accelerates the tumorigenesis of pancreatic cancer

description: Additional file 2: Table S1. Source files of bioinformatics analysis on HSF1 and its related proteins (mainly TCGA PAAD datasets).
DOI: 10.6084/m9.figshare.13551072.v1
title: Additional file 2 of The EGFR-HSF1 axis accelerates the tumorigenesis of pancreatic cancer

description: Additional file 2: Table S1. Source files of bioinformatics analysis on HSF1 and its related proteins (mainly TCGA PAAD datasets).
DOI: 10.6084/m9.figshare.13551078.v1
title: Additional file 4 of The EGFR-HSF1 axis accelerates the tumorigenesis of pancreatic cancer

description: Additional file 4: Table S3. Source files of bioinformatics analysis on EGFR pathway (GEO GSE98399 datasets).
DOI: 10.6084/m9.figshare.12502547
title: Additional file 7 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 7. Table S5. The performance comparison results of our RNA-Seq pipeline.
DOI: 10.6084/m9.figshare.12502547.v1
title: Additional file 7 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 7. Table S5. The performance comparison results of our RNA-Seq pipeline.
DOI: 10.6084/m9.figshare.12502568
title: Additional file 9 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 9. Table S7. In silico (using SpliceAI, TraP, S-CAP, and CADD) predictions for all transcript-deleterious variants in this cohort that were empirically tested.
DOI: 10.6084/m9.figshare.12502568.v1
title: Additional file 9 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

description: Additional file 9. Table S7. In silico (using SpliceAI, TraP, S-CAP, and CADD) predictions for all transcript-deleterious variants in this cohort that were empirically tested.
DOI: 10.6084/m9.figshare.14677118
title: Additional file 5 of Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

description: Additional file 5: Table S10
DOI: 10.6084/m9.figshare.14677118.v1
title: Additional file 5 of Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

description: Additional file 5: Table S10
DOI: 10.6084/m9.figshare.14677124
title: Additional file 7 of Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

description: Additional file 7: Table S12
DOI: 10.6084/m9.figshare.14677124.v1
title: Additional file 7 of Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

description: Additional file 7: Table S12
DOI: 10.6084/m9.figshare.23512633
title: Additional file 1 of RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

description: Additional file 1: Supplementary File 1. Metadata of this study.
DOI: 10.6084/m9.figshare.23512633.v1
title: Additional file 1 of RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

description: Additional file 1: Supplementary File 1. Metadata of this study.
DOI: 10.6084/m9.figshare.23512645
title: Additional file 4 of RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

description: Additional file 4: Supplementary File 4. Metadata of five studies.
DOI: 10.6084/m9.figshare.23512645.v1
title: Additional file 4 of RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

description: Additional file 4: Supplementary File 4. Metadata of five studies.
DOI: 10.34740/kaggle/dsv/7717987
title: Arthritis Profile Dataset (APDDataset)
DOI: 10.6084/m9.figshare.23512648
title: Additional file 5 of RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

description: Additional file 5: Supplementary File 5. OTU table obtained from bioBakery workflow of five 16S-RNA-seq studies.
DOI: 10.6084/m9.figshare.23512651
title: Additional file 6 of RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

description: Additional file 6: Supplementary File 6. Differentially significant taxa in the comparative study (part 4) from MaAsLin 2
DOI: 10.6084/m9.figshare.23512648.v1
title: Additional file 5 of RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

description: Additional file 5: Supplementary File 5. OTU table obtained from bioBakery workflow of five 16S-RNA-seq studies.
DOI: 10.6084/m9.figshare.23512651.v1
title: Additional file 6 of RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

description: Additional file 6: Supplementary File 6. Differentially significant taxa in the comparative study (part 4) from MaAsLin 2
DOI: 10.15468/3c5ruq
title: 25 - Programme d'inventaire MycoflAURA - MycoflAURA RT 2013

description: MycoflAURA RT 2013 / Acquisition de données d'inventaire de la fonge d'Auvergne-Rhône-Alpes dans le cadre d'une convention entre la FMBDS et les associations ou les mycologues régionaux
DOI: 10.15468/snzkwv
title: Unveiling the Mushrooms Diversity of Lumle, Nepal, in a High-Precipitation Environment

description: In 2005, Shiva Devkota successfully completed a dissertation at the Central Department of Botany, Tribhuvan University, as a requirement for earning a Master of Science in Botany (MSC Botany). This dissertation, titled "Mushroom Diversity in the Lumle (Kaski) Area and a Study of Clavariales in the Lumle Region and the Vicinity of Kathmandu Valley, Nepal," is available for reference at this link: https://lib.icimod.org/record/333. The dataset presented here is a product of Shiva Devkota's research, which was primarily focused on the systematic examination of mushrooms within the Lumle Village Development Committee (VDC), which is currently known as Annapurna Rural Municipality. This study area is situated in Nepal's meso-thermal zone. Despite its elevated location and exposure to cold winds from the snow-covered Annapurna range, it consistently maintains a humid-temperate microclimate. Lumle is renowned for its substantial annual rainfall, with precipitation levels ranging from 5000 mm to 6000 mm, predominantly occurring between June and September, spanning four months and encompassing more than 70 rainy days. These environmental conditions make the studied area an ideal habitat for a diverse range of mushroom species. This research reveals a gradient in the distribution of mushroom species with changing altitudes, characterized by low spatial turnover. This suggests a relatively homogeneous distribution of mushroom flora in the region. The presence of a substantial number of mushroom species within a narrow ecological range, displaying a homogeneous distribution, implies that the Lumle area holds the potential to serve as a significant fungal reservoir. Additionally, this study documented the local community's beliefs regarding mushrooms, traditional methods for distinguishing edible from poisonous varieties, and practices employed to minimize the risk of poisoning. For further exploration and access to additional research publications based on this dataset, please visit the following link: https://www.researchgate.net/profile/Shiva-Devkota/research
DOI: 10.6084/m9.figshare.14677130
title: Additional file 9 of Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

description: Additional file 9: Table S14
DOI: 10.15468/4maap4
title: Hongos y Liquenes del Sur Argentino, campaña 2015-2017 del Museo Botánico CORD - IMBIV

description: Hongos del sur de Argentina, colectados durante las campañas de los años 2015-2017 conjuntamente con el herbario University of Florida Herbarium (FLAS)
DOI: 10.6084/m9.figshare.14677130.v1
title: Additional file 9 of Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

description: Additional file 9: Table S14
DOI: 10.6084/m9.figshare.11454060
title: Additional file 1 of The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers

description: Additional file 1 Supplementary tables. This is an MS Excel file. This file includes 32 supplementary tables.
DOI: 10.6084/m9.figshare.11454060.v1
title: Additional file 1 of The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers

description: Additional file 1 Supplementary tables. This is an MS Excel file. This file includes 32 supplementary tables.
DOI: 10.6084/m9.figshare.11454081
title: MOESM1 of NmSEER V2.0: a prediction tool for 2′-O-methylation sites based on random forest and multi-encoding combination

description: Additional file 1: Table S1. Training set for both HeLa and HEK293. Table S2. Testing set for both HeLa and HEK293. Table S3. Training set for individual HeLa. Table S4. Testing set for individual HeLa. Table S5. Training set for individual HEK293. Table S6. Testing set for individual HEK293. Table S7. Optimized hyper-parameters of each encoding.
DOI: 10.6084/m9.figshare.11454081.v1
title: MOESM1 of NmSEER V2.0: a prediction tool for 2′-O-methylation sites based on random forest and multi-encoding combination

description: Additional file 1: Table S1. Training set for both HeLa and HEK293. Table S2. Testing set for both HeLa and HEK293. Table S3. Training set for individual HeLa. Table S4. Testing set for individual HeLa. Table S5. Training set for individual HEK293. Table S6. Testing set for individual HEK293. Table S7. Optimized hyper-parameters of each encoding.
DOI: 10.6084/m9.figshare.25303751
title: Zipfile containing code in MATLAB and R. from Oscillatory differentiation dynamics fundamentally restricts the resolution of pseudotime reconstruction algorithms

description: The challenge to understand differentiation and cell lineages in development has resulted in many bioinformatics software tools, notably those working with gene expression data obtained via single-cell RNA sequencing obtained at snapshots in time. Reconstruction methods for trajectories often proceed by dimension reduction, data clustering and then computation of a tree graph in which edges indicate closely related clusters. Cell lineages can then be deduced by following paths through the tree. In the case of multipotent cells undergoing differentiation, this trajectory reconstruction involves the reconstruction of multiple distinct lineages corresponding to commitment to each of a set of distinct fates. Recent work suggests that there may be cases in which the cell differentiation process involves trajectories that explore, in a dynamic and oscillatory fashion, propensity to differentiate into a number of possible cell fates before commitment finally occurs. Here, we show theoretically that the presence of such oscillations provides intrinsic constraints on the quality and resolution of the trajectory reconstruction process, even for idealizzed noise-free data. These constraints point to inherent common limitations of current methodologies and serves both to provide additional challenge in the development of software tools, and also may help to understand features observed in recent experiments.
DOI: 10.6084/m9.figshare.25303751.v1
title: Zipfile containing code in MATLAB and R. from Oscillatory differentiation dynamics fundamentally restricts the resolution of pseudotime reconstruction algorithms

description: The challenge to understand differentiation and cell lineages in development has resulted in many bioinformatics software tools, notably those working with gene expression data obtained via single-cell RNA sequencing obtained at snapshots in time. Reconstruction methods for trajectories often proceed by dimension reduction, data clustering and then computation of a tree graph in which edges indicate closely related clusters. Cell lineages can then be deduced by following paths through the tree. In the case of multipotent cells undergoing differentiation, this trajectory reconstruction involves the reconstruction of multiple distinct lineages corresponding to commitment to each of a set of distinct fates. Recent work suggests that there may be cases in which the cell differentiation process involves trajectories that explore, in a dynamic and oscillatory fashion, propensity to differentiate into a number of possible cell fates before commitment finally occurs. Here, we show theoretically that the presence of such oscillations provides intrinsic constraints on the quality and resolution of the trajectory reconstruction process, even for idealizzed noise-free data. These constraints point to inherent common limitations of current methodologies and serves both to provide additional challenge in the development of software tools, and also may help to understand features observed in recent experiments.
DOI: 10.6084/m9.figshare.23512715
title: Additional file 2 of 5-Methylcytosine-related lncRNAs: predicting prognosis and identifying hot and cold tumor subtypes in head and neck squamous cell carcinoma

description: Additional file 2: Table S1. Results for ceRNA in tumor based on LncSEA database.
DOI: 10.6084/m9.figshare.23512715.v1
title: Additional file 2 of 5-Methylcytosine-related lncRNAs: predicting prognosis and identifying hot and cold tumor subtypes in head and neck squamous cell carcinoma

description: Additional file 2: Table S1. Results for ceRNA in tumor based on LncSEA database.
DOI: 10.6084/m9.figshare.11454072
title: Additional file 1 of JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants

description: Additional file 1. The transcriptome data sources of Jatropha curcas.
DOI: 10.6084/m9.figshare.11454093
title: MOESM2 of wtest: an integrated R package for genetic epistasis testing

description: Additional file 2 Reference table of sample size estimation. When the averaged MAF is 0.3 and the sample size is greater than the estimated sample size, no more than 25% cells have averaged cell count less than 2 in the contingency tables.
DOI: 10.6084/m9.figshare.11454072.v1
title: Additional file 1 of JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants

description: Additional file 1. The transcriptome data sources of Jatropha curcas.
DOI: 10.6084/m9.figshare.11454093.v1
title: MOESM2 of wtest: an integrated R package for genetic epistasis testing

description: Additional file 2 Reference table of sample size estimation. When the averaged MAF is 0.3 and the sample size is greater than the estimated sample size, no more than 25% cells have averaged cell count less than 2 in the contingency tables.
DOI: 10.34740/kaggle/dsv/7718145
title: SOD1 structures mutations
DOI: 10.6084/m9.figshare.12502682
title: Additional file 2 of CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

description: Additional file 2. Additional tables. This file contains information about benchmark samples (tab 1), performance evaluation of benchmark samples by different algorithms (tab 2), sample information about TCGA GBM cohort (tab 3), cancer gene fusions identified in TCGA GBM cohort (tab 4 & 5) and reference files used in CICERO analysis (tab 6).
DOI: 10.6084/m9.figshare.12502682.v1
title: Additional file 2 of CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

description: Additional file 2. Additional tables. This file contains information about benchmark samples (tab 1), performance evaluation of benchmark samples by different algorithms (tab 2), sample information about TCGA GBM cohort (tab 3), cancer gene fusions identified in TCGA GBM cohort (tab 4 & 5) and reference files used in CICERO analysis (tab 6).
DOI: 10.6084/m9.figshare.11454108
title: MOESM3 of Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)

description: Additional file 3. KEGG pathways and the corresponding unigene numbers and IDs in the transcriptome of Lei bamboo.
DOI: 10.6084/m9.figshare.11454108.v1
title: MOESM3 of Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)

description: Additional file 3. KEGG pathways and the corresponding unigene numbers and IDs in the transcriptome of Lei bamboo.
DOI: 10.6084/m9.figshare.12502688
title: Additional file 3 of CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

description: Additional file 3. Additional tables. This file shows the results of false positive rate of different fusion detection methods based on the analysis of 80 cases that have both WGS and RNA-seq.
DOI: 10.6084/m9.figshare.12502688.v1
title: Additional file 3 of CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

description: Additional file 3. Additional tables. This file shows the results of false positive rate of different fusion detection methods based on the analysis of 80 cases that have both WGS and RNA-seq.
DOI: 10.6084/m9.figshare.11454117
title: MOESM4 of Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)

description: Additional file 4. Summary of the GO enrichment analysis of the DEGs in each comparison.
DOI: 10.6084/m9.figshare.11454117.v1
title: MOESM4 of Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)

description: Additional file 4. Summary of the GO enrichment analysis of the DEGs in each comparison.
DOI: 10.6084/m9.figshare.23512759
title: Additional file 6 of Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genus Pseudozyma (Ustilaginales)

description: Additional file 6: Telomere annotation.
DOI: 10.6084/m9.figshare.23512756
title: Additional file 5 of Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genus Pseudozyma (Ustilaginales)

description: Additional file 5: Meiosis and mating gene functional domains.