cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7628099
title: Additional file 3: of Guide RNAs with embedded barcodes boost CRISPR-pooled screens

description: Table S4. Results of the human genome-scale sgRNAiBAR library screening at different MOI for the cytotoxicity of TcdB using conventional MAGeCK analysis. Table S5. Results of the human genome-scale sgRNAiBAR library screening for the cytotoxicity of 6-TG using MAGeCKiBAR analysis. Table S6. Results of the human genome-scale sgRNAiBAR library screening for the cytotoxicity of 6-TG using conventional MAGeCK analysis. Table S7. Top 20 gene list of two biological replicates using MAGeCKiBAR and MAGeCK analysis. Table S8. sgRNA design for the functional validation of candidate genes from 6-TG screening and sgRNA design for the test of iBAR effects on activity. Table S9. Primers used for PCR amplification of the genomic DNAs and for library construction. Table S10. Comparison of the numbers of cells required for CRISPR library construction for TcdB screenings at different MOIs. (XLSX 12014 kb)
DOI: 10.5281/zenodo.10666958
title: Dataset related to article "An in vitro model of drug-resistant seizures for selecting clinically effective antiseizure medications in Febrile Infection-Related Epilepsy Syndrome"

description: Dataset related to the article
DOI: 10.5281/zenodo.10666959
title: Dataset related to article "An in vitro model of drug-resistant seizures for selecting clinically effective antiseizure medications in Febrile Infection-Related Epilepsy Syndrome"

description: Dataset related to the article
DOI: 10.6084/m9.figshare.11300159.v1
title: MOESM3 of Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida

description: Additional file 3: Table S2. Arabidopsis and rice GRAS genes used for phylogenetic analysis. (XLS 26 kb)
DOI: 10.6084/m9.figshare.21258729.v1
title: Additional file 10 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

description: Additional file 10: Table S10. SNPs, SNP density, and gene density of all 29,269 high-quality SNPs on all 17 pear chromosomes.
DOI: 10.6084/m9.figshare.7628120
title: MOESM3 of Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1

description: Additional file 3. Dataset S2. Biomass composition of Alternaria sp. MG1.
DOI: 10.6084/m9.figshare.7628129
title: MOESM4 of Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1

description: Additional file 4. Dataset S3. Detailed information about model iYL1539.
DOI: 10.6084/m9.figshare.7628144
title: MOESM6 of Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1

description: Additional file 6. Dataset S5. Flux distribution with the resveratrol production rate increased from 0.0073 to 0.02Â mmol/gDW/h.
DOI: 10.6084/m9.figshare.14966174.v1
title: Additional file 6 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

description: Additional file 6: Table S5. The estimated recombination rate.
DOI: 10.6084/m9.figshare.8152502
title: Tree-based ensemble methods for individualized treatment rules

description: There is a growing interest in the development of statistical methods for personalized medicine or precision medicine, especially for deriving optimal individualized treatment rules (ITRs). An ITR recommends a patient to a treatment based on the patient's characteristics. The common parametric methods for deriving an optimal ITR, which model the clinical endpoint as a function of the patient's characteristics, can have suboptimal performance when the conditional mean model is misspecified. Recent methodology development has cast the problem of deriving optimal ITR under a weighted classification framework. Under this weighted classification framework, we develop a weighted random forests (W-RF) algorithm that derives an optimal ITR nonparametrically. In addition, with the W-RF algorithm, we propose the variable importance measures for quantifying relative relevance of the patient's characteristics to treatment selection, and the out-of-bag estimator for the population average outcome under the estimated optimal ITR. Our proposed methods are evaluated through intensive simulation studies. We illustrate the application of our methods using data from Clinical Antipsychotic Trials of Intervention Effectiveness Alzheimer's Disease Study.
DOI: 10.6084/m9.figshare.14966165.v1
title: Additional file 3 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

description: Additional file 3: Table S2. The size and location of the assembled centromere in the hap-Y genome.
DOI: 10.6084/m9.figshare.7628246.v1
title: Additional file 3: of Transcriptome analysis of genes and metabolic pathways associated with nicotine degradation in Aspergillus oryzae 112822

description: Table S1. DEGs between the YD and Nic libraries. Table S2. COG classification of DEGs. Table S3. GO classification and enrichment analysis of DEGs. Table S4. KEGG pathway annotation of DEGs. Table S5. Candidate genes involved in the demethylation pathway of nicotine degradation in A. oryzae 112822. Table S6. DEGs associated with energy production in A. oryzae 112822 exposed to nicotine. Table S7. DEGs encoding enzymes involved in oxidative stress responses. Table S8. DEGs encoding enzymes involved in phase II detoxification. Table S9. DEGs encoding transporters involved in efflux of nicotine and its metabolites. Table S10. Information for the primers used in the qRT-PCR analysis. (XLSX 1155 kb)
DOI: 10.6084/m9.figshare.7628111.v1
title: MOESM2 of Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1

description: Additional file 2. Dataset S1. Metabolites detected inside cells and in the cell-free culture by setting the identification standard of similarity value greater than 200.
DOI: 10.6084/m9.figshare.14442978
title: Additional file 3 of Bioinformatic analysis identifies potential biomarkers and therapeutic targets of septic-shock-associated acute kidney injury

description: Additional file 3. Differentially expressed genes involved in septic shock samples within 24 hours.
DOI: 10.6084/m9.figshare.7103531
title: Additional file 5: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

description: Table S3. Gene annotation statistics of SN265 and R99. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.7103537.v1
title: Additional file 6: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

description: Table S4. Predicted non-coding RNAs, pseudogenes, and motifs. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.8152502.v1
title: Tree-based ensemble methods for individualized treatment rules

description: There is a growing interest in the development of statistical methods for personalized medicine or precision medicine, especially for deriving optimal individualized treatment rules (ITRs). An ITR recommends a patient to a treatment based on the patient's characteristics. The common parametric methods for deriving an optimal ITR, which model the clinical endpoint as a function of the patient's characteristics, can have suboptimal performance when the conditional mean model is misspecified. Recent methodology development has cast the problem of deriving optimal ITR under a weighted classification framework. Under this weighted classification framework, we develop a weighted random forests (W-RF) algorithm that derives an optimal ITR nonparametrically. In addition, with the W-RF algorithm, we propose the variable importance measures for quantifying relative relevance of the patient's characteristics to treatment selection, and the out-of-bag estimator for the population average outcome under the estimated optimal ITR. Our proposed methods are evaluated through intensive simulation studies. We illustrate the application of our methods using data from Clinical Antipsychotic Trials of Intervention Effectiveness Alzheimer's Disease Study.
DOI: 10.6084/m9.figshare.10251590
title: MOESM1 of Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex

description: Additional file 1: Table S1. The number of SRG-positive and SRG-negative cells in the population of glutamatergic neuron, GABAergic neuron and non-neuronal cell.
DOI: 10.6084/m9.figshare.14442972.v1
title: Additional file 1 of Bioinformatic analysis identifies potential biomarkers and therapeutic targets of septic-shock-associated acute kidney injury

description: Additional file 1. Differentially expressed genes involved in AKI samples.
DOI: 10.6084/m9.figshare.7103552.v1
title: Additional file 24: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: FEELnc Coding Potential Scores for Pig LncRNAs. The coding potential scores calculated by FEELnc. The “coding_potential” column is the coding potential score, with 0 being the least likely to be coding and 1 being most likely. The “label” column is 0 or 1 to indicate if the score lies above or below the cutoff determined by FEELnc using cross validation. 0 indicates a predicted lncRNA while 1 is a predicted coding transcript. (XLSX 323 kb)
DOI: 10.6084/m9.figshare.10251590.v1
title: MOESM1 of Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex

description: Additional file 1: Table S1. The number of SRG-positive and SRG-negative cells in the population of glutamatergic neuron, GABAergic neuron and non-neuronal cell.
DOI: 10.6084/m9.figshare.7103555
title: Additional file 1: of The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants

description: Table S1. Kinase domain annotation of 758 pineapple protein kinases. Table S2. Family classification of pineapple protein kinases and their related information. Table S3. The numbers of pineapple PK genes in different families. Table S4. Domain organization of 758 pineapple PKs. Table S5. List of 70 pineapple protein kinases containing multiple kinase domains. Table S6. Pineapple PK genes generated by segmental duplication. Table S7. Pineapple PK genes generated by tandem duplication. Table S8. Segmental and tandem duplication events and Ka/Ks values of pineapple protein kinases. Table S9. Alternative splicing types of PK genes in pineapple. Table S10. Average FPKM expression values of 758 pineapple kinase genes in 14 different tissues among developmental stages. Table S11. 494 genes in ten clusters with different expression patterns during development. Table S12. Average FPKM expression values of 758 pineapple kinase genes during 24-h in green leaf tip. Table S13. Average FPKM expression values of 758 pineapple kinase genes during 24-h in white leaf base. Table S14. Genes in ten clusters with different expression patterns. Table S15. Expression values of pineapple kinase genes generated by duplication during 24-h in both green and white leaf tissues. Table S16. The orthologs of 20 pineapple PKs in Arabidopsis. (XLSX 336 kb)
DOI: 10.6084/m9.figshare.7103555.v1
title: Additional file 1: of The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants

description: Table S1. Kinase domain annotation of 758 pineapple protein kinases. Table S2. Family classification of pineapple protein kinases and their related information. Table S3. The numbers of pineapple PK genes in different families. Table S4. Domain organization of 758 pineapple PKs. Table S5. List of 70 pineapple protein kinases containing multiple kinase domains. Table S6. Pineapple PK genes generated by segmental duplication. Table S7. Pineapple PK genes generated by tandem duplication. Table S8. Segmental and tandem duplication events and Ka/Ks values of pineapple protein kinases. Table S9. Alternative splicing types of PK genes in pineapple. Table S10. Average FPKM expression values of 758 pineapple kinase genes in 14 different tissues among developmental stages. Table S11. 494 genes in ten clusters with different expression patterns during development. Table S12. Average FPKM expression values of 758 pineapple kinase genes during 24-h in green leaf tip. Table S13. Average FPKM expression values of 758 pineapple kinase genes during 24-h in white leaf base. Table S14. Genes in ten clusters with different expression patterns. Table S15. Expression values of pineapple kinase genes generated by duplication during 24-h in both green and white leaf tissues. Table S16. The orthologs of 20 pineapple PKs in Arabidopsis. (XLSX 336 kb)
DOI: 10.6084/m9.figshare.21258735.v1
title: Additional file 12 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

description: Additional file 12: Table S12. Two significant SNPs associated with fruit firmness.
DOI: 10.6084/m9.figshare.7103573
title: Additional file 2: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Sequences of Cattle LncRNAs. A fasta file containing all the lncRNA sequences from cattle. (FA 14461 kb)
DOI: 10.6084/m9.figshare.7103582
title: Additional file 3: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Sequences of Pig LncRNAs. A fasta file containing all the lncRNA sequences from pigs. (FA 21227 kb)
DOI: 10.6084/m9.figshare.7103582.v1
title: Additional file 3: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Sequences of Pig LncRNAs. A fasta file containing all the lncRNA sequences from pigs. (FA 21227 kb)
DOI: 10.6084/m9.figshare.10251596
title: MOESM2 of Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex

description: Additional file 2: Table S2. The ratio of SRG-positive cells to total cells in human versus mouse V1 cortex. The Îş2 and p value were shown for each SRG. The red color indicates significant difference between human and mouse.
DOI: 10.6084/m9.figshare.10251596.v1
title: MOESM2 of Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex

description: Additional file 2: Table S2. The ratio of SRG-positive cells to total cells in human versus mouse V1 cortex. The Îş2 and p value were shown for each SRG. The red color indicates significant difference between human and mouse.
DOI: 10.6084/m9.figshare.21258710
title: Additional file 1 of Interaction analysis of lipid accumulation product and family history of diabetes on impaired fasting glucose and diabetes risk in population with normotension in Eastern China: a community-based cross-sectional survey

description: Additional file 1.
DOI: 10.6084/m9.figshare.21258732.v1
title: Additional file 11 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

description: Additional file 11: Table S11. A summary of the categorized SNPs.
DOI: 10.6084/m9.figshare.7103630
title: Additional file 7: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Mapping to NONCODE. The NONCODE IDs for each lncRNA found in the NONCODE database, as described in the Methods section. For lncRNA that had multiple matches in the NONCODE database, the NONCODE ID for the match with the highest bit score is used. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.7103630.v1
title: Additional file 7: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Mapping to NONCODE. The NONCODE IDs for each lncRNA found in the NONCODE database, as described in the Methods section. For lncRNA that had multiple matches in the NONCODE database, the NONCODE ID for the match with the highest bit score is used. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.21258729
title: Additional file 10 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

description: Additional file 10: Table S10. SNPs, SNP density, and gene density of all 29,269 high-quality SNPs on all 17 pear chromosomes.
DOI: 10.6084/m9.figshare.7103525
title: Additional file 21: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Multiple Sequence Alignments for Conserved LncRNAs. A multiple sequence alignment file generated by ClustalW is included for each of the 39 groups of lncRNAs associated with orthologous genes across all five species. (ZIP 445 kb)
DOI: 10.6084/m9.figshare.11300174
title: MOESM5 of Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida

description: Additional file 5: Table S4. The expression data of the ItfGRAS genes in various tissues. (XLS 32 kb)
DOI: 10.6084/m9.figshare.7103534
title: Additional file 22: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: FEELnc Coding Potential Scores for Chicken LncRNAs. The coding potential scores calculated by FEELnc. The “coding_potential” column is the coding potential score, with 0 being the least likely to be coding and 1 being most likely. The “label” column is 0 or 1 to indicate if the score lies above or below the cutoff determined by FEELnc using cross validation. 0 indicates a predicted lncRNA while 1 is a predicted coding transcript. (XLSX 217 kb)
DOI: 10.6084/m9.figshare.7627967.v1
title: Additional file 15: of Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum

description: Expression patterns of MGT genes across leaf gradient segments in maize and rice [88]. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.11300174.v1
title: MOESM5 of Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida

description: Additional file 5: Table S4. The expression data of the ItfGRAS genes in various tissues. (XLS 32 kb)
DOI: 10.6084/m9.figshare.7627922.v1
title: Additional file 10: of Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum

description: The non-synonymous (Ka) and synonymous (Ks) substitution ratios of each MGTs from 10 representative plants. (XLSX 804 kb)
DOI: 10.6084/m9.figshare.7628381
title: MOESM10 of Transcriptome analysis unraveled potential mechanisms of resistance to Haemonchus contortus infection in Merino sheep populations bred for parasite resistance

description: Additional file 10. Significant transcript isoforms between resistant and susceptible lines in response to Haemonchus contortus infection. These isoforms were detected using the TopHat2-Cuffdiff pipeline.
DOI: 10.6084/m9.figshare.14443080.v1
title: Additional file 2 of Chromatin accessibility landscapes of immune cells in rheumatoid arthritis nominate monocytes in disease pathogenesis

description: Additional file 2: Table S1. List of information for patients with RA and OA.
DOI: 10.6084/m9.figshare.7103534.v1
title: Additional file 22: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: FEELnc Coding Potential Scores for Chicken LncRNAs. The coding potential scores calculated by FEELnc. The “coding_potential” column is the coding potential score, with 0 being the least likely to be coding and 1 being most likely. The “label” column is 0 or 1 to indicate if the score lies above or below the cutoff determined by FEELnc using cross validation. 0 indicates a predicted lncRNA while 1 is a predicted coding transcript. (XLSX 217 kb)
DOI: 10.6084/m9.figshare.10251602
title: MOESM3 of Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex

description: Additional file 3: Table S3. The ratio of SRG-positive glutamatergic neurons to total glutamatergic neurons in human versus mouse V1 cortex. The Îş2 and p value were shown for each SRG. The red color indicates significant difference between human and mouse.
DOI: 10.6084/m9.figshare.14966140.v1
title: Additional file 2 of Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

description: Additional file 2: Table S1. Sequence of TADs and origins (TAD1 & TAD2).
DOI: 10.6084/m9.figshare.21258735
title: Additional file 12 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

description: Additional file 12: Table S12. Two significant SNPs associated with fruit firmness.
DOI: 10.6084/m9.figshare.7103573.v1
title: Additional file 2: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Sequences of Cattle LncRNAs. A fasta file containing all the lncRNA sequences from cattle. (FA 14461 kb)
DOI: 10.6084/m9.figshare.7103642.v1
title: Additional file 8: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: LncRNA Classes from Chickens. (TSV 3281 kb)
DOI: 10.6084/m9.figshare.10251602.v1
title: MOESM3 of Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex

description: Additional file 3: Table S3. The ratio of SRG-positive glutamatergic neurons to total glutamatergic neurons in human versus mouse V1 cortex. The Îş2 and p value were shown for each SRG. The red color indicates significant difference between human and mouse.
DOI: 10.6084/m9.figshare.14966168
title: Additional file 4 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

description: Additional file 4: Table S3. Expression levels of genes in the SLR.
DOI: 10.22008/fk2/b674ar/gmspo1
title: r_TOA_16.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/yzv5cv
title: r_TOA_17.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/m5ohbm
title: r_TOA_18.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/w4zaax
title: r_TOA_19.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/uhjvdo
title: r_TOA_20.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/iuecuh
title: r_TOA_21.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/0xjzcn
title: r_TOA_S5.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/kojhbu
title: SAA.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/94qufb
title: SZA.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/og31ii
title: WV.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/eidqdi
title: O3.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/arguse
title: OAA.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/gloxk9
title: OZA.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.22008/fk2/b674ar/sqrcjg
title: r_TOA_01.tif

description: SICE version: Cloud removed, PPGC, SNAP7
DOI: 10.6084/m9.figshare.13297718
title: Supplemental materials for incidence of complications in 25 adult patients with X-linked hypophosphatemia.

description: This is the dataset of clinical data of 25 adults with X-linked hypophosphatemia, which was the supplementary material for the paper entitled: "Incidence of complications in 25 adults patients with X-linked hypophosphatemia".