cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6449159
title: Additional file 6: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S5. Interconnected loops in core regulatory circuits. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.6449159.v1
title: Additional file 6: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S5. Interconnected loops in core regulatory circuits. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.6449153
title: MOESM2 of In silico identification of drug target pathways in breast cancer subtypes using pathway cross-talk inhibition

description: Additional file 2. Shows the network efficiency after inhibition of individual and combined pathway(s) in luminal B BC.
DOI: 10.6084/m9.figshare.6449153.v1
title: MOESM2 of In silico identification of drug target pathways in breast cancer subtypes using pathway cross-talk inhibition

description: Additional file 2. Shows the network efficiency after inhibition of individual and combined pathway(s) in luminal B BC.
DOI: 10.6084/m9.figshare.6449150
title: Additional file 5: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S4. Category of methylation change. (XLSX 5313Â kb)
DOI: 10.6084/m9.figshare.6449150.v1
title: Additional file 5: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S4. Category of methylation change. (XLSX 5313Â kb)
DOI: 10.6084/m9.figshare.6449135
title: MOESM1 of In silico identification of drug target pathways in breast cancer subtypes using pathway cross-talk inhibition

description: Additional file 1. Shows the network efficiency after inhibition of individual and combined pathway(s) in luminal A BC.
DOI: 10.6084/m9.figshare.6449135.v1
title: MOESM1 of In silico identification of drug target pathways in breast cancer subtypes using pathway cross-talk inhibition

description: Additional file 1. Shows the network efficiency after inhibition of individual and combined pathway(s) in luminal A BC.
DOI: 10.6084/m9.figshare.6449129
title: Additional file 4: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S3. sgRNA-primer of DRE tested. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6449129.v1
title: Additional file 4: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S3. sgRNA-primer of DRE tested. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6449114
title: Additional file 1 of Evaluation of gold fiducial marker manual localisation for magnetic resonance-only prostate radiotherapy

description: [1.] GeneralGuidelineFMloc.pdf which presents a short description of the procedure; [2.] PracticalInstructionFMloc.pdf which describes step-by-step the procedure; [3.] Checklist_Obs.pdf which is aimed at supporting the RTTs during the procedure in keeping track and annotate for which patient the localisation was found problematic. (ZIP 194 kb)
DOI: 10.6084/m9.figshare.6449114.v1
title: Additional file 1 of Evaluation of gold fiducial marker manual localisation for magnetic resonance-only prostate radiotherapy

description: [1.] GeneralGuidelineFMloc.pdf which presents a short description of the procedure; [2.] PracticalInstructionFMloc.pdf which describes step-by-step the procedure; [3.] Checklist_Obs.pdf which is aimed at supporting the RTTs during the procedure in keeping track and annotate for which patient the localisation was found problematic. (ZIP 194 kb)
DOI: 10.6084/m9.figshare.6449111
title: Additional file 3: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S2. DREs identified from 11 cancers. (XLSX 5825Â kb)
DOI: 10.6084/m9.figshare.6449111.v1
title: Additional file 3: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S2. DREs identified from 11 cancers. (XLSX 5825Â kb)
DOI: 10.6084/m9.figshare.6449102
title: Additional file 1: of Immune oncology, immune responsiveness and the theory of everything

description: List of individual genes and corresponding models related to immune suppression used for the Theory of Everything (TOE). (TXT 11 kb)
DOI: 10.6084/m9.figshare.6449102.v1
title: Additional file 1: of Immune oncology, immune responsiveness and the theory of everything

description: List of individual genes and corresponding models related to immune suppression used for the Theory of Everything (TOE). (TXT 11 kb)
DOI: 10.6084/m9.figshare.6449096
title: Additional file 4: of Safety and efficacy of human embryonic stem cell-derived astrocytes following intrathecal transplantation in SOD1G93A and NSG animal models

description: Table S2. Percent of cell presence and percent of frequency scores greater than, or equal to â 2â (one to three foci of 10-20 cells per foci) for each follow up time (4, 17 and 39 weeks after hES-AS transplantation). Supplementary materials and methods. (ZIP 150 kb)
DOI: 10.6084/m9.figshare.6449096.v1
title: Additional file 4: of Safety and efficacy of human embryonic stem cell-derived astrocytes following intrathecal transplantation in SOD1G93A and NSG animal models

description: Table S2. Percent of cell presence and percent of frequency scores greater than, or equal to â 2â (one to three foci of 10-20 cells per foci) for each follow up time (4, 17 and 39 weeks after hES-AS transplantation). Supplementary materials and methods. (ZIP 150 kb)
DOI: 10.6084/m9.figshare.6449090
title: Additional file 2: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S1. Barcode of TCGA samples. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.6449090.v1
title: Additional file 2: of MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

description: Table S1. Barcode of TCGA samples. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.6449069
title: Additional file 9: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_CPP02_vs_Pmnk6_CPP27. High-confidence single nucleotide polymorphisms between tropical kudzu CPP02 (reference: Ref) and a composite transcriptome comprising reads from kudzu accessions CPP27 and Pmnk6 (variant: Var). Abbreviations as described for Additional file 6. (XLSX 11520 kb)
DOI: 10.6084/m9.figshare.6449057
title: Additional file 9: of Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

description: Table S7. List of deregulated genes of the indepentent cohort of patients.Â (XLSX 95 kb)
DOI: 10.6084/m9.figshare.6449057.v1
title: Additional file 9: of Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

description: Table S7. List of deregulated genes of the indepentent cohort of patients.Â (XLSX 95 kb)
DOI: 10.6084/m9.figshare.6449051
title: Additional file 8: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_CPP02_vs_Pmnk6. High-confidence single nucleotide polymorphisms between tropical kudzu CPP02 (reference: Ref) and kudzu accession Pmnk6 (variant: Var). Abbreviations as described for Additional file 6. (XLSX 11073 kb)
DOI: 10.6084/m9.figshare.6449051.v1
title: Additional file 8: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_CPP02_vs_Pmnk6. High-confidence single nucleotide polymorphisms between tropical kudzu CPP02 (reference: Ref) and kudzu accession Pmnk6 (variant: Var). Abbreviations as described for Additional file 6. (XLSX 11073 kb)
DOI: 10.6084/m9.figshare.6449042
title: Additional file 2: of Collective interaction effects associated with mammalian behavioral traits reveal genetic factors connecting fear and hemostasis

description: Table S3. Lists of highlyÂ ranked pathways for mouse and dog behavioral traits. Pathways with Pâ
DOI: 10.6084/m9.figshare.6449042.v1
title: Additional file 2: of Collective interaction effects associated with mammalian behavioral traits reveal genetic factors connecting fear and hemostasis

description: Table S3. Lists of highlyÂ ranked pathways for mouse and dog behavioral traits. Pathways with Pâ
DOI: 10.6084/m9.figshare.6449033
title: Additional file 7: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_CPP02_vs_CPP27. High-confidence single nucleotide polymorphisms between tropical kudzu CPP02 (reference: Ref) and kudzu accession CPP27 (variant: Var). Abbreviations as described for Additional file 6. (XLSX 4932 kb)
DOI: 10.6084/m9.figshare.6449033.v1
title: Additional file 7: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_CPP02_vs_CPP27. High-confidence single nucleotide polymorphisms between tropical kudzu CPP02 (reference: Ref) and kudzu accession CPP27 (variant: Var). Abbreviations as described for Additional file 6. (XLSX 4932 kb)
DOI: 10.6084/m9.figshare.6449018
title: Additional file 6: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_Pmnk6_vs_CPP27. High-confidence single nucleotide polymorphisms between US kudzu accessions Pmnk6 (variant: Var) and CPP27 (reference: Ref). Accno: contig in reference; Pos: position; Nuc: nucleotide; Total Depth: number of variant reads aligned against the reference; Var Freq: frequency of variant SNP within aligned reads; # Fwd: number of forward reads with variant; # Rev.: number of reverse reads with variant; # Fwd Total: number of forward-aligned reads total; # Rev. Total: number of reverse-aligned reads total. (XLSX 578 kb)
DOI: 10.6084/m9.figshare.6449018.v1
title: Additional file 6: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_Pmnk6_vs_CPP27. High-confidence single nucleotide polymorphisms between US kudzu accessions Pmnk6 (variant: Var) and CPP27 (reference: Ref). Accno: contig in reference; Pos: position; Nuc: nucleotide; Total Depth: number of variant reads aligned against the reference; Var Freq: frequency of variant SNP within aligned reads; # Fwd: number of forward reads with variant; # Rev.: number of reverse reads with variant; # Fwd Total: number of forward-aligned reads total; # Rev. Total: number of reverse-aligned reads total. (XLSX 578 kb)
DOI: 10.6084/m9.figshare.6448994
title: MOESM8 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 8. Essential genes and partially essential genes predicted by iZZ1342. Excel file with the list of Essential genes and partially essential genes predicted by iZZ1342.
DOI: 10.6084/m9.figshare.6448994.v1
title: MOESM8 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 8. Essential genes and partially essential genes predicted by iZZ1342. Excel file with the list of Essential genes and partially essential genes predicted by iZZ1342.
DOI: 10.6084/m9.figshare.6448988
title: MOESM9 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 9. Not normalised read counts per GATC fragment for all sequenced samples mapped on dm3 genome annotation.
DOI: 10.6084/m9.figshare.6448988.v2
title: MOESM9 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 9. Not normalised read counts per GATC fragment for all sequenced samples mapped on dm3 genome annotation.
DOI: 10.6084/m9.figshare.6448988.v1
title: MOESM9 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 9. Not normalised read counts per GATC fragment for all sequenced samples mapped on dm3 genome annotation.
DOI: 10.6084/m9.figshare.6448982
title: MOESM7 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 7. The central carbon metabolic fluxes simulated with iZZ1342 and from 13C labeled experiments. Flux values (in mmol/gDCW/h) for reactions that produce in S. erythraea NRRL23338 metabolism which are simulated by GEM iZZ1342 and from experiments. Reactions names can be traced in reaction list in Additional file 3.
DOI: 10.6084/m9.figshare.6448982.v1
title: MOESM7 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 7. The central carbon metabolic fluxes simulated with iZZ1342 and from 13C labeled experiments. Flux values (in mmol/gDCW/h) for reactions that produce in S. erythraea NRRL23338 metabolism which are simulated by GEM iZZ1342 and from experiments. Reactions names can be traced in reaction list in Additional file 3.
DOI: 10.6084/m9.figshare.6448967
title: MOESM8 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 8. Â Pc binding intensities (log2), normalized to Dam-binding and averaged between two replicates, and the corresponding results from the three-state HMM analysis for all three biological samples (early and lat wild type wing imaginal discs, and scrib1 wing imaginal discs) mapped on dm3 genome annotation.
DOI: 10.6084/m9.figshare.6448967.v2
title: MOESM8 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 8. Â Pc binding intensities (log2), normalized to Dam-binding and averaged between two replicates, and the corresponding results from the three-state HMM analysis for all three biological samples (early and lat wild type wing imaginal discs, and scrib1 wing imaginal discs) mapped on dm3 genome annotation.
DOI: 10.6084/m9.figshare.6448967.v1
title: MOESM8 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 8. Â Pc binding intensities (log2), normalized to Dam-binding and averaged between two replicates, and the corresponding results from the three-state HMM analysis for all three biological samples (early and lat wild type wing imaginal discs, and scrib 1 wing imaginal discs) mapped on dm3 genome annotation.
DOI: 10.6084/m9.figshare.6448964
title: MOESM6 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 6. The expressed genes from transcriptomics analysis result of S. erythraea NRRL23338.
DOI: 10.6084/m9.figshare.6448964.v1
title: MOESM6 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 6. The expressed genes from transcriptomics analysis result of S. erythraea NRRL23338.
DOI: 10.6084/m9.figshare.6448961
title: Additional file 3: of Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

description: Table S2. List of significant deregulated genesÂ in RECs versus PRs.Â (XLSX 39 kb)
DOI: 10.6084/m9.figshare.6448961.v1
title: Additional file 3: of Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

description: Table S2. List of significant deregulated genesÂ in RECs versus PRs.Â (XLSX 39 kb)
DOI: 10.6084/m9.figshare.6448958
title: MOESM7 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 7: SF1 Script developed by A. Ivankin used to perform the three-state HMM analysis based on the previously published BioHMM algorithm (Marioni et al. [66]).
DOI: 10.6084/m9.figshare.6448958.v2
title: MOESM7 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 7: SF1 Script developed by A. Ivankin used to perform the three-state HMM analysis based on the previously published BioHMM algorithm (Marioni et al. [66]).
DOI: 10.6084/m9.figshare.6448958.v1
title: MOESM7 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 7: SF1 Script developed by A. Ivankin used to perform the three-state HMM analysis based on the previously published BioHMM algorithm (Marioni et al. [66]).
DOI: 10.6084/m9.figshare.6448952
title: Additional file 7: of MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

description: Sourcecode. Some core code of our method. (TXT 5Â kb)
DOI: 10.6084/m9.figshare.6448952.v1
title: Additional file 7: of MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

description: Sourcecode. Some core code of our method. (TXT 5Â kb)
DOI: 10.6084/m9.figshare.6448949
title: MOESM5 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 5. Metabolites in iZZ1342. Excel file with the total list of metabolites in iZZ1342 and other detailed information about the metabolites.
DOI: 10.6084/m9.figshare.6448949.v1
title: MOESM5 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 5. Metabolites in iZZ1342. Excel file with the total list of metabolites in iZZ1342 and other detailed information about the metabolites.
DOI: 10.6084/m9.figshare.6448940
title: MOESM2 of Hematological abnormalities in patients with malaria and typhoid in Tamale Metropolis of Ghana

description: Additional file 2. Data set of the subjects. This is a SPSS document containing data transribed from the questionnaire.
DOI: 10.6084/m9.figshare.6448940.v1
title: MOESM2 of Hematological abnormalities in patients with malaria and typhoid in Tamale Metropolis of Ghana

description: Additional file 2. Data set of the subjects. This is a SPSS document containing data transribed from the questionnaire.
DOI: 10.6084/m9.figshare.6448937
title: MOESM6 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 6: SF4 WIG file containing the results of the three-state HMM analysis of wild type wing imaginal discs in early third instar stage for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = −1.
DOI: 10.6084/m9.figshare.6448937.v2
title: MOESM6 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 6: SF4 WIG file containing the results of the three-state HMM analysis of wild type wing imaginal discs in early third instar stage for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = −1.
DOI: 10.6084/m9.figshare.6448937.v1
title: MOESM6 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 6: SF4 WIG file containing the results of the three-state HMM analysis of wild type wing imaginal discs in early third instar stage for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = −1.
DOI: 10.6084/m9.figshare.6448928
title: MOESM4 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 4. iZZ1342 in SBML format.
DOI: 10.6084/m9.figshare.6448928.v1
title: MOESM4 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 4. iZZ1342 in SBML format.
DOI: 10.6084/m9.figshare.6448913
title: MOESM5 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 5: Table S2 i-cisTarget Analysis of group II and III genes; List of regulatory elements identified by i-cisTarget that either represent transcription and chromatin-binding factors or specific histone modifications enriched within the presumptive regulatory region (2.5 kb upstream to 1.5 kb downstream of the transcriptional start sites (TSS)) of genes belonging to group II (RNA – down regulated; Pc binding – gain); group III (RNA – up regulated; Pc binding – loss).
DOI: 10.6084/m9.figshare.6448913.v2
title: MOESM5 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 5: Table S2 i-cisTarget Analysis of group II and III genes; List of regulatory elements identified by i-cisTarget that either represent transcription and chromatin-binding factors or specific histone modifications enriched within the presumptive regulatory region (2.5 kb upstream to 1.5 kb downstream of the transcriptional start sites (TSS)) of genes belonging to group II (RNA – down regulated; Pc binding – gain); group III (RNA – up regulated; Pc binding – loss).
DOI: 10.6084/m9.figshare.6448913.v1
title: MOESM5 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 5: Table S2 i-cisTarget Analysis of group II and III genes; List of regulatory elements identified by i-cisTarget that either represent transcription and chromatin-binding factors or specific histone modifications enriched within the presumptive regulatory region (2.5 kb upstream to 1.5 kb downstream of the transcriptional start sites (TSS)) of genes belonging to group II (RNA – down regulated; Pc binding – gain); group III (RNA – up regulated; Pc binding – loss).
DOI: 10.6084/m9.figshare.6448901
title: MOESM3 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 3. iZZ1342 reactions associated with gene annotations. Excel file with the list of S. erythraea iZZ1342 model reactions and other information about the reactions.
DOI: 10.6084/m9.figshare.6448901.v1
title: MOESM3 of In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

description: Additional file 3. iZZ1342 reactions associated with gene annotations. Excel file with the list of S. erythraea iZZ1342 model reactions and other information about the reactions.