cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10027829.v1
title: MOESM2 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin

description: Additional file 2. Doxorubicin-gene interaction data; Tables S1-S8. Tables S1-S4 are the genome-wide experiment: Table S1. YKO/KD strains in HLEG. Table S2. Reference cultures in HLEG. Table S3. YKO/KD strains in HLD. Table S4. Reference cultures in HLD. Tables S5-S8 are the validation study: Table S5. YKO/KD strains in HLEG. Table S6. Reference cultures in HLEG. Table S7. YKO/KD strains in HLD. Table S8. Reference cultures in HLD.
DOI: 10.6084/m9.figshare.10027820.v1
title: MOESM12 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin

description: Additional file 12. Comparisons between yeast studies of doxorubicin in the context of integrating cancer pharmacogenomics data. Overlapping and unique sets of genes reported from the different studies of doxorubicin, using the YKO/KD libraries, are assessed with regard to correlation with cancer pharmacogenomics data.
DOI: 10.6084/m9.figshare.10027811
title: MOESM11 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin

description: Additional file 11. Integration of yeast phenomic and cancer cell line pharmacogenomic data to predict human genes that modify doxorubicin toxicity in cancer cells. (A) Tables of UES and OES human genes and whether their yeast homologs were found to be deletion enhancing or deletion suppressing, respectively. (B-C) Overlap between the gCSI and GDSC1000 databases with regard to UES and OES human genes (B) across all tissues or (C) for individual tissues. Note: the intersection of UES with OES between gCSI and GDSC was used as a negative control for assessing UES and OES overlap. (D-E) Yeast phenomic doxorubicin-gene interaction profiles for homologs of human UES or OES genes, sub-classified according to interaction type (deletion enhancing or suppressing) and Warburg-dependence of the interaction, for the (D) gCSI or (E) GDSC1000 databases. Similar to Fig. 11, yeast-human homology relationships are shown to the left of heatmaps (blue - one to one; green - one to many; red - many to many). (F-I) Interactive plots for yeast-human homologs, comparing the p-value of human genes to L interaction scores for yeast counterparts in (F, G) HLD or (H, I) HLEG from (F, H) gCSI or (G, I) GDSC1000. For the standardized coefficient (â estimateâ ; color gradient), a negative value (purple) indicates UES, while a positive value (orange) indicates OES. Thus, the model would predict causality for a human gene if its yeast homolog has a positive L interaction (deletion enhancing) and is colored purple (UES), or a negative L interaction (deletion suppressing) and colored orange (OES). Genes are only plotted if the human homolog was significant (p-value &lt; 0.05).
DOI: 10.6084/m9.figshare.10027802
title: MOESM10 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin

description: Additional file 10: Table S13. HLD-specific gene deletion enhancement, not associated with ‘shift’ / growth deficiency. Data were selected for yeast-human homologs if the respective YKO/KD strains generated growth curves in both HLD and HLEG media (in the absence doxorubicin), and either of the following two sets of criteria were met: (1) HLD L interaction &gt; 2 and HLEG L interaction &lt; 2; these data were further filtered for HLD L Interaction - HLD L Shift &gt; 4, and are presented in Additional file 1: Figure S8A.; or (2) HLD L Interaction – HLEG L interaction &gt; 4 and HLEG K interaction &gt; - 10; these data were further filtered for HLD L Interaction - HLD L Shift &gt; 4, and are presented in Additional file 1: Figure S8B. Data included in Additional file 1: Figure S8 are indicated in the last column.
DOI: 10.6084/m9.figshare.10027811.v1
title: MOESM11 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin

description: Additional file 11. Integration of yeast phenomic and cancer cell line pharmacogenomic data to predict human genes that modify doxorubicin toxicity in cancer cells. (A) Tables of UES and OES human genes and whether their yeast homologs were found to be deletion enhancing or deletion suppressing, respectively. (B-C) Overlap between the gCSI and GDSC1000 databases with regard to UES and OES human genes (B) across all tissues or (C) for individual tissues. Note: the intersection of UES with OES between gCSI and GDSC was used as a negative control for assessing UES and OES overlap. (D-E) Yeast phenomic doxorubicin-gene interaction profiles for homologs of human UES or OES genes, sub-classified according to interaction type (deletion enhancing or suppressing) and Warburg-dependence of the interaction, for the (D) gCSI or (E) GDSC1000 databases. Similar to Fig. 11, yeast-human homology relationships are shown to the left of heatmaps (blue - one to one; green - one to many; red - many to many). (F-I) Interactive plots for yeast-human homologs, comparing the p-value of human genes to L interaction scores for yeast counterparts in (F, G) HLD or (H, I) HLEG from (F, H) gCSI or (G, I) GDSC1000. For the standardized coefficient (â estimateâ ; color gradient), a negative value (purple) indicates UES, while a positive value (orange) indicates OES. Thus, the model would predict causality for a human gene if its yeast homolog has a positive L interaction (deletion enhancing) and is colored purple (UES), or a negative L interaction (deletion suppressing) and colored orange (OES). Genes are only plotted if the human homolog was significant (p-value &lt; 0.05).
DOI: 10.6084/m9.figshare.10027802.v1
title: MOESM10 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin

description: Additional file 10: Table S13. HLD-specific gene deletion enhancement, not associated with ‘shift’ / growth deficiency. Data were selected for yeast-human homologs if the respective YKO/KD strains generated growth curves in both HLD and HLEG media (in the absence doxorubicin), and either of the following two sets of criteria were met: (1) HLD L interaction &gt; 2 and HLEG L interaction &lt; 2; these data were further filtered for HLD L Interaction - HLD L Shift &gt; 4, and are presented in Additional file 1: Figure S8A.; or (2) HLD L Interaction – HLEG L interaction &gt; 4 and HLEG K interaction &gt; - 10; these data were further filtered for HLD L Interaction - HLD L Shift &gt; 4, and are presented in Additional file 1: Figure S8B. Data included in Additional file 1: Figure S8 are indicated in the last column.
DOI: 10.6084/m9.figshare.10027700
title: MOESM9 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 9: Table S7. Strain-specific genes of V. harveyi 345.
DOI: 10.6084/m9.figshare.10027700.v1
title: MOESM9 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 9: Table S7. Strain-specific genes of V. harveyi 345.
DOI: 10.6084/m9.figshare.10027688
title: MOESM7 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 7: Table S5. Genomic islands in a single chromosome (CP025538) of V. harveyi 345.
DOI: 10.6084/m9.figshare.10027691
title: MOESM1 of Multi-center screening of the Pathogen Box collection for schistosomiasis drug discovery

description: Additional file 1: Table S1. Descriptors and associated severity scores applied by UCSD. Table S2. Concordance between the 3 groups for active and inactive compounds. Table S3. Data transformation. Table S4. Unique hits per group. Table S5. Active compounds shared by all three groups (‘core actives’). Table S6. Transformed activity of the reference compounds. Table S7. Comparisons with data previously generated for the same compounds. Table S8. Transformed activity by disease set. Table S9. Core active compounds compared to activity measured previously by the Swiss TPH against adult S. mansoni.
DOI: 10.6084/m9.figshare.10027694
title: MOESM8 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 8: Table S6. Prophage sequences present in V. harveyi 345 chromosomes.
DOI: 10.6084/m9.figshare.10027685
title: MOESM6 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 6: Table S4. Genomic islands in a single chromosome (CP025537) of V. harveyi 345.
DOI: 10.6084/m9.figshare.10027688.v1
title: MOESM7 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 7: Table S5. Genomic islands in a single chromosome (CP025538) of V. harveyi 345.
DOI: 10.6084/m9.figshare.10027694.v1
title: MOESM8 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 8: Table S6. Prophage sequences present in V. harveyi 345 chromosomes.
DOI: 10.6084/m9.figshare.10027691.v1
title: MOESM1 of Multi-center screening of the Pathogen Box collection for schistosomiasis drug discovery

description: Additional file 1: Table S1. Descriptors and associated severity scores applied by UCSD. Table S2. Concordance between the 3 groups for active and inactive compounds. Table S3. Data transformation. Table S4. Unique hits per group. Table S5. Active compounds shared by all three groups (‘core actives’). Table S6. Transformed activity of the reference compounds. Table S7. Comparisons with data previously generated for the same compounds. Table S8. Transformed activity by disease set. Table S9. Core active compounds compared to activity measured previously by the Swiss TPH against adult S. mansoni.
DOI: 10.6084/m9.figshare.10027673
title: MOESM5 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 5: Table S3. Details of virulence factors predicted with the VFDB database.
DOI: 10.6084/m9.figshare.10027685.v1
title: MOESM6 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 6: Table S4. Genomic islands in a single chromosome (CP025537) of V. harveyi 345.
DOI: 10.6084/m9.figshare.10027673.v1
title: MOESM5 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 5: Table S3. Details of virulence factors predicted with the VFDB database.
DOI: 10.6084/m9.figshare.10027643
title: MOESM2 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 2: Table S2. Gene information and gene statistics for 31â V. harveyi strains.
DOI: 10.6084/m9.figshare.10027643.v1
title: MOESM2 of Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

description: Additional file 2: Table S2. Gene information and gene statistics for 31â V. harveyi strains.
DOI: 10.6084/m9.figshare.10027592
title: MOESM1 of High frequency audible calls in northern birch mice Sicista betulina in response to handling: effects of individuality, sex and body mass on the acoustics

description: Additional file 1: Table S1. Data table with body mass and acoustic measurements of discomfort-related sonic calls of the study northern birch mice.
DOI: 10.6084/m9.figshare.10027592.v1
title: MOESM1 of High frequency audible calls in northern birch mice Sicista betulina in response to handling: effects of individuality, sex and body mass on the acoustics

description: Additional file 1: Table S1. Data table with body mass and acoustic measurements of discomfort-related sonic calls of the study northern birch mice.
DOI: 10.6084/m9.figshare.10027559
title: MOESM11 of Genome rearrangements induce biofilm formation in Escherichia coli C â an old model organism with a new application in biofilm research

description: Additional file 11: Table S1. Gene content comparison between five E. coli strains.
DOI: 10.6084/m9.figshare.10027559.v1
title: MOESM11 of Genome rearrangements induce biofilm formation in Escherichia coli C â an old model organism with a new application in biofilm research

description: Additional file 11: Table S1. Gene content comparison between five E. coli strains.
DOI: 10.6084/m9.figshare.10027544
title: MOESM1 of Rapid adaptation of signaling networks in the fungal pathogen Magnaporthe oryzae

description: Additional file 1: SVs summary.
DOI: 10.6084/m9.figshare.10027544.v1
title: MOESM1 of Rapid adaptation of signaling networks in the fungal pathogen Magnaporthe oryzae

description: Additional file 1: SVs summary.
DOI: 10.6084/m9.figshare.10027532
title: MOESM4 of Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization

description: Additional file 4.Â Dominant fungal orders (relative abundance &gt; 1%) in the rhizosphere and root samples.
DOI: 10.6084/m9.figshare.10027535
title: MOESM5 of Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization

description: Additional file 5.Â Dominant fungal genera (relative abundance &gt; 1%) in the rhizosphere and root samples.
DOI: 10.6084/m9.figshare.10027529
title: MOESM6 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 6. Map information for the 36,625 (pruned) SNPs used for the GWAS, containing the corresponding chromosome, SNP name, physical position (in bp) and alleles (A1: minor allele, A2: major allele)
DOI: 10.6084/m9.figshare.10027529.v1
title: MOESM6 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 6. Map information for the 36,625 (pruned) SNPs used for the GWAS, containing the corresponding chromosome, SNP name, physical position (in bp) and alleles (A1: minor allele, A2: major allele)
DOI: 10.6084/m9.figshare.10027532.v1
title: MOESM4 of Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization

description: Additional file 4.Â Dominant fungal orders (relative abundance &gt; 1%) in the rhizosphere and root samples.
DOI: 10.6084/m9.figshare.10027526
title: MOESM3 of Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization

description: Additional file 3.Â Dominant bacterial genera (relative abundance &gt; 1%) in the rhizosphere and root samples.
DOI: 10.6084/m9.figshare.10027520
title: MOESM5 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 5. Genotypic and phenotypic information used for the GWAS. Genotypes for the 36,625 (pruned) SNPs are coded as allele dosage (0, 1, 2) for the minor allele (A1) for each individual (first row). Phenotypic information for sex (1: male, 2: female) for each individual is also included (second row). Missing values are coded as NA
DOI: 10.6084/m9.figshare.10027523
title: MOESM2 of Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization

description: Additional file 2.Â Dominant bacterial genera (relative abundance &gt; 1%) in the rhizosphere and root samples.
DOI: 10.6084/m9.figshare.10027526.v1
title: MOESM3 of Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization

description: Additional file 3.Â Dominant bacterial genera (relative abundance &gt; 1%) in the rhizosphere and root samples.
DOI: 10.6084/m9.figshare.10027520.v1
title: MOESM5 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 5. Genotypic and phenotypic information used for the GWAS. Genotypes for the 36,625 (pruned) SNPs are coded as allele dosage (0, 1, 2) for the minor allele (A1) for each individual (first row). Phenotypic information for sex (1: male, 2: female) for each individual is also included (second row). Missing values are coded as NA
DOI: 10.5281/zenodo.4001764
title: Replication package: the mind is a powerful place

description: This package contains a replication package for: "The Mind Is a Powerful Place: How Showing Code Comprehensibility Metrics Influences Code Understanding", double blind, ICSE 2021 submission. - The `data` folder contains dataset, R analysis script, and figures for the paper<br> - the `material` folder contains the snippets used for the experimental tasks (`code snippets` subfolder) and the task sheet form to evaluate comprehension. The R analysis script allows to reproduce all statistical analysis steps of the paper as well as its figures. We recommend calling `setwd()` before running the script contents, so that the dataset can be properly loaded. For ethics and privacy reasons, we had to drop the following potentially identifying fields from the openly released dataset, because the fields might enable participants to identify their peers: - Age<br> - Gender<br> - Subject (study plan)<br> - Program<br> - Semester no. These missed details will still allow full reproducibility of the study.
DOI: 10.6084/m9.figshare.10027505
title: MOESM2 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 2. Information relative to candidate regions identified in the GWAS for chromosomes Ssa02 and Ssa21contained in the Salmo salar annotation (Salmo_salar-annotation.gff3)
DOI: 10.6084/m9.figshare.10027511
title: MOESM3 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 3. Results of the BLAST analysis of sex-related genes previously identified in other species of the class Actinopterygii against the Salmo salar reference genome (assembly ICSASG_v2), indicating the corresponding chromosome match and position in Salmo salar and BLAST parameters
DOI: 10.6084/m9.figshare.10027502
title: MOESM1 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 1. Information relative to SNPs significantly associated with sex identified in the GWAS
DOI: 10.6084/m9.figshare.10027505.v1
title: MOESM2 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 2. Information relative to candidate regions identified in the GWAS for chromosomes Ssa02 and Ssa21contained in the Salmo salar annotation (Salmo_salar-annotation.gff3)
DOI: 10.6084/m9.figshare.10027511.v1
title: MOESM3 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 3. Results of the BLAST analysis of sex-related genes previously identified in other species of the class Actinopterygii against the Salmo salar reference genome (assembly ICSASG_v2), indicating the corresponding chromosome match and position in Salmo salar and BLAST parameters
DOI: 10.6084/m9.figshare.10027502.v1
title: MOESM1 of Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

description: Additional file 1. Information relative to SNPs significantly associated with sex identified in the GWAS
DOI: 10.6084/m9.figshare.10027487
title: MOESM5 of The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

description: Additional file 5: Table S4. with MaxQuant analysis of MS data from the proteome analysis from MKRN1 KD2 in HEK293T cells. (XLSX 2270 kb)
DOI: 10.6084/m9.figshare.10027481
title: MOESM4 of The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

description: Additional file 4: Table S3. with MaxQuant analysis of MS data from the ubiquitin remnant profiling from MKRN1 KD2 in HEK293T cells. (XLSX 7940 kb)
DOI: 10.6084/m9.figshare.10027487.v1
title: MOESM5 of The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

description: Additional file 5: Table S4. with MaxQuant analysis of MS data from the proteome analysis from MKRN1 KD2 in HEK293T cells. (XLSX 2270 kb)
DOI: 10.6084/m9.figshare.10027481.v1
title: MOESM4 of The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

description: Additional file 4: Table S3. with MaxQuant analysis of MS data from the ubiquitin remnant profiling from MKRN1 KD2 in HEK293T cells. (XLSX 7940 kb)
DOI: 10.6084/m9.figshare.10027463
title: MOESM2 of The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

description: Additional file 2: Table S1. with MaxQuant analysis of MS data from the SILAC-AP for GFP-MKRN1wt, GFP-MKRN1PAM2mut, and GFP-MKRN1RINGmut. (XLSX 1409 kb)
DOI: 10.6084/m9.figshare.10027463.v1
title: MOESM2 of The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

description: Additional file 2: Table S1. with MaxQuant analysis of MS data from the SILAC-AP for GFP-MKRN1wt, GFP-MKRN1PAM2mut, and GFP-MKRN1RINGmut. (XLSX 1409 kb)
DOI: 10.6084/m9.figshare.10027448
title: MOESM3 of De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

description: Additional file 3: File S1. Sequences of the discussed sex-related genes.
DOI: 10.6084/m9.figshare.10027448.v1
title: MOESM3 of De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

description: Additional file 3: File S1. Sequences of the discussed sex-related genes.
DOI: 10.6084/m9.figshare.10027436
title: MOESM1 of A visual approach for analysis and inference of molecular activity spaces

description: Additional file 1: Figure S1a. Test set projection over PSMA with KMDS. b Test set projection over PSMA with SM. c Test set projection over PSMA with t-SNE. Figure S2a. DRD5 shepard plot for PCooA, KMDS, SM and t-SNE. b HRH1 shepard plot for PCooA, KMDS, SM and t-SNE. c SIGMAR1 shepard plot for PCooA, KMDS, SM and t-SNE.
DOI: 10.6084/m9.figshare.10027439
title: MOESM1 of De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

description: Additional file 1: Table S1. Annotation table of the non-redundant P. serratus ovary and testis transcriptome. Table S2. Full list of up-regulated genes in ovary. Table S3. Full list of up-regulated genes in testis. Table S4. Results of GO enrichment analyses.
DOI: 10.6084/m9.figshare.10027442
title: MOESM2 of A visual approach for analysis and inference of molecular activity spaces

description: Additional file 2. Contains all data sets (SIGMAR1, HRH1, HERG,and DRD5) retrieved from ChEMBL23, their computed NAMS similarities and R source code for analysis and inference of molecular activity spaces.