Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Has reproduction · 73
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.
PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups
De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp
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Has reproduction
Inter- and Intraspecific Venom Variation in the Reclusive Rear-Fanged Black-Striped Snakes (Coniophanes).
PMID 41745774 · PMC12945099 · Toxins · 2026 · 8 claims · 4 setups
This is the first characterization of the venom profiles (transcriptomic and proteomic) of the genus Coniophanes.
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Has reproduction · 62
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.
PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups
H. caudiculatum (lower canopy) exhibits about twice as many differentially expressed genes as H. dentatum (upper canopy), with a higher proportion of both increased and decreased gene abundance during dehydration.
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Has reproduction · 45
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.
PMID 29451882 · PMC5815590 · PloS one · 2018 · 7 claims · 7 setups
This is the first de novo transcriptomic analysis of Cornus officinalis, providing fundamental gene and biosynthetic pathway information.
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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Has reproduction · 52
Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.
PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups
A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity
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Has reproduction · 95
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.
PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups
transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms
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Has reproduction · 91
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.
PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups
SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes
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Has reproduction · 70
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).
PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups
AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella
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Has reproduction · 97
Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle.
PMID 32523568 · PMC7261829 · Frontiers in microbiology · 2020 · 6 claims · 6 setups
Photosynthesis-related and translational transcripts are upregulated at midday (high light) compared to night/darkness in the pond microeukaryotic community
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Has reproduction · 84
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.
PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups
The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species
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Has reproduction · 76
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.
PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups
The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.
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Pathway analysis of kidney cancer using proteomics and metabolic profiling.
PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups
31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue
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Has reproduction · 95
Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.
PMID 32111840 · PMC7048732 · Nature communications · 2020 · 6 claims · 8 setups
SuSr-D1 encodes Med15b.D, a subunit of the conserved Mediator complex that regulates transcription of protein-coding genes.
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Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups
Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.
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Has reproduction · 63
RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data.
PMID 42172220 · PMC13196991 · PloS one · 2026 · 8 claims · 8 setups
RAGER integrates widely-used bioinformatics tools into an automated Snakemake-based pipeline for joint analysis of RNA-seq and ATAC-seq data
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Has reproduction · 79
pyrpipe: a Python package for RNA-Seq workflows.
PMID 34085037 · PMC8168212 · NAR genomics and bioinformatics · 2021 · 8 claims · 3 setups
pyrpipe enables development of flexible, reproducible, and easy-to-debug RNA-Seq computational pipelines purely in Python, in an object-oriented manner
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Has reproduction · 58
Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.
PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups
Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.