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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Species-specific protein sequence and fold optimizations.
PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups
Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes
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Has reproduction · 83
Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.
PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 5 setups
CHCT, a hierarchical classification tool, splits classification of 30 cancer types into ten smaller subproblems using a two-tier architecture to classify primary cancer by methylation profile
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MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.
PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups
MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources
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MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.
PMID 19798417 · PMC2749450 · PloS one · 2009 · 7 claims · 7 setups
High grade serous carcinomas with and without BRCA1/2 abnormalities show very similar miRNA expression profiles, with no clear clustering separation by BRCA1/2 status
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 86
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.
PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups
CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome
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Has reproduction · 90
Inferring a spatial code of cell-cell interactions across a whole animal body.
PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups
cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells
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Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.
PMID 18704688 · PMC2597685 · Reviews in endocrine & metabolic disorders · 2008 · 8 claims · 8 setups
Genetic predisposition determines susceptibility and rate of progression to ESRD in diabetic patients, in addition to environmental factors
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Has reproduction · 95
Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.
PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 8 claims · 7 setups
254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs) were detected in the P. ostreatus CCEF00389 genome assembly, the first genome-scale identification of sncRNAs for a basidiomycete.
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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 · 64
Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.
PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups
Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important
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g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.
PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups
g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis
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Has reproduction · 30
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.
PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups
MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.