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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ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.
PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups
ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format
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Has reproduction · 88
Comprehensive benchmarking of large language models for RNA secondary structure prediction.
PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups
Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.
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A large-scale proteomic analysis of human embryonic stem cells.
PMID 18162134 · PMC2211323 · BMC genomics · 2007 · 8 claims · 5 setups
Two large-scale western blot systems (PowerBlot, Kinexus) identify over 600 proteins expressed in undifferentiated hESCs across 18 functional classes
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High-accuracy proteome maps of human body fluids.
PMID 17140426 · PMC1794581 · Genome biology · 2006 · 8 claims · 5 setups
Large-scale, high-accuracy MS analyses of tear fluid, urine, and seminal plasma provide high-quality datasets useful for biomarker discovery
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The VIZIER project: preparedness against pathogenic RNA viruses.
PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups
Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.
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G2Cdb: the Genes to Cognition database.
PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups
G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.
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Has reproduction · 95
A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.
PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups
ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids
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Has reproduction · 49
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.
PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups
oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.
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Next-generation sequencing.
PMID 20030863 · PMC2797692 · Breast cancer research : BCR · 2009 · 8 claims · 7 setups
Massively parallel sequencing can simultaneously capture base-pair mutations, copy number aberrations and somatic rearrangements of a cancer genome in a single experiment
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Discovery and hypothesis generation through bioinformatics.
PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups
Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data
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High-throughput genomic technology in research and clinical management of breast cancer. Evolving landscape of genetic epidemiological studies.
PMID 16834767 · PMC1557740 · Breast cancer research : BCR · 2006 · 8 claims · 5 setups
Candidate polymorphism-based genetic epidemiological studies have yielded little success in identifying low-penetrance breast cancer susceptibility genes, largely due to poor genomic coverage and inadequate statistical power.
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The mitochondrial genome, a growing interest inside an organelle.
PMID 18488415 · PMC2526360 · International journal of nanomedicine · 2008 · 8 claims · 8 setups
mtDNA mutations are causally linked to a wide range of mitochondrial diseases, aging, and chronic degenerative diseases
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A catalog of human cDNA expression clones and its application to structural genomics.
PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups
A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli
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Has reproduction · 99
The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.
PMID 40926267 · PMC12421755 · Genome biology · 2025 · 8 claims · 3 setups
Over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available in publications or public repositories.
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Improvements to cardiovascular gene ontology.
PMID 19046747 · PMC2706316 · Atherosclerosis · 2009 · 8 claims · 8 setups
Gene Ontology (GO) provides a controlled vocabulary that links current functional knowledge of genes to high-throughput genomic and proteomic datasets, aiding data interpretation.
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Locus-specific and activity-independent gene repositioning during early tumorigenesis.
PMID 18195100 · PMC2213600 · The Journal of cell biology · 2008 · 7 claims · 6 setups
The genome undergoes global spatial reorganization during both normal and tumorigenic mammary epithelial differentiation, as shown by reduced nucleolar number.
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GenBank.
PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups
GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.