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).

• A large-scale proteomic analysis of human embryonic stem cells.

  PMID 18162134 · PMC2211323 · BMC genomics · 2007 · 8 claims · 5 setups

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  Two large-scale western blot systems (PowerBlot, Kinexus) identify over 600 proteins expressed in undifferentiated hESCs across 18 functional classes

  bg01 bg03 hescs powerblot kinexus immunofluorescence

• 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

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  ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format

  sequences parsed bacillus anopheles large-scale sequence orf

• High-accuracy proteome maps of human body fluids.

  PMID 17140426 · PMC1794581 · Genome biology · 2006 · 8 claims · 5 setups

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  Large-scale, high-accuracy MS analyses of tear fluid, urine, and seminal plasma provide high-quality datasets useful for biomarker discovery

  tear-duct urine seminal blood lc-ms large-scale decoy

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant

• The VIZIER project: preparedness against pathogenic RNA viruses.

  PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

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  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.

  viruses virus coli soluble large-scale bioinformatic recombinant

• Genome sequences and great expectations.

  PMID 11178275 · PMC150431 · Genome biology · 2001 · 8 claims · 3 setups

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  Function is known or can be predicted for an average of 62% of proteins across 31 analyzed genomes.

  complete annotated haemophilus automated benchmarking temporal

• Complex genetic diseases: controversy over the Croesus code.

  PMID 11532206 · PMC138948 · Genome biology · 2001 · 8 claims · 3 setups

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  The common disease/common variant hypothesis is predicted by population genetic theory (founder population dynamics, mutation-drift-selection balance) and supported by empirical examples such as APOE*E4.

  chromosome northern disease large-scale genome-wide database

• Human genome research in China.

  PMID 15168679 · PMC7079922 · Journal of molecular medicine (Berlin, Germany) · 2004 · 8 claims · 8 setups

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  China completed its assigned 1% share of the international Human Genome Project sequencing effort and contributed ~10% of the HapMap effort

  genome chinese high-risk nb4 large-scale mutation positional

• Fractional ridge regression: a fast, interpretable reparameterization of ridge regression.

  PMID 33252656 · PMC7702219 · GigaScience · 2020 · 7 claims · 2 setups

  Has reproduction · 84

  Ridge regression can be reparameterized in terms of the fraction γ between the L2-norms of the regularized and unregularized coefficient solutions (fractional ridge regression, FRR).

  synthetic brain benchmarking general

• Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

  PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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  Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

  blood-derived blood crisp father mlpa long-range field

• Comprehensive benchmarking of large language models for RNA secondary structure prediction.

  PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

  Has reproduction · 88

  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.

  archiveii bprna large-scale secondary cross-family self-supervised

• 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

  Has reproduction · 49

  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.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored

• Systems biology approaches for the study of multiple sclerosis.

  PMID 18505469 · PMC3865652 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

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  The MHC locus on chromosome 6p21 is the strongest genetic region linked to MS susceptibility.

  patients lesion osteopontin monocyte-depleted genetic large-scale gene

• Gene function in the mammalian genome, courtesy of the mouse.

  PMID 12537544 · PMC151280 · Genome biology · 2003 · 8 claims · 8 setups

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  Mosaicism of Mus musculus domesticus and Mus musculus musculus haplotypes exists across the inbred laboratory mouse genome, and genome-wide haplotype mapping can enhance positional cloning

  inbred genome mice model genome-wide large-scale phenotypic

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental

• 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

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  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.

  breast large-scale candidate single candidate ultra medium-throughput

• G2Cdb: the Genes to Cognition database.

  PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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  G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

  brain nervous genome synaptic proteomic large-scale sequence

• FGF: a web tool for Fishing Gene Family in a whole genome database.

  PMID 17584790 · PMC1933194 · Nucleic acids research · 2007 · 6 claims · 3 setups

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  FGF efficiently searches and identifies gene families in whole-genome databases and outputs visual phylogenetic trees annotated with gene structure, chromosome position, duplication fate, and selective pressure (Ka/Ks)

  genome rice gene large-scale

• Wireless sensor network design with reliable and long network lifetime.

  PMID 41981015 · PMC13083951 · Scientific reports · 2026 · 6 claims · 3 setups

  Has reproduction · 65

  All four fundamental WSN design problems and network reliability can be addressed together in an integrated set of mixed-integer mathematical models.

  simulated medium mixed-integer lagrangian reliability

• Pharokka: a fast scalable bacteriophage annotation tool.

  PMID 36453861 · PMC9805569 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  Pharokka is a one-line, fast, scalable bacteriophage annotation tool producing standards-compliant outputs, installable via a two-line bioconda command

  enterobacteria staphylococcus crass-like predicted genome large-scale homology