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).

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

  Full-text index only

  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

  Full-text index only

  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3.

  PMID 41559189 · PMC13047044 · Molecular systems biology · 2026 · 8 claims · 6 setups

  Full-text index only

  Pooled-AlphaFold3 prediction improves accuracy of genome-scale PPI screens compared to a paired approach while reducing inference time (~2-fold) and job count (~100-fold)

  mycoplasma subset genitalium simulated pooled paired benchmarking

• Exploring the immunome: A brave new world for human vaccine development.

  PMID 20009527 · PMC2919815 · Human vaccines · 2009 · 7 claims · 7 setups

  Full-text index only

  Screening the Mtb proteome in silico for epitopes ('fishing for antigens using epitopes as bait') revealed a remarkable diversity of human immune responses to Mtb proteins without an ascribed function, suggesting human immune response to Mtb is omnivorous rather than focused on single immunodominant proteins.

  mycobacterium subjects francisella autologous epitope-mapping response epitope

• Detection of ras gene mutations in human lung cancer: comparison of two screening assays based on the polymerase chain reaction.

  PMID 1486847 · PMC1519635 · Environmental health perspectives · 1992 · 8 claims · 3 setups

  Full-text index only

  Somatic K-ras mutations were found in one-third of lung carcinomas studied, but no N-ras mutations were detected.

  lung plasmid pcr-based denaturing

• Global analysis of community-associated methicillin-resistant Staphylococcus aureus exoproteins reveals molecules produced in vitro and during infection.

  PMID 17217429 · PMC2064037 · Cellular microbiology · 2007 · 6 claims · 3 setups

  Full-text index only

  Proteomic analysis (2-DGE coupled with ADI-MS/MS) identified 250 unique exoproteins produced by MW2 and LAC culture supernatants during growth in vitro.

  mw2 mice neutrophils 2-dimensional infection confocal

• Rapid detection of carriers with BRCA1 and BRCA2 mutations using high resolution melting analysis.

  PMID 18298804 · PMC2266761 · BMC cancer · 2008 · 8 claims · 3 setups

  Full-text index only

  HRM correctly detects and distinguishes the three Ashkenazi Jewish BRCA1/BRCA2 founder mutations (185delAG, 5382insC, 6174delT) from wild type

  peripheral high

• AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

  PMID 17485433 · PMC5947781 · Bioinformatics (Oxford, England) · 2007 · 7 claims · 2 setups

  Full-text index only

  AutoCSA is an automated algorithm, extended from the CSA protocol, that detects DNA sequence variants in cancer genomes with minimal manual intervention

  training kinase capillary targeted

• SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

  PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

  Full-text index only

  Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

  genomic cdna known sequence homology transcript

• Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

  PMID 16469098 · PMC1409804 · BMC bioinformatics · 2006 · 7 claims · 3 setups

  Full-text index only

  AUGUSTUS+ extends the AUGUSTUS GHMM by combining intrinsic sequence information with extrinsic hints via an extended emission alphabet, so the GHMM jointly models the DNA sequence, gene structure, and hint collection.

  chromosome genomic training ghmm-based sequence parameter

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk

• The UCSC Proteome Browser.

  PMID 15608236 · PMC540054 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  The UCSC Proteome Browser is tightly integrated with the UCSC Genome Browser, giving users simultaneous access to genome and proteome data.

  swiss-prot sequence domain isoelectric

• Patents and translational research in genomics.

  PMID 17621295 · PMC1955681 · Nature biotechnology · 2007 · 8 claims · 2 setups

  Full-text index only

  Gene patents can impede the use of genes for research, diagnosis and treatment, thereby hindering translational genomics research

  publicly mutation patent

• Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.

  PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 8 setups

  Has reproduction · 30

  Single-cell transcriptomic analysis of GBA-N370S iPSC-derived dopamine neurons identifies a progressive axis of gene expression variation leading to endoplasmic reticulum stress.

  facs-purified ipsc-derived core bulk single-cell facs

• Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

  PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  Dutch traditional chicken breeds show a complex and admixed subdivided population structure that partly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).

  chickens dutch individuals phased whole-genome principal neighbor-joining

• Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

  PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups

  Has reproduction · 79

  196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions

  rhizobium strains genotype genome whole-genome orthologous snp

• Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

  PMID 41490125 · PMC12768360 · PloS one · 2026 · 6 claims · 5 setups

  Has reproduction · 69

  The original BRAKER3-based NWR annotation was of poor quality: only 51% of transcripts were correctly called, many were assigned uninformative protein names, and some were misassigned to incorrect or bacterial sequences.

  granulosa nwr aligned unassigned bulk reference transcript

• Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

  PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups

  Has reproduction · 67

  Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies

  frugiperda satellite million contigs comparative homology divergence

• Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

  PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

  Has reproduction · 50

  Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

  sars-cov-2 publicly simulated simulated amplicon-based variant

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome