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).

• MILANO--custom annotation of microarray results using automatic literature searches.

  PMID 15661078 · PMC547913 · BMC bioinformatics · 2005 · 7 claims · 4 setups

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  MILANO annotates microarray gene lists by counting literature co-occurrences of each gene with user-defined secondary terms

  well-known list over-producing known medline generif microarray

• Use of modified U1 snRNAs to inhibit HIV-1 replication.

  PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

  hiv-1 293t hela bioinformatic western reporter

• CancerGenes: a gene selection resource for cancer genome projects.

  PMID 17088289 · PMC1781153 · Nucleic acids research · 2007 · 6 claims · 4 setups

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  CancerGenes is a gene list-centric web resource that combines expert-annotated gene lists with data from public databases (Entrez Gene, Ensembl BioMart, Kim et al. promoter data, Sanger COSMIC) to support gene selection for cancer re-sequencing projects.

  genes chip-on-chip literature entrez

• Predicting candidate genes for human deafness disorders: a bioinformatics approach.

  PMID 16854223 · PMC1564145 · BMC genomics · 2006 · 8 claims · 4 setups

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  A bioinformatic approach combining expression databases and protein interaction data narrows ~2400 candidate genes across deafness loci to a manageable set of candidates.

  genomic developing proteins positional expression protein-protein

• MACSIMS: multiple alignment of complete sequences information management system.

  PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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  MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

  balibase-derived sequences same query automatic database initio

• Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

  PMID 16504056 · PMC1402321 · BMC genetics · 2006 · 7 claims · 8 setups

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  No statistical evidence of a major association between T1D and any of the interferon or interferon-related genes tested (IFNA cluster, IFNB1, IFNW1, IFNG, ICSBP1)

  t1d european warren resequencing database tag

• The RCSB PDB information portal for structural genomics.

  PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

  structural nih genome sequence target production

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

  PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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  Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

  organisms cide cideb hmmer tblastn sequence

• SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

  PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

  randomly heirs seattlesnps african resequencing genome-wide tag

• Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

  PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

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  A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

  hcv 5'ncr serum maximum sequence recombination

• Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

  PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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  Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

  tumors cancer tumor lung direct database quantitative

• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

  PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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  Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

  gingivalis whole-cell comparative gene

• PPDPF is not a key regulator of human pancreas development.

  PMID 40193385 · PMC12037078 · PLoS genetics · 2025 · 8 claims · 8 setups

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  PPDPF is not a key regulator of human pancreas development, in contrast to its zebrafish orthologue exdpf

  fetuses fetal hesc population situ proteome qpcr

• MCPmed: a call for Model Context Protocol-enabled bioinformatics web services for LLM-driven discovery.

  PMID 41729821 · PMC12927880 · Briefings in bioinformatics · 2026 · 8 claims · 3 setups

  Has reproduction · 80

  Adapting MCP to bioinformatics web server backends provides a standardized, machine-actionable semantic layer that associates API endpoints with scientific concepts and metadata.

  geo string ucsc mcp

• An SVM-based system for predicting protein subnuclear localizations.

  PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

  single-localization multi-localization same svm sequence

• SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

  PMID 15980532 · PMC1160243 · Nucleic acids research · 2005 · 7 claims · 3 setups

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  SOP 3 v2 is a web-based application that outputs recommended forward/reverse PCR primers plus a sequencing primer optimized for sequence-based genotyping of human and mouse polymorphisms

  genomic ncbi laboratory primer genomic

• aCLImatise: automated generation of tool definitions for bioinformatics workflows.

  PMID 33325479 · PMC8016486 · Bioinformatics (Oxford, England) · 2021 · 6 claims · 3 setups

  Has reproduction · 93

  aCLImatise automatically generates workflow-language tool definitions by parsing a command-line tool's help output

  samtools single bioconda automated large-scale

• An XML-based system for synthesis of data from disparate databases.

  PMID 16501185 · PMC1513665 · Journal of the American Medical Informatics Association : JAMIA · 2006 · 8 claims · 2 setups

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  An XML-based data management framework (built on Mobius) supports integration of disparate data sources and large data sets for biomedical research applications.

  snp swisprot phylogenetic integration

• The archives are half-empty: an assessment of the availability of microbial community sequencing data.

  PMID 32859925 · PMC7455719 · Communications biology · 2020 · 8 claims · 6 setups

  Has reproduction · 95

  A large proportion of 16S rRNA amplicon sequencing studies contain data that is not available or not reusable despite being reported as deposited.

  publications randomly studies v3–v4 literature manual database