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).

• Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics.

  PMID 18783599 · PMC2559821 · Theoretical biology & medical modelling · 2008 · 8 claims · 2 setups

  Full-text index only

  Probability landscapes permit systematic detection, analysis, and utilization of feature context-dependency in genomic data.

  specified probability microarray

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

  Full-text index only

  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• Blood Pressure Sunday: introducing genomics to the community through family history.

  PMID 15888234 · PMC1327717 · Preventing chronic disease · 2005 · 7 claims · 5 setups

  Full-text index only

  Family history is a significant, longstanding risk factor for high blood pressure and can serve as a practical 'genomic tool' for public health given that routine DNA-based risk testing is not yet available.

  family detroit u.s parish readability community national

• Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.

  PMID 19063745 · PMC2613935 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  Gene Prospector is a Web-based application that selects and prioritizes potential disease-related genes using a curated, updated literature database of genetic association studies

  huge pdgene snps3d dbsnp curated comparative snp

• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

  Full-text index only

  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• 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

  Has reproduction · 99

  Across 253 manually curated studies (164,000+ samples), over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available overall.

  randomly repositories geo manual automated

• Web services and workflow management for biological resources.

  PMID 16351751 · PMC1866383 · BMC bioinformatics · 2005 · 8 claims · 4 setups

  Full-text index only

  Workflow management systems combined with Web Services are a promising ICT approach for automating access to and integration of biomedical data.

  cabri iarc taverna web workflow database

• StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

  PMID 24627795 · PMC3938176 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 43

  StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics, backed by an SQL (MySQL) database with Perl and Java APIs.

  fastq mysql perl java fastqc relational programmatic

• scSAMAC: saliency-adjusted masking induced attention contrastive learning for single-cell clustering.

  PMID 40131310 · PMC11934584 · Briefings in bioinformatics · 2025 · 8 claims · 1 setups

  Has reproduction · 85

  scSAMAC integrates contrastive learning and negative binomial (NB) losses into a VAE, extracting features via contrastive unit similarity while preserving intrinsic data characteristics to enhance robustness and generalization in clustering.

  scrna-seq scrna-seq

• Systems biology in human health and disease.

  PMID 17893698 · PMC2013921 · Molecular systems biology · 2007 · 8 claims · 5 setups

  Full-text index only

  High-throughput quantitative proteomics of signaling networks (e.g., HER2 overexpression) can be correlated with biological responses like proliferation and migration to better understand pathways deregulated in cancer.

  her2 biological prostate model quantitative combinatorial genome-wide

• UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data.

  PMID 37478378 · PMC10516365 · Briefings in bioinformatics · 2023 · 5 claims · 3 setups

  Has reproduction · 60

  UNMF is designed for tidy data format and structure, allowing it to handle a wide range of data structures and formats in a unified manner without requiring format-specific preprocessing.

  simulated specified simulation metagenomics sequencing

• GeMI: interactive interface for transformer-based Genomic Metadata Integration.

  PMID 35657113 · PMC9216561 · Database : the journal of biological databases and curation · 2022 · 8 claims · 5 setups

  Has reproduction · 64

  GeMI is a web tool that uses a fine-tuned GPT2 model to extract 15 structured key-value attributes from free-text GEO sample metadata.

  cistrome encode geo fine-tuned manual batch transformer-based

• KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.

  PMID 36430895 · PMC9694301 · International journal of molecular sciences · 2022 · 8 claims · 6 setups

  Has reproduction · 57

  KARAJ automates end-to-end querying and downloading of genomic/transcriptomic sequence data from a list of PMCIDs, URLs, or accession numbers

  fastq gse126379 research sequence download parallel literature

• Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

  PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

  Full-text index only

  Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

  pubmed genes same randomly geneseeker evoc disease

• An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

  PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

  Full-text index only

  Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

  private disease uniprot snps database controlled sequence

• ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

  PMID 16845044 · PMC1538898 · Nucleic acids research · 2006 · 8 claims · 2 setups

  Full-text index only

  The ASPIC algorithm, using an optimization procedure that minimizes splice site predictions and transcript isoforms from multiple EST-genome alignments, outperforms other similar AS-prediction tools in sensitivity and selectivity

  hnrpr specified comparative algorithm

• Ensembl 2005.

  PMID 15608235 · PMC540092 · Nucleic acids research · 2005 · 8 claims · 4 setups

  Full-text index only

  Ensembl's automatic gene build system can flexibly and reliably annotate a wide variety of genomes with limited species-specific evidence.

  chicken genomes vertebrate annotated experimental gene pairwise

• D2H2: diabetes data and hypothesis hub.

  PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 6 setups

  Has reproduction

  D2H2 is a web-based portal integrating hundreds of curated diabetes-relevant transcriptomics datasets with bioinformatics tools for gene/gene set queries

  brain top curated d2h2 differential gene bulk

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

  PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

  user-submitted string pubmed protein-coding gene hierarchical text-mining

• COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.

  PMID 36350658 · PMC9825429 · Nucleic acids research · 2023 · 8 claims · 6 setups

  Has reproduction · 84

  COXPRESdb version 8 adds CoexMap (UMAP-based genome-scale coexpression visualization), KEGG pathway enrichment summaries, and CoexPub (literature-linking tool) as new analysis features.

  animal same coexpression gene rnaseq-based microarray-based pathway