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).

• Representing and querying disease networks using graph databases.

  PMID 27462371 · PMC4960687 · BioData mining · 2016 · 7 claims · 8 setups

  Has reproduction · 77

  Graph databases are well suited for representing biological information that is highly connected, semi-structured, and unpredictable.

  uniprot proteome asthma tissues all-versus-all graph protein-protein

• Wide-Open: Accelerating public data release by automating detection of overdue datasets.

  PMID 28594819 · PMC5464523 · PLoS biology · 2017 · 7 claims · 5 setups

  Has reproduction · 74

  Wide-Open is a general text-mining approach that automatically detects overdue datasets by scanning PubMed articles for dataset accession identifiers and querying repositories to determine if the datasets remain private.

  open-access geo sra text database web

• Analysis of the glutathione S-transferase (GST) gene family.

  PMID 15607001 · PMC3500200 · Human genomics · 2004 · 8 claims · 4 setups

  Full-text index only

  The complete human GST gene family comprises 16 genes in six subfamilies: alpha (GSTA), mu (GSTM), omega (GSTO), pi (GSTP), theta (GSTT) and zeta (GSTZ).

  genome gst gst-related gstk1 gene sequence phylogenetic

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

  nci60 lymphoma fep go-annotated cdna recursive hypergeometric

• Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

  PMID 16403238 · PMC1351203 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  No NPC proteome database existed prior to this work despite availability of other cancer proteome databases

  nasopharyngeal excised subset monoisotopic 2-de maldi-tof q-tof

• The Genographic Project public participation mitochondrial DNA database.

  PMID 17604454 · PMC1904368 · PLoS genetics · 2007 · 7 claims · 4 setups

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  The Genographic Project created the largest standardized human mtDNA database to date, comprising 78,590 genotypes from the first 18 months of public participation.

  buccal reference entire direct coding-region leave-one-out

• Cataloging coding sequence variations in human genome databases.

  PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

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  A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

  coding hapmap concurrent nssnps database hapmap amino

• Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

  PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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  PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

  subset drosophila ensembl lc-ms icat peptide-to-genome

• Landscape of allele-specific transcription factor binding in the human genome.

  PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 82

  A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.

  gtrd k562 mcf7 types chip-seq variant bayesian

• Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.

  PMID 16790052 · PMC1534064 · BMC bioinformatics · 2006 · 8 claims · 7 setups

  Full-text index only

  The Sequential Minimal Optimization (SMO) SVM algorithm was the best-performing classifier among 26 WEKA classifiers for predicting catalytic residues

  benchmarking same pirsf pdb supervised wrapper sequence

• Metatranscriptomics of the human oral microbiome during health and disease.

  PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

  Has reproduction · 62

  Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

  patient-matched subset health rna-seq rrna comparison metatranscriptomics

• Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines.

  PMID 18005451 · PMC2216041 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Parepro, an SVM-based method integrating three attribute sets (RD, MI, IE) derived from evolutionary and residue-property information, predicts whether an nsSNP is deleterious or neutral.

  sequences target svm benchmark homology

• Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

  PMID 17672919 · PMC1973086 · BMC bioinformatics · 2007 · 6 claims · 8 setups

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  The Not-N algorithm, incorporated into the Minimum SNPs program, identifies small marker sets diagnostic for user-defined subgroups of genetic variants with 0% false negatives

  hcv campylobacter yersinia clostridium snp comparative cgh

• Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

  PMID 18769673 · PMC2518838 · PloS one · 2008 · 8 claims · 6 setups

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  The protein sequence-structure map behaves as a noisy digital communication channel whose capacity C exceeds the transmission rate R for native structures, satisfying Shannon's noisy channel theorem

  chains pdbselect25 same single-domain statistical channel negative

• A catalog of human cDNA expression clones and its application to structural genomics.

  PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups

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  A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli

  hex1 ensembl coli recombinant small-scale tag-sequencing blastp

• Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

  PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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  SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

  genome autosomal hapmap chromosome snp chromosomal minor

• Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

  PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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  The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

  clinical concatenated cereus isolates multilocus phylogenetic pcr

• Genetic variation in an individual human exome.

  PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

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  The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

  huref genes subset whole-genome allele functional

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

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

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  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

• Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

  PMID 16515697 · PMC1448207 · BMC medical genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  CMS compares IBS allele/genotype sharing between distantly related (beyond grandparental) affected and unaffected individuals from founder populations to detect disease loci while reducing confounding from population stratification and genetic heterogeneity.

  amish unrelated same overall microsatellite combinatorial permutation