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).

• Oligomeric protein structure networks: insights into protein-protein interactions.

  PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

  Full-text index only

  Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

  non-redundant same known complexes structure hub comparison

• Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

  PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

  Full-text index only

  Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

  pools individual same parental pooled individual test-retest

• Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

  PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

  Full-text index only

  SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

  independent ceph same unrelated snp individual simulated

• FeatureScan: revealing property-dependent similarity of nucleotide sequences.

  PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

  Full-text index only

  FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

  randomly fully same chimpanzee signal-theoretic featurescan blast

• Automatic discovery of cross-family sequence features associated with protein function.

  PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

  Full-text index only

  A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

  non-redundant same evolved eukaryotic self-supervised experiment self-organizing

• fREDUCE: detection of degenerate regulatory elements using correlation with expression.

  PMID 17941998 · PMC2174516 · BMC bioinformatics · 2007 · 6 claims · 5 setups

  Full-text index only

  fREDUCE is a computational method that detects weak or degenerate binding motifs from gene expression or ChIP-chip data by exhaustive search of degenerate IUPAC oligonucleotides

  saccharomyces cerevisiae hepatocytes chip-chip motif-finding gene

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

  Full-text index only

  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome.

  PMID 34561431 · PMC8463674 · Nature communications · 2021 · 8 claims · 7 setups

  Has reproduction · 100

  revTWMR, a reverse transcriptome-wide Mendelian Randomization approach integrating GWAS and whole-blood trans-eQTL summary statistics, is proposed to estimate the causal effect of a phenotype on gene expression.

  blood ra-associated genome-wide revtwmr transcriptome-wide reverse functional

• GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

  PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

  Has reproduction · 96

  gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

  avian comparative correlation robustness

• Sources of variability and effect of experimental approach on expression profiling data interpretation.

  PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups

  Full-text index only

  Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling

  skeletal muscle spleen myogenic affymetrix duplicate unsupervised

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue.

  PMID 28346411 · PMC5699924 · Nature medicine · 2017 · 8 claims · 8 setups

  Has reproduction · 78

  12,13-diHOME is a cold-induced lipokine that stimulates BAT activity

  plasma bat serum mice lc-ms correlation 18f-fdg

• Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.

  PMID 15799778 · PMC1080126 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

  Full-text index only

  Dart shooting introduces an allohormone that inhibits digestion of donated sperm, increasing the amount reaching the spermathecae and fertilizing eggs, thereby manipulating the mating partner's sperm storage.

  dart-possessing same land cantareus 28s shimodaira-hasegawa principal

• Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis.

  PMID 16517937 · PMC1390686 · Nucleic acids research · 2006 · 8 claims · 6 setups

  Full-text index only

  QD-mediated two-color fluorescence coincidence detection combined with oligonucleotide ligation assay (OLA) enables separation-free, homogeneous point mutation detection.

  synthetic same β-globin kras ola fluorescence photon

• Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

  PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

  Full-text index only

  The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

  PMID 20003400 · PMC2806376 · BMC genetics · 2009 · 7 claims · 4 setups

  Full-text index only

  Pooled genotyping on the Affymetrix 500k platform using PPC yields highly accurate allele frequency estimates (correlation 0.988) comparable to or better than the 10k/100k platforms.

  case hapmap snp individual allele

• Geometric Reliability of Super-Resolution Reconstructed Images from Clinical Fetal MRI in the Second Trimester.

  PMID 37284977 · PMC10406722 · Neuroinformatics · 2023 · 7 claims · 8 setups

  Has reproduction

  NiftyMIC and MIALSRTK provide reliable SR reconstructed volumes suitable for biometric assessments

  fetal same reconstructed t2w b-ffe super-resolution

• Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

  PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

  full-length alternative refseq genome pairwise mitochondrial signal

• A comprehensive catalogue of somatic mutations from a human cancer genome.

  PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

  Full-text index only

  Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

  colo-829 additional whole-genome conventional pcr

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized