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).

• Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

  PMID 18588693 · PMC2446391 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  A decision tree built on 10 selected sequence-derived features classifies SAPs as Disease or Polymorphism with 82.6% accuracy and 0.607 MCC in cross-validation.

  sap sequence-derived humvar same decision independent greedy

• Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

  PMID 16840528 · PMC1524903 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  MS-PET, which dimerizes PETs prior to 454 multiplex sequencing, achieves an approximate 100-fold efficiency increase over standard Sanger-based PET analysis

  mcf7 hct116 flcdna gis-pet chip-pet quantitative

• Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

  PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 100

  TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

  hesc hescs long-read short-read rt-pcr

• A novel mutation in GRK1 causes Oguchi disease in a consanguineous Pakistani family.

  PMID 19753316 · PMC2742643 · Molecular vision · 2009 · 8 claims · 6 setups

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  A novel nonsense mutation (c.614C>A; p.S205X) in exon 1 of GRK1 causes disease in family RP19

  affected family rp19 selected genome-wide microsatellite direct

• A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm.

  PMID 16002787 · PMC1174901 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  An evolution-mimicking algorithm (EMA) that shuffles and mutates loop sequences while keeping the G-quartet intact can screen DNA aptamers based on inhibitory activity rather than binding affinity.

  plasma bovine clot-inhibition binding

• CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

  PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 62

  CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons

  cask ko1 day mature bulk qrt-pcr western

• Protein ranking by semi-supervised network propagation.

  PMID 16723003 · PMC1810311 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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  RankProp, a diffusion-based network propagation algorithm on a PSI-BLAST-derived protein similarity network, significantly outperforms local search methods (BLAST/PSI-BLAST) at detecting remote homologs.

  scop similarity same psi-blast rankprop probabilistic

• Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

  PMID 18842779 · PMC3014055 · The American journal of clinical nutrition · 2008 · 8 claims · 4 setups

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  A significant gene x diet interaction exists between 5-LO promoter short alleles (3,4 repeats) and dietary AA intake in determining MI risk

  costa buffy genetic real-time allele-specific

• Constructing support vector machine ensembles for cancer classification based on proteomic profiling.

  PMID 16689692 · PMC5173238 · Genomics, proteomics & bioinformatics · 2005 · 7 claims · 4 setups

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  CSVME, built by selecting a subset of base SVMs via SVM-RFE ranking and fusing them with a trained upper-layer SVM, achieves better classification performance than an ensemble of all base SVMs.

  serum computational seldi-tof svm-rfe-based 10-fold

• A common missense variant in BRCA2 predisposes to early onset breast cancer.

  PMID 16280055 · PMC1410744 · Breast cancer research : BCR · 2005 · 7 claims · 4 setups

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  BRCA2 C5972T homozygosity (TT genotype) is rare but confers a roughly five-fold increased risk of breast cancer.

  peripheral blood-derived blood case-control genotyping sequencing mutation

• Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

  PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

  user-supplied ranked gene fasta-formatted functional gene novo

• Indirect genomic effects on survival from gene expression data.

  PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups

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  A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.

  dutch uppsala dlbcl gene gene literature permutation

• QuickSNP: an automated web server for selection of tagSNPs.

  PMID 17517769 · PMC1933212 · Nucleic acids research · 2007 · 7 claims · 3 setups

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  QuickSNP is a freely available automated web server for selecting tagSNPs from a chromosomal region, genes within a region, or a specified gene list, with a gene-centric selection option

  genes selected chromosome automated gene-centric tagsnp

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

  PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

  arabidopsis pacbio randomly illumina pacbio nanopore

• Inferring a spatial code of cell-cell interactions across a whole animal body.

  PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 90

  cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

  elegans computational single-cell random genetic

• Information extraction from full text scientific articles: where are the keywords?

  PMID 12775220 · PMC166134 · BMC bioinformatics · 2003 · 8 claims · 5 setups

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  The keyword content of the five article sections (A, I, M, R, D) is heterogeneous, i.e., different sections carry different kinds of information.

  corpus same articles keyword validation qualitative

• Functional restoration of BRCA2 protein by secondary BRCA2 mutations in BRCA2-mutated ovarian carcinoma.

  PMID 19654294 · PMC2754824 · Cancer research · 2009 · 8 claims · 7 setups

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  Secondary BRCA2 mutations restore BRCA2 protein/reading frame and thereby cause acquired platinum and PARP inhibitor resistance in BRCA2-mutated ovarian carcinoma

  ovarian peo1 v-c8-dr-gfp western brca2 crystal

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript