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).

• An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

  PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

  osteoarthritic articular chondrocyte microarray computational high-throughput

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

  PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

  aeruginosa differentially paired rna-seq tn-seq computational

• Mutations in NYX of individuals with high myopia, but without night blindness.

  PMID 17392683 · PMC2642916 · Molecular vision · 2007 · 7 claims · 5 setups

  Full-text index only

  Two novel NYX missense mutations (Cys48Trp and Arg191Gln) were found in unrelated males with high myopia but no night blindness.

  unrelated individuals high model direct sequencing electroretinogram

• Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

  PMID 20011630 · PMC2790479 · Molecular vision · 2009 · 8 claims · 5 setups

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  MDH1 is not the causative gene for RP28-linked autosomal recessive retinitis pigmentosa

  genomic lr-pcr uhts v-4 long-range ultra sanger

• Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

  PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups

  Has reproduction · 50

  2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B

  flower roots analysis parental high-throughput quantitative pcr

• A restricted spectrum of NRAS mutations causes Noonan syndrome.

  PMID 19966803 · PMC3118669 · Nature genetics · 2010 · 8 claims · 6 setups

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  Germline NRAS mutations (T50I, G60E) cause a subset of Noonan syndrome cases via enhanced MAPK activation

  cohort cos-7 recombinant nras mutation western ras

• Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model.

  PMID 41672067 · PMC13174225 · Cell genomics · 2026 · 7 claims · 7 setups

  Full-text index only

  A segregation analysis in an F2 medaka cross identified 16 QTLs linked to embryonic heart rate variation across temperatures

  mikk medaka discovered informed high-throughput heart shallow

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• Rbfox2 controls autoregulation in RNA-binding protein networks.

  PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

  Has reproduction · 48

  Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

  v6.5 fhfox2 top introns iclip sequencing rt-pcr

• Sequence variations of GRM6 in patients with high myopia.

  PMID 19862333 · PMC2765235 · Molecular vision · 2009 · 7 claims · 8 setups

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  Three novel GRM6 variations with predicted functional consequences (c.67-82delCAGGCGGGCCTGGCGCinsT, c.858-5a>g, c.1537G>A) were found in high myopia patients but absent in 96 controls

  genomic pcr mglur6 grm6 pcr heteroduplex pcr-restriction

• Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

  PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

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  DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

  standard dsic-labeled immunodepleted serum labeling quantitative in-solution

• IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.

  PMID 41851882 · PMC13113378 · Genome biology · 2026 · 8 claims · 2 setups

  Full-text index only

  IFDlong is the only tool that can discover fusion transcripts at isoform resolution

  in-silico type long-read computational

• Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.

  PMID 37948380 · PMC10637681 · PloS one · 2023 · 8 claims · 8 setups

  Has reproduction · 90

  Stemness-related genes ORC1L, KIF20A, and DLGAP5 are upregulated in LUAD and correlate with altered immune cell infiltration (Th2, MDSC, HSC) and reduced patient survival.

  tcga gse40419 gse31210 gene bulk microarray univariate

• Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

  PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

  Has reproduction · 98

  Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

  hg38 hela hek293t induced genome-wide high-throughput chip-seq

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

  PMID 18489799 · PMC2413254 · BMC cancer · 2008 · 8 claims · 6 setups

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  Pathogenic BRCA1/BRCA2 mutations were identified in 294 of 1,010 (29.1%) unrelated high-risk Czech probands

  genomic pcr-amplified brca1 pha-stimulated truncation heteroduplex direct

• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

  PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

  Full-text index only

  Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

  liver saccharomyces mdeg independent microarray transcription chromosomal

• Prevalence of mutations in ELANE, GFI1, HAX1, SBDS, WAS and G6PC3 in patients with severe congenital neutropenia.

  PMID 19775295 · PMC2783282 · British journal of haematology · 2009 · 8 claims · 4 setups

  Full-text index only

  ELANE mutations were detected in 90 of 162 SCN patients (55.6%), making it the most commonly mutated gene in SCN.

  peripheral whole-genome-amplified gfi1 sanger high-throughput sift

• Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

  PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

  Has reproduction · 88

  Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

  arabidopsis deg promoter selected meta-analysis transcription hexamer