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 common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

  PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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  A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

  gbs clinical bioinformatic eburst kinetic

• SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

  PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

  genome affymetrix probe database microarray interactive

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.

  PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments

  tcga-blca famc1-3 differentially gse32894 bulk consensus gene

• A distinct epigenetic signature at targets of a leukemia protein.

  PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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  Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

  32d sequence gene bioinformatic real-time

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• Mining novel biomarkers for prognosis of gastric cancer with serum proteomics.

  PMID 19740432 · PMC2753349 · Journal of experimental & clinical cancer research : CR · 2009 · 7 claims · 4 setups

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  A 5-peak prognosis pattern (4474, 4542, 6443/6643, 4988, 6685 Da) predicts poor vs good prognosis in GC with higher sensitivity/specificity than CEA and TNM stage

  serum seldi seldi-tof-ms chemiluminescence bioinformatic

• Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.

  PMID 35013236 · PMC8748982 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Aβ (APP/PS1) and Tau (MAPT P301S) pathology induce distinct but overlapping astrocyte translatome signatures

  astrocytes aldh1l1_egfp-rpl10a astrocyte ageing trap-seq immunofluorescence ribosome

• Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

  PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 50

  BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

  bovine direct amplified synthetic

• Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

  PMID 16855283 · PMC1524921 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  Four novel brain-specific paternally expressed transcripts (BB077283, BM117114, AK080843, AV328498) were identified and validated on proximal Chr 7.

  tissues inter-subspecies placenta genomic microarray rt-pcr sequencing

• Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

  PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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  Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

  saliva amplified extracted differentially genome quality extraction

• Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

  PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 44

  The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI

  spinal brown sci microarray functional protein-protein