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).

• Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

  PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 7 setups

  Has reproduction · 72

  edgeR identifies 9 DEGs associated with pCR and 13 DEGs associated with relapse from 579 immune genes in a small TNBC sample set (n=55)

  ffpe same nanostring training nanostring immunohistochemistry differential

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

  PMID 15809229 · PMC1074396 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Comparative gene finding (SGP2) between human and chicken, followed by RT-PCR verification, adds at most ~0.2% new genes to the multi-exonic human gene catalog

  chicken predicted human-chicken cdna comparative blastp pairwise

• Mutation screening of HSF4 in 150 age-related cataract patients.

  PMID 18941546 · PMC2569895 · Molecular vision · 2008 · 8 claims · 4 setups

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  Five new HSF4 sequence variants (c.1020-25G>A, c.1078A>G, c.1223C>T, c.1256+25C>T, c.1286C>T) were found in age-related cataract patients but not in 220 controls.

  peripheral hsf4b hsf4 genomic secondary sequence

• Identification of four novel cytochrome P4501B1 mutations (p.I94X, p.H279D, p.Q340H, and p.K433K) in primary congenital glaucoma patients.

  PMID 20057908 · PMC2802296 · Molecular vision · 2009 · 8 claims · 4 setups

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  Mutations in CYP1B1 are a major cause of PCG in the studied patient cohort

  genomic cyp1b1 pcg pcr missense clinical

• Mutational analysis of TARDBP in neurodegenerative diseases.

  PMID 20031275 · PMC2889148 · Neurobiology of aging · 2011 · 8 claims · 4 setups

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  TARDBP mutations are not a significant cause of AD or PD

  als tdp-43 pcr pathogenicity

• Prediction and assessment of splicing alterations: implications for clinical testing.

  PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

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  Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

  brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene

• Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

  PMID 40990923 · PMC12687342 · Evolution; international journal of organic evolution · 2025 · 8 claims · 5 setups

  Has reproduction · 64

  The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families

  caecilian caecilia archival lws pcr eye histology

• Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

  PMID 16429166 · PMC1342637 · PLoS genetics · 2005 · 8 claims · 5 setups

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  PANTHER subPSEC scores correctly predicted the functional impact of >94% (16/17) of tested naturally occurring ABCA1 variants

  abca1 stably subpsec cholesterol rt-pcr

• The evolution and genomic landscape of CGB1 and CGB2 genes.

  PMID 17055150 · PMC2599907 · Molecular and cellular endocrinology · 2007 · 8 claims · 5 setups

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  CGB1 and CGB2 arose via insertion of a DNA fragment (736/724 bp) replacing part of the ancestral hCGβ promoter and 5'-UTR, creating a novel exon 1 and causing a frameshift that produces a completely different 132-aa protein unrelated to hCGβ

  genomic great cgb1 chimpanzee pcr population hka

• Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.

  PMID 18162506 · PMC7611804 · Diabetes · 2008 · 8 claims · 8 setups

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  Heterozygous INS mutations are a common cause of permanent neonatal diabetes (PNDM) diagnosed before 6 months of age

  peripheral patients mody young-onset pcr microsatellite variant

• Mutation analysis in a German family identified a new cataract-causing allele in the CRYBB2 gene.

  PMID 17653036 · PMC2774456 · Molecular vision · 2007 · 8 claims · 4 setups

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  A novel heterozygous mutation (383A>T; D128V) in exon 5 of CRYBB2 cosegregates with congenital cataract in all three affected family members and is absent in unaffected relatives.

  genomic pcr-amplified computational pcr restriction pcr-rflp

• Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

  PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

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  OPTC is a candidate gene involved in POAG pathogenesis

  genomic pcr optc retinal pcr-sscp dhplc sequencing

• Two novel myocilin mutations in a Chinese family with primary open-angle glaucoma.

  PMID 18776955 · PMC2530518 · Molecular vision · 2008 · 7 claims · 4 setups

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  Two novel MYOC mutations, Pro13Leu (38C→T) and Gln337Stop (1009C del), are likely responsible for POAG pathogenesis in this pedigree

  genomic family myoc pcr-rflp sequencing clinical

• Autosomal dominant hereditary spastic paraplegia: novel mutations in the REEP1 gene (SPG31).

  PMID 18644145 · PMC2492855 · BMC medical genetics · 2008 · 8 claims · 6 setups

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  Pathogenic REEP1 mutations were identified in 4.3% (7/162) of autosomal dominant 'pure' HSP cases

  genomic pcr-amplified reep1 pcr dhplc direct

• A nonsense mutation in CRYGC associated with autosomal dominant congenital nuclear cataract in a Chinese family.

  PMID 18618005 · PMC2447816 · Molecular vision · 2008 · 6 claims · 4 setups

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  A heterozygous c.327C>A transversion in exon 3 of CRYGC causes a nonsense mutation (C109X) that cosegregates with autosomal dominant congenital nuclear cataract in a Chinese family.

  genomic type family γc-crystallin pcr comparative clinical

• A missense mutation in LIM2 causes autosomal recessive congenital cataract.

  PMID 18596884 · PMC2442473 · Molecular vision · 2008 · 7 claims · 5 setups

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  A homozygous missense mutation (Gly154Glu, c.587G>A) in LIM2 causes autosomal recessive congenital cataract in a human family

  genomic mp19 patients pcr sscp cosegregation

• Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

  PMID 18552984 · PMC2426732 · Molecular vision · 2008 · 8 claims · 4 setups

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  Coding/flanking regions of RHO, PRPF31, and IMPDH1, plus exons 4F/4G/4H of RP1, were PCR-amplified and directly sequenced in 48 isolated and 53 adRP Indian patients and 75 controls

  genomic peripheral probands identified pcr reverse clinical

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant

• Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

  PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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  Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

  msi-h computational rb1cc1 normal pcr nonlinear real-time