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).

• Biased exon/intron distribution of cryptic and de novo 3' splice sites.

  PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups

  Full-text index only

  Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns

  disease authentic hek293t nuclear literature shapiro-senapathy splicing

• A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

  PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 6 claims · 5 setups

  Has reproduction

  The glycosyltransferase gene AsRCOM is the most critical disease-resistance gene against agave purple curl leaf disease, and its overexpression significantly enhances resistance.

  agave a.h11648 bulk wgcna qpcr

• Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

  PMID 16595074 · PMC3500179 · Human genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  50 novel α-Gal A mutations were identified in 49 of 66 unrelated families with classic Fabry disease.

  genomic α-gal cos-7 transcripts pcr southern microsatellite

• SNAP predicts effect of mutations on protein function.

  PMID 18757876 · PMC2562009 · Bioinformatics (Oxford, England) · 2008 · 8 claims · 3 setups

  Full-text index only

  SNAP is a publicly available web-server implementation predicting functional effects (neutral/non-neutral) of single amino acid substitutions.

  mutant insulin neural alanine mutation

• Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.

  PMID 19890111 · PMC2787406 · The New England journal of medicine · 2009 · 8 claims · 8 setups

  Full-text index only

  Homozygous loss-of-function mutations in IL10RA or IL10RB cause severe early-onset enterocolitis

  consanguineous patients ebv-transformed pbmcs genetic-linkage single-nucleotide-polymorphism candidate-gene

• Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

  PMID 41758938 · PMC12947870 · Science advances · 2026 · 7 claims · 8 setups

  Has reproduction · 84

  MYOD1 L122R-mutant SRMS comprises three coexisting tumor cell states (MYOD1-enriched progenitor-like, proliferative transition, and partially differentiated with reduced MYOD1 activity) reflecting disrupted myogenic differentiation.

  six myod1 independent paired single-nucleus targeted bulk

• CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

  PMID 16995941 · PMC1592126 · BMC bioinformatics · 2006 · 7 claims · 5 setups

  Full-text index only

  CROPPER is a web-based software resource that combines genomic data from heterogeneous sources using identifier and orthologous gene information from the Ensembl database.

  mus substantia transgenic mptp-lesioned western microarray self-organizing

• Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

  PMID 18654622 · PMC2447880 · PLoS computational biology · 2008 · 8 claims · 5 setups

  Full-text index only

  Bongo identifies mutations causing local and global structural effects with a remarkably low false positive rate

  p53 1bpi mutations disease-associated graph correlation structural

• A novel splice-site mutation of TULP1 underlies severe early-onset retinitis pigmentosa in a consanguineous Israeli Muslim Arab family.

  PMID 18432314 · PMC2329669 · Molecular vision · 2008 · 6 claims · 5 setups

  Full-text index only

  A novel homozygous splice-site mutation, c.1495+2_1495+3insT, in the donor splice-site of TULP1 intron 14 underlies autosomal recessive early-onset RP in family TB13.

  genomic tulp1 y79 haplotype direct mismatch-primer

• Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

  PMID 20037586 · PMC2812627 · Nature genetics · 2010 · 8 claims · 8 setups

  Full-text index only

  Heterozygous missense mutations in TRPV4 (c.805C>T/R269C and c.806G>A/R269H) cause CMT2C

  cmt2c affected spinal drg genetic sanger quantitative

• Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

  PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups

  Full-text index only

  Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis

  alzheimer brain alzheimer's presenilin-1 microarray proteomic transgenic

• Analysis of mitochondrial DNA sequences in childhood encephalomyopathies reveals new disease-associated variants.

  PMID 17895983 · PMC1976591 · PloS one · 2007 · 8 claims · 5 setups

  Full-text index only

  Sequencing of complete mtDNA genomes in 23 pediatric patients identified 27 significant variants (12 novel, 15 known) associated with mitochondrial encephalomyopathies.

  blood-derived lymphocytes maternal wild-type complete respiratory pcr-rflp

• MutDB: update on development of tools for the biochemical analysis of genetic variation.

  PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

  Full-text index only

  MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

  proteins mutdb nonsynonymous genes sequence web functional

• Molecular dissection of ALS-associated toxicity of SOD1 in transgenic mice using an exon-fusion approach.

  PMID 18424447 · PMC2465800 · Human molecular genetics · 2008 · 6 claims · 8 setups

  Full-text index only

  Nonsense-mediated mRNA decay (NMD) degrades mutant SOD1 mRNA carrying a PTC in non-terminal exons (1-4), explaining why ALS-associated PTC mutations are found only in exon 5

  transgenic nih hsod1 lumbar southern northern rt-pcr

• Minisequencing mitochondrial DNA pathogenic mutations.

  PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

  Full-text index only

  A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

  blood-derived same genomic pcr minisequencing automatic multiplex

• What have we learned from the congenital myasthenic syndromes.

  PMID 19688192 · PMC3050586 · Journal of molecular neuroscience : MN · 2010 · 8 claims · 8 setups

  Full-text index only

  CMS have been traced to mutations in at least 11 disease genes encoding proteins at the neuromuscular junction

  endplate endplates cos bacterially electron intracellular density

• Mutation analysis of the PTEN / MMAC1 gene in Japanese patients with Cowden disease.

  PMID 10920277 · PMC5926416 · Japanese journal of cancer research : Gann · 2000 · 7 claims · 4 setups

  Full-text index only

  Sequencing of all PTEN/MMAC1 coding regions identified five different germline mutations, four of them novel, in 5 of 12 unrelated Japanese CD patients

  genomic unaffected pcr targeted restriction

• Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

  PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Mutations in GLE1, an mRNA export mediator, cause LCCS1

  lccs1 laahd finnish healthy genomic microsatellite carrier

• A need for a 'whole-istic functional genomics' approach in complex human diseases: arthritis.

  PMID 12718747 · PMC165036 · Arthritis research & therapy · 2003 · 8 claims · 6 setups

  Full-text index only

  A systems ('whole-istic') functional genomics approach integrating multiple technologies and biological levels (cell, tissue, organ, organism) is necessary to understand complex diseases like arthritis.

  oa-affected cartilage type zebrafish gene differential genetic

• Iterative class discovery and feature selection using Minimal Spanning Trees.

  PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

  Full-text index only

  Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

  simulated breast acute diffuse synthetic cdna microarray