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).

• A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report.

  PMID 20003495 · PMC2802351 · Orphanet journal of rare diseases · 2009 · 8 claims · 7 setups

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  A novel FAH gene mutation, c.103G>A (Ala35Thr), causes a mild, atypical form of tyrosinemia type I

  fibroblasts liver genomic tnt northern western liver

• High-throughput crystallography for structural genomics.

  PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

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  SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

  recombinant recalcitrant hundred family hydrogen situ site-directed

• Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

  PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

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  Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

  hiv-1 longitudinal 0-month single pseudovirus single site-directed

• A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.

  PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 7 claims · 6 setups

  Has reproduction · 78

  MERLIN-P-TFA network inference on 18 curated public RNA-seq datasets produced a genome-wide GRN resource for A. fumigatus called GRAsp.

  aspergillus fumigatus bulk computational chip-seq-based

• Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.

  PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 84

  TEPs from NSCLC patients show 111 upregulated and 108 downregulated genes compared to platelets from non-cancer donors

  platelets degs platelet-specific tep-specific transcriptome pathway k-means

• Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

  PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

  breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence

• Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

  PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

  Has reproduction · 90

  MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

  pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent

• Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.

  PMID 35508485 · PMC9068813 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  eRNAs longer than 200 nucleotides that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release

  cortical transcribed reconstituted erna-bound gro-seq exo-seq shape-map

• 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

• Intracellular sorting and targeting of melanosomal membrane proteins: identification of signals for sorting of the human brown locus protein, gp75.

  PMID 7642699 · PMC2199968 · The Journal of cell biology · 1995 · 7 claims · 7 setups

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  The 36-amino acid cytoplasmic tail of gp75 alone is sufficient to direct intracellular retention and targeting of chimeric CD8 proteins to the endosomal/lysosomal compartment in fibroblasts

  melanoma sk-mel-19 immunoprecipitated coli immunofluorescence immunoelectron protease

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

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

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  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

• VIRGO: computational prediction of gene functions.

  PMID 16845022 · PMC1538839 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  VIRGO constructs a functional linkage network (FLN) from gene expression and molecular interaction data, labels genes with GO annotations, and propagates these labels to predict functions of unlabelled genes

  cerevisiae sapiens leave-one-out gene protein-protein

• 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

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  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

• An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

  PMID 17984082 · PMC2239001 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  The Biodefense Proteomics Resource Center (RC) is a public cyberinfrastructure that stores, integrates, and disseminates experimental data from seven Proteomics Research Centers (PRCs) on biodefense pathogens and host interactions

  brucella toxoplasma bacillus homo label-free mass genomic

• In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

  PMID 17726045 · PMC2094079 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Two exonic mutations, PINK1 E417G and PARK7 E64D, disrupt binding to U1 snRNA and cause skipping of the mutation-harboring exon

  hek293 genome lymphocytes minigene artificial genome-wide

• A novel missense mutation in DAX-1 with an unusual presentation of X-linked adrenal hypoplasia congenita.

  PMID 17308433 · PMC3479083 · Hormone research · 2007 · 7 claims · 6 setups

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  A novel C794G transversion causing missense mutation T265R in DAX1 (NR0B1) is responsible for X-linked adrenal hypoplasia congenita in this kindred

  genomic tsa201 unspecified proband sequence modified full-length

• Phosphoproteomics: unraveling the signaling web.

  PMID 18922462 · PMC2754874 · Molecular cell · 2008 · 8 claims · 8 setups

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  Integrating discovery-based MS phosphoproteomics with targeted protein microarray technologies yields a more complete picture of signaling networks and improves clinical translation of findings.

  ddr atr-deficient hela mammary phosphospecific phospho-motif scx

• Relation of response to treatment with dorzolamide in X-linked retinoschisis to the mechanism of functional loss in retinoschisin.

  PMID 18834580 · PMC2668603 · American journal of ophthalmology · 2009 · 6 claims · 4 setups

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  A positive response of macular cysts to dorzolamide can occur across all three known mechanisms of retinoschisin dysfunction (absent secretion, decreased expression, non-functional secretion).

  eyes blood-derived ebna xlrs optical genetic transfection

• The clinical course and genetic defect in the PCFT gene in a 27-year-old woman with hereditary folate malabsorption.

  PMID 18718264 · PMC3835188 · The Journal of pediatrics · 2008 · 6 claims · 5 setups

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  The patient carries two identical homozygous mutations (GC>AA at positions 197/198) in exon 1 of PCFT, causing a premature stop codon (C66X)

  parental rfc hela blood genomic [3h]5-methyltetrahydrofolate northern

• A novel GCAP1(N104K) mutation in EF-hand 3 (EF3) linked to autosomal dominant cone dystrophy.

  PMID 18706439 · PMC2584361 · Vision research · 2008 · 8 claims · 7 setups

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  A novel N104K mutation in GCAP1's third EF-hand (EF3) motif was identified in two affected members of a family with autosomal dominant cone dystrophy, the first naturally occurring mutation in the EF3 Ca2+-binding loop.

  genomic patients high recombinant pcr full-field paired-flash