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).

• EpiToolKit--a web server for computational immunomics.

  PMID 18440979 · PMC2447732 · Nucleic acids research · 2008 · 7 claims · 3 setups

  Full-text index only

  EpiToolKit is a web server integrating five MHC class I and two MHC class II epitope prediction methods in a unified, user-friendly interface.

  randomly novel minor mhc polymorphic

• 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

• A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

  PMID 15238985 · PMC2364794 · British journal of cancer · 2004 · 7 claims · 6 setups

  Full-text index only

  A novel A-1012G (adenine-guanine) polymorphism exists in the VDR exon 1a promoter region, identified by SSCP screening and sequencing

  blood variant patients same sscp sanger pcr-rflp

• Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

  PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

  Full-text index only

  SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

  blood family unrelated subjects snp family-based linkage

• Mutation analysis of the MSMB gene in familial prostate cancer.

  PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

  Full-text index only

  No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

  germline blood 161-nt genotype sanger taqman transcription

• Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

  PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

  Full-text index only

  Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

  genomic pnmt promoter pcr population haplotype

• Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

  PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

  Full-text index only

  MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

  prostate subset lncap 22rv1 microrna quantitative western

• FOXP1 is differentially active during development of murine vasopressin and oxytocin magnocellular neurons.

  PMID 42088346 · PMC13138059 · iScience · 2026 · 8 claims · 7 setups

  Full-text index only

  FOXP1 participates in MCN development and is differentially active in OXT MCNs relative to AVP MCNs

  hypothalamus hypothalamic avp neuro-2a single-cell gene fate

• Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

  PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

  Full-text index only

  The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

  bac heart ccs genomic genomic rt-pcr transcription

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

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

  Full-text index only

  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

• N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

  PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

  Full-text index only

  NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

  random reference healthy long-term resequencing quantitative sequence

• Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection.

  PMID 16953805 · PMC1859983 · Cellular microbiology · 2007 · 7 claims · 8 setups

  Full-text index only

  Ile-91 is the primary docking residue required for binding of all tested Nm and Hi strains to CEACAM1, despite structural diversity of bacterial ligands

  ceacam1 meningitidis influenzae ha3 homology site-directed receptor

• DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

  PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

  Has reproduction · 93

  Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

  homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic

• Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

  PMID 41953002 · PMC13053772 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 78

  PARP1, PTPN1, and ITGA4 are core PAH protein targets identified via PPI network analysis and XGBoost feature selection from AD-associated DEGs

  brain geo predicted gse44771 wgcna differential protein-protein

• Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

  PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

  Full-text index only

  The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

  ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence

• 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

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.

  PMID 40314147 · PMC12774851 · Genetics · 2026 · 8 claims · 8 setups

  Full-text index only

  TF2TG is an online resource integrating motif scan data, ChIP-seq peaks (modENCODE/modERN), Hi-C (TADs), REDfly-curated CRMs, ATAC-seq, protein-protein interaction data, and tissue-specific expression to predict TF-target gene relationships in Drosophila

  drosophila combined motif chip-seq whole-animal

• Protocadherin 20 Is a POU Class 2 Homeobox 3 Target Gene Required for Proper Tuft Cell Microvillus Organization.

  PMID 41619969 · PMC13051935 · Cellular and molecular gastroenterology and hepatology · 2026 · 8 claims · 8 setups

  Full-text index only

  POU2F3 ChIP-seq in isolated murine tuft cells identifies high-confidence POU2F3 binding sites/target genes enriched at gene promoters and the POU consensus motif

  facs-isolated pou2f3 duodenal non-small-cell chip-seq novo bulk

• Identification of functional SNPs in the 5-prime flanking sequences of human genes.

  PMID 15717931 · PMC550646 · BMC genomics · 2005 · 6 claims · 5 setups

  Full-text index only

  7 of 10 candidate SNPs tested by EMSA showed reproducible allele-specific differences in TF-DNA complex binding/stability

  flanking synthetic genomic cloned comparative electrophoretic rflp