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).

• Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

  PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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  15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

  orthologues repair case-control phosphorylation cross-species database

• Cross-species prediction reveals chromatin regions with increased accessibility in humans.

  PMID 41984952 · PMC13082337 · Science advances · 2026 · 8 claims · 8 setups

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  CNNs trained exclusively on human ATAC-seq data achieve cross-species prediction performance in chimpanzees and macaques comparable to species-specific models

  lymphoblastoid prefrontal six chimpanzee bulk single-cell cnn

• Structural organization and interactions of transmembrane domains in tetraspanin proteins.

  PMID 15985154 · PMC1190194 · BMC structural biology · 2005 · 8 claims · 5 setups

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  TM1, TM2 and TM3 of human tetraspanins display a distinct heptad repeat motif (abcdefg)n, while TM4 lacks this motif.

  tetraspanin cd9 gfp single-cysteine sequence cross-species fluorescence

• In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

  PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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  A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

  genomic genome pan blood snp sequence cross-species

• In silico promoters: modelling of cis-regulatory context facilitates target predictio.

  PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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  An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

  serca2 rantes genes podocyte-associated literature-based promoter cross-referenced

• Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

  PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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  APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

  urothelial urothelial-specific ureter hek293t single-cell poly fluorescence

• Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

  PMID 19023448 · PMC2584772 · Molecular vision · 2008 · 8 claims · 7 setups

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  Mutations in USH2A are responsible for most cases of USH2

  genomic family probands ush2a direct restriction single

• Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

  PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

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  Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

  chicken turkey broiler chromosome single fish

• The functional landscape of alternative splicing in hematopoietic lineage commitment.

  PMID 41593078 · PMC12946277 · Nature communications · 2026 · 7 claims · 8 setups

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  FAScore, a Random Forest model integrating 19 dynamic, structural, and conservation features, predicts functional exon-skipping AS events with high accuracy in a species- and lineage-specific manner.

  umbilical bone fetal zebrafish bulk machine exon

• PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

  PMID 16430766 · PMC1434729 · BMC medical genetics · 2006 · 7 claims · 8 setups

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  Linkage analysis can pre-select which gene (PKD1 or PKD2) to screen for mutations in ADPKD families with sufficient samples

  genomic pcr additional cat linkage direct heteroduplex

• 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

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

  genomic pnmt promoter pcr population haplotype

• Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

  PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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  Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

  5'-flanking upstream transiently genomic comparative tfbs promoter-reporter

• Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

  PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

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  The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

  turmoil-1 rrm elegans predicted pairwise maximum genome-wide

• Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

  PMID 18203199 · PMC2578871 · American journal of medical genetics. Part A · 2008 · 6 claims · 8 setups

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  Two novel homozygous missense mutations in BBS5 (p.Gly72Ser and p.Thr183Ala) were identified in non-Caucasian BBS patients (Somali and Sri Lankan)

  genomic somali sri ethnically dhplc snp sanger

• A novel mutation I522N within the TGFBI gene caused lattice corneal dystrophy I.

  PMID 19956413 · PMC2786890 · Molecular vision · 2009 · 7 claims · 4 setups

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  A novel missense mutation (1565T→A) in exon 12 of TGFBI, causing an I522N amino acid substitution, causes lattice corneal dystrophy type I in the studied Chinese family.

  genomic patients affected tgfbi pcr clinical visual

• Sequence variations of GRM6 in patients with high myopia.

  PMID 19862333 · PMC2765235 · Molecular vision · 2009 · 7 claims · 8 setups

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  Three novel GRM6 variations with predicted functional consequences (c.67-82delCAGGCGGGCCTGGCGCinsT, c.858-5a>g, c.1537G>A) were found in high myopia patients but absent in 96 controls

  genomic pcr mglur6 grm6 pcr heteroduplex pcr-restriction

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

  PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

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  Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

  identified cst csts comparative coding exon

• Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

  PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

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  RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

  peripheral patient-parent genomic crebbp karyotyping bac microsatellite