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).

• In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

  PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

  subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription

• Genome-wide survey for biologically functional pseudogenes.

  PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

  Full-text index only

  A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

  human-mouse chimpanzee cross-species maximum-likelihood synteny

• The EH1 motif in metazoan transcription factors.

  PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

  Full-text index only

  There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

  homeobox-containing forkhead-containing complete combined meme hmm logistic

• ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

  PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

  orthologous literature sequence pairwise

• A third approach to gene prediction suggests thousands of additional human transcribed regions.

  PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

  Full-text index only

  A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

  genome 4.4-mb known nucleotide repeat polyadenylation

• DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

  PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

  Full-text index only

  DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

  normal dld1 beas2b ramos tss comparative

• Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

  PMID 40281430 · PMC12032694 · BMC genomics · 2025 · 7 claims · 8 setups

  Full-text index only

  A large repository of nascent run-on RNA-seq samples (DBNascent) was assembled and uniformly processed to identify sites of bidirectional transcription genome-wide.

  bidirectional across high-quality nascent comparative eqtl

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental

• 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

  Full-text index only

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

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

• RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

  PMID 41755635 · PMC12956339 · Nucleic acids research · 2026 · 7 claims · 8 setups

  Full-text index only

  RAPseq is a novel in vitro, antibody-free and cross-linking-free method that profiles RBP binding to native cellular RNA transcriptome-wide using recombinant Halo-tagged RBPs and affinity purification followed by sequencing.

  hepg2 hur igf2bp1 ythdf1 rapseq cross-species co-rapseq

• Predicting enhancers in mammalian genomes using supervised hidden Markov models.

  PMID 30917778 · PMC6437899 · BMC bioinformatics · 2019 · 8 claims · 8 setups

  Has reproduction · 70

  eHMM predicts enhancers with high precision and recall comparable to state-of-the-art methods and consistently outperforms them in accuracy and resolution

  esc atac-seq chip-seq cage

• Development of double-positive thymocytes at single-cell resolution.

  PMID 33771202 · PMC8004397 · Genome medicine · 2021 · 7 claims · 8 setups

  Has reproduction · 86

  DP thymocytes can be classified into blast, rearrangement, and selection subtypes, distinguishable by surface markers CD2 and Ly6d

  thymocytes sorted thymocyte scrna-seq flow immunofluorescence

• Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

  PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 59

  Short-term stress and long-term adaptations share common metabolic pathways

  great embryonic gef mapk1 bulk gene transcription

• 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

  Full-text index only

  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

• F-SNP: computationally predicted functional SNPs for disease association studies.

  PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

  Full-text index only

  F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

  genome protein-coding genomic genome-wide non-synonymous exonic nonsense

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• Given the complexity of the human genome, can 'personalised medicine' or 'individualised drug therapy' ever be achieved?

  PMID 19706359 · PMC3525196 · Human genomics · 2009 · 7 claims · 3 setups

  Full-text index only

  The human genome is far too complex, given current understanding, for personalised medicine or individualised drug therapy to be realised in the near term

  populations genome genome-wide genome

• 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

• Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

  PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

  Full-text index only

  MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

  macrorna sequence comparative mouse-human population