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).

• The lords of the genomes.

  PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them

  drosophila cdna-derived saccharomyces acid reporter-gene enhancer chromatin

• The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

  PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

  genome drosophila transfac b99 profile sequence case-study

• Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

  PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

  Full-text index only

  eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

  drosophila caenorhabditis xenopus five pairwise evoprint comparison

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative

• Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

  PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes

  melanogaster dgrp drosophila genes bulk locomotor gene

• Identifying cis-regulatory sequences by word profile similarity.

  PMID 19730735 · PMC2731932 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  WPH-finder identifies putative co-regulated CRMs by scanning the genome for sequences with word profiles similar to a known CRM, without explicitly defining binding sites

  stripe pair-rule nrsf-bound eve genome-wide chip-chip chip-seq

• Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

  PMID 18257909 · PMC2374702 · Genome biology · 2008 · 8 claims · 3 setups

  Full-text index only

  Compiled a list of 120 core presynaptic gene prototypes (PS120) and catalogued their conservation across insect proteomes.

  insect vamp2 ps120 comparative sequence protein-protein

• 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

• Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

  PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

  Full-text index only

  Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

  gria2 drosophila nova1 cd45 splicing sirna hits-clip

• A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

  PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 6 claims · 8 setups

  Has reproduction · 76

  Hnf4a is a major transcriptional regulator of Dnajc22.

  mus tissues liver-specific kidney bulk microarray chip-seq

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• Comprehensive splice-site analysis using comparative genomics.

  PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

  Full-text index only

  Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

  refseq u2-type genes comparative information phylogenetic

• Sequencing the regulatory genome.

  PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

  interphase nine beta-globin drosophila nuclear digital chip

• Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

  PMID 36373634 · PMC9723646 · Nucleic acids research · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells (OSCs)

  drosophila ovarian osc melanogaster chip-seq sirna western

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

  Full-text index only

  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic

• Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.

  PMID 41345108 · PMC12789597 · Nature communications · 2025 · 7 claims · 8 setups

  Has reproduction · 93

  SIRT6 is an evolutionarily conserved regulator of tryptophan catabolism that balances tryptophan usage between the kynurenine and serotonin/melatonin pathways

  embryonic brains sirt6 serum untargeted rna-seq microarray

• Database resources of the National Center for Biotechnology Information.

  PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

  genbank genomic eukaryotic completely sequence rapid est