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).

• Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

  PMID 17335570 · PMC1828162 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  An initial diversification of bHLHs occurred in the pre-Cambrian, prior to metazoan cladogenesis

  metazoan identified amphimedon nematostella genome sequence gene

• Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

  PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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  Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

  hgmd refseq aligned svm svm reciprocal inter-species

• RPS4Y gene family evolution in primates.

  PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

  primate chromosomes rps4x concatenated pcr fluorescence repeat

• The Proteomics Identifications database: 2010 update.

  PMID 19906717 · PMC2808904 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  PRIDE has become one of the main repositories for MS-based proteomics data, with substantial growth in data holdings over the last two years.

  species plasma caenorhabditis secretory ms-based quantitative

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk

• Eight previously unidentified mutations found in the OA1 ocular albinism gene.

  PMID 16646960 · PMC1468396 · BMC medical genetics · 2006 · 7 claims · 5 setups

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  Sequencing of the nine OA1 exons in 72 individuals identified ten different mutations across seven unrelated families and three sporadic cases.

  genomic oa1 direct long-range splice-site

• Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

  PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups

  Has reproduction · 100

  NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.

  garlic pepper pear grapevine rna-seq mrna-seq transcriptome

• Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

  PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

  aspergillus circularized core orthologous mitogenome read organellar

• Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.

  PMID 15799778 · PMC1080126 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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  Dart shooting introduces an allohormone that inhibits digestion of donated sperm, increasing the amount reaching the spermathecae and fertilizing eggs, thereby manipulating the mating partner's sperm storage.

  dart-possessing same land cantareus 28s shimodaira-hasegawa principal

• Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

  PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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  BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

  genomic unrelated best1 best1-4 direct chromosome pathogenicity

• Mutation analysis of SLC26A4 in mainland Chinese patients with enlarged vestibular aqueduct.

  PMID 19786220 · PMC3309400 · Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery · 2009 · 7 claims · 5 setups

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  SLC26A4 mutations are highly prevalent in Chinese patients with SNHL and EVA, with mutations found in 100% (32/32) of subjects.

  blood-derived subjects mutation pure high-resolution

• A Reference DNA Barcode Library for UK Fungi associated with Bark and Ambrosia Beetles.

  PMID 41022899 · PMC12480477 · Scientific data · 2025 · 6 claims · 6 setups

  Has reproduction · 44

  A reference DNA barcode library of fungi associated with over 1000 UK bark and ambrosia beetles (25 native Scolytinae species) was generated, yielding 5274 identified fungal OTUs.

  bark sites sequencing fungal its2 passive sequence

• Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

  PMID 16034026 · PMC1179734 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  L1 insertions are directly responsible for genomic deletions (L1IMDs) confirmed in both human and chimpanzee genomes

  hg16 genomic individuals element computational pcr pcr-based

• Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

  PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

  otx sea elegans endo16 windowed reporter comparative

• 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

• Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

  PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups

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  Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.

  blood schizophrenia sjl serum proteomic differential comparative

• Exome sequencing identifies the cause of a mendelian disorder.

  PMID 19915526 · PMC2847889 · Nature genetics · 2010 · 8 claims · 7 setups

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  Exome sequencing of a small number of unrelated affected individuals, combined with filtering against public SNP databases and HapMap exomes, is sufficient to identify the causal gene for a monogenic disorder of unknown etiology.

  patients chromosomes dhodh utero exome directed sanger

• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

  PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

  genome random cd4+ six average mutual chip-seq

• 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

• Mutation screening of HSF4 in 150 age-related cataract patients.

  PMID 18941546 · PMC2569895 · Molecular vision · 2008 · 8 claims · 4 setups

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  Five new HSF4 sequence variants (c.1020-25G>A, c.1078A>G, c.1223C>T, c.1256+25C>T, c.1286C>T) were found in age-related cataract patients but not in 220 controls.

  peripheral hsf4b hsf4 genomic secondary sequence