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).

• What makes species unique? The contribution of proteins with obscure features.

  PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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  POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

  eukaryotic animal cerevisiae homo hmmpfam blast tblastn

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members were identified in the wheat genome and classified into six phylogenetic groups

  triticum taiqd wheat rice genome-wide phylogenetic gene

• POCUS: mining genomic sequence annotation to predict disease genes.

  PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

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  Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

  omim genome disease comparative pocus expression-id

• Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

  PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 8 claims · 8 setups

  Has reproduction

  114 CNGC genes were identified across the genomes of four cotton species (G. arboreum, G. raimondii, G. barbadense, G. hirsutum)

  arboreum cotton hirsutum ghcngc genome-wide phylogenetic gene

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

  PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups

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  P. falciparum encodes substantially more membrane transport proteins than originally annotated

  falciparum genome-wide bioinformatic quantification

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• The integrated world of functional genomics.

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

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  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

• Identity rather than 3D position informs splicing of rare introns in the human genome.

  PMID 41561379 · PMC12814444 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 98

  Rare intron classes (minor, minor-like, hybrid, non-canonical) are largely dispersed across the linear human genome, with only two notable clusters (GBP on chr1, TSPY on chrY)

  reference genome k562 computational genome-wide chromomap hi-c

• Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

  PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

  genome genomic kinase psi-blast comparative genscan

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• Patterns of evolutionary constraints on genes in humans.

  PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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  BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

  mammalian hapmap panther significant comparative population chi-square

• Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

  PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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  Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

  family p2ry5 affected snp microsatellite sanger

• Protein structure and function by the sea.

  PMID 11983051 · PMC139342 · Genome biology · 2002 · 8 claims · 8 setups

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  High-throughput structural genomics (X-ray crystallography and NMR) can rapidly expand the number of solved protein structures far beyond what is currently in the Protein Data Bank.

  proteins membrane proteasome bacterial high-throughput electron x-ray

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

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

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  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

• The UCSC Proteome Browser.

  PMID 15608236 · PMC540054 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  The UCSC Proteome Browser is tightly integrated with the UCSC Genome Browser, giving users simultaneous access to genome and proteome data.

  swiss-prot sequence domain isoelectric

• Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

  PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

  Has reproduction · 67

  Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

  vibrio coli anguillarum transposon-insertion conjugative functional

• Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

  PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction · 58

  SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

  rms rh4 h3k27ac pooled chip-seq

• Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates.

  PMID 16620374 · PMC1464127 · BMC genomics · 2006 · 8 claims · 6 setups

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  Syndecan-encoding sequences are present in Cnidaria and throughout the Bilateria, showing deep conservation of the family.

  invertebrate syndecan full-length chicken wu-blastp clustalw tcoffee

• Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

  PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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  Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

  serous same lmp braf-mutant gene hotspot erbb2