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 excess of 5' introns in eukaryotic genomes.

  PMID 16314314 · PMC1292992 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  All 21 eukaryotic genomes studied show a statistically significant 5′-biased distribution of introns in protein-coding genes

  eukaryotic same housekeeping comparative chi-square bidirectional

• EGASP: Introduction.

  PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups

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  Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.

  genome computational manual rt-pcr

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 7 setups

  Has reproduction · 77

  HIV-1 recurrently integrates into genes that are proximal to super-enhancer (SE) genomic elements in both patients and in vitro T cell cultures.

  activated cd4+ cd3 uninfected hiv-1 chip-seq rna-seq

• Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

  PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups

  Has reproduction · 91

  A chromosome-level genome assembly of G. vermiculophylla was generated by combining DNBSeq short reads, Nanopore long reads, and Hi-C data.

  gracilaria whole-genome nanopore hi-c

• geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

  PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 4 setups

  Has reproduction · 75

  geneshot is a gene-level metagenomic bioinformatics tool that clusters de novo assembled protein-coding genes into co-abundant gene groups (CAGs) to reduce dimensionality and generate testable hypotheses from WGS microbiome data

  stool deduplicated reference whole-genome taxonomic functional

• The DNA sequence of the human X chromosome.

  PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

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  The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

  pac selected chromosome clone-based shotgun comparative

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

  PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

  est unannotated trans-sa tus computational coding hybridization

• G-quadruplexes: the beginning and end of UTRs.

  PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

  genome 5'-utr simulated protein-coding computational high-resolution utr

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

  PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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  41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

  genome transcriptome gene genes full-length genome cdna

• Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.

  PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups

  Has reproduction · 92

  A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)

  panax ginseng whole-genome genome rna-seq

• Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

  PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

  genome chimpanzee pseudogenes genomic megablast blat sequence

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence

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

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

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  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

• Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

  PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups

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  Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99

  ulcerans collection snp whole-genome comparative read

• Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

  PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome

  genome transcripts tissues proteins comparative taf250 cpg