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).

• Reference based annotation with GeneMapper.

  PMID 16600017 · PMC1557983 · Genome biology · 2006 · 7 claims · 6 setups

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  GeneMapper transfers reference gene annotations to target genomes with higher accuracy than GeneWise and Projector

  orthologous human-mouse chicken encode reference-based multi-species reciprocal

• Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

  PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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  ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

  paralogous human-mouse duplicated comparative ortholog binomial

• A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

  PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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  SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

  bac kidney genomic marathon genomic cdna pcr

• Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

  PMID 15809229 · PMC1074396 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Comparative gene finding (SGP2) between human and chicken, followed by RT-PCR verification, adds at most ~0.2% new genes to the multi-exonic human gene catalog

  chicken predicted human-chicken cdna comparative blastp pairwise

• Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

  PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

  hg18 zebrafish bystander human-mouse comparative synteny orthologous

• Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

  PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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  Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

  chicken comparative amino phylogenetic

• 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

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• Organismal complexity, cell differentiation and gene expression: human over mouse.

  PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

  human-mouse oligonucleotide exon comparative

• Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

  PMID 18334962 · PMC2268858 · Molecular vision · 2008 · 8 claims · 4 setups

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  Two MYOC sequence variants were identified in Japanese POAG patients: a novel non-synonymous variant p.Gln297His and a previously reported variant p.Ala363Thr.

  genomic myoc poag pcr amino clinical

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

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

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  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

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read

• Discovering cancer genes by integrating network and functional properties.

  PMID 19765316 · PMC2758898 · BMC medical genomics · 2009 · 8 claims · 6 setups

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  Cancer genes have distinct PPI network topology (higher connectivity, higher clustering coefficient, shorter path length to known cancer genes) compared to non-cancer genes

  genes gene colon ppi pfam term

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

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

  Has reproduction · 91

  Assembled the first chromosome-level genome of G. vermiculophylla: 77.5 Mb, 22 pseudochromosomes, contig N50 2.61 Mb, scaffold N50 3.16 Mb

  vermiculophylla assembled predicted genome short-read nanopore hi-c

• Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43.

  PMID 34647802 · PMC8515887 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

  Has reproduction · 88

  The complete, chromosome-scale genome sequence of Porcisia hertigi (isolate C119, strain LV43) was assembled using combined short- and long-read sequencing technologies.

  porcisia hertigi parasite extraction short-read