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).

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome

• 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

• Discovery and characterization of Alu repeat sequences via precise local read assembly.

  PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups

  Has reproduction · 69

  Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads

  hgdp insertion-supporting candidate assembled genome discordant novo

• Recent segmental and gene duplications in the mouse genome.

  PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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  33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

  genome gene ensembl-annotated chromosome pairwise gene blat

• 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

• Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

  PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

  full-length alternative refseq genome pairwise mitochondrial signal

• Mitochondrial diversity within modern human populations.

  PMID 17439969 · PMC1888801 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  Modern humans show extremely low divergence from the mitochondrial consensus sequence, differing on average by only 21.6 nucleotide sites

  full-length mitochondrial mtdna additional sequence site-by-site regional

• Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.

  PMID 18757892 · PMC2553571 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  3'-most (L type) poly(A) sites are more conserved than upstream F/M type sites, while intronic (C/H type) sites are the least conserved

  consensus poly comparative transposable

• Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.

  PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 57

  t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes

  calanus same 11k degs bulk dimensionality differential

• Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

  PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

  Has reproduction · 81

  A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

  lung sequencing assembled deer high-throughput metagenomic reference

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn

• Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

  PMID 18588689 · PMC2474586 · BMC medical genetics · 2008 · 8 claims · 6 setups

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  A region spanning the gene RAI and the 5' portion of XPD is associated with postmenopausal breast cancer

  peripheral genomic genotype independent linkage targeted genotyping

• 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 TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

  PMID 16288651 · PMC1314899 · BMC genomics · 2005 · 8 claims · 6 setups

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  Human genomic DNA sequence can be leveraged to obtain 3' end sequence of NHP orthologs, which can then be used to generate NHP oligonucleotide microarrays

  refseq macaca genomic rhesus exon pcr molecular

• The distribution of SNPs in human gene regulatory regions.

  PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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  SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

  gene mammalian promoter experimentally genome-wide computational binding

• Personalized copy number and segmental duplication maps using next-generation sequencing.

  PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups

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  mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.

  genomes genomic interphase na18507 whole-genome array fluorescence

• Natural clines and human management impact the genetic structure of Algerian honey bee populations.

  PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups

  Has reproduction · 55

  No significant admixture from European subspecies was detected in Algerian honey bees, suggesting large-scale queen imports have not occurred in Algeria.

  apis algerian ld-pruned reference whole-genome read identity-by-descent

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

  PMID 10027313 · PMC2362434 · British journal of cancer · 1999 · 7 claims · 5 setups

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  Allelic distribution of the Cyp19 intron 4 STRP differs significantly between breast cancer cases and controls

  peripheral ceph individuals cases strp genotyping fluorescent