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).

• Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

  PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

  gossypium transcripts uq-normalized differentially comparative coding bulk

• Seasonality of influenza A(H3N2) virus: a Hong Kong perspective (1997-2006).

  PMID 18648550 · PMC2481298 · PloS one · 2008 · 7 claims · 4 setups

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  Influenza A(H3N2) seasonality is largely explained by global viral migration, with similar viruses appearing in different countries at different times

  influenza same hong gene maximum-likelihood protein-coding

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene

• Empirical codon substitution matrix.

  PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

  orthologous million codon same pairwise empirical comparative

• Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

  PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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  The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

  bac heart ccs genomic genomic rt-pcr transcription

• Designating eukaryotic orthology via processed transcription units.

  PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

  ortholog blat exon-intron blast-based

• 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

• Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

  PMID 16336695 · PMC1325232 · Respiratory research · 2005 · 6 claims · 8 setups

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  There is overall little sequence variation in the conserved non-coding elements (CNEs) on 5q31, including none detected in CNE-B/CNS-1

  genomic pcr large outbred comparative denaturing pcr

• Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

  PMID 16179648 · PMC1236720 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Deeply conserved human-zebrafish non-coding elements are enriched for in vivo cis-acting transcriptional regulatory activity.

  ncbi genes zebrafish comparative annotation gfp

• SVC: structured visualization of evolutionary sequence conservation.

  PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

  orthologous exonic tblastx blastn sliding-window

• Dcode.org anthology of comparative genomic tools.

  PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.

  dlx1 hoxa prothrombin gene comparative multi-species phylogenetic

• 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

• Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

  PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

  chromosome genomic comparative phylohmmcons conserved

• Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

  PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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  8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

  unique hmpv sequence neighbor-joining codon

• CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

  PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

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  CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

  genome sequence drosophila novo gene coding

• Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

  PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

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  The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

  turmoil-1 rrm elegans predicted pairwise maximum genome-wide

• In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

  PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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  Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

  strains genomic celera blast-based targeted phred

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• EGenBio: a data management system for evolutionary genomics and biodiversity.

  PMID 17118150 · PMC1683573 · BMC bioinformatics · 2006 · 7 claims · 7 setups

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  EGenBio is a web-based system for integrated management, filtering, curation, and visualization of large-scale genomic sequences, alignments, and phylogenetic trees for evolutionary genomics and biodiversity research.

  vertebrate sequence mutant phylogenetic sequence coevolution saturation

• Vertebrate gene finding from multiple-species alignments using a two-level strategy.

  PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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  DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

  genomic encode entire chromosome multi-species hmm-based classifier