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).

• Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

  PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

  redundant mammalian genomic vertebrates blast pattern-hit tblastn

• Simple models of genomic variation in human SNP density.

  PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

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  Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

  genome observed simulated genome hierarchical coalescent

• Genetic distance and heterogenecity between quasispecies is a critical predictor to IFN response in Egyptian patients with HCV genotype-4.

  PMID 17300723 · PMC1805740 · Virology journal · 2007 · 7 claims · 7 setups

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  Genetic distance and heterogeneity between HCV quasispecies is a critical predictor of IFN response in Egyptian genotype-4 patients

  serum pcr cloned 5'utr rt-pcr molecular sequencing

• PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

  PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

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  PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

  natural aligned ns3 denv sequence pcp-consensus physicochemical

• 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

• Use of modified U1 snRNAs to inhibit HIV-1 replication.

  PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

  hiv-1 293t hela bioinformatic western reporter

• PigGIS: Pig Genomic Informatics System.

  PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

  million pig matched wgs blastx repeat sequence

• Conservation, variability and the modeling of active protein kinases.

  PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

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  A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

  active-conformation same chak rio2 sequence-order pairwise structural

• Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

  PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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  14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

  h3n2 meme sequence entropy

• SARS-CoV genome polymorphism: a bioinformatics study.

  PMID 16144519 · PMC5172477 · Genomics, proteomics & bioinformatics · 2005 · 8 claims · 6 setups

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  SARS-CoV isolates can be classified into groups/subgroups based on the number and distribution of SNVs and INDELs relative to a 'profile' sequence, and this classification aligns with phylogenetic tree relationships and epidemiological spread.

  sars-cov annotated spike whole-genome positional codon

• TFBScluster web server for the identification of mammalian composite regulatory elements.

  PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

  imr90 tissues dog transgenic microarray-based gene

• BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.

  PMID 17965094 · PMC2238987 · Nucleic acids research · 2008 · 7 claims · 5 setups

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  BioHealthBase BRC is a public integrated bioinformatics database and analysis resource for influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin.

  avian pb2 dkxi35 ns1 sequence genome t-cell

• Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

  PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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  A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

  primate hepg2 32p-labeled sequence rt-pcr luciferase

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 8 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign is the first RNA sequence/structure pairwise alignment algorithm based on incremental ensemble mountain distance, running in O(n^3) time and O(n^2) space for two sequences of length n.

  sequences sequence trna target pairwise global single

• Ab initio identification of putative human transcription factor binding sites by comparative genomics.

  PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

  human-mouse conserved gene consensus comparative statistical gene

• U7 snRNAs: a computational survey.

  PMID 18267300 · PMC5054213 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 6 setups

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  A computational (BLAST-based) survey identified bona fide U7 snRNA genes with characteristic upstream promoter elements (PSE) across most vertebrate genomes examined, plus numerous pseudogenes.

  mammalian drosophilid aligned basal blast sequence consensus

• Developments in CORG: a gene-centric comparative genomics resource.

  PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

  upstream gene overlapping c-fos pairwise sequence comparative

• Ensembl's 10th year.

  PMID 19906699 · PMC2808936 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  Ensembl provides comprehensive gene annotation and integrated genomic resources (variation, regulation, comparative genomics) across a growing set of chordate genomes

  anole western genome cd4+ whole-genome gene cross-database

• A third approach to gene prediction suggests thousands of additional human transcribed regions.

  PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

  genome 4.4-mb known nucleotide repeat polyadenylation

• 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