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 post-genomic era for a select few.

  PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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  The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

  takifugu physcomitrella coli vibrio comparative genetic dna-microarray

• Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.

  PMID 17982171 · PMC2238866 · Nucleic acids research · 2008 · 6 claims · 5 setups

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  StellaBase Disease houses homology data for 155,904 invertebrate isoforms of human disease genes across four model systems, including 14,874 predicted Nematostella genes

  nematostella blastp est snp

• Genomics: applications in mechanism elucidation.

  PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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  Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

  extract panel saccharomyces inbred affinity cytotoxicity genome-wide

• Mutations in UCP2 in congenital hyperinsulinism reveal a role for regulation of insulin secretion.

  PMID 19065272 · PMC2588657 · PloS one · 2008 · 6 claims · 5 setups

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  Heterozygous UCP2 coding variants (parentally inherited) were identified in 2 of 10 CHI patients with no mutations in known CHI genes

  peripheral saccharomyces yeast ins-1e dhplc proton western

• Information-based methods for predicting gene function from systematic gene knock-downs.

  PMID 18959798 · PMC2596148 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  Information-based metrics, which incorporate a phenotype's genomic frequency, outperform non-information-based metrics for detecting gene-gene functional similarity from phenotypic knock-down profiles.

  caenorhabditis elegans saccharomyces interference computational genome-wide

• Genetical genomics: spotlight on QTL hotspots.

  PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

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  Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

  adipose saccharomyces genome-wide permutation gene

• A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

  PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

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  Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

  genes hela proteins worm co-expression quantitative functional

• Repeatability of gene expression evolution in experimental environmental adaptation.

  PMID 41587990 · PMC12946262 · Nature communications · 2026 · 6 claims · 8 setups

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  Gene expression evolution during experimental adaptation is far more repeatable across replicate populations than expected by chance, whether measured by shared DEGs, shared direction of change, or shared direction plus magnitude of change

  coli yeast fly copepod microarray rna-seq

• The limits of reductionism in medicine: could systems biology offer an alternative?

  PMID 16681415 · PMC1459480 · PLoS medicine · 2006 · 8 claims · 3 setups

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  Reductionist medical science (focus on singular causal factors, homeostasis-as-normal-range, one-risk-factor epidemiology, additive treatment of comorbidities) has inherent limitations for explaining complex disease behavior

  escherichia population genome mathematical epidemiological genome

• Mutations of the mitochondrial holocytochrome c-type synthase in X-linked dominant microphthalmia with linear skin defects syndrome.

  PMID 17033964 · PMC1698567 · American journal of human genetics · 2006 · 7 claims · 4 setups

  Has reproduction · 75

  Heterozygous de novo point mutations in HCCS (missense p.R217C and nonsense p.R197X) cause X-linked dominant MLS in females with normal karyotypes

  patients family saccharomyces cho-k1 mutation deletion yeast

• Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters.

  PMID 11897022 · PMC139022 · Genome biology · 2002 · 8 claims · 8 setups

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  Trans-splicing generates cell-specific protocadherin mRNAs in human neurons

  individual cancer pre-b saccharomyces reverse-transcriptase karyotypic spectral

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• Translating genome sequences into biological understanding.

  PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups

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  Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.

  embryonic transfectable drosophila computational gene-trap pooled cross-species

• Mutations associated with HNPCC predisposition -- Update of ICG-HNPCC/INSiGHT mutation database.

  PMID 15528792 · PMC3839397 · Disease markers · 2004 · 8 claims · 4 setups

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  The ICG-HNPCC/INSiGHT mutation database has grown from 126 predisposing mutations (1997) to 448 mutations occurring in 748 families (2003 update)

  hnpcc tumor yeast families germline microsatellite functional

• The lords of the genomes.

  PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups

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  Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them

  drosophila cdna-derived saccharomyces acid reporter-gene enhancer chromatin

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

  PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

  uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain

• GenBank.

  PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

  sapiens organisms genbank large-scale genome expressed blast

• Defining the proteome.

  PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups

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  Integration of multi-omics data is an important step toward a systems-biology approach to the proteome

  brain chicken bacillus yeast proteome proteomics two-dimensional

• A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length.

  PMID 38638702 · PMC11025885 · NAR genomics and bioinformatics · 2024 · 8 claims · 7 setups

  Has reproduction · 98

  Ribosome drop-off events occur at a significant rate in S. cerevisiae cultured in standard conditions

  cerevisiae ribo-seq ribosome rna-seq read

• From genomes to systems.

  PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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  Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

  serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr