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).

• pmid-41890963

  PMID 41890963 · PMC13014971 · 8 claims · 7 setups

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  Dauers induced by different environmental (starvation, pheromone, heat) or genetic (daf-2, daf-7, ilc-17.1, cep-1 OE) stimuli are transcriptionally distinct from each other and from continuously developing WT L2/L3 and adults

  elegans bulk principal likelihood

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

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  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna

• SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

  PMID 18315851 · PMC2259403 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  SNP@Promoter is a database of human SNPs within putative promoter regions and predicted transcription factor binding sites

  genome predicted target computational snp evolutionary

• Genome sequences and great expectations.

  PMID 11178275 · PMC150431 · Genome biology · 2001 · 8 claims · 3 setups

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  Function is known or can be predicted for an average of 62% of proteins across 31 analyzed genomes.

  complete annotated haemophilus automated benchmarking temporal

• A golden age of brain exploration.

  PMID 15660159 · PMC544547 · PLoS biology · 2005 · 8 claims · 3 setups

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  Over 99% of neuroscience literature focuses on only 1% of the ~15,000–16,000 genes expressed in the brain, leaving most brain-expressed genes uncharacterized.

  brain transgenic situ microarray bacterial

• TRED: a transcriptional regulatory element database, new entries and other development.

  PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups

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  TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes

  cancer-related computational literature database

• Subfunctionalization of duplicated genes as a transition state to neofunctionalization.

  PMID 15831095 · PMC1112588 · BMC evolutionary biology · 2005 · 8 claims · 2 setups

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  Subfunctionalization plays an important role in duplicate gene retention but functions as a transition state leading to neofunctionalization rather than as a terminal fate.

  model lattice

• Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

  PMID 16549007 · PMC1544357 · BMC bioinformatics · 2006 · 7 claims · 2 setups

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  A methodology combining Cox proportional hazards models with a compound covariate, cross-validated log partial likelihood (ACVL) for predictive accuracy, and permutation-based significance testing can identify an optimal subset of significant genes for survival prediction

  simulated diffuse simulation cdna

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

  Has reproduction · 53

  spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

  bistable three-gene emt circuits simulation mixed-state grn

• Systems biology of SNPs.

  PMID 16820779 · PMC1681509 · Molecular systems biology · 2006 · 8 claims · 2 setups

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  Co-sets are groups of enzymatic reactions that are perfectly correlated (correlation coefficient of 1) in a reconstructed metabolic network and represent functional modules.

  mitochondrial genome-scale database

• Vibrio cholerae pathogenic clones.

  PMID 16318732 · PMC3367346 · Emerging infectious diseases · 2005 · 8 claims · 1 setups

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  The US Gulf clone, the Australian clone, and 3 prepandemic El Tor strains are related to the seventh pandemic clone.

  vibrio multilocus

• The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements.

  PMID 18353860 · PMC2377421 · Nucleic acids research · 2008 · 7 claims · 1 setups

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  A large number of upstream PQSSs incorporate the SP1-binding element, establishing a clear link between PQSS occurrence and SP1 elements

  genome genome-wide

• 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

• KEGG for linking genomes to life and the environment.

  PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

  protein-coding newly microarray kegg sequence computational glycan

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat

• Survival analysis with high-dimensional covariates.

  PMID 19654171 · PMC4806549 · Statistical methods in medical research · 2010 · 8 claims · 1 setups

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  The classical Cox proportional hazards model cannot be fit when p >> n because the partial likelihood maximizer is not unique and the matrix X^T A X is singular in the IRLS procedure

  renal gene

• Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

  PMID 19958472 · PMC2788361 · BMC genomics · 2009 · 8 claims · 6 setups

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  88 full paper submissions were peer-reviewed for InCoB2009, with 49 shortlisted for oral presentation and 34 accepted into this BMC Genomics supplement, reflecting an overall acceptance rate of 50% across venues.

  nhe1 cancer mammalian bovine computational microarray quantile

• Olden times: looking back on a career at the NIEHS.

  PMID 15289171 · PMC1247486 · Environmental health perspectives · 2004 · 8 claims · 3 setups

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  Kenneth Olden served 13 years as director of NIEHS and the National Toxicology Program, the first African American to head an NIH institute

  environmentally genome gene microarray transgenic

• Web-based resources for comparative genomics.

  PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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  Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

  yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood

• PI3K inhibitors protect against glucocorticoid-induced skin atrophy.

  PMID 30737086 · PMC6441871 · EBioMedicine · 2019 · 8 claims · 8 setups

  Has reproduction · 76

  Drug repurposing screen of the LINCS transcriptional signature database identified PI3K/mTOR/Akt inhibitors as the most prominent pharmacological class capable of repressing REDD1/FKBP51 expression.

  keratinocytes hacat skin ear computational rt-pcr western