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).

• Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

  PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

  postmortem genes gene proteins microarray protein-protein hierarchical

• Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

  PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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  Current syndromic disease classification lacks specificity despite historically serving clinicians well

  prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene

• Association of the SerCys DISC1 polymorphism with human hippocampal formation gray matter and function during memory encoding.

  PMID 19046394 · PMC2865560 · The European journal of neuroscience · 2008 · 8 claims · 5 setups

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  Individuals homozygous for the DISC1 Ser allele show greater HF (parahippocampal) gray matter volume than Cys allele carriers

  healthy extracted voxel-based task psychophysiological

• Seeded Bayesian Networks: constructing genetic networks from microarray data.

  PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

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  Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

  leukemia interactome pubmed-indexed computational microarray yeast literature

• PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.

  PMID 18487273 · PMC2447794 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  PolySearch supports more than 50 different classes of queries against nearly a dozen types of text, abstract, or bioinformatic databases

  manually biomedical text feature real-life

• Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

  PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

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  NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

  cancer proteome pten genome orthology protein-protein

• A new paradigm for MAPK: structural interactions of hERK1 with mitochondria in HeLa cells.

  PMID 19847302 · PMC2760858 · PloS one · 2009 · 8 claims · 8 setups

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  hERK1 translocates to the mitochondria of HeLa cells upon a proliferative stimulus

  hela confocal immunofluorescence western

• Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

  PMID 19844207 · PMC2797562 · Molecular psychiatry · 2010 · 8 claims · 7 setups

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  rs1344706 in ZNF804A is associated with schizophrenia in the Irish ICCSS sample, replicating the original Cardiff finding

  irish iccss postmortem genomic snp haplotype logistic

• Point mutations in GLI3 lead to misregulation of its subcellular localization.

  PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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  The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

  hela immunofluorescence real-time luciferase

• Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

  PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

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  A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

  macrophage hela vaccinia bacillus gene protein-protein comparative

• Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.

  PMID 19638617 · PMC2889494 · Science signaling · 2009 · 8 claims · 6 setups

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  Pathway reconstruction can be modeled as a prize-collecting Steiner tree problem, balancing penalties for excluding terminal nodes against costs for including edges, controlled by a parameter β.

  saccharomyces phosphoproteomic expression curated

• Protein co-evolution, co-adaptation and interactions.

  PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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  The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

  nuoe intra-protein coli interacting phylogenetic correlated domain-restricted

• Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.

  PMID 18676414 · PMC2639365 · International journal of epidemiology · 2009 · 7 claims · 2 setups

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  Conventional power calculations for case-control studies disregard analytic complexity (e.g. clinical assessment errors, unmeasured aetiological determinants) and can seriously underestimate true sample size requirements

  simulated simulation-based simulated

• Detecting tipping points of complex diseases by network information entropy.

  PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 78

  NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data

  real stringdb individual genes network background sample-specific

• Phenotypic variation meets systems biology.

  PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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  Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

  thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing

• Plexin B3 promotes neurite outgrowth, interacts homophilically, and interacts with Rin.

  PMID 16122393 · PMC1215486 · BMC neuroscience · 2005 · 8 claims · 8 setups

  Has reproduction

  Plexin B3 strongly and plexin B2 moderately stimulate neurite outgrowth of primary murine cerebellar neurons

  cos-7 cerebellar nih-3t3 yeast northern western situ

• Genetic Variants in ARHGEF6 Cause Congenital Anomalies of the Kidneys and Urinary Tract in Humans, Mice, and Frogs.

  PMID 36414417 · PMC10103091 · Journal of the American Society of Nephrology : JASN · 2023 · 7 claims · 7 setups

  Has reproduction · 85

  Hemizygous variants in the X-linked gene ARHGEF6 cause X-linked CAKUT in humans

  international kidney expressing madin-darby exome cdc42 lamellipodia

• The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

  PMID 30899024 · PMC6428865 · Nature communications · 2019 · 7 claims · 8 setups

  Has reproduction · 85

  Xrn1 promotes translation of a specific group of mRNAs encoding membrane/secretome proteins, acting at translation initiation.

  cerevisiae yeast xrn1∆ western luciferase polysome

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms

  pubmed invasive geo genes semantic computational gene

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 8 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share a transcriptional overlap of 239 unique common differentially expressed genes (DEGs), 237 of which are up-regulated

  patients pbmcs plasma derived bulk single-cell quantitative