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).

• Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

  PMID 18598366 · PMC2474618 · BMC bioinformatics · 2008 · 7 claims · 6 setups

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  Experimentally measured protein-protein interaction sub-networks are not random samples of their parent networks.

  yeast drosophila networks dppi reanalysis computer repeated

• 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

• A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.

  PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 8 claims · 5 setups

  Has reproduction · 78

  A comprehensive genome-wide gene regulatory network resource for A. fumigatus (GRAsp) was constructed from 18 RNA-seq datasets using MERLIN-P-TFA.

  aspergillus fumigatus bulk computational chip-seq-based

• Integrative network modeling reveals mechanisms underlying T cell exhaustion.

  PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 6 setups

  Has reproduction · 59

  An integrative, literature-curated and data-driven gene regulatory network underlies CD8+ T cell exhaustion and accurately captures expression states in chronic infection and tumor settings.

  cd8+ tce activated manual gene principal

• Oligomeric protein structure networks: insights into protein-protein interactions.

  PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

  non-redundant same known complexes structure hub comparison

• Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

  PMID 18053250 · PMC2246260 · Genome biology · 2007 · 8 claims · 4 setups

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  Loss-of-function phenotypes in yeast are predictable from a gene's connections in a functional gene network via guilt-by-association.

  saccharomyces guilt-by-association comparison network-guided

• The 32nd Annual Congress of the Society of Critical Care Medicine, 28 January - 2 February 2003, San Antonio, USA.

  PMID 12720569 · PMC270663 · Critical care (London, England) · 2003 · 8 claims · 8 setups

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  Proteomics is more useful than genomics for identifying regulatory pathways and druggable targets in disease because transcriptional responses to different stimuli often converge while protein interaction networks reveal distinct regulatory nodes

  macrophages patients animal ards gene histological mechanical

• Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

  PMID 19073697 · PMC2632920 · Nucleic acids research · 2009 · 8 claims · 5 setups

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  Combining high protein-interaction network scores with significant PID-related GO terms identifies novel PID candidate genes

  immunome known protein-interaction gene comparative

• 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

• Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer.

  PMID 33729159 · PMC8012062 · eLife · 2021 · 7 claims · 6 setups

  Has reproduction · 94

  Discrete (Boolean/Ising) and continuous (RACIPE) simulations of the SCLC regulatory network yield similar multistable phenotypic distributions, with four dominant steady states (X1-X4) that map onto experimentally observed SCLC molecular subtypes.

  sclc randomized mutant boolean racipe network

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

• YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

  PMID 15929789 · PMC1175843 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  YANA integrates METATOOL to provide a graphical, platform-independent front-end for editing, calculating, visualizing, and comparing elementary flux modes, with SBML support.

  redox elementary flux evolutionary

• Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

  PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

  Has reproduction · 88

  Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

  arabidopsis deg promoter selected meta-analysis transcription hexamer

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  H. caudiculatum (lower canopy) exhibits about twice as many differentially expressed genes as H. dentatum (upper canopy), with a higher proportion of both increased and decreased gene abundance during dehydration.

  hymenophyllum dark-adapted annotated differentially bulk relative chlorophyll

• miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.

  PMID 34637468 · PMC8509996 · PloS one · 2021 · 7 claims · 6 setups

  Has reproduction · 100

  RBPs beyond Drosha/DGCR8/Dicer are involved in regulating miRNA biogenesis and explain its spatio-temporal nature

  tissues computational rbps clip-seq rna-seq srna-seq

• Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.

  PMID 35726533 · PMC9542029 · Molecular ecology · 2022 · 7 claims · 8 setups

  Has reproduction · 93

  Italian sparrow testis exhibits extensive transgressive gene expression relative to both parental species

  testis ovary house differentially bulk gene protein-protein

• Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

  PMID 24715956 · PMC3962008 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 67

  Cyrface is a Cytoscape app/Java library providing a general interface from Cytoscape (Java) to any R function or package.

  cytoscape generated prior-knowledge iris software datarail logic

• Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

  PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

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  Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

  coli cerevisiae comparative machine single-gene

• 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

• Predicting position along a looping immune response trajectory.

  PMID 30296270 · PMC6175499 · PloS one · 2018 · 8 claims · 5 setups

  Has reproduction · 98

  Looper is an automated computational method that identifies gene pairs that trace looping trajectories when plotted against each other in longitudinally sampled data

  monocytes blood pbmcs montreal microarray qrt-pcr topological