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).

• 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

• Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

  PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 7 claims · 7 setups

  Has reproduction · 71

  HIV-1 and PAH share 109 co-expressed genes primarily enriched in type I interferon (IFN) pathways.

  pbmc shared gene microarray kegg

• Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.

  PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups

  Has reproduction · 74

  Autoencoder networks based on 266 shared DEGs reveal a comorbidity (positive) relationship between Alzheimer's disease and lung cancer.

  brain lung integrated shared microarray differential autoencoder

• Analysis of protein sequence and interaction data for candidate disease gene prediction.

  PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

  ophid biocarta kegg pfam-annotated common benchmarking multiple-interval

• Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

  PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

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  Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

  saccharomyces correlated chip-chip gene

• RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data.

  PMID 42172220 · PMC13196991 · PloS one · 2026 · 8 claims · 8 setups

  Has reproduction · 63

  RAGER integrates widely-used bioinformatics tools into an automated Snakemake-based pipeline for joint analysis of RNA-seq and ATAC-seq data

  embryonic cd34+ shared promoter rna-seq atac-seq gsea

• Dissecting lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.

  PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups

  Has reproduction · 50

  lncRNA-mRNA ceRNA networks differ substantially between control and cytokine-treated islet exosomes, sharing lncRNAs more than mRNAs, implying state-dependent regulatory functions

  pancreatic database-derived plasma saliva sequencing exosome lncrna-mirna

• Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

  PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 75

  All three mouse models (hAβ-KI, 5xFAD, APP/PS1) share more differentially expressed genes, GO biological processes, and KEGG pathways with LOAD than with EOAD patients.

  haβ-ki models degs app bulk functional master

• From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

  PMID 17983265 · PMC2062474 · PLoS computational biology · 2007 · 8 claims · 7 setups

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  There has been a large turnover of the mitochondrial proteome during evolution: cell envelope synthesis proteins virtually disappeared, and replication, transcription, cell division, transport, regulation, and signal transduction proteins were replaced by eukaryotic proteins

  alpha-proteobacterial reclinomonas reconstructed yeast comparative phylogenomic cog

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• WebGestalt: an integrated system for exploring gene sets in various biological contexts.

  PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

  genes gene est-based enrichment kegg

• Polyploidy and the petal transcriptome of Gossypium.

  PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

  Has reproduction · 51

  Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

  petal rna-seq commonly polyploid rna-seq read universal