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 gene interactions associated with disease from gene expression data using synergy networks.

  PMID 18234101 · PMC2258206 · BMC systems biology · 2008 · 8 claims · 4 setups

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  Synergy of a gene pair with respect to disease, defined as I(G1,G2;C) - [I(G1;C)+I(G2;C)], identifies gene pairs that interact cooperatively with respect to a phenotype rather than independently.

  prostate simulated microarray simulated permutation

• Vector algebra in the analysis of genome-wide expression data.

  PMID 11897023 · PMC88809 · Genome biology · 2002 · 8 claims · 6 setups

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  The angle θ between expression (experiment) vectors is the geometric counterpart of the Pearson correlation coefficient r, providing a rigorous measure of similarity between profiles.

  saccharomyces microarray

• An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

  PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

  osteoarthritic articular chondrocyte microarray computational high-throughput

• Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.

  PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups

  Has reproduction · 71

  Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.

  breast colorectal brca representative gene comparative multi-omic

• Sources of variability and effect of experimental approach on expression profiling data interpretation.

  PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups

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  Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling

  skeletal muscle spleen myogenic affymetrix duplicate unsupervised

• 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

• A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

  PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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  Expression context is largely conserved between orthologs across four eukaryote species.

  elegans pairwise orthologs cerevisiae microarray ortholog functional

• Application of functional genomics to primate endometrium: insights into biological processes.

  PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

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  Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

  endometrial uterus whole-genome cdna oligonucleotide

• Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

  PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction

  SDSD constitutes a distinct taxonomic entity within S. dysgalactiae, with a mean intra-subspecies average nucleotide identity of 99%.

  dysgalactiae sdse sdsd isolates genome multilocus pangenome

• Geographical genomics of human leukocyte gene expression variation in southern Morocco.

  PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

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  Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.

  peripheral blood genotype randomly genome-wide population admixture

• PubMatrix: a tool for multiplex literature mining.

  PMID 14667255 · PMC317283 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  PubMatrix is a web-based CGI tool that queries PubMed with two lists of terms (search terms vs modifier terms) and returns a matrix of pairwise co-occurrence frequency counts

  pubmed ovarian genome literature cdna

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• TFBScluster web server for the identification of mammalian composite regulatory elements.

  PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

  imr90 tissues dog transgenic microarray-based gene

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based

• From single cells to whole organisms.

  PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

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  The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

  saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species

• 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

• Human genetics branches out in Barcelona.

  PMID 18710599 · PMC2575509 · Genome biology · 2008 · 8 claims · 8 setups

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  A meta-analysis of three GWAS scans (DIAGRAM) identifies new type 2 diabetes susceptibility loci (JAZF1, CDC123/CAMK1D, ADAMTS9, THADA) with modest individual effect

  patients families lymphoblastoid genome genome-wide gwas genetic

• CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

  PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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  CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

  cd4+ hela imr90 embryonic chip-seq computational gene

• 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