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).

• 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

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

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

  Full-text index only

  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

• 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

• Promoting human promoters.

  PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

  Full-text index only

  A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

  gene liver cycle genes computational expression time-course

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna

• The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease.

  PMID 38839750 · PMC11153611 · Nature communications · 2024 · 8 claims · 8 setups

  Has reproduction · 70

  Intestinal epithelial cell-specific deletion of Slc39a8 causes systemic manganese (Mn) deficiency in blood and multiple organs.

  c57bl frozen tissues slc39a8-iec qpcr immunofluorescence icp-ms

• 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

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• 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

• 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

  Full-text index only

  Current syndromic disease classification lacks specificity despite historically serving clinicians well

  prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data.

  PMID 17204155 · PMC1774579 · BMC bioinformatics · 2007 · 6 claims · 5 setups

  Full-text index only

  FLAME captures non-linear relationships and non-globular clusters by approximating fuzzy membership from each object's nearest neighbors rather than global centroids

  reduced yeast hypoxia tissues microarray gene

• Machine learning-based DNA microarray analysis for disease detection using the MICRO-AI framework.

  PMID 41925147 · PMC13051084 · Science progress · 2026 · 8 claims · 1 setups

  Has reproduction · 22

  MICRO-AI's attention-weighted feature fusion reduces dimensionality by over 99% (from ~20,000 to ~127 genes) without loss of biological significance

  breast microarray

• 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

  Full-text index only

  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

• 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

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• Genome Network and FANTOM3: assessing the complexity of the transcriptome.

  PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

  fantom3 genome large-scale mammalian cage full-length genome

• Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

  PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

  user-supplied ranked gene fasta-formatted functional gene novo

• Visualization-based discovery and analysis of genomic aberrations in microarray data.

  PMID 15953389 · PMC1181623 · BMC bioinformatics · 2005 · 8 claims · 7 setups

  Full-text index only

  ChARMView integrates dynamic visualization with automated statistical analysis (EM-based breakpoint detection, one-sample sign test, permutation mean test) to discover chromosomal aberrations from array CGH and gene expression data

  saccharomyces breast yeast array gene

• 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