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).

• CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

  PMID 41566196 · PMC12895761 · BMC bioinformatics · 2026 · 6 claims · 6 setups

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  CRESCENT is a Snakemake workflow performing fully automated, comprehensive RNA-Seq analysis integrating differential expression, differential alternative splicing (DAS), differential transcript usage (DTU), and GO enrichment

  arabidopsis bulk rna-seq-based rna-seq

• Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.

  PMID 41578372 · PMC12911049 · Biology of sex differences · 2026 · 8 claims · 8 setups

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  48 tumor-specific sex-biased (TSSB) microRNAs were identified in bladder cancer, mostly located on autosomes rather than sex chromosomes

  tcga tssb blca mirna-seq bulk kegg

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons.

  PMID 34194426 · PMC8236716 · Frontiers in immunology · 2021 · 8 claims · 8 setups

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  Genes in the SRP-dependent cotranslational protein targeting to membrane (ER translocation) pathway and ribosomal subunit genes are strongly and specifically enriched for arginine and lysine residues, suggesting high susceptibility to gingipain cleavage.

  protein-coding coli recombinant postmortem proteome-wide gene gingipain

• Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.

  PMID 41736854 · PMC12927100 · iScience · 2026 · 7 claims · 6 setups

  Has reproduction · 70

  Early-stage (prodromal) aSyn pathology in M83+/+ mouse brainstem is associated with upregulation of ATP/energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)

  sagittal st-derived spatial immunofluorescence cell-cell

• Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes.

  PMID 41882679 · PMC13019944 · Genome biology · 2026 · 8 claims · 7 setups

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  The majority of long-range intronic RNA duplexes detected genome-wide are mediated by inverted Alu-repeat elements.

  k562 hek293t chimpanzee computational splash eclip-seq

• Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.

  PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups

  Has reproduction · 85

  Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.

  liver huh-7 bulk sirna lipid

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

  PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

  blood charlesbogerti reptile annotated whole-genome novo repeat

• Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

  PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups

  Has reproduction · 50

  2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B

  flower roots analysis parental high-throughput quantitative pcr

• Discovery and hypothesis generation through bioinformatics.

  PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

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  Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

  genome chemokine gene-expression proteins genome-wide phylogenetic microarray

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman

• Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

  PMID 18772397 · PMC2848990 · Science (New York, N.Y.) · 2008 · 8 claims · 6 setups

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  Pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations

  pancreatic computational targeted prevalence snp

• Report of the 9th HLPP Workshop October 2007, Seoul, Korea.

  PMID 18683817 · PMC4601560 · Proteomics · 2008 · 8 claims · 8 setups

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  An integrated separating-identifying platform identified 6788 proteins (≥2 peptides, 95% confidence) in Chinese human liver samples, including 3721 new to liver and 977 hypothetical proteins

  chinese liver hbv-related mammalian shotgun transcriptome yeast

• Physiology engages with functional genomics - at last.

  PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups

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  Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic

  wild-type caenorhabditis kidney pcr qtl enu copas

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 77

  Recurrently targeted HIV-1 integration genes (RIGs) are proximal to super-enhancer (SE) genomic elements

  activated cd4+ cd3 jurkat chip-seq hiv-1 sequencing

• Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.

  PMID 41484656 · PMC12857045 · Genome biology · 2026 · 8 claims · 8 setups

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  pRIC-seq, an adaptation of RIC-seq for plants, enables genome-wide mapping of RNA-RNA spatial interactions in diploid and tetraploid cotton

  diploid tetraploid cotton nicotiana pric-seq gro-cap chip-seq