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).

• Age Deceleration and Reversal Gene Patterns in Dauer Diapause.

  PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption

  daf-2 wild-type same dauer developmental lifespan brood

• Phagosome maturation: going through the acid test.

  PMID 18813294 · PMC2908392 · Nature reviews. Molecular cell biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Maturation of apoptotic cell-containing phagosomes proceeds via machinery mechanistically distinct from receptor-mediated endocytosis

  caenorhabditis elegans swiss phagosomes rnai genetic acridine

• Have microarrays failed to deliver for developmental biology?

  PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

  Full-text index only

  Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

  drosophila caenorhabditis developing xenopus cdna genome-wide microarray

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental

• The changing face of genomics.

  PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

  yeast drosophila zebrafish elegans chip-chip comparative insertional

• A comparison of programmed cell death between species.

  PMID 11178240 · PMC138857 · Genome biology · 2000 · 8 claims · 8 setups

  Full-text index only

  The core apoptotic pathway (CED-3/caspases, CED-4/Apaf-1, CED-9/Bcl-2, EGL-1) is conserved across C. elegans, Drosophila, and mammals.

  elegans mammalian drosophila transgenic whole-genome kinetic ectopic

• A conversation with John Sulston.

  PMID 14580111 · PMC2588810 · The Yale journal of biology and medicine · 2002 · 8 claims · 5 setups

  Full-text index only

  C. elegans, with about 1,000 cells, is an ideal model for studying how cells divide, communicate, differentiate, and undergo programmed death, bridging single-celled organisms and complex animals

  elegans genomic survey lineage ablation physical

• Intronic alternative splicing regulators identified by comparative genomics in nematodes.

  PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

  elegans database transgenic comparative est cross-species

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• The genome of Brugia malayi - all worms are not created equal.

  PMID 18952001 · PMC2668601 · Parasitology international · 2009 · 8 claims · 8 setups

  Full-text index only

  Comparative genome analysis shows conserved long-range synteny but divergent local gene order between B. malayi and C. elegans, reflecting distinct evolutionary trajectories of parasitic and free-living lineages.

  malayi elegans wbm-infected filarial whole-genome genome-wide comparative

• Advances in the study of SR protein family.

  PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

  Full-text index only

  SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

  nuclear bovine drosophila caenorhabditis selex rna-binding splicing

• Genomic organization of zebrafish microRNAs.

  PMID 18510755 · PMC2427041 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  Using sequence conservation and prediction algorithms, 35 new zebrafish miRNAs were identified, bringing the total to 415.

  zebrafish candidate hairpin blast secondary comparative

• The Proteomics Identifications database: 2010 update.

  PMID 19906717 · PMC2808904 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  PRIDE has become one of the main repositories for MS-based proteomics data, with substantial growth in data holdings over the last two years.

  species plasma caenorhabditis secretory ms-based quantitative