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).

• Population structure analysis of Salmonella serovar Muenchen to redefine geno-serotyping using genome indexing approaches.

  PMID 41743541 · PMC12929376 · Frontiers in microbiology · 2025 · 6 claims · 6 setups

  Has reproduction · 54

  Integrating genome-indexing (bettercallsal, DNA sketching + genome proximity) with SeqSero2 yields complementary serovar calls that improve discrimination of genomically distinct but antigenically similar serovars while retaining historical nomenclature

  salmonella megahit-assembled genome genome-indexing in-silico cgmlst

• Identity rather than 3D position informs splicing of rare introns in the human genome.

  PMID 41561379 · PMC12814444 · iScience · 2026 · 8 claims · 7 setups

  Has reproduction · 98

  Splicing efficiency depends on intron identity rather than nuclear (SPAD) position; despite shared SPAD proximity, major-like and minor-like introns are less efficiently spliced than major and minor introns

  k562 reference intron-class-containing hi-c tsa-seq damid-seq

• A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.

  PMID 40323688 · PMC12584591 · The Journal of heredity · 2025 · 6 claims · 8 setups

  Has reproduction · 99

  This paper presents the first de novo, haplotype-resolved reference-quality genome assembly of Sebastes paucispinis (bocaccio rockfish).

  sebastes assembled pacbio omni-c k-mer

• Lamin C is required to establish genome organization after mitosis.

  PMID 34775987 · PMC8591896 · Genome biology · 2021 · 7 claims · 6 setups

  Has reproduction · 76

  Lamin C, and not lamin A or lamin B1, is required for LAD:LAD cohesion, retention of LADs near the nuclear envelope, and overall chromosome territory organization.

  embryonic mefs clonal western growth damid-seq

• 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

• Firefly genomes illuminate parallel origins of bioluminescence in beetles.

  PMID 30324905 · PMC6191289 · eLife · 2018 · 8 claims · 8 setups

  Has reproduction · 93

  Bioluminescence evolved independently at least twice in beetles: once in the firefly ancestor and once in the bioluminescent click beetle ancestor.

  photinus aquatica ignelater pyralis hybrid whole-genome linked-read

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

  Full-text index only

  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• Evolutionarily conserved human targets of adenosine to inosine RNA editing.

  PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

  panel brain chicken flna comparative rt-pcr homology

• Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.

  PMID 38918881 · PMC11373658 · G3 (Bethesda, Md.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  Improved E. guineensis genome assembly achieved with substantially increased continuity and completeness compared to prior assemblies

  guineensis oleifera root pacbio proximity optical

• Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

  PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction · 58

  SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

  rms rh4 h3k27ac pooled chip-seq

• Cohesin regulates alternative splicing.

  PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

  Full-text index only

  Cohesin regulates alternative splicing independently of its effects on transcription.

  hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity

• 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

  Full-text index only

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

  pancreatic computational targeted prevalence snp