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).

• ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

  PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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  Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

  ductal same sporadic paired cdna quantitative genotyping

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma.

  PMID 26895470 · PMC4924754 · Oncotarget · 2016 · 8 claims · 8 setups

  Has reproduction · 36

  160 lncRNAs are differentially expressed between normal plasma cells and MGUS, SMM, MM, or PCL patients, with 31 lncRNAs shared across at least three comparisons

  bone gene plasma normal microarray custom unsupervised

• Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

  PMID 17386095 · PMC1868932 · Genome biology · 2007 · 8 claims · 4 setups

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  More than 55,000 totally intronic noncoding (TIN) RNAs are transcribed from the introns of 74% of unique RefSeq genes.

  dbest liver cultures refseq est oligoarray polymerase

• Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins.

  PMID 40191587 · PMC11970367 · NAR genomics and bioinformatics · 2025 · 8 claims · 5 setups

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  44 individuals' fully haplotyped diploid genome assemblies (88 haplotypes) from the 1000 Genomes Project were used to comprehensively assess homozygous and heterozygous sequence variations around and within 5'ss

  healthy reconstructed same 5'ss long-read computational statistical

• 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

• Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

  PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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  Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

  nb4 tf1 tracheobronchial moser affymetrix cdna microarray

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read