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).

• Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.

  PMID 19823582 · PMC2756628 · PloS one · 2009 · 8 claims · 8 setups

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  M. tuberculosis isolates with identical DNA fingerprints can harbour substantial genomic diversity at the whole-genome level

  tuberculosis whole-genome is6110 spoligotyping

• Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G (p.I2285V) variant.

  PMID 19795481 · PMC3501199 · Human mutation · 2009 · 7 claims · 8 setups

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  BRCA2 c.6853A>G (p.I2285V) co-occurs in trans with the deleterious founder mutation c.5946delT, supporting classification as a neutral variant

  lymphocytes brca2 brca2-null ashkenazi rt-pcr splicing allelic

• A simple and efficient algorithm for genome-wide homozygosity analysis in disease.

  PMID 19756043 · PMC2758715 · Molecular systems biology · 2009 · 8 claims · 4 setups

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  A genome-wide AH analysis (GAHA) algorithm can identify disease-associated loci by comparing frequencies of homozygous segments between cases and controls using a z-statistic proportion test

  unrelated simulated selected genes genome-wide statistical logistic

• Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

  PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups

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  The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.

  asian fgf5 woolly savanna pcr structural blast

• Identifying cis-regulatory sequences by word profile similarity.

  PMID 19730735 · PMC2731932 · PloS one · 2009 · 8 claims · 8 setups

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  WPH-finder identifies putative co-regulated CRMs by scanning the genome for sequences with word profiles similar to a known CRM, without explicitly defining binding sites

  stripe pair-rule nrsf-bound eve genome-wide chip-chip chip-seq

• Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.

  PMID 19694819 · PMC4286260 · Genes, brain, and behavior · 2009 · 6 claims · 6 setups

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  A family-based clustering strategy using neurocognitive test scores (CPT, WCST) can identify more homogeneous subgroups of schizophrenia families for genetic association analysis

  multiplex affected subjects cluster-specific family-based continuous wisconsin

• PPDPF is not a key regulator of human pancreas development.

  PMID 40193385 · PMC12037078 · PLoS genetics · 2025 · 8 claims · 8 setups

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  PPDPF is not a key regulator of human pancreas development, in contrast to its zebrafish orthologue exdpf

  fetuses fetal hesc population situ proteome qpcr

• Developments in CORG: a gene-centric comparative genomics resource.

  PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

  upstream gene overlapping c-fos pairwise sequence comparative

• A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes.

  PMID 16510851 · PMC1388096 · Nucleic acids research · 2006 · 6 claims · 3 setups

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  MDHA extends the range of classical DHA from ~20 kb increments to intervals approaching 100 kb using agarose-embedded nuclei, FIGE, and long-range Southern blotting

  jurkat specified mdha northern

• Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

  PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

  Has reproduction

  SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

  dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial

• Mutational analysis of BRCA1 gene in ovarian and breast-ovarian cancer families in Japan.

  PMID 9197534 · PMC5921420 · Japanese journal of cancer research : Gann · 1997 · 5 claims · 2 setups

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  Germline BRCA1 mutations were detected in 7 of 19 Japanese cancer families (4 breast-ovarian, 3 site-specific ovarian)

  genomic tumor single-strand loss

• The meso-genomic era.

  PMID 11516332 · PMC139414 · Genome biology · 2001 · 8 claims · 8 setups

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  Linkage disequilibrium (LD) between SNPs extends much further in Northern European populations (~120 kb) than in a Nigerian population (<10 kb), reflecting differing population histories (bottlenecks vs. constant expansion).

  genome chromosome families tomato snp haplotype genetic

• The many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• With the finished human genome in hand, what next?

  PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

  domestic saccharomyces systemic schistosoma comparative functional genetic

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat

• Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes.

  PMID 38566006 · PMC10985947 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 7 setups

  Has reproduction · 64

  Significant genetic introgression from commercial European pigs (EP) into the Lijiang pig (LJP) and other domestic Chinese pig breeds was detected.

  unrelated chinese ljp individuals whole-genome d-statistic local

• Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

  PMID 33690630 · PMC7978347 · PLoS genetics · 2021 · 8 claims · 4 setups

  Has reproduction · 97

  Paramutation between R and S HPT epialleles occurs only in tetraploid (RRSS) F2 progeny, not in diploid (RS) F2 progeny, reducing the ratio of hygromycin-resistant plants below Mendelian expectation.

  diploid 14-day-old tetraploid type hygromycin small crispr-cas9

• Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution.

  PMID 35977485 · PMC9644345 · Cell reports · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Bmp4 treatment instructs ESCs to downregulate pluripotency genes and upregulate genes associated with formative pluripotency and fate specification

  escs naive facs-isolated freshly bulk atac-seq chip-seq

• Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.

  PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation

  quiescent satellite regenerating situ atac-seq rna-seq motif

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid