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).

• MatchMiner: a tool for batch navigation among gene and gene product identifiers.

  PMID 12702208 · PMC154578 · Genome biology · 2003 · 8 claims · 3 setups

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  MatchMiner's LookUp function automates batch translation of an input list of gene identifiers into a matching list of a different identifier type.

  nci-60 fish-mapped random batch fish-mapped cross-validation

• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 7 claims · 6 setups

  Has reproduction · 64

  Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut).

  rimicaris foregut deferribacteres shotgun fluorescence yoyo-1

• Characterisation of p53 status at the gene, chromosomal and protein levels in oesophageal adenocarcinoma.

  PMID 14583777 · PMC2394414 · British journal of cancer · 2003 · 8 claims · 4 setups

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  p53 gene mutations are infrequent in oesophageal adenocarcinoma (9.6%)

  formalin-fixed oesophageal evaluable pooled rflp fluorescence immunohistochemistry

• Human and mouse oligonucleotide-based array CGH.

  PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb

  bt474 normal gm01750 mda-mb-468 array fish

• Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

  PMID 16254605 · PMC1270012 · PLoS genetics · 2005 · 8 claims · 6 setups

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  Comparative net alignment of human and chimpanzee genome assemblies identifies 1,576 putative inverted regions covering more than 154 Mb of DNA

  build chimpanzee unrelated ceph comparative three-color pcr

• Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

  PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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  Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

  cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish

• Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

  PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

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  RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

  peripheral patient-parent genomic crebbp karyotyping bac microsatellite

• Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

  PMID 17626639 · PMC1952070 · BMC cancer · 2007 · 7 claims · 4 setups

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  EGFR mutations (exon 19 deletions, exon 21 L858R) did not correlate with gefitinib response in this cohort

  microdissected formalin-fixed archival clinical pcr fluorescence laser

• Evolutionary toggling of the MAPT 17q21.31 inversion region.

  PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

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  The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

  chimpanzee lymphoblastoid donor whole-genome reciprocal bac

• Epidermal growth factor receptor abnormalities in the pathogenesis and progression of lung adenocarcinomas.

  PMID 19138956 · PMC3369271 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 4 setups

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  EGFR mutations and protein overexpression are early phenomena in the pathogenesis of lung adenocarcinoma, occurring in histologically normal bronchial/bronchiolar epithelium (NBE)

  lung microdissection fluorescence immunohistochemistry

• Stable in a genome of instability: an interview with Evan Eichler. Interview by Jane Gitschier.

  PMID 18654618 · PMC2442658 · PLoS genetics · 2008 · 8 claims · 5 setups

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  Loss of AGG interruptions in CGG repeat tracts predisposes FMR1 alleles to instability and faster progression toward premutation/disease state

  fmr1 xq28 genome agg fluorescence genome-wide

• Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

  PMID 18559093 · PMC2440550 · Molecular cancer · 2008 · 7 claims · 6 setups

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  Gain of chromosome 5p is the most frequent genomic alteration in invasive cervical cancer

  cervical tumors pap tumor snp fluorescence fish

• RPS4Y gene family evolution in primates.

  PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

  primate chromosomes rps4x concatenated pcr fluorescence repeat

• Locus-specific and activity-independent gene repositioning during early tumorigenesis.

  PMID 18195100 · PMC2213600 · The Journal of cell biology · 2008 · 7 claims · 6 setups

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  The genome undergoes global spatial reorganization during both normal and tumorigenic mammary epithelial differentiation, as shown by reduced nucleolar number.

  mcf-10a.b2 immunofluorescence interphase quantitative

• Approaching the genomics of risk-taking behavior.

  PMID 20109660 · PMC3961474 · Advances in genetics · 2009 · 8 claims · 8 setups

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  Candidate genes (e.g., DRD4, SERT, MAOA) explain only a small fraction of total genetic variation in risk-taking-related behaviors, motivating a whole-genome approach.

  wild-caught three-spined sticklebacks open-field-like predator repeated-measures

• Divide and conquer: progress in the molecular stratification of cancer.

  PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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  Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

  breast nsclc colon early-stage immunohistochemistry gene comparative

• Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin.

  PMID 33833454 · PMC7610777 · Nature genetics · 2021 · 8 claims · 8 setups

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  In human embryos, intra-adrenal sympathoblasts are directly derived from nerve-associated Schwann cell precursors (SCPs), similarly to chromaffin cells

  embryo sympathoadrenal embryonic adrenal scrna-seq velocity immunohistochemistry

• Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture.

  PMID 34248892 · PMC8264503 · Frontiers in microbiology · 2021 · 7 claims · 6 setups

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  Natural seasonality is the primary driver of aquatic bacterial community structure in the fishponds and reservoir

  pond filtered phytoplankton common 16s photosynthetic inorganic

• Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

  PMID 33722289 · PMC7962346 · Genome biology · 2021 · 7 claims · 8 setups

  Has reproduction · 66

  A three-base-pair (HDR) or single-base (PE2) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder, but not heart or brain

  tissues zygotes aorta spleen qrt-pcr allele-specific restriction

• An Erg-driven transcriptional program controls B cell lymphopoiesis.

  PMID 32541654 · PMC7296042 · Nature communications · 2020 · 7 claims · 8 setups

  Has reproduction · 81

  Erg is essential for early B lymphoid differentiation

  erg b220+ prob wild-type lacz rna-seq flow