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).

• Neuroscience in the era of functional genomics and systems biology.

  PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

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  Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

  developing hippocampus bac-transgenic fetal situ gene bac-transgenic

• Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

  PMID 17470268 · PMC1868757 · BMC genomics · 2007 · 8 claims · 7 setups

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  graCNV uses re-annotated Affymetrix expression microarray probe sets and the WPP algorithm to measure DNA copy number variation at a median resolution of ~17,500 bp without genomic complexity reduction.

  neuroblastoma same normal megabladder acgh bac principal

• 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

• Complex landscapes of somatic rearrangement in human breast cancer genomes.

  PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

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  There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

  breast subset confirmed paired-end fish exon-exon

• Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.

  PMID 19720790 · PMC2780873 · Diabetes · 2009 · 7 claims · 8 setups

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  INSR is disrupted by the chromosome 19 breakpoint, causing INSR haploinsufficiency (monoallelic expression) that explains the insulin resistance/dysglycemia phenotype

  metaphase genomic ebv-transformed serum fluorescence multiplex sanger

• 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

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

  pancreatic computational targeted prevalence snp

• The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer.

  PMID 33772001 · PMC7998036 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  AAMDC is an amplified/overexpressed oncogene in a subgroup of ER-positive breast cancers (IntClust2) associated with poor prognosis

  breast luminal sum52pe t-47d immunohistochemistry fluorescence qrt-pcr

• A genome-wide screen for copy number alterations in Aicardi syndrome.

  PMID 19760649 · PMC3640635 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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  Aicardi syndrome is thought to result from heterozygous defects in an essential X-linked gene, or from a sex-limited autosomal gene defect, due to its occurrence almost exclusively in females and in 47,XXY males.

  genomic subject array quantitative fluorescence

• 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

• Large-scale discovery and validation of functional elements in the human genome.

  PMID 15774039 · PMC1088940 · Genome biology · 2005 · 8 claims · 8 setups

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  Genome-wide tiling microarray hybridization reveals large, diverse sets of transcripts, many of which lack existing gene annotations

  liver genome yeast lines tiling computational dnase

• Genomic activation of the EGFR and HER2-neu genes in a significant proportion of invasive epithelial ovarian cancers.

  PMID 18182111 · PMC2266762 · BMC cancer · 2008 · 8 claims · 4 setups

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  No somatic mutations were found in the entire tyrosine kinase domain (exons 18-24) of EGFR or HER2-neu in 68 tissue samples from 52 ovarian cancer patients.

  invasive ovarian lung dgge immunohistochemistry fluorescence

• Genetics and irritable bowel syndrome: from genomics to intermediate phenotype and pharmacogenetics.

  PMID 19655247 · PMC2903621 · Digestive diseases and sciences · 2009 · 8 claims · 8 setups

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  Candidate gene association studies with IBS symptom phenotype (e.g., SLC6A4, GNB3, IL-10) have generally produced inconsistent, unreplicated results.

  ibs ibs-d ibs-c subjects candidate genotyping mutational

• Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

  PMID 36373634 · PMC9723646 · Nucleic acids research · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells (OSCs)

  drosophila ovarian osc melanogaster chip-seq sirna western

• The use of laser capture microscopy in proteomics research--a review.

  PMID 15502248 · PMC3839334 · Disease markers · 2004 · 8 claims · 8 setups

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  LCM allows purification of specific, histologically defined cell populations from heterogeneous tissue for downstream proteomic analysis

  breast prostate esophageal head maldi-tof automated two-dimensional

• A sequence-based survey of the complex structural organization of tumor genomes.

  PMID 18364049 · PMC2397511 · Genome biology · 2008 · 8 claims · 6 setups

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  End sequencing profiling (ESP) can identify all classes of genome rearrangements in tumor genomes by paired-end sequencing of BAC clones

  tumors breast bac bt474 bac low-coverage fluorescence

• The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

  PMID 19956657 · PMC2777318 · PloS one · 2009 · 6 claims · 4 setups

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  The FOXL2 c.402C>G mutation is not commonly found in a wide variety of other cancers and is likely pathognomonic for A-GCTs and closely related tumors.

  tumor ovarian kgn high sanger taqman

• The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients.

  PMID 19756916 · PMC2778706 · Targeted oncology · 2009 · 8 claims · 5 setups

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  Genomic/gene expression profiling alone is insufficient to identify tumors with molecular pathway changes predictive of treatment outcome; protein-level functional assessment (activation states, PTMs, interactions) is also required

  microarray ffpe models cancer immunohistochemistry fret fret-flim

• Proteomics technologies and challenges.

  PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

  serum myeloid formalin-fixed general maldi-tof phage maldi

• Extensive variation between chromosomes of North American and European hop.

  PMID 42204144 · PMC13216280 · Nature communications · 2026 · 8 claims · 8 setups

  Has reproduction · 87

  Chromosome-scale, haplotype-resolved genome assemblies of the hybrid hop cultivar Apollo were generated using hifiasm, ALLHiC, and TRITEX pipelines with PacBio HiFi and Hi-C data

  hop feral biparental accessions pacbio busco fluorescence

• Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila.

  PMID 32900993 · PMC7479620 · Nature communications · 2020 · 8 claims · 8 setups

  Has reproduction · 86

  Single-cell RNA-seq of developing Drosophila lymph glands resolves heterogeneity of hemocytes and identifies major and sub cell types.

  drosophila lymph single single-cell bulk gene