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).

• Activating mutations in ALK provide a therapeutic target in neuroblastoma.

  PMID 18923525 · PMC2587486 · Nature · 2008 · 8 claims · 8 setups

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  Non-synonymous ALK kinase domain mutations occur in 8% of primary neuroblastomas, with F1174L being the most frequent

  neuroblastoma kelly fish sequencing cytokine-independence

• Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

  PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups

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  An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.

  mg-thymoma colon exon fluorescent reverse

• Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).

  PMID 19929093 · PMC2945731 · The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association · 2009 · 8 claims · 4 setups

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  The translocation breakpoints disrupt SLC31A1 (intron 1) on chromosome 9 and a predicted gene containing CCL2 (5'UTR/exons) on chromosome 17

  family genomic case-control case fluorescence long-range mutation

• Molecular genetics and structural genomics of the human protein kinase C gene module.

  PMID 11897026 · PMC88812 · Genome biology · 2002 · 8 claims · 4 setups

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  The nine human PKC genes are dispersed throughout the genome, with five isotypes (α, β, δ, ζ, ι) previously incorrectly assigned to chromosomes in the literature.

  metaphase genome pkc genomic fluorescence bioinformatic snp

• PIK3CA alterations in Middle Eastern ovarian cancers.

  PMID 19638206 · PMC2724395 · Molecular cancer · 2009 · 8 claims · 7 setups

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  PIK3CA gene amplification is frequent in Middle Eastern EOC, found in 54/152 (35.5%) cases

  eoc fluorescence pcr step-down

• Rare mutations predisposing to familial adenomatous polyposis in Greek FAP patients.

  PMID 15833136 · PMC1097718 · BMC cancer · 2005 · 8 claims · 6 setups

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  A 250 Kbp deletion spanning intron 5 to beyond exon 15 of APC was identified in one FAP patient using MLPA, karyotyping, and FISH.

  genomic peripheral metaphase dhplc sequencing rt-pcr

• Bone marrow ectopic expression of a non-coding RNA in childhood T-cell acute lymphoblastic leukemia with a novel t(2;11)(q11.2;p15.1) translocation.

  PMID 18947387 · PMC2579299 · Molecular cancer · 2008 · 8 claims · 8 setups

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  A novel t(2;11)(q11.2;p15.1) translocation was identified as the sole cytogenetic abnormality in a childhood T-ALL case

  bone genomic da926692 g-banding fish vectorette

• Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

  PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

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  Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

  chicken turkey broiler chromosome single fish

• Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

  PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

  Has reproduction · 70

  AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

  head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• 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

• Pathogenesis of vestibular schwannoma in ring chromosome 22.

  PMID 19772601 · PMC2758865 · BMC medical genetics · 2009 · 8 claims · 7 setups

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  Tumours in ring chromosome 22 patients arise from the combination of loss of the ring chromosome (first hit) and a pathogenic somatic NF2 mutation on the remaining chromosome 22 (second hit)

  peripheral schwann skin-biopsy vestibular karyotyping fish array

• 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

• 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

• Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

  PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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  GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

  genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

• Free circular introns with an unusual branchpoint in neuronal projections.

  PMID 31697236 · PMC6879206 · eLife · 2019 · 8 claims · 7 setups

  Has reproduction · 99

  A set of free circular introns with a non-canonical (C) branchpoint is enriched in distal neuronal projections; these appear to be tailless lariats that escape debranching.

  hippocampal cytoplasmic rrna-depleted polya-site ribosome

• 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

• SVC: structured visualization of evolutionary sequence conservation.

  PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

  orthologous exonic tblastx blastn sliding-window

• Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

  PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

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  Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

  imr-32 subtracted mycn-amplified suppression differential array

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic