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).

• A universal mechanism ties genotype to phenotype in trinucleotide diseases.

  PMID 18039028 · PMC2082501 · PLoS computational biology · 2007 · 8 claims · 5 setups

  Full-text index only

  A universal mechanism of somatic, length-dependent trinucleotide repeat expansion toward a disease-specific pathological threshold explains genotype-phenotype correlations common to trinucleotide diseases

  dominant recessive patients homozygous computer mathematical

• Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.

  PMID 17517123 · PMC1899181 · BMC genomics · 2007 · 8 claims · 4 setups

  Full-text index only

  A new method combining known LRR structures, multiple sequence alignment, and secondary structure prediction identifies and aligns LRRs in TLRs more accurately than PFAM/InterPro/SMART

  tlrs lrr-containing tlr2 mammalian comparative structural secondary

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

  Full-text index only

  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

  PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

  Full-text index only

  TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

  scop-derived malt nr-70 scop profile-based dali remote

• Sequence determinants of human microsatellite variability.

  PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups

  Full-text index only

  Mean and maximum number of repeats across individuals are positively correlated with heterozygosity

  hgdp-ceph genome calibrated microsatellite blastn sequence

• GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.

  PMID 19910367 · PMC2808900 · Nucleic acids research · 2010 · 7 claims · 7 setups

  Full-text index only

  GenomeRNAi is a database integrating RNAi phenotypes, reagents, and gene annotations from cell-based screens in Drosophila and human cells

  drosophila hela genome-scale image-based rna-seq

• Association of replication error positive phenotype with lymphocyte infiltration in endometrial cancers.

  PMID 9818024 · PMC5921952 · Japanese journal of cancer research : Gann · 1998 · 7 claims · 4 setups

  Full-text index only

  RER+ phenotype (microsatellite instability at ≥2 of 7 loci) occurs in a subset (21-23%) of sporadic endometrioid endometrial adenocarcinomas but not in other histological types or endometrial hyperplasia

  paired tumor hematoxylin-eosin-stained pcr sequencing histopathological

• COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

  PMID 19906727 · PMC2808858 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  COSMIC is the largest public resource for information on somatically acquired mutations in human cancer, freely available without restriction

  cancer tumour manual semi-automated candidate

• Telomere-to-telomere assembly of a complete human X chromosome.

  PMID 32663838 · PMC7484160 · Nature · 2020 · 8 claims · 8 setups

  Full-text index only

  Produced the first gapless, telomere-to-telomere assembly of a human chromosome (the X chromosome) using the CHM13 cell line

  chm13htert chm13 ultra-long-read pacbio linked-read

• Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

  PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

  Full-text index only

  No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

  nigerian same novel sanger targeted repeat

• Cryptococcus neoformans strains and infection in apparently immunocompetent patients, China.

  PMID 18439357 · PMC2600263 · Emerging infectious diseases · 2008 · 8 claims · 8 setups

  Full-text index only

  71% (91/129) of Chinese cryptococcosis clinical isolates (1985-2006) came from patients with no apparent risk factor, versus only 8.5% from AIDS patients, contrasting sharply with other countries

  clinical neoformans randomly balb pcr ura5 igs1-5.8s

• Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

  PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

  sheep bac dot tandem

• Analysis of recent segmental duplications in the bovine genome.

  PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

  bos bovine genes cattle genome fluorescent repeat

• High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

  PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups

  Full-text index only

  Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature

  yoruba selected subset whole-genome targeted pcr

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

  Full-text index only

  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

  PMID 20035629 · PMC2806268 · BMC medical genetics · 2009 · 8 claims · 7 setups

  Full-text index only

  All UK vCJD cases tested (147/147) are methionine homozygous (MM) at PRNP codon 129

  vcjd scjd scottish controls pcr-rflp full chi-squared

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

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

  Full-text index only

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

  breast subset confirmed paired-end fish exon-exon