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).

• Current status of use of high throughput nucleotide sequencing in rheumatology.

  PMID 33408124 · PMC7789458 · RMD open · 2021 · 8 claims · 4 setups

  Has reproduction · 83

  RNA-Seq is the most represented HTS assay in rheumatology research (n=457, 65%), used for biomarker identification in blood or synovial tissue

  pubmed sequence icd-11 sle semiautomated sequencing disease-name

• Genomics, proteomics and bioinformatics: all in the same boat.

  PMID 12374575 · PMC244909 · Genome biology · 2002 · 8 claims · 8 setups

  Full-text index only

  Microarray sensitivity has improved enough to analyze clinical samples as small as 10-50 nanograms, and many early microarray experiments may need to be repeated due to data quality issues

  clinical oligonucleotide-immobilized dendritic blood microarray chip combined

• VGEA: an RNA viral assembly toolkit.

  PMID 34567846 · PMC8428259 · PeerJ · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  VGEA is a Snakemake workflow that chains existing tools (fastp, BWA, SAMtools, IVA, shiver, SeqKit, QUAST, MultiQC) into an all-in-one RNA viral genome assembly pipeline

  sars-cov-2 lassa hiv-1 ngs-based computational comparative

• TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

  PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

  Has reproduction · 43

  TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.

  mdr-tb paired-end raw bam whole-genome kraken raw

• COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.

  PMID 19958500 · PMC2788389 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  COMUS is a bioinformatics system for detecting and depositing new mutations from patient DNA with a clinician-friendly interface

  ab1 fasta mutation hemophilia base-calling sequence known-variant

• An online database for brain disease research.

  PMID 16594998 · PMC1489945 · BMC genomics · 2006 · 7 claims · 5 setups

  Full-text index only

  SMRIDB is a comprehensive web-based database integrating gene expression data and clinical metadata to aid understanding of the genetic effects of brain disease (bipolar disorder, schizophrenia, depression)

  postmortem individual disease studies microarray array gene-by-gene

• Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.

  PMID 30648934 · PMC6412060 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  The S. Adjame outbreak produced a heterogeneous phylogeny with multiple temporally/geographically linked sub-clusters, atypical of a point-source Salmonella outbreak and consistent with contamination from an endemic mixed-strain source (imported South Asian herbs/spices).

  salmonella adjame outbreak commonly genome reference-based cgmlst

• The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.

  PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups

  Has reproduction · 90

  The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application

  tuberculosis outlier whole-genome maximum-likelihood read

• Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.

  PMID 39009986 · PMC11247842 · Genetics, selection, evolution : GSE · 2024 · 6 claims · 8 setups

  Has reproduction · 69

  Meta-analysis of GWAS across multiple breeds for CM and SCS identified 58 lead markers associated with mastitis incidence, including 16 loci not overlapping previously identified QTL in AnimalQTLdb.

  six multi-breed per-breed bovine genome-wide single-trait trans-ethnic

• poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

  PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data

  porecov sars-cov-2 nanopore fastq gisaid workflow real-world

• 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

  Full-text index only

  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

• Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data.

  PMID 28045932 · PMC5207757 · PloS one · 2017 · 7 claims · 5 setups

  Has reproduction · 78

  Metavisitor is an open-source suite of modular Galaxy tools and preset workflows enabling non-experts to detect and assemble viral genomes from deep sequence data.

  drosophila deep srp013822 small novo long-read

• Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

  PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

  epithelial-based tcga gdsc muscle-invasive differential co-expression signature

• Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

  PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups

  Full-text index only

  GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage

  pools pcr genomic gs-flx massively sanger pcr

• Segregation of a M404V mutation of the p62/sequestosome 1 (p62/SQSTM1) gene with polyostotic Paget's disease of bone in an Italian family.

  PMID 16277682 · PMC1297578 · Arthritis research & therapy · 2005 · 6 claims · 4 setups

  Full-text index only

  The M404V mutation in p62/SQSTM1 exon 8 segregates with the polyostotic form of PDB in the F01 Italian family

  genomic serum affected pcr pcr biochemical clinical

• Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

  PMID 16515697 · PMC1448207 · BMC medical genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  CMS compares IBS allele/genotype sharing between distantly related (beyond grandparental) affected and unaffected individuals from founder populations to detect disease loci while reducing confounding from population stratification and genetic heterogeneity.

  amish unrelated same overall microsatellite combinatorial permutation

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

  Full-text index only

  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine

• Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

  PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

  Full-text index only

  A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

  gbs clinical bioinformatic eburst kinetic

• The novel Y371D myocilin mutation causes an aggressive form of juvenile open-angle glaucoma in a Caucasian family from the Middle-East.

  PMID 19784393 · PMC2751802 · Molecular vision · 2009 · 6 claims · 4 setups

  Full-text index only

  A novel MYOC missense mutation, Y371D (1111t→g), causes an aggressive, autosomal dominant form of JOAG in this family.

  genomic caucasian patients blood direct mutation clinical

• Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

  PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups

  Full-text index only

  SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.

  serum seldi dlbcl pooled seldi-tof-ms proteinchip decision