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).

• EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

  PMID 35561186 · PMC9113274 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 5 setups

  Has reproduction · 49

  EDGE COVID-19 (EC-19) is a web-based platform that automates QC, reference-based variant/consensus calling, lineage determination, and submission of SARS-CoV-2 genomes and metadata to GenBank, GISAID and INSDC for both Illumina and ONT data.

  sars-cov-2 srr illumina ont amplicon lineage cross-workflow

• Genome-wide diversity and selective pressure in the human rhinovirus.

  PMID 17477878 · PMC1892812 · Virology journal · 2007 · 7 claims · 6 setups

  Full-text index only

  Whole genome and subgenomic phylogenies of HRV are essentially identical at every locus, indicating consistent phylogenetic patterns across the genome.

  diverse hrv fully hrva genome phylogenetic pairwise

• Comparative genomics of multidrug resistance in Acinetobacter baumannii.

  PMID 16415984 · PMC1326220 · PLoS genetics · 2006 · 7 claims · 5 setups

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  A. baumannii strain AYE contains an 86-kb genomic resistance island (AbaR1) clustering 45 of its 52 resistance genes, the largest resistance island described to date

  baumannii resistance clinical whole-genome comparative sequence

• Of mice and men: comparative proteomics of bronchoalveolar fluid.

  PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

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  Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

  pooled oxidative unpooled balf shotgun functional protein-protein

• Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data.

  PMID 32528441 · PMC7262952 · Frontiers in microbiology · 2020 · 8 claims · 5 setups

  Has reproduction · 100

  WGS-derived antibiotic resistance gene (ARG) coverage can be used to predict antimicrobial resistance in Gram-negative bacteria via machine learning

  gram-negative in-house args curated shotgun genome phenotypic

• geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

  PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 6 setups

  Has reproduction · 75

  geneshot identifies microbial genomic islands consistently associated with ICI response across independent cohorts

  stool deduplicated cag reference gene-level novo co-abundance

• Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

  PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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  Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

  pooled computational identified additional label-free lspad pathway-associated

• Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

  PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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  An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

  hla-b44 plasma macrophages complement proteomics shotgun cap

• Science star over Asia.

  PMID 16149850 · PMC1201306 · PLoS biology · 2005 · 8 claims · 7 setups

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  Ariff Bongso and associates at Singapore's National University Hospital were the first to derive human embryonic stem cells, from a five-day-old discarded human embryo in 1994, and showed the cells were pluripotent with therapeutic transplant potential.

  blastocyst embryonic fugu rice embryo culture whole-genome

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups

  Has reproduction · 66

  Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level

  prostate bulk weighted reverse

• Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

  PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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  Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

  serum frozen ig-depleted clinical seldi-tof maldi lc-ms

• Versatile and open software for comparing large genomes.

  PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups

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  MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances

  escherichia chromosome drosophila anopheles suffix-tree whole-genome protein-level