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).

• De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.

  PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups

  Has reproduction · 87

  A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).

  euglena gracilis five transcriptomes bulk novo transcriptome

• Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

  PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

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  Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

  five cichlid pairwise lake low-coverage blastx multi-species

• A virtual computer lab for distance biomedical technology education.

  PMID 18366629 · PMC2292716 · BMC medical education · 2008 · 6 claims · 4 setups

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  A 'virtual computer lab' combining videoconferencing with VNC-based desktop sharing can replicate the functionality of a physical computer lab for distance biomedical technology education

  graduate students nlm five-point open-ended informal

• Evaluation of classification and forecasting methods on time series gene expression data.

  PMID 33156855 · PMC7647064 · PloS one · 2020 · 6 claims · 3 setups

  Has reproduction · 74

  Deep learning based methods generally outperform traditional approaches for time series gene expression classification

  five gene microarray time

• How can developing countries harness biotechnology to improve health?

  PMID 18053180 · PMC2238767 · BMC public health · 2007 · 8 claims · 2 setups

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  Five Executive Courses on Genomics and Public Health Policy were held in five developing-world regions (Africa, India, Eastern Mediterranean, Latin America/Caribbean, Western Pacific/Southeast Asia) to generate recommendations on harnessing biotechnology for health.

  developing-world course structured participant

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• Genetic diversity among five T4-like bacteriophages.

  PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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  A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

  bacteriophages five conserved aeh1 genome orf trna

• Proteomics as a tool for biomarker discovery.

  PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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  A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

  serum laser ovarian seldi-tof two-dimensional gene

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups

  Has reproduction · 67

  A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.

  mammary five singlecellexperiment individual droplet-based quality doublet

• 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

• A metadata approach for clinical data management in translational genomics studies in breast cancer.

  PMID 19948017 · PMC3225860 · BMC medical genomics · 2009 · 8 claims · 5 setups

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  A metadata/CDE-based approach using CancerGrid's semantic web tools enables automatic integration of heterogeneous clinical datasets without loss of original detail

  clinical breast metadata estrogen her2

• Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?

  PMID 41627342 · PMC12862982 · Briefings in bioinformatics · 2026 · 7 claims · 3 setups

  Has reproduction · 89

  No single existing SOTA imputation method consistently performs well across newer SRT platforms/datasets

  datasets srt same computational proposed

• Molecular genetic diagnosis of von Hippel-Lindau disease: analysis of five Japanese families.

  PMID 8641976 · PMC5921130 · Japanese journal of cancer research : Gann · 1996 · 5 claims · 3 setups

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  Four of five Japanese VHL disease families showed germ line VHL gene mutations, comprising 2 missense mutations, 1 deletion, and 1 splice-site mutation

  blood-derived hemangioblastoma single-strand direct sscp

• COVID-19 vaccination atlas using an integrative systems vaccinology approach.

  PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 7 setups

  Has reproduction · 69

  Distinct immune markers differentiate between vaccine types and infection statuses.

  pbmcs immune immune-related pbmc-derived bulk spearman gene

• Human genomic variation.

  PMID 11178257 · PMC138878 · Genome biology · 2000 · 8 claims · 7 setups

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  Lewontin's 1972 analysis of 17 blood-group/protein loci found 85% of human genetic variation lies within individuals of a nation/tribe, 8% between populations within races, and only 6% between races

  populations individuals composite genome blood-group marker mitochondrial

• Chipping away at 'stemness'.

  PMID 15287966 · PMC507869 · Genome biology · 2004 · 8 claims · 6 setups

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  Global gene-expression analyses across five independent studies identify known and new candidate regulators of human ES-cell growth, self-renewal, and pluripotency.

  microarray sage custom

• Empirical codon substitution matrix.

  PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

  orthologous million codon same pairwise empirical comparative

• In silico analysis of missense substitutions using sequence-alignment based methods.

  PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

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  Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

  clinically sequence curated deep blosum62 sift align-gvgd

• Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

  PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum

  sycon ciliatum sponges differential go-term genome

• Autoantibody profiling for the study and treatment of autoimmune disease.

  PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups

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  Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.

  serum antigen-antibody antigens fetal spotted elisa microarray