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 method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

  PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups

  Full-text index only

  Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.

  fecal assembled predicted gut whole-genome gene reciprocal

• Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm.

  PMID 33295865 · PMC8116671 · Microbial genomics · 2020 · 8 claims · 4 setups

  Has reproduction · 98

  wCtub and wDcau (863 988 bp and 863 427 bp) are the smallest Wolbachia genomes sequenced to date and are the first genomes representing supergroup J.

  wolbachia filarial six target-enrichment whole-genome novo

• Exome sequencing of a multigenerational human pedigree.

  PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

  genomic eluted captured pcr microarray-based qpcr next-generation

• Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

  PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

  Has reproduction · 81

  A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

  lung sequencing assembled deer high-throughput metagenomic reference

• The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

  PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

  Has reproduction · 58

  The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

  developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Enrichment of sequencing targets from the human genome by solution hybridization.

  PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

  Full-text index only

  Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

  genome genomic same technical capture solution-hybridization sequence

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

  Full-text index only

  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

  PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

  schizosaccharomyces pombe rna-seq lasso lariat-specific

• Single-cell transcriptional dynamics of flavivirus infection.

  PMID 29451494 · PMC5826272 · eLife · 2018 · 8 claims · 6 setups

  Has reproduction · 90

  viscRNA-Seq simultaneously quantifies whole single-cell host transcriptome and intracellular viral RNA from the same cell, including non-polyadenylated viruses via a virus-specific oligo

  hepatoma single huh7 denv-infected single-cell qpcr loss-of-function

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read

• IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.

  PMID 33522913 · PMC7852101 · BMC bioinformatics · 2021 · 8 claims · 2 setups

  Has reproduction · 78

  IsomiR Window is an integrated, user-friendly platform that systematically identifies, quantifies, and functionally explores isomiR expression in small-RNA-seq datasets without requiring computational skills

  simulated basal small-rna-seq

• Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.

  PMID 37085932 · PMC10120106 · Environmental microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes

  root musa assembled prokka-annotated shotgun culture-free metagenome

• RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data.

  PMID 42172220 · PMC13196991 · PloS one · 2026 · 8 claims · 8 setups

  Has reproduction · 63

  RAGER integrates widely-used bioinformatics tools into an automated Snakemake-based pipeline for joint analysis of RNA-seq and ATAC-seq data

  embryonic cd34+ shared promoter rna-seq atac-seq gsea

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  ChIRP-MS identifies 309 host proteins that bind SARS-CoV-2 RNA during active infection across Huh7.5 and Vero E6 cells.

  huh7.5 host lung chirp-ms chirp-rna-seq sds-page