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).

• The sequence and de novo assembly of the giant panda genome.

  PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

  Full-text index only

  A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

  giant panda whole-genome novo read

• Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

  PMID 18637199 · PMC2483709 · BMC microbiology · 2008 · 8 claims · 5 setups

  Full-text index only

  A RecA- phenotype increases genetic stability and may help restrict ongoing genome evolution of BCG substrains while maintaining protective efficacy

  bovis bcg genomic cell-free allelic southern sequencing

• Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer.

  PMID 40145684 · PMC11948951 · Current protocols · 2025 · 6 claims · 5 setups

  Has reproduction · 90

  Streaming minimap2 alignment output directly into HLAminer via Unix pipe (-a stream mode) enables HLA class I and II allele prediction without storing bulky SAM alignment files on disk

  wgs

• Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

  PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 7 setups

  Has reproduction · 80

  After long-term ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin locations, most prominently centromeric satellite/micro-satellite DNA.

  pbmc single cd4 flip-seq mip-seq prip-seq

• hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

  PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

  Full-text index only

  hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

  mgc cloned orfs genome gateway orf blat

• ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae.

  PMID 40364978 · PMC12067309 · Bio-protocol · 2025 · 8 claims · 6 setups

  Has reproduction · 100

  siQ-ChIP measures absolute protein–DNA interaction (IP efficiency) genome-wide without relying on exogenous spike-in chromatin, overcoming limitations of spike-in normalization.

  cerevisiae pombe concatenated chip-seq chip-seq high-throughput fastq

• Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

  PMID 19958472 · PMC2788361 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  88 full paper submissions were peer-reviewed for InCoB2009, with 49 shortlisted for oral presentation and 34 accepted into this BMC Genomics supplement, reflecting an overall acceptance rate of 50% across venues.

  nhe1 cancer mammalian bovine computational microarray quantile

• Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

  PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups

  Has reproduction · 88

  Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life

  zymo bacterial reference shotgun comparative reference

• Compression of structured high-throughput sequencing data.

  PMID 24260313 · PMC3832420 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 43

  Leveraging an explicit data schema (separate field encoding, field modeling, template compression, domain modeling) enables stronger compression of HTS alignment data than general-purpose compression of serialized bytes.

  benchmark ten rna-seq exome genome

• Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

  PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

  Has reproduction · 83

  MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

  pooled hc227 contig sets shotgun novo alignment-free

• Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.

  PMID 36057548 · PMC9441065 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 6 setups

  Has reproduction · 90

  Commercially available bovine arrays are ineffective at capturing variants segregating among African indicine animals, with only 6% of high-LD (r2>0.8) variants captured by the best arrays versus 17% in African taurine and 25% in European taurine.

  global ndama target illumina whole-genome array genotype

• Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

  PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

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  Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

  genomic rmrp family non-finnish sequencing comparative microsatellite

• Rise of the machines.

  PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

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  New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

  bacillus independent subtilis whole-genome read

• Analysis of chimpanzee history based on genome sequence alignments.

  PMID 18421364 · PMC2278377 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Bonobos and common chimpanzees separated approximately 1.29 million years ago

  bonobo bonobos chimpanzee simulated shotgun sequenom principal

• Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

  PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 6 claims · 8 setups

  Has reproduction · 82

  Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis

  klebsiella isolate a55848 assembled short-read phenotypic genome-based

• TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

  PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 69

  TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.

  ppm1d-transgenic genome genome read touchdown-pcr

• Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

  PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

  Has reproduction · 95

  Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

  solar saltern combined individual metagenomic taxonomic functional

• Molecular correlates of host specialization in Staphylococcus aureus.

  PMID 17971880 · PMC2040198 · PloS one · 2007 · 8 claims · 6 setups

  Full-text index only

  Genome sequencing of ET3-1 revealed genomic elements not previously identified in S. aureus, including homologs of virulence factors from other Gram-positive pathogens

  aureus sequenced et3-1 bovine whole-genome comparative substitution

• Analysis of virulence factors of Helicobacter pylori isolated from a Vietnamese population.

  PMID 19698173 · PMC2739534 · BMC microbiology · 2009 · 8 claims · 5 setups

  Full-text index only

  Three distinct deletion patterns (39-bp, 18-bp, no deletion) exist upstream of the cagA EPIYA repeat region (pre-EPIYA region), providing a novel genotyping marker.

  pylori gastric pcr sequence comparative

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome