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).

• 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

• Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

  PMID 20042177 · PMC3026437 · American journal of ophthalmology · 2010 · 6 claims · 4 setups

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  The Gln192Arg PON1 polymorphism is associated with decreased susceptibility to AMD, particularly wet AMD, indicating a protective effect

  genomic pcr-amplified case-control pon1 single-strand direct genetic

• Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

  PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

  Has reproduction · 87

  Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

  leaf trimmed species concatenated genome novo reference-assisted

• Bases and spaces: resources on the web for accessing the draft human genome.

  PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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  By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

  bac whole-genome draft submitted bac radiation initio

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Alignoth: portable and interactive visualization of read alignments.

  PMID 41392197 · PMC12777968 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

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  Alignoth is a command-line tool that generates self-contained, portable HTML reports of DNA sequencing read alignment pileups, with export to PNG, SVG, PDF, and JSON.

  synthetic test genomic report browser output

• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

  PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

  Has reproduction

  Retrotransposons mobilize via a copy-and-paste mechanism involving transcription of an RNA intermediate and reinsertion as a cDNA copy, unlike DNA transposons which cut-and-paste.

  drosophila normal genomic genome synthetic whole-genome computational

• Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

  PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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  Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

  mcf7 arabidopsis specified different chip-seq microarray array-based

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence