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).

• SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.

  PMID 36875992 · PMC9978240 · F1000Research · 2022 · 7 claims · 8 setups

  Has reproduction · 67

  SnakeMAGs is a simple, efficient, flexible and scalable Snakemake workflow that processes Illumina reads from raw data to MAG classification and relative abundance estimation

  publicly bins quality-filtered assembled workflow genome megahit

• Detecting natural selection by empirical comparison to random regions of the genome.

  PMID 19783549 · PMC2778377 · Human molecular genetics · 2009 · 8 claims · 5 setups

  Full-text index only

  Comparing candidate loci to empirically matched random genomic regions (ENCODE data) avoids the strong demographic/mutation assumptions required by theoretical neutral models and provides a robust test for selection

  ceu genomic simulated long-read snp population

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

  PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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  Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

  genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis

• BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.

  PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length

  rfam plant lncrna-mirna sequences unsupervised mirna-lncrna length-binned

• Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

  PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

  Full-text index only

  C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

  chimpanzee intergenic genome-wide chi-square nucleotide-content

• Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

  PMID 18788775 · PMC3744223 · Journal of proteome research · 2008 · 7 claims · 4 setups

  Full-text index only

  PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.

  trypsin-digested mix serum same shotgun sequest lc-ms

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• The use of urine proteomic and metabonomic patterns for the diagnosis of interstitial cystitis and bacterial cystitis.

  PMID 15258332 · PMC3850593 · Disease markers · 2003 · 6 claims · 2 setups

  Full-text index only

  Urine MS and 1H-NMR spectral patterns can be used to discriminate IC-affected, BC-affected, and unaffected individuals with approximately 84% success rate.

  urine surface-binding high-resolution

• Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

  PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  Dutch traditional chicken breeds display a complex, admixed, subdivided population structure that broadly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).

  individuals dutch phased drenthe whole-genome principal phylogenetic

• 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.

  PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups

  Has reproduction · 78

  A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.

  interrogans canine syrian smrt bulk rt-qpcr