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).

• Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data.

  PMID 32528441 · PMC7262952 · Frontiers in microbiology · 2020 · 8 claims · 4 setups

  Has reproduction · 100

  WGS data enables prediction of antimicrobial resistance in Gram-negative bacteria using machine learning

  baumannii gram-negative in-house cchmc whole-genome xgboost antimicrobial

• Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

  PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups

  Full-text index only

  An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes

  genome training svm support leave-one-out sensitivity

• Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

  PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 8 claims · 5 setups

  Has reproduction

  The nasal methylome shows differential DNA methylation in intergenic regions and low methylated regions (LMRs), highlighting distal regulatory/enhancer-like elements in COVID-19 gene regulation

  nasal aggregated severe differentially genome methylation differential

• RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.

  PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups

  Has reproduction · 79

  RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report

  wgs single whole-genome nested capillary

• Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

  PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

  parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr

• Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

  PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

  Full-text index only

  The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

  non-identical gene3d cath whole-gene domain transmembrane

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

  Full-text index only

  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

  Full-text index only

  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel

• 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

• Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.

  PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups

  Has reproduction · 89

  Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa

  aureus reduced genome cgmlst comparative

• Systematic identification of pseudogenes through whole genome expression evidence profiling.

  PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

  genome ensembl vega celera spliced protein-to-genome pseudogene

• Detecting transcriptionally active regions using genomic tiling arrays.

  PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

  anopheles chromosomes simulated genomic high-density sequence-based

• Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

  PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

  Full-text index only

  The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

  chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr

• CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

  PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

  Full-text index only

  CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

  genome sequence drosophila novo gene coding

• Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

  PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

  gossypium transcripts uq-normalized differentially comparative coding bulk

• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

  PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

  genome random cd4+ six average mutual chip-seq

• Long-range regulation is a major driving force in maintaining genome integrity.

  PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups

  Full-text index only

  Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.

  opossum genome comparative identification statistical

• VISTA Enhancer Browser--a database of tissue-specific human enhancers.

  PMID 17130149 · PMC1716724 · Nucleic acids research · 2007 · 8 claims · 2 setups

  Full-text index only

  Comparative genome analysis can identify candidate human enhancer elements whose tissue-specific in vivo activity can then be experimentally validated in transgenic mice.

  genomic genome transgenic comparative

• Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.

  PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups

  Has reproduction · 99

  Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.

  coli lymphoblastoid na12878 mixture nanopore cas9-targeted whole-genome