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).

• Unexpected major geomagnetic storm caused by faint eruption of a solar trans-equatorial flux rope.

  PMID 39448608 · PMC11502832 · Nature communications · 2024 · 8 claims · 8 setups

  Has reproduction · 96

  The March 23, 2023 severe geomagnetic storm (Dragon Day Event) originated from the eruption of a trans-equatorial, longitudinal, low-density magnetic flux rope with weak coronal emission and no chromospheric signatures.

  near-earth earth's solar full-halo in-situ geomagnetic euv

• 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

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read

• Electron Energy Partition across Interplanetary Shocks. I. Methodology and Data Product.

  PMID 31806920 · PMC6894189 · The Astrophysical journal. Supplement series · 2019 · 7 claims · 3 setups

  Has reproduction · 92

  Solar wind electron VDFs below ~1.2 keV are best modeled as the sum of three components: a cold dense core, a hot tenuous halo, and a field-aligned beam/strahl.

  solar electron quasi-static proton

• Biocomputing enters its adolescence.

  PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

  bank antibody-antigen yeast genome protein-protein empirical integrative

• The future is genome-wide.

  PMID 16934105 · PMC1779592 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Noncoding SNPs near NRG1 associated with schizophrenia likely act by influencing NRG1 expression level

  schizophrenia myocardial individuals infectious genetic candidate gene

• Extreme conservation of noncoding DNA near HoxD complex of vertebrates.

  PMID 15462684 · PMC524357 · BMC genomics · 2004 · 7 claims · 7 setups

  Full-text index only

  Three blocks of extremely conserved non-coding DNA (CR1, CR2, CR3) exist within 7 kb upstream of the HoxD complex, 3' of Evx-2, conserved from fish to human.

  hoxd genomic pcr pcr-amplified comparative pcr southern

• 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

• Immunopathogenic interaction of environmental triggers and genetic susceptibility in diabetes: is epigenetics the missing link?

  PMID 19033405 · PMC2584121 · Diabetes · 2008 · 8 claims · 3 setups

  Full-text index only

  Epigenetic modification of histones and DNA provides a plausible common mechanism linking environmental triggers to genetic susceptibility regions in autoimmune type 1 diabetes.

  lymphocytes genetic nonobese chip-on-chip bioinformatic congenic

• Incorporating genetics and genomics in risk assessment for inhaled manganese: from data to policy.

  PMID 19646473 · PMC2765692 · Neurotoxicology · 2009 · 8 claims · 7 setups

  Full-text index only

  Inhaled manganese bypasses normal homeostatic regulation and can accumulate in the brain, unlike dietary manganese which is readily excreted

  occupationally residents mn-exposed marietta biological postural rflp

• Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.

  PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups

  Has reproduction · 75

  Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.

  testes normal gene rna-seq sapas cdna

• Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection.

  PMID 16102740 · PMC7124242 · Clinica chimica acta; international journal of clinical chemistry · 2006 · 6 claims · 7 setups

  Full-text index only

  The Luminex xMAP system uses spectrally distinct dyed microspheres (up to 100 sets) read by dual lasers to enable simultaneous multiplexed analysis of up to 100 reactions in one vessel.

  genomic apoe hla whole-genome direct oligonucleotide single

• A novel Twinkle (PEO1) gene mutation in a Chinese family with adPEO.

  PMID 18989381 · PMC2579934 · Molecular vision · 2008 · 8 claims · 5 setups

  Full-text index only

  Two-point linkage analysis maps this Chinese adPEO family to the PEO1 (Twinkle) locus on chromosome 10q23.3-24.3, with the other three candidate genes excluded.

  members family biceps proband two-point direct muscle

• ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

  PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

  Full-text index only

  ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

  genome cytomegalovirus six probabilistic 5-fold directional

• Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.

  PMID 29590198 · PMC5874073 · PloS one · 2018 · 8 claims · 8 setups

  Has reproduction · 99

  Verrucomicrobia is highly prevalent in north-temperate freshwater lakes, on average the 4th most abundant phylum (range 1.7–41.7%).

  southeastern lake muskegon lake-type 16s within-phylum phylogenetic

• Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor.

  PMID 30576656 · PMC6310685 · Molecular cell · 2018 · 8 claims · 8 setups

  Has reproduction

  Depletion of Rap1 induces divergent noncoding transcription at a large fraction of Rap1-regulated gene promoters

  cerevisiae rap1-aid northern western poly

• Revealing an unexpectedly low electron injection threshold via reinforced shock acceleration.

  PMID 39805850 · PMC11730962 · Nature communications · 2025 · 8 claims · 4 setups

  Has reproduction · 68

  A reinforced shock acceleration model combining foreshock transients, wave-particle interactions, and variable stellar wind conditions operating across multiple scales enables electrons to consistently reach relativistic energies

  mms artemis foreshock six situ wave multi-event

• Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.

  PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 6 claims · 7 setups

  Has reproduction · 50

  A computational method using high-quality scRNA-seq reference data can estimate per-sample, per-cell-type off-target contamination coefficients in sctRNA-seq datasets.

  brain cortex allen lcm-seq lcm-seq scrna-seq marker

• 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