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).

• Comprehensive data for studying serum exosome microRNA transcriptome in Parkinson's disease patients.

  PMID 39406833 · PMC11480472 · Scientific data · 2024 · 8 claims · 5 setups

  Has reproduction · 100

  A serum exosome miRNA transcriptome dataset from four Japanese cohorts (96 PD patients, 80 matched controls, plus 96 PD patients before/after one year of rasagiline) with anonymised demographic, clinical, and neuroimaging data is provided.

  serum patients skin small mirna 123i-metaiodobenzylguanidine

• Statistical framework for calling allelic imbalance in high-throughput sequencing data.

  PMID 39966391 · PMC11836314 · Nature communications · 2025 · 8 claims · 6 setups

  Has reproduction · 89

  MIXALIME is a versatile computational framework for calling allele-specific variants (ASVs) from diverse high-throughput omics data

  wa01 left heart chip-seq rna-seq cage-seq

• Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

  PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 5 setups

  Has reproduction · 67

  fRNA-seq transcript counts are best fit by the negative binomial distribution, with little evidence supporting zero-inflated extensions

  compendium frna-seq nb-generated breast ffpe distribution synthetic

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 78

  INVADE-seq simultaneously captures host and bacterial transcripts to map bacteria-host interactions across diverse testicular cell types at single-cell resolution

  testes testis young testicular invade-seq histology sperm

• huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.

  PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups

  Has reproduction · 50

  huSA is a publicly accessible database integrating data from 17 skin diseases and 63 independent datasets, including 1434 scRNA-seq, 63 spatial transcriptomics, and 1502 bulk RNA-seq samples

  skin scrna-seq single prurigo scrna-seq bulk spatial

• A comparative study on recombination activity in cattle.

  PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups

  Has reproduction · 93

  Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)

  six paternal alphasimr-simulated brown snp recombination simulation

• Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

  PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups

  Has reproduction · 73

  De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp

  suaeda rna-seq novo blastx

• Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

  PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction

  SDSD constitutes a distinct taxonomic entity within S. dysgalactiae, with a mean intra-subspecies average nucleotide identity of 99%.

  dysgalactiae sdse sdsd isolates genome multilocus pangenome

• Genomics research and malaria control: great expectations.

  PMID 14624242 · PMC261879 · PLoS biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Genomics research on humans, P. falciparum, and An. gambiae holds great promise for developing new drugs, vaccines, diagnostics, and vector control tools for malaria.

  plasmodium anopheles malaria whole-genome computational microarray

• Continued colonization of the human genome by mitochondrial DNA.

  PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

  Full-text index only

  NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

  homo genomic chimpanzee genome genome-wide pcr sanger

• Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

  PMID 15339345 · PMC517707 · BMC bioinformatics · 2004 · 7 claims · 5 setups

  Full-text index only

  A Bayesian mixture model is proposed to account for within-class biological variability in SAGE/Digital-Northern/MPSS tag counting data.

  astrocytoma same sage classical beta-binomial

• Candida albicans genome sequence: a platform for genomics in the absence of genetics.

  PMID 15239821 · PMC463275 · Genome biology · 2004 · 8 claims · 5 setups

  Full-text index only

  Publication of the complete diploid C. albicans genome sequence will accelerate research into the pathogenesis of Candida infections

  candida sc5314 whole-genome fingerprinting multi-locus

• Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.

  PMID 15207009 · PMC449699 · BMC bioinformatics · 2004 · 8 claims · 8 setups

  Full-text index only

  New classifiers (SVMs, ensembles) and new wavelet-derived (Gabor, Daubechies) features improve recognition of protein subcellular location patterns over the previous neural network approach

  hela automated stepwise training-set-size

• Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

  PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.

  sequenced cmr-derived uniprot cogent computational genome sequence

• A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

  PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups

  Has reproduction · 69

  Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.

  mus chuniphyes hormiphora pleuromamma rna-seq homology

• Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

  PMID 16179648 · PMC1236720 · Nucleic acids research · 2005 · 8 claims · 4 setups

  Full-text index only

  Deeply conserved human-zebrafish non-coding elements are enriched for in vivo cis-acting transcriptional regulatory activity.

  ncbi genes zebrafish comparative annotation gfp

• Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

  PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups

  Full-text index only

  145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013

  complete mutation sars-cov spike sequence phylogenetic selection

• Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

  PMID 16093549 · PMC1184218 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  Created the Mammalian Orthologous Intron Database (MOID) containing orthologous introns of human, mouse and rat identified via conserved reading-frame position

  introns ribosomal rrna comparative orthologous pairwise

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

  Full-text index only

  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold

• Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

  PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

  predicted non-masked genome interpro hmm tblastn inter-species