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).

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

  PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups

  Has reproduction

  m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow

  paired hl-60 gene aml nanopore functional kaplan-meier

• 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

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

  Full-text index only

  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

  PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

  Full-text index only

  85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

  paired list differentially oscc 2-de gene interaction

• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

  PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

  user-assembled archs4 generif-derived aggregated gene gene-gene literature

• Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

  PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

  Has reproduction · 27

  A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

  radish assembled rna-seq novo functional

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

  PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

  Full-text index only

  QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

  paired colorectal genome normal quma auma bioinformatic

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases

  hymenophyllum caudiculatum annotated rna-seq chlorophyll relative

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read

• Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

  PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 74

  RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).

  pericarp green cuiguan illumina bulk qrt-pcr light

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

  PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)

  preimplantation single uniparental embryos rna-seq paired gene

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

  Full-text index only

  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.

  PMID 34090257 · PMC8182229 · EBioMedicine · 2021 · 8 claims · 6 setups

  Has reproduction · 53

  1,613 genes were differentially expressed in leprosy progressors before diagnosis (t=1) compared to household contacts.

  blood rna-seq rt-qpcr differentially rna-seq rt-qpcr random

• Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

  PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 80

  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read

• Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

  PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

  immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime