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).

• Impact of short-read sequencing on the misassembly of a plant genome.

  PMID 33530937 · PMC7852129 · BMC genomics · 2021 · 7 claims · 6 setups

  Full-text index only

  Short-read tomato assembly has substantial high-coverage (0.6%, 5.1 Mb) and low-coverage (9.7%, 79.6 Mb) regions relative to background coverage

  tomato whole-genome cnv machine

• Systems biology: where it's at in 2005.

  PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

  saccharomyces drosophila environmental literature systematic genome-wide

• SLDMS: A Tool for Calculating the Overlapping Regions of Sequences.

  PMID 35046988 · PMC8761809 · Frontiers in plant science · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  SLDMS is a novel method for computing overlapping regions of sequencing reads using suffix array (SA), longest common prefix (LCP) array, document array (DA), and a monotonic stack.

  sequencing concatenated pacbio-hifi third-generation running-time suffix overlap

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

  a549 sequence same bulk pathway gene

• Expression in human prostate of drug- and carcinogen-metabolizing enzymes: association with prostate cancer risk.

  PMID 9823980 · PMC2063181 · British journal of cancer · 1998 · 7 claims · 5 setups

  Full-text index only

  CYP2D6, CYP3A, and an N-acetyltransferase enzyme activity are functionally expressed in human prostate tissue

  peripheral prostate genomic allele-specific enzymatic determination

• PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

  PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

  Full-text index only

  The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

  individually reference equimolar independently snp reference pooled

• SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

  PMID 15961730 · PMC1151590 · Nucleic acids research · 2005 · 7 claims · 5 setups

  Full-text index only

  SW-ARRAY, an adaptation of the Smith-Waterman dynamic programming algorithm, provides a sensitive and robust method for identifying copy-number changes in array CGH data

  chromosome 16p array probe-by-probe sw-array

• Somatic and germline mutation in GRIM-19, a dual function gene involved in mitochondrial metabolism and cell death, is linked to mitochondrion-rich (Hurthle cell) tumours of the thyroid.

  PMID 15841082 · PMC2361763 · British journal of cancer · 2005 · 8 claims · 5 setups

  Full-text index only

  Somatic missense GRIM-19 mutations occur in a subset of sporadic Hürthle cell carcinomas but not in non-Hürthle cell thyroid carcinomas or blood donors

  sporadic hürthle pcr loss semi-quantitative

• Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates.

  PMID 17127215 · PMC5054070 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 4 setups

  Full-text index only

  Incorporating more sequence evolution features (transition/transversion bias, nucleotide/codon frequency bias) into Ka/Ks estimation methods yields more accurate and reliable estimates.

  simulated computer

• Comparative genomics search for losses of long-established genes on the human lineage.

  PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

  Full-text index only

  A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

  dog genome chimp gorilla comparative overlap visual

• Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

  PMID 18929582 · PMC2599865 · Mutation research · 2008 · 8 claims · 5 setups

  Full-text index only

  Overall MSY1 mutation frequencies in sperm (2.68%) and blood (1.88%) are not significantly different

  sperm donor hgr1b3 single-molecule fluorescent radioactive

• A chromosome-level reference genome and pangenome for barn swallow population genomics.

  PMID 36662619 · PMC10044405 · Cell reports · 2023 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level, karyotype-validated reference genome (bHirRus1) was assembled using the VGP pipeline combining PacBio CLR, 10x Linked-Reads, Bionano optical maps, and Hi-C data

  single barn bhirrus1 rustica genome cytogenetic reference-free

• Chromosome-scale genome assembly and annotation of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae).

  PMID 41678355 · PMC13042277 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-scale genome assembly of the white-eyed mutant G. bimaculatus strain was generated using ONT + PacBio HiFi long reads integrated with Hi-C data

  bimaculatus nanopore pacbio hi-c

• An SVM-based system for predicting protein subnuclear localizations.

  PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

  single-localization multi-localization same svm sequence

• Mutational analysis of BRCA1 gene in ovarian and breast-ovarian cancer families in Japan.

  PMID 9197534 · PMC5921420 · Japanese journal of cancer research : Gann · 1997 · 5 claims · 2 setups

  Full-text index only

  Germline BRCA1 mutations were detected in 7 of 19 Japanese cancer families (4 breast-ovarian, 3 site-specific ovarian)

  genomic tumor single-strand loss

• Current status of use of high throughput nucleotide sequencing in rheumatology.

  PMID 33408124 · PMC7789458 · RMD open · 2021 · 8 claims · 8 setups

  Has reproduction · 83

  RNA-Seq is the most represented HTS assay used in rheumatology research, primarily for biomarker identification in blood or synovial tissue.

  pubmed sequence blood patients systematic sra rna-seq

• Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.

  PMID 30578418 · PMC6365102 · Nature genetics · 2019 · 7 claims · 8 setups

  Has reproduction

  208 novel common blood pressure SNPs and 53 rare variants were discovered in GWASs of SBP, DBP and pulse pressure in up to 776,078 participants from MVP and collaborating studies.

  multi-ethnic mvp tissues kidney genome-wide exome transcriptome-wide

• Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.

  PMID 33461502 · PMC7812657 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 5 setups

  Has reproduction · 90

  Gene expression, exon expression, and intron excision ratio (splicing) molecular phenotypes are significantly heritable in sheep liver and muscle

  liver sheep sequencing snp heritability

• Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.

  PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 6 setups

  Has reproduction · 89

  GRF identifies effective features that form highly connected sub-graphs on the underlying biological network

  synthetic tcga embryonic simulation sub-graph reproducibility

• Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics.

  PMID 36854789 · PMC10119117 · The ISME journal · 2023 · 8 claims · 4 setups

  Has reproduction · 84

  Across all 16 replicate co-cultures of P. putida and P. lacustris, bacteria show a consistent succession of defense strategies over five weeks (~35 predator generations).

  pseudomonas filamentous axenically semi-continuous morphometric whole-genome