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).

• Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

  PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 7 setups

  Has reproduction · 90

  Replacing Scc1 with Rec8 in mitosis impairs sister chromosome cohesion, advances the timing of genome replication, and reduces reproductive fitness by 45%

  saccharomyces cerevisiae competitive live-cell flow

• Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.

  PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 7 setups

  Has reproduction · 49

  S100A3 shows consistent discriminatory performance across the training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort

  blood degs bulk single-gene gene

• Using prototyping to choose a bioinformatics workflow management system.

  PMID 33630841 · PMC7906312 · PLoS computational biology · 2021 · 7 claims · 6 setups

  Has reproduction

  Prototyping a subset of the RiboViz workflow in each candidate system gives more insight into suitability, ease of use, and documentation quality than reading documentation or working through developer tutorials alone

  workflow snakemake cwltool toil web repository prototype

• A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

  PMID 35019679 · PMC8754136 · Microbiology spectrum · 2022 · 8 claims · 9 setups

  Has reproduction · 36

  Microbulbifer sp. YX04 shows high algicidal activity against P. globosa, peaking at 93.2% in the declining growth phase

  phaeocystis strain yx04 globosa algicidal 16s scanning

• Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.

  PMID 35177610 · PMC8854666 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  SHARC uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA

  model dipicolinic hek293t 28s crosslinking nmr crosslink

• αPIX Is a Trafficking Regulator that Balances Recycling and Degradation of the Epidermal Growth Factor Receptor.

  PMID 26177020 · PMC4503440 · PloS one · 2015 · 8 claims · 8 setups

  Has reproduction

  αPIX interacts with c-Cbl, including as endogenous proteins

  cho-k1 cos-7 cho αpix co-immunoprecipitation time-course stability

• Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

  PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

  Full-text index only

  None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

  breast quantitative fragment gene-expression

• Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.

  PMID 15673719 · PMC548352 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  Presence of CENP-B box elements is required for efficient de novo centromere formation in HAC vectors

  ht1080 coli ht1080-derived synthetic novo gel transposition

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

  Full-text index only

  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip

• Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

  PMID 16412238 · PMC1368963 · BMC medical genetics · 2006 · 8 claims · 6 setups

  Full-text index only

  A novel PPARG nonsense mutation, Y355X, was identified in a mother and daughter with FPLD3-consistent phenotypes and was absent from unaffected relatives and 260 healthy controls

  subjects nih3t3 subject healthy sequencing luciferase western

• Nutrigenomics: the genome--food interface.

  PMID 18087577 · PMC2137135 · Environmental health perspectives · 2007 · 8 claims · 8 setups

  Full-text index only

  Nutrigenomics integrates genomic science with nutrition to study how dietary components affect gene expression, the proteome, and the metabolome.

  general humans lymphocytes healthy snp controlled micronucleus

• Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans.

  PMID 18987626 · PMC2656577 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 5 setups

  Full-text index only

  DNM1 SNP rs3003609 is significantly associated with Smoking Quantity (SQ) and Heaviness of Smoking Index (HSI) in the European-American (EA) sample, surviving correction for multiple testing.

  nuclear same sh-sy5y snp haplotype-based quantitative

• Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

  PMID 18654622 · PMC2447880 · PLoS computational biology · 2008 · 8 claims · 5 setups

  Full-text index only

  Bongo identifies mutations causing local and global structural effects with a remarkably low false positive rate

  p53 1bpi mutations disease-associated graph correlation structural

• Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

  PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

  Full-text index only

  PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

  hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag

• The role of medical structural genomics in discovering new drugs for infectious diseases.

  PMID 19855826 · PMC2756625 · PLoS computational biology · 2009 · 8 claims · 6 setups

  Full-text index only

  Structure-based drug design using X-ray/NMR protein structures has contributed to the development of numerous approved and improved therapeutics.

  bacteria plasmodium candidate burkholderia high-throughput animal compound-target

• Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP.

  PMID 19784376 · PMC2747018 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  Native human U1 snRNP shows differential incorporation of four protein isoforms (U1-70k isoforms 1/2, Sm-B/B')

  native snrna intact denatured proteomic denaturing nucleic

• A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

  PMID 19725976 · PMC2742551 · BMC cancer · 2009 · 7 claims · 5 setups

  Full-text index only

  Three protein spots (beta-actin, HSP60, PDI) show low expression variability across tumourous, non-tumourous cirrhotic, and normal liver tissues by 2-DE (ANOVA p>0.99 ranking)

  liver 2-de western immunohistochemistry

• Deep-Learning Tool ScVital Enables Species-Agnostic Integration of Cancer Cell States.

  PMID 41223329 · PMC13053053 · Cancer research · 2026 · 7 claims · 7 setups

  Full-text index only

  scVital is a variational autoencoder with an adversarially trained discriminator that embeds scRNA-seq data from different species into a species-agnostic latent space to overcome batch effect.

  pbmc normal pancreatic lung scrna-seq

• BLIT: an R package for seamless integration of command-line bioinformatics tool universe.

  PMID 42164079 · PMC13183670 · Bioinformatics advances · 2026 · 8 claims · 5 setups

  Full-text index only

  BLIT provides a unified R6-based framework for seamless integration of command-line bioinformatics tools within R, replacing fragile string-based system() calls.

  core circrna clinical europe unit pipeline production

• SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

  PMID 15980532 · PMC1160243 · Nucleic acids research · 2005 · 7 claims · 3 setups

  Full-text index only

  SOP 3 v2 is a web-based application that outputs recommended forward/reverse PCR primers plus a sequencing primer optimized for sequence-based genotyping of human and mouse polymorphisms

  genomic ncbi laboratory primer genomic