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).

• MuPlex: multi-objective multiplex PCR assay design.

  PMID 15980531 · PMC1160138 · Nucleic acids research · 2005 · 8 claims · 3 setups

  Full-text index only

  MuPlex is a web-enabled system that designs multiplex PCR assays by selecting primer pairs for SNPs and partitioning them into multiplex-compatible tube sets.

  user-submitted candidate genomic multiplex primer homogeneous

• SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

  PMID 15774022 · PMC1274256 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  SNPHunter allows ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data (physical position, function class, flanking sequences at user-defined lengths, heterozygosity) from NCBI dbSNP

  ncbi candidate tnf batch-mode snp gene

• Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass.

  PMID 18824761 · PMC2629397 · Circulation · 2008 · 8 claims · 3 setups

  Full-text index only

  CP/CPB causes multiple consistent, reproducible changes in the human myocardial (right atrial) protein profile

  right excised 2-dimensional tandem sds-page

• Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

  PMID 18257909 · PMC2374702 · Genome biology · 2008 · 8 claims · 3 setups

  Full-text index only

  Compiled a list of 120 core presynaptic gene prototypes (PS120) and catalogued their conservation across insect proteomes.

  insect vamp2 ps120 comparative sequence protein-protein

• BOAT: Basic Oligonucleotide Alignment Tool.

  PMID 19958483 · PMC2788372 · BMC genomics · 2009 · 7 claims · 3 setups

  Full-text index only

  BOAT can accurately and efficiently map sequencing reads to a reference genome while handling several substitutions and indels simultaneously

  same short-read snp

• Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets.

  PMID 41808435 · PMC13012599 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

  Full-text index only

  Souporcell3 can robustly demultiplex pooled scRNA-seq data from up to 64 donors

  pooled scrna-seq doublet genotype-based umap-based

• YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

  PMID 15929789 · PMC1175843 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  YANA integrates METATOOL to provide a graphical, platform-independent front-end for editing, calculating, visualizing, and comparing elementary flux modes, with SBML support.

  redox elementary flux evolutionary

• randPedPCA: rapid approximation of principal components from large pedigrees.

  PMID 40877802 · PMC12392600 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 2 setups

  Has reproduction · 84

  Matrix-vector multiplication with the dense additive relationship matrix A can be performed implicitly and efficiently via forward/backward substitution using the sparse inverse relationship (Cholesky) factor L^-1, avoiding explicit construction of A.

  simulated kennel computational pedigree

• Quantum pixel representations and compression for N-dimensional images.

  PMID 35546151 · PMC9095730 · Scientific reports · 2022 · 8 claims · 2 setups

  Has reproduction · 87

  QPIXL is a uniform framework that overarches (I)FRQI, (I)NEQR, MCRQI, and (I)NCQI representations

  simulated example quantum image

• CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.

  PMID 15796777 · PMC1274267 · BMC bioinformatics · 2005 · 8 claims · 2 setups

  Full-text index only

  CGMIM is a Perl program that text-mines OMIM entries to identify cancer-gene associations and genetically-related cancer type pairs.

  omim automated manual

• Statistical analysis of real-time PCR data.

  PMID 16504059 · PMC1395339 · BMC bioinformatics · 2006 · 8 claims · 2 setups

  Full-text index only

  Four statistical models (multiple regression, ANCOVA, t-test, Wilcoxon test) were developed to estimate ΔΔCt with associated significance/confidence intervals

  real-time linear

• Dinucleotide repeat polymorphism in Fms-like tyrosine kinase-1 (Flt-1) gene is not associated with preeclampsia.

  PMID 18631405 · PMC2496902 · BMC medical genetics · 2008 · 7 claims · 2 setups

  Full-text index only

  The Flt-1 d(TG)n repeat polymorphism is not associated with the development of preeclampsia in Korean pregnant women

  genomic same pcr clinical

• A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

  PMID 19681055 · PMC2782493 · Proteomics · 2009 · 8 claims · 2 setups

  Full-text index only

  PDA_stFFT is a novel automatic peak detection method for prOTOF MS data that does not require a priori knowledge of protein masses

  peptide serum maldi-tof

• Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding.

  PMID 12590655 · PMC149451 · BMC evolutionary biology · 2003 · 6 claims · 1 setups

  Full-text index only

  RNA secondary structure folding shows a clear prevalence of antagonistic epistasis (β < 1) among reference sequences

  randomly

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• Human genome research in China.

  PMID 15168679 · PMC7079922 · Journal of molecular medicine (Berlin, Germany) · 2004 · 8 claims · 8 setups

  Full-text index only

  China completed its assigned 1% share of the international Human Genome Project sequencing effort and contributed ~10% of the HapMap effort

  genome chinese high-risk nb4 large-scale mutation positional

• A European focus on proteomics.

  PMID 15128441 · PMC416463 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  MALDI-MS and ESI-MS are complementary techniques that identify overlapping but distinct subsets of proteins

  ribosomal breast ovarian prostate maldi-ms laser-capture fticr-ms

• From single cells to whole organisms.

  PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

  saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai

• Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

  PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

  Full-text index only

  An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

  hla-b44 plasma macrophages complement proteomics shotgun cap

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage