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).

• Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

  PMID 39592593 · PMC11599844 · Nature communications · 2024 · 8 claims · 2 setups

  Has reproduction · 90

  Weak selection conferred by HSC variation created before birth can reliably yield clonal hematopoiesis later in life, demonstrated via shared prenatal circulation of monozygotic (MZ) twins.

  blood simulated fluctuating single-cell

• A Bayesian approach to accurate and robust signature detection on LINCS L1000 data.

  PMID 32003771 · PMC7203754 · Bioinformatics (Oxford, England) · 2020 · 6 claims · 4 setups

  Has reproduction · 37

  A novel Bayesian-based peak deconvolution algorithm gives unbiased likelihood estimations for peak locations and characterizes peaks with probability-based z-scores.

  lincs simulated l1000 l1000 simulated student's

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy.

  PMID 16984653 · PMC1618409 · BMC bioinformatics · 2006 · 8 claims · 6 setups

  Full-text index only

  The proposed feature set outperforms existing published feature sets for predicting effects of amino acid substitutions

  coli bacteriophage lac proteins svm simulated pearson

• HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

  PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 5 setups

  Has reproduction · 67

  HASCAD, a DNN-based cell composition deconvolution model, predicts the fractions of up to 15 immune cell types from bulk RNA-seq.

  pbmc bulk tcga-lihc harmony-symphony scrna-seq simulated bulk

• ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion.

  PMID 34844559 · PMC8628418 · BMC genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  scLRTC imputes dropout entries closest to the original expression values on simulated datasets, outperforming other state-of-the-art methods by SSE and PCC.

  usoskin pollen zeisel yan scrna-seq umap masking

• Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

  PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

  Full-text index only

  The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

  transmembrane simulated age duplicate maximum kernel monte

• Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

  PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

  Full-text index only

  The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Involvement of the modifier gene of a human Mendelian disorder in a negative selection process.

  PMID 19888326 · PMC2765618 · PloS one · 2009 · 7 claims · 4 setups

  Full-text index only

  The frequency of SAA1 alpha/alpha homozygotes is much higher among Armenian FMF patients (24%) than Karabakhian FMF patients (4%)

  genomic population simulated pcr pearson monte

• CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 6 setups

  Has reproduction · 87

  CoINcIDE is a methodological framework that discovers replicable patient subtypes (meta-clusters) across multiple datasets by finding consensus across dataset-specific clusterings, requiring no between-dataset transformations.

  breast ovarian simulated gene semi-supervised novo

• Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

  PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 6 setups

  Has reproduction

  Selective linkage disequilibrium pruning (SLDP) refines whole-genome SNP sets using GWAS prior information to improve genomic prediction accuracy.

  duroc 1000-individual real low-coverage genome-wide genomic

• A hybrid empirical and parametric approach for managing ecosystem complexity: Water quality in Lake Geneva under nonstationary futures.

  PMID 35733249 · PMC9245694 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 7 claims · 6 setups

  Has reproduction · 69

  A hybrid model combining empirical dynamic modeling (EDM/S-map) for biogeochemical sink terms with the equation-based Simstrat hydrodynamic model for physical source terms produces substantially better historical DOB forecasts than conventional parametric models.

  lake convergent multivariate s-map

• Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

  PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

  olfactory present same anova-significant microarray step-down peddada

• Natural clines and human management impact the genetic structure of Algerian honey bee populations.

  PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups

  Has reproduction · 55

  No significant admixture from European subspecies was detected in Algerian honey bees, suggesting large-scale queen imports have not occurred in Algeria.

  apis algerian ld-pruned reference whole-genome read identity-by-descent