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).

• Application of two machine learning algorithms to genetic association studies in the presence of covariates.

  PMID 19014573 · PMC2620353 · BMC genetics · 2008 · 8 claims · 3 setups

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  The relative performance of RF and MARS for detecting genotype-trait associations depends on both the strategy used to handle covariates and the true underlying model of association (e.g., confounding vs. mediation vs. interaction).

  simulated cohort simulation applied

• Validation of analytic methods for biomarkers used in drug development.

  PMID 18829475 · PMC2744124 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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  Analytical method validation (assessing assay performance/reproducibility) is a distinct process from clinical qualification (linking a biomarker to biological processes and clinical endpoints), though the two are intertwined.

  specified biological cancer-associated biofluids immunohistochemistry immunoassay microarray

• ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.

  PMID 17710137 · PMC1940324 · PloS one · 2007 · 8 claims · 4 setups

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  ADaCGH implements eight CNA detection methods, including the best-performing ones from recent reviews (CBS, GLAD, CGHseg, HMM)

  30-node web-based cluster simulated computational web comparison

• Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

  PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 6 claims · 3 setups

  Has reproduction · 90

  Representing the genome as a binary string (1/0) of peak presence and computing Hamming distances enables hierarchical clustering of ATAC-seq samples with reduced computational cost while preserving cell-type classification.

  leukemia hematopoietic atac-seq rna-seq

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

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  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna

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

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

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  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

• Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis.

  PMID 18444230 · PMC2729096 · Statistics in medicine · 2008 · 8 claims · 3 setups

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  A statistical test (delta method and Steiger-Browne optimal linear composites) is developed to test equality of the marginal correlation and the partial correlation of two gene expression traits conditional on a set of covariates.

  simulated real analytical simulation application

• Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite.

  PMID 17488846 · PMC1933128 · Nucleic acids research · 2007 · 8 claims · 2 setups

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  Asterias is an integrated, open-source, web-based software suite for analysis of gene expression and aCGH data

  asterias pomelo functional cross-browser

• treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.

  PMID 34001188 · PMC8127214 · Genome biology · 2021 · 7 claims · 6 setups

  Has reproduction · 73

  treeclimbR proposes multiple candidate resolutions on a tree and selects the optimal one in a data-driven manner using three criteria (FDR-controlling range of t, number of rejected leaves, fewest internal nodes)

  synthetic semi-simulated microbiome mirna differential microbiome microrna

• Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

  PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

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  Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

  pools individual same parental pooled individual test-retest

• QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

  PMID 16381937 · PMC1347390 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  QTL MatchMaker integrates QTL information with physical, genetic and cytogenetic maps across human, mouse and rat genomes

  pubmed ucsc laser-captured literature genome comparative

• Gene-disease relationship discovery based on model-driven data integration and database view definition.

  PMID 19042916 · PMC2639000 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 4 setups

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  Explicit gene–disease relationships can be formulated as candidate gene definitions (e.g., co-localization, dysregulation, functional similarity) that may include intermediary orthologous or interacting genes

  acgr disease term-based database case

• A searchable database of genetic evidence for psychiatric disorders.

  PMID 18548508 · PMC2574546 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 8 claims · 4 setups

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  SLEP (Sullivan Lab Evidence Project) is a freely available, searchable web database of findings from psychiatric genetics for non-commercial use.

  psychiatric relational genomewide microarray database

• A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

  PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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  A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

  duke nci-60 mayo spanish gene cdna igvh

• Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

  PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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  A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

  panel breast 250-gene candidate genome growth pathway

• MuPlex: multi-objective multiplex PCR assay design.

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

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  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

• From single cells to whole organisms.

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

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  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

• A network-guided protocol to discover susceptibility genes in genome-wide association studies using stability selection.

  PMID 36609152 · PMC9850185 · STAR protocols · 2023 · 5 claims · 5 setups

  Has reproduction · 92

  The protocol identifies genes that are both statistically associated with a phenotype and functionally interconnected in a biological network

  case-control gene-gene fictional familial snp-phenotype gene-level network-guided

• Filtering high-throughput protein-protein interaction data using a combination of genomic features.

  PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

  saccharomyces bank caenorhabditis homo yeast mass naive

• Evaluation of models to predict BRCA germline mutations.

  PMID 17016486 · PMC2360540 · British journal of cancer · 2006 · 7 claims · 7 setups

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  Four commonly used BRCA risk prediction models (BRCAPRO, Manchester, Penn, Myriad-Frank) have only modest ability to rule in or rule out BRCA1/2 germline mutation carrier status at a 10% probability threshold.

  proband pedigrees randomly brca1 brcapro manchester