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).

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

  Has reproduction · 86

  A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

  known tnbc unique unknown gene machine term

• The HIV positive selection mutation database.

  PMID 17108357 · PMC1669717 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  The database provides codon-level Ka/Ks selection pressure maps for HIV protease and the first 381 codons of RT, built from a novel ~50,000-sample clinical dataset.

  hiv-1 stanford codon-specific selection conditional

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

  PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  Dutch traditional chicken breeds display a complex, admixed, subdivided population structure that broadly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).

  individuals dutch phased drenthe whole-genome principal phylogenetic

• Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

  PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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  8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

  unique hmpv sequence neighbor-joining codon

• A model-based approach to selection of tag SNPs.

  PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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  The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

  hapmap encode enr112 tag cross-validated entropy tagged

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• Analysis of protein sequence and interaction data for candidate disease gene prediction.

  PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

  ophid biocarta kegg pfam-annotated common benchmarking multiple-interval

• Animal models of gene-nutrient interactions.

  PMID 19037208 · PMC2703433 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 5 setups

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  Mice and rats are well-suited models for human food selection because they share food preferences with humans and are supported by extensive genetic tools (sequenced genome, inbred strains, gene targeting, Cre-lox).

  interbred inbred pubmed genome qtl strain bibliometric

• G-quadruplexes: the beginning and end of UTRs.

  PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

  genome 5'-utr simulated protein-coding computational high-resolution utr

• Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

  PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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  E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

  e2348 hep-2 blast colony transformation

• Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

  PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 6 claims · 7 setups

  Has reproduction · 62

  Combining four de novo models (PWM, diPWM, BaMM, InMoDe) significantly increases the fraction of recognized peaks versus PWM alone (by 26.3%).

  hg38 foxa2 pwm whole-genome chip-seq pwm dipwm

• Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

  PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting

  normal aneuploid same genomiphi-amplified array-cgh

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

  PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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  Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

  cynomolgus 3-year-old macaque est full-insert oligonucleotide

• The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

  PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

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  Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

  genome protein-protein genes artificial kappa clustering gene

• Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

  PMID 18948297 · PMC2602764 · Nucleic acids research · 2008 · 6 claims · 8 setups

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  Incorporating a biotin tag into the HTA probe enables purification of labeled heteroduplexes and direct sequencing of the separated query strand, allowing recovery of minor variant sequences

  hiv-1 biotin-hta-purified original recovered heteroduplex rt-pcr sanger