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).

• BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

  PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

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  BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

  french-canadian families brca1-positive same targeted full-length multiplex

• Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

  PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 7 setups

  Has reproduction · 72

  edgeR identifies 9 DEGs associated with pCR and 13 DEGs associated with relapse from 579 immune genes in a small TNBC sample set (n=55)

  ffpe same nanostring training nanostring immunohistochemistry differential

• In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

  PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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  In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

  hmlh1 same cos-7 hela ese splice minigene

• Experimental identification and in silico prediction of bacterivory in green algae.

  PMID 33649548 · PMC8245530 · The ISME journal · 2021 · 7 claims · 6 setups

  Has reproduction · 93

  Five prasinophyte strains (Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, Dolichomastix tenuilepis CCMP3274) ingest live fluorescently labeled bacteria, detected by microscopy and/or flow cytometry

  prasinophyte same green pelagibaca flow epifluorescence gene-based

• GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

  PMID 16845010 · PMC1538901 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  GeneAlign predicts coding exons by using signal detection (GeneSplicer/WMM) combined with CORAL, a heuristic linear-time alignment tool, to align candidate signal-flanked regions against annotated exons of a homologous organism's genes

  homologous human-mouse same gene comparative parameter micro-exon

• Using ESTs to improve the accuracy of de novo gene prediction.

  PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome

  elegans genome chromosome novo gene partial

• The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

  PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

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  P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

  sequences orthomcl yeast orthomcl jaccard phylogenetic

• Inferring combinatorial regulation of transcription in silico.

  PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

  upstream monocytes same tfbs microarray permutation

• Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.

  PMID 18627636 · PMC2575532 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

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  27 deleterious BRCA1/BRCA2 mutations were detected in 28 breast cancer patients (14 in BRCA1, 13 in BRCA2) among 187 tested

  blood-derived family brca1 direct multiplex boadicea

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

  PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

  quintessentialset-88 hth same newly lcs svm traditional

• Mutation analysis of the ATR gene in breast and ovarian cancer families.

  PMID 15987455 · PMC1175065 · Breast cancer research : BCR · 2005 · 8 claims · 5 setups

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  ATR mediates the DNA damage response by phosphorylating tumor suppressors such as p53, BRCA1 and CHK1, making it a plausible candidate breast/ovarian cancer susceptibility gene

  index atr variant mutation direct variant

• Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

  PMID 19758473 · PMC2745591 · BMC bioinformatics · 2009 · 8 claims · 8 setups

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  None of 39 tested structural properties can be used as a sole classification criterion to separate neutral SNPs from disease mutations.

  ensembl swissprot same structural foldx side

• Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

  PMID 38940130 · PMC11256924 · Bioinformatics (Oxford, England) · 2024 · 7 claims · 5 setups

  Has reproduction · 87

  Forseti is the first probabilistic model for resolving the splicing status of exonic scRNA-seq reads by scoring putative fragments linking read alignments to proximate priming sites

  training simulated held-out paired-end cubic mlp

• Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.

  PMID 35348734 · PMC9756952 · Nucleic acids research · 2022 · 7 claims · 6 setups

  Has reproduction · 91

  A nascent intermediate central helix forms in the yxjA riboswitch that is mutually exclusive with both the aptamer's P1 helix and the expression platform's intrinsic terminator hairpin.

  coli yxja refolded flow bulk cotranscriptional

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• ATM variants and cancer risk in breast cancer patients from Southern Finland.

  PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

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  Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

  familial brca1 same genotype genotyping denaturing direct

• fREDUCE: detection of degenerate regulatory elements using correlation with expression.

  PMID 17941998 · PMC2174516 · BMC bioinformatics · 2007 · 6 claims · 5 setups

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  fREDUCE is a computational method that detects weak or degenerate binding motifs from gene expression or ChIP-chip data by exhaustive search of degenerate IUPAC oligonucleotides

  saccharomyces cerevisiae hepatocytes chip-chip motif-finding gene

• Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

  PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

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  No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

  nigerian same novel sanger targeted repeat

• Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

  PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

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  Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

  peripheral mhc2ta pcr sanger bisulfite cpg