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).

• Hit selection with false discovery rate control in genome-scale RNAi screens.

  PMID 18628291 · PMC2504311 · Nucleic acids research · 2008 · 8 claims · 3 setups

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  A Bayesian FDR-controlling methodology for hit selection in genome-scale RNAi HTS is proposed, using a direct posterior probability approach analogous to Newton et al.

  hela hepatitis simulated genome-scale simulation

• 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

• The genomic analysis of lactic acidosis and acidosis response in human cancers.

  PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

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  Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

  mammary hmec gene breast gene real-time bayesian

• Seeded Bayesian Networks: constructing genetic networks from microarray data.

  PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

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  Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

  leukemia interactome pubmed-indexed computational microarray yeast literature

• An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

  PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 7 setups

  Has reproduction · 67

  An individualized causal analysis framework can discover tumor-specific intercellular communication networks (ICNs) from transcriptomic data

  hnscc pooled cd45+ cd8+ single-cell nhdp celda

• Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus.

  PMID 41803193 · PMC13179358 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 64

  HLA-DRB5 and ODAPH are causal risk genes for keratoconus, supported by SMR and Bayesian colocalization (HLA-DRB5 PP4=0.844, SMR p=0.001, OR=1.768; ODAPH PP4=1.0, SMR p=0.013, OR=202.851).

  corneal gwas string bulk summary-data two-sample

• PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

  PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC

  homo peroxisomal bona eukaryotic annotation comparative sequence

• Function2Gene: a gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge.

  PMID 18631403 · PMC2500032 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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  Function2Gene is a set of Perl programs that queries public databases (NCBI, GeneCards, Harvester, with Uniprot/Ensembl also supported) using expert-selected keywords to rank genes by prior probability of disease association.

  gene nuclear sle tdt keyword-based snp transmission

• Adaptations to climate in candidate genes for common metabolic disorders.

  PMID 18282109 · PMC2242814 · PLoS genetics · 2008 · 8 claims · 7 setups

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  A network-based bioinformatics approach (Molecular Triangulation) was used to select 82 candidate genes belonging to the core subnetwork of metabolic syndrome phenotypes.

  individuals population genic compiled snp spearman bayesian

• miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.

  PMID 34637468 · PMC8509996 · PloS one · 2021 · 7 claims · 6 setups

  Has reproduction · 100

  RBPs beyond Drosha/DGCR8/Dicer are involved in regulating miRNA biogenesis and explain its spatio-temporal nature

  tissues computational rbps clip-seq rna-seq srna-seq

• Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

  PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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  Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

  brasiliensis gp43 ratio codon-based mutational

• Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

  PMID 15892868 · PMC1175952 · Genome biology · 2005 · 8 claims · 6 setups

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  Two quantitative benchmarks (functional-annotation-based and physical-interaction-based log likelihood ratio scores) can measure relative accuracy of human PPI datasets

  medline annotated interactions consolidated conditional co-citation bayesian

• Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

  PMID 19922616 · PMC2784454 · BMC biology · 2009 · 8 claims · 7 setups

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  The ratio of homologous recombination to mutation in B. pseudomallei is over two times higher than in Streptococcus pneumoniae, the highest yet reported in bacteria.

  isolates genome snp snps multilocus genome bayesian

• GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.

  PMID 35087491 · PMC8787282 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

  Has reproduction · 50

  GAL08 is a dominant bacterial clade in a neutral hot spring, comprising up to 29.2% of the community by relative read abundance and up to 4.7 × 10^5 16S rRNA gene copies per gram sediment.

  dewar dchs_gal08 hoodoo gal08 16s qpcr single

• Systems biology: where it's at in 2005.

  PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

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  High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

  saccharomyces drosophila environmental literature systematic genome-wide

• Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

  PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups

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  The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.

  rumen blood beef metagenome snp longitudinal

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Genetical genomics: spotlight on QTL hotspots.

  PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

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  Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

  adipose saccharomyces genome-wide permutation gene

• 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