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).

Publications 1.3k Datasets 392.5k Experiments 96

System / cell line: analysis ✕ Assay: probability ✕ Clear

Stability analysis of mixtures of mutagenetic trees.

PMID 18366778 · PMC2335279 · BMC bioinformatics · 2008 · 7 claims · 5 setups

Full-text index only

Mutagenetic trees mixture models capture multiple alternative pathways of ordered accumulation of genetic events (e.g., HIV resistance mutations, cancer chromosomal aberrations).

simulated hiv-1 hiv timed simulation genotypic mutagenetic
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

Full-text index only

Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics.

PMID 18783599 · PMC2559821 · Theoretical biology & medical modelling · 2008 · 8 claims · 2 setups

Full-text index only

Probability landscapes permit systematic detection, analysis, and utilization of feature context-dependency in genomic data.

specified probability microarray
Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.

PMID 24555103 · PMC3892923 · F1000Research · 2013 · 8 claims · 8 setups

Has reproduction · 71

The distance between consecutive backbone Cα atoms in high-quality structures is normally distributed with mean 3.8 Å and standard deviation 0.04 Å, justifying a reference state in which all consecutive Cα atoms are 3.8 Å apart.

top100h decoys i-tasser non-homologous statistical rdcc comparative
Direct inference of SNP heterozygosity rates and resolution of LOH detection.

PMID 18052545 · PMC2098867 · PLoS computational biology · 2007 · 6 claims · 7 setups

Full-text index only

A large proportion of SNPs in dbSNP have high-variance HET rate estimates, limiting their reliability for LOH study design.

dbsnp theoretical simulated hapmap snp probability sequential
The genomic analysis of lactic acidosis and acidosis response in human cancers.

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

Full-text index only

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
An analysis of human microRNA and disease associations.

PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

Full-text index only

MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

literature-derived diseases mirnas mirna literature bipartite mirna
Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

Full-text index only

Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection
Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

PMID 39256359 · PMC11387733 · Nature communications · 2024 · 8 claims · 7 setups

Has reproduction · 87

Heterozygous missense or loss-of-function variants in LRRC7 cause a dominant neurodevelopmental disorder in 33 identified individuals

genomes genematcher affected 293t genetic exome phenotype
Phylogenetic analysis of RhoGAP domain-containing proteins.

PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

Full-text index only

RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

rhogap aligned bayesian domain sequence maximum bayesian
Evaluation of models to predict BRCA germline mutations.

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

Full-text index only

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
A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

Full-text index only

A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

cases patients postmortem whole-genome cox linear
Identification and analysis of co-occurrence networks with NetCutter.

PMID 18781200 · PMC2526157 · PloS one · 2008 · 8 claims · 4 setups

Full-text index only

Random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency, and the edge-swapping (ES) model closely approximates this and is the preferred null-model among six tested.

publime bipartite randomized co-occurrence null-model signal-to-noise
Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.

PMID 37217248 · PMC10231005 · Journal for immunotherapy of cancer · 2023 · 8 claims · 8 setups

Has reproduction · 76

High expression of IFN-I signaling/response genes predicts favorable clinical outcome (longer relapse-free survival) in B-ALL patients

cog b-all eμ-myc crispra relapse-free flow mass
Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups

Has reproduction · 89

Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM

european cis-pqtl myocardial geo mendelian bayesian differential
Genomic variability within an organism exposes its cell lineage tree.

PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

Full-text index only

Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

robinia arabidopsis randomly genotyping multiplex computer
Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

Full-text index only

A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

rts rtsβ ccrf-cem comparative mitochondrial subcellular
Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

Full-text index only

Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold

simulated real chromosome randomly simulation multiplex coverage-vs-n
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

Full-text index only

The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

non-identical gene3d cath whole-gene domain transmembrane
A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

Full-text index only

Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

simulated same mcmc-based direct original

Experiments

Stability analysis of mixtures of mutagenetic trees.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics.

Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.

Direct inference of SNP heterozygosity rates and resolution of LOH detection.

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

An analysis of human microRNA and disease associations.

Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

Phylogenetic analysis of RhoGAP domain-containing proteins.

Evaluation of models to predict BRCA germline mutations.

A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

Identification and analysis of co-occurrence networks with NetCutter.

Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.

Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

Genomic variability within an organism exposes its cell lineage tree.

Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.