7 Result(s)
within
Joel S. Bader
English
Algorithms
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Article
Open AccessPriors, population sizes, and power in genome-wide hypothesis tests
Genome-wide tests, including genome-wide association studies (GWAS) of germ-line genetic variants, driver tests of cancer somatic mutations, and transcriptome-wide association tests of RNAseq data, carry a hig...
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Article
Open AccessResolving the structure of interactomes with hierarchical agglomerative clustering
Graphs provide a natural framework for visualizing and analyzing networks of many types, including biological networks. Network clustering is a valuable approach for summarizing the structure in large networks...
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Article
Open AccessPredicting functional associations from metabolism using bi-partite network algorithms
Metabolic reconstructions contain detailed information about metabolic enzymes and their reactants and products. These networks can be used to infer functional associations between metabolic enzymes. Many meth...
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Article
Open AccessNeMo: Network Module identification in Cytoscape
As the size of the known human interactome grows, biologists increasingly rely on computational tools to identify patterns that represent protein complexes and pathways. Previous studies have shown that densel...
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Article
Open AccessAnalytical approximations for the amplitude and period of a relaxation oscillator
Analysis and design of complex systems benefit from mathematically tractable models, which are often derived by approximating a nonlinear system with an effective equivalent linear system. Biological oscillato...
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Article
Open AccessGenetic interaction motif finding by expectation maximization – a novel statistical model for inferring gene modules from synthetic lethality
Synthetic lethality experiments identify pairs of genes with complementary function. More direct functional associations (for example greater probability of membership in a single protein complex) may be infer...
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Article
Open AccessCommensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast
In a genetic interaction, the phenotype of a double mutant differs from the combined phenotypes of the underlying single mutants. When the single mutants have no growth defect, but the double mutant is lethal ...
