21 Result(s)
within
Joel S. Bader
English
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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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Open AccessNext-generation large-scale binary protein interaction network for Drosophila melanogaster
Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of...
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Open AccessIdentifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure
Mycobacterium avium subsp. hominissuis (MAH) is increasingly recognized as a significant cause of morbidity, particularly in elderly patients or those with immune deficiency or underlying lung impairment. Disease...
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Open AccessGenome analysis of Mycobacterium avium subspecies hominissuis strain 109
Infection with Mycobacterium avium is a significant cause of morbidity and its treatment requires the use of multiple antibiotics for more than 12 months. In the current work, we provide the genome sequence, gene...
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Open AccessPR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity
Electrocardiographic PR interval measures atrio-ventricular depolarization and conduction, and abnormal PR interval is a risk factor for atrial fibrillation and heart block. Our genome-wide association study o...
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Open AccessHeterozygous diploid and interspecies SCRaMbLEing
SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution) is a genome restructuring technique that can be used in synthetic genomes such as that of Sc2.0, the synthetic yeast ge...
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Open AccessTranscriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism
Recent studies of genomic variation associated with autism have suggested the existence of extreme heterogeneity. Large-scale transcriptomics should complement these results to identify core molecular pathways...
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Open AccessRNA-Seq optimization with eQTL gold standards
RNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, map**, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of dif...
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Retraction Note: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK
In response to a concern raised by a reader about inconsistencies in our Letter between the results from the primary microarray screen and cell growth validation studies (Supplementary Table 2), we reviewed th...
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Open AccessEarly innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits
Pulmonary infection of humans by Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), results in active disease in 5-10% of individuals, while asymptomatic latent Mtb infection (LTBI) is es...
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Open AccessMolecular immunologic correlates of spontaneous latency in a rabbit model of pulmonary tuberculosis
Infection of humans with Mycobacterium tuberculosis (Mtb) results in latent tuberculosis infection (LTBI) in 90-95% of immune competent individuals, with no symptoms of active disease. The World Health Organizati...
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Grand network convergence
A report of the Systems Biology: Networks meeting, Cold Spring Harbor, USA, 22-26 March 2011.
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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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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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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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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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Correction: Corrigendum: Genome sequencing in microfabricated high-density picolitre reactors
Nature 437, 376–380 (2005) In this paper, the second name of Chun Heen Ho was misspelled as He. In the earlier Corrigendum (Nature 439, 502; 2006) the surnames of Stephen K. Hutchison and Brian C. Godwin were ...
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Correction: Corrigendum: Genome sequencing in microfabricated high-density picolitre reactors
Nature 437, 376–380 (2005)10.1038/nature03959 The following were omitted from the original author listing: Alex de Winter, James Drake, Robin Forte, Steve Hutchinson, William L. Lee, Michael Reifler and David ...
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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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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 ...
