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Article
Open AccessIntegrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases
Neurodegenerative diseases share common pathologic features including neuroinflammation, mitochondrial dysfunction and protein aggregation, suggesting common underlying mechanisms of neurodegeneration. We unde...
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Article
Open AccessIntegrating multiple ‘omics’ analyses identifies serological protein biomarkers for preeclampsia
Preeclampsia (PE) is a pregnancy-related vascular disorder which is the leading cause of maternal morbidity and mortality. We sought to identify novel serological protein markers to diagnose PE with a multi-’o...
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Article
Open AccessWhole genome sequencing in support of wellness and health maintenance
Whole genome sequencing is poised to revolutionize personalized medicine, providing the capacity to classify individuals into risk categories for a wide range of diseases. Here we begin to explore how whole ge...
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Article
Open AccessContent-based microarray search using differential expression profiles
With the expansion of public repositories such as the Gene Expression Omnibus (GEO), we are rapidly cataloging cellular transcriptional responses to diverse experimental conditions. Methods that query these re...
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Open AccessComparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants
Combining the results of studies using highly parallelized measurements of gene expression such as microarrays and RNAseq offer unique challenges in meta analysis. Motivated by a need for a deeper understandin...
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Article
Open AccessTranslational bioinformatics in the cloud: an affordable alternative
With the continued exponential expansion of publicly available genomic data and access to low-cost, high-throughput molecular technologies for profiling patient populations, computational technologies and info...
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Article
Likelihood ratios for genome medicine
Patients are beginning to present to healthcare providers with the results of high-throughput individualized genoty**, and interpreting these results in the context of the explosive growth of literature link...
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Article
Open AccessOverview of BioCreative II gene normalization
The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a cha...
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Article
Open AccessAutomating document classification for the Immune Epitope Database
The Immune Epitope Database contains information on immune epitopes curated manually from the scientific literature. Like similar projects in other knowledge domains, significant effort is spent on identifying...
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Article
Open AccessData preparation and interannotator agreement: BioCreAtIvE Task 1B
We prepared and evaluated training and test materials for an assessment of text mining methods in molecular biology. The goal of the assessment was to evaluate the ability of automated systems to generate a li...
