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UnknownA novel bi-level meta-analysis approach: applied to biological pathway analysis.

Motivation

The accumulation of high-throughput data in public repositories creates a pressing need for integrative analysis of multiple datasets from independent experiments. However, study heterogeneity, study bias, outliers and the lack of power of available methods present real challenge ...
S-EPMC5006307 | biostudies-literature
UnknownBabel's tower revisited: a universal resource for cross-referencing across annotation databases.

Motivation

Annotation databases are widely used as public repositories of biological knowledge. However, most of these resources have been developed by independent groups which used different designs and different identifiers for the same biological entities. As we show in this article, inco...
S-EPMC2435247 | biostudies-literature
UnknownMAGPEL: an autoMated pipeline for inferring vAriant-driven Gene PanEls from the full-length biomedical literature.
In spite of the efforts in developing and maintaining accurate variant databases, a large number of disease-associated variants are still hidden in the biomedical literature. Curation of the biomedical literature in an effort to extract this information is a challenging task due to: (i) the complexi...
S-EPMC7378213 | biostudies-literature
UnknownIdentifying significantly impacted pathways: a comprehensive review and assessment.

Background

Many high-throughput experiments compare two phenotypes such as disease vs. healthy, with the goal of understanding the underlying biological phenomena characterizing the given phenotype. Because of the importance of this type of analysis, more than 70 pathway analysis methods hav...
S-EPMC6784345 | biostudies-literature
UnknownA novel approach for predicting upstream regulators (PURE) that affect gene expression.
External factors such as exposure to a chemical, drug, or toxicant (CDT), or conversely, the lack of certain chemicals can cause many diseases. The ability to identify such causal CDTs based on changes in the gene expression profile is extremely important in many studies. Furthermore, the ability to...
S-EPMC10616115 | biostudies-literature
UnknownNovel T7 Phage Display Library Detects Classifiers for Active Mycobacterium Tuberculosis Infection.
Tuberculosis (TB) is caused by Mycobacterium tuberculosis (MTB) and transmitted through inhalation of aerosolized droplets. Eighty-five percent of new TB cases occur in resource-limited countries in Asia and Africa and fewer than 40% of TB cases are diagnosed due to the lack of accurate and e...
S-EPMC6070804 | biostudies-literature
UnknownDetecting qualitative changes in biological systems.
Currently, most diseases are diagnosed only after significant disease-associated transformations have taken place. Here, we propose an approach able to identify when systemic qualitative changes in biological systems happen, thus opening the possibility for therapeutic interventions before the occur...
S-EPMC7235093 | biostudies-literature
TranscriptomicsTranscription profiling of human placenta from women presenting at term with villitis of unknown etiology
Placental villous tissue from women at term presenting various degrees of villitis of unknown etiology were analysed using Affymetrix microarrays. The severity of inflammation was graded using four levels: 0(no inflammation), 1(mild inflammation - multifocal low grade villitis), 2(moderate inflammat...
ORGANISM(S): Homo sapiens 
2009-01-04 | E-TABM-577 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human amniotic fluid after `amnion treatment with surfactant protein-A
We investigated a potential role for SP-A in human pregnancy and parturition by examining SP-A expression patterns in amniotic fluid and the amnion
ORGANISM(S): Homo sapiens 
2010-04-12 | E-TABM-741 | biostudies-arrayexpress
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