Validating pathophysiological models of aging using clinical electronic medical records
Bioinformatics methods that leverage the vast amounts of clinical data promises to provide insights into underlying molecular mechanisms that help explain human physiological processes. One of these processes is adolescent development. The utility of ...
Simulated pathogenic conformational switch regions matched well with the biochemical findings
Pathogenic conformational conversion is a general causation of many disease, such as transmissible spongiform encephalopathy (TSE) caused by misfolding of prion, sickle cell anemia, and etc. In such structural changes, misfolding occurs in regions ...
Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data
BackgroundKinase inhibition is an increasingly popular strategy for pharmacotherapy of human diseases. Although many of these agents have been described as "targeted therapy", they will typically inhibit multiple kinases with varying potency. Pre-...
Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures
Characterizing the biomolecular systems' properties underpinning prognosis signatures derived from gene expression profiles remains a key clinical and biological challenge. In breast cancer, while different "poor-prognosis" sets of genes have predicted ...
On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers
- Rosalia Maglietta,
- Angela Distaso,
- Ada Piepoli,
- Orazio Palumbo,
- Massimo Carella,
- Annarita D'Addabbo,
- Sayan Mukherjee,
- Nicola Ancona
One of the major problems in genomics and medicine is the identification of gene networks and pathways deregulated in complex and polygenic diseases, like cancer. In this paper, we address the problem of assessing the variability of results of pathways ...
Evaluation of probabilistic and logical inference for a SNP annotation system
Genome wide association studies (GWAS) are an important approach to understanding the genetic mechanisms behind human diseases. Single nucleotide polymorphisms (SNPs) are the predominant markers used in genome wide association studies, and the ability ...
An automated reasoning framework for translational research
In this paper we propose a novel approach to the design and implementation of knowledge-based decision support systems for translational research, specifically tailored to the analysis and interpretation of data from high-throughput experiments. Our ...
BING
High throughput parallel genomic sequencing (Next Generation Sequencing, NGS) shifts the bottleneck in sequencing processes from experimental data production to computationally intensive informatics-based data analysis. This manuscript introduces a ...
TMA-TAB
The importance of tissue microarrays (TMA) as clinical validation tools for cDNA microarray results is increasing, whereas researchers are still suffering from TMA data management issues. After we developed a comprehensive data model for TMA data ...
MeSHing molecular sequences and clinical trials
The centralized and public availability of molecular sequence and clinical trial data presents an opportunity to identify potentially valuable linkages across the bench-to-bedside "T1" translational barrier. In this study, we sought to leverage keyword ...
Formal representation of eligibility criteria
Standards-based, computable knowledge representations for eligibility criteria are increasingly needed to provide computer-based decision support for automated research participant screening, clinical evidence application, and clinical research ...
