Search results for "INFORMATICS"
showing 10 items of 2542 documents
BANΔIT: B’‐factor Analysis for Drug Design and Structural Biology
2020
The analysis of B‐factor profiles from X‐ray protein structures can be utilized for structure‐based drug design since protein mobility changes have been associated with the quality of protein‐ligand interactions. With the BANΔIT (B’‐factor analysis and ΔB’ interpretation toolkit), we have developed a JavaScript‐based browser application that provides a graphical user interface for the normalization and analysis of B’‐factor profiles. To emphasize the usability for rational drug design applications, we have analyzed a selection of crystallographic protein‐ligand complexes and have given exemplary conclusions for further drug optimization including the development of a B’‐factor‐supported pha…
Retraction: Alcohol consumption and hormonal alterations related to muscle hypertrophy: a review
2014
Detrimental effects of acute and chronic alcohol (ethanol) consumption on human physiology are well documented in the literature. These adversely influence neural, metabolic, cardiovascular, and thermoregulatory functions. However, the side effects of ethanol consumption on hormonal fluctuations and subsequent related skeletal muscle alterations have received less attention and as such are not entirely understood. The focus of this review is to identify the side effects of ethanol consumption on the major hormones related to muscle metabolism and clarify how the hormonal profiles are altered by such consumption.
BOGENVI: A Biomedical Ontology for Modelling Gene*Environment Interactions on Intermediate Phenotypes in Nutrigenomics Research
2008
Nutritional Genomics is demanding computing models and technological platforms in order to support acquisition, storage, management and presentation of all the information generated coming from heterogeneous sources: genotypes, environmental factors (diet and other life-style factors) and phenotypes (intermediate and final phenotypes). Our aim is to build a biomedical ontology in order to modelling gene*environment interactions on intermediate phenotypes by means of formalising and integrating genomic, environmental and phenotypic data, in the field of research on Nutritional Genomics applied to cardiovascular diseases and associated phenotypes. This ontology is part of a Health Information…
Classification and retrieval on macroinvertebrate image databases
2011
Aquatic ecosystems are continuously threatened by a growing number of human induced changes. Macroinvertebrate biomonitoring is particularly efficient in pinpointing the cause-effect structure between slow and subtle changes and their detrimental consequences in aquatic ecosystems. The greatest obstacle to implementing efficient biomonitoring is currently the cost-intensive human expert taxonomic identification of samples. While there is evidence that automated recognition techniques can match human taxa identification accuracy at greatly reduced costs, so far the development of automated identification techniques for aquatic organisms has been minimal. In this paper, we focus on advancing …
UPC++ for bioinformatics: A case study using genome-wide association studies
2014
Modern genotyping technologies are able to obtain up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as SNP-SNP interactions, in Genome-Wide Association Studies is an important but time-consuming operation since statistical computations have to be performed for each pair of measured markers. Therefore, a variety of HPC architectures have been used to accelerate these studies. In this work we present a parallel approach for multi-core clusters, which is implemented with UPC++ and takes advantage of the features available in the Partitioned Global Address Space and Object Oriented Programming models. Our solution is base…
Integrative bioinformatics and omics data source interoperability in the next-generation sequencing era-Editorial.
2021
With the advent of high-throughput and next-generation sequencing (NGS) technologies [1], huge amounts of ‘omics’ data (i.e. data from genomics, proteomics, pharmacogenomics, metagenomics, etc.) are continuously produced. Combining and integrating diverse omics data types is important in order to investigate the molecular machinery of complex diseases, with the hope for better disease prevention and treatment [2]. Experimental data repositories of omics data are publicly available, with the main aim of fostering the cooperation among research groups and laboratories all over the world. However, despite their openness, the effective integrated use of available public sources is hampered by t…
Frequent chromosomal gains in recurrent juvenile nasopharyngeal angiofibroma.
2007
Juvenile nasopharyngeal angiofibroma (JNA) is a rare benign tumor, mostly affecting adolescent males. Some patients develop recurrences after surgery independently of completeness of removal. Only very limited data concerning underlying chromosomal changes are available. We therefore analyzed samples of 22 JNAs, including six recurrences, with comparative genomic hybridization (CGH). Additionally, quantitative image cytometry was used for measurement of DNA aneuploidy in representative samples. Of the 13 primary JNAs without later recurrence, DNA gains were identified on autosomes in only two samples. Four patients with one or two recurrences were included in the study; for one of these, no…
Serum proteome profiling of primary breast cancer indicates a specific biomarker profile.
2011
Non-invasive biomarkers for early breast cancer detection are urgently needed, as the risk of recurrent morbidity and mortality is closely related to the stage of the disease at the time of primary surgery. Currently, there are no established clinical biomarkers for breast cancer. Evaluation of protein expression patterns in body fluids using proteomic technologies can be used to discover new biomarkers for the detection of breast cancer. The aim of this study was to identify a biomarker signature identifying primary non-metastatic breast cancer and healthy controls. We screened 91 serum samples including 45 breast cancer patients and 46 healthy women using a proteomic approach. We found 14…
Progression-free survival as a surrogate for overall survival in advanced/recurrent gastric cancer trials: a meta-analysis.
2013
The traditional endpoint for assessing efficacy of chemotherapies for advanced/recurrent gastric cancer is overall survival (OS), but OS requires prolonged follow-up. We investigated whether progression-free survival (PFS) is a valid surrogate for OS. Using individual patient data from the GASTRIC meta-analysis, surrogacy of PFS was assessed through the correlation between the endpoints and through the correlation between the treatment effects on the endpoints. External validation of the prediction based on PFS was also evaluated. Individual data from 4069 patients in 20 randomized trials were analyzed. The rank correlation coefficient between PFS and OS was 0.853 (95% confidence interval […
SnapShot: Hepatocellular carcinoma.
2014
Hepatocellular carcinoma is the sixth most common cancer globally and the second most lethal cancer worldwide. This SnapShot depicts the molecular and morphological features of this heterogeneous disease, as well as outlines associated prognostic factors, current and emerging therapies, and challenges ahead.