Search results for "Bioinformatic"

Modelling swarm-intelligent systems for medical applications

2017

Modeling swarm intelligent systems has attracted attention of researchers over the last decade, as the attributes such as self-organization, self-regulation or collective behavior exhibited by the system entities while following a certain set of rules, can be implemented with the aim at investigating complexity of the problems that an individual would be unable to tackle in real world. In this keynote paper, meta-heuristics and paradigms of modeling swarm-intelligent systems will be discussed with respect to their application areas for medical purposes.

An inducible mouse model of colon carcinogenesis for the analysis of sporadic and inflammation-driven tumor progression.

2007

Colorectal cancer is a life-threatening disease that can develop spontaneously or as a complication of inflammatory bowel diseases. Mouse models are essential tools for the preclinical testing of novel therapeutic options in vivo. Here, we provide a highly reliable protocol for an experimental mouse model to study the development of colon cancers. It is based on the mutagenic agent azoxymethane (AOM), which exerts colonotropic carcinogenicity. Repeated intraperitoneal administration of AOM results in the development of spontaneous tumors within 30 weeks. As an alternative option, inflammation-dependent tumor growth can be investigated by combining the administration of AOM with the inflamma…

Prognostic and predictive factors in colorectal cancer: Kirsten Ras in CRC (RASCAL) and TP53CRC collaborative studies.

2005

Mutations in the Ki-ras and TP53 genes are the most frequently observed genetic alterations in colorectal cancer (CRC). Ki-ras mutations are mostly found in codons 12 and 13, and less in codon 61. The majority of the TP53 mutations occur in the core domain which contains the sequence-specific DNA binding activity of the protein, and they results in loss of DNA binding. Few centres have sufficient patients to collect detailed information in the large numbers required to determine the impact of individual ki-ras and TP53 genotypes on outcome. Moreover, it has been reported that specific genetic alterations, and not any mutation, might play a different biological role in cancer progression. Fo…

Snapshot liver transcriptome in hepatocellular carcinoma

2012

Lately, advances in high throughput technologies in biomedical research have led to a dramatic increase in the accessibility of molecular insights at different levels of cancer biology such as genome, epigenome, transcriptome, proteome, and others. Among the diverse biological layers, the transcriptome has been most extensively studied especially due to the successful and broad introduction of the microarray technology. The future prospect of broad disposability of deep sequencing technology will furthermore lead to a more sensitive detection of lowly expressed transcripts and to an increase in the number of newly identified transcripts, but also to increase the discovery and characterizati…

Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics

2021

To date, computational approaches have been recognized as a key component in drug design and discovery workflows. Developed to help researchers save time and reduce costs, several computational tools have been developed and implemented in the last twenty years. At present, they are routinely used to identify a therapeutic target, understand ligand–protein and protein–protein interactions, and identify orthosteric and allosteric binding sites, but their primary use remains the identification of hits through ligand-based and structure-based virtual screening and the optimization of lead compounds, followed by the estimation of the binding free energy. The repurposing of an old drug for the tr…

Quantitative Analysis of Dynamic Association in Live Biological Fluorescent Samples

2014

Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed. Point-pattern matching provides a measure of correspondence between two point-sets under various changes between the sets. Thus, it can be used for robust quantitative analysis of vesicle …

Unreliable predictions about COVID‐19 infections and hospitalizations make people worry: The case of Italy

2021

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

2007

Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric) has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rath…

Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics

2008

Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems

2015

This is a post-peer-review, pre-copyedit version of an article published in IEEE - ACM Transactions on Computational Biology and Bioinformatics. The final authenticated version is available online at: http://dx.doi.org/10.1109/TCBB.2015.2389958 [Abstract] High-throughput genotyping technologies (such as SNP-arrays) allow the rapid collection of up to a few million genetic markers of an individual. Detecting epistasis (based on 2-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. Computational methods to detect epistasis therefore suffer from prohibitively lon…