bioinformatics Articles
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Complexity metrics for ontology based information
An ontology defines technical terms and shows interrelationships between terms for particular application areas. XML-based standards such as OWL and DAML provide mechanisms to produce XML based ontologies. Ontologies are used in service matching and dynamic web service composition, and are heavily used in bioinformatics and genomics to characterise the structure of living things. Our research ...
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UPNT: uniform projection and neighbourhood thresholding method for motif discovery
Motif discovery is a significant problem in Bioinformatics. According to the complexity of most signals in biologic sequences, there are no extremely good models or dependable algorithms to solve this problem. This paper introduces the Uniform Projection and Neighbourhood Thresholding (UPNT) algorithm, which is based on two efficient strategies: Uniform Projection and Neighbourhood-based ...
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Nomadic genetic algorithm for multiple sequence alignment (MSANGA)
Genetic algorithms (GA) are adaptive search procedures that try to produce a globally optimum solution for problems of huge search space. This paper speaks about a variant of the standard genetic algorithm (SGA) called nomadic genetic algorithm (NGA) which is based on the concept of 'birds of the same feather flock together'. This NGA is found to maintain the diversity of individuals in the ...
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The Medical University of South Carolina - Case study
Medical University of South Carolina (MUSC) is South Carolina’s only comprehensive academic health science center. Its purpose is to preserve and optimize human life in South Carolina through the vision to lead health innovation for the lives it touches. Ludivine Renaud has a Bachelor’s degree in marine biology from the College of Charleston, a Master’s degree in environmental ...
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National Institutes of Health – Perinatology Research Branch - Case Study
The Perinatology Research Branch (PRB) is the only Clinical Branch in the Division of Intramural Research (DIR) of the National Institutes of Health (NIH) to focus its research on human pregnancy and unborn children. It is currently housed at the Detroit Medical Center in Detroit, Michigan through a service contract. The Branch has thrived in this environment, earning a national and international ...
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The Applications of Bioinformatics in Microbial Technology
Bioinformatics is a discipline developed on the basis of biology, mathematics and computer science. It effectively acquires and analyzes biological data such as nucleic acid sequences and protein structures, so as to conduct comprehensive and accurate biological analysis. Bioinformatics is an extremely important tool to study the microorganisms, which are widespread and highly varied. ...
By CD Genomics
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Project - VIBE Education Edition
Project Summary 1. Project Design Throughout the project, INCOGEN collaborated closely with a team of professionals from the College of William & Mary (W&M) and other institutions to develop an effective plan for assessment and design of the educational software and its introduction into the classroom. This team was comprised of bioinformatics educators from the Departments of Biology, ...
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How biotechnology changes pharma R&D: a managerial perspective
In recent years, pharmaceutical R&D has increasingly been affected by two main factors. On the one hand, there is a technology push factor related to the development of biotechnology and, on the other hand, there is the demand pull related to the growing R&D performance required by the market. In this paper, on the basis of the empirical study, the main R&D related cost and revenue drivers ...
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Integration of KnetMiner tools - Case Study
Integration of data mining and bioinformatic tools to enable scientists to accelerate genomics-based crop improvement and ...
By Genestack
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The generalised k-truncated suffix tree for time-and space-efficient searches in multiple DNA or protein sequences
Efficient searching for specific subsequences in a set of longer sequences is an important component of many bioinformatics algorithms. Generalised suffix trees and suffix arrays allow searches for a pattern of length n in time proportional to n independent of the length of the sequences, and are thus attractive for a variety of applications. Here, we present an algorithm termed the generalised ...
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How do you validate a pathway analysis method? How do you compare such methods?
My previous post, Pathway Analysis vs Gene Set Analysis, ended with an interesting question: has anybody really compared side-by-side gene set analysis methods and pathway analysis methods on the same data sets? Well, the answer is: not yet! The main reason for this is that it is extremely difficult to objectively validate the results of a pathway analysis method. It is even more difficult to ...
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Dr Parag Mallick in conversation with Adam M Hill. `Extra Time` podcast.
Adam talks to Dr Parag Mallick from Stanford University where he is a Professor. Having originally trained as an engineer biochemist, Parag's research is diverse and spans computational and experimental systems biology, cancer biology, and nanotechnology. Parag talks about the diverse applications of proteomics and the value of bringing together different perspectives and disciplines to tackle ...
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Research Highlight: Stanford University - Case Study
AdvaitaBio’s IPathwayGuide plays significant role in the research of a Stanford investigator. Stanford University is one of the world’s leading research and teaching institutions. With a 1.69 billion dollar annual sponsored research budget, Stanford has been delivering breakthrough discoveries in numerous domains. For over 6 years, Dr. Linda Yip has been conducting research at ...
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Bioinformatics Workflow for Whole Genome Sequencing
Whole genome sequencing (WGS) has the capacity to greatly enhance genomic knowledge and understand mysteries of life by utilizing the most advanced genetic sequencing technologies. WGS can be used for variant calling, genome annotation, phylogenetic analysis, reference genome construction, and more. WGS tries to cover the whole genome, but actually covers 95% of the genome with technical ...
By CD Genomics
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The University of Chicago - Case Study
The research goals of Carole Ober’s laboratory at the University of Chicago are to identify genetic variants that influence gene expression and epigenetic patterns in tissues relevant to complex phenotypes, especially related to asthma and fertility. The lab uses both freshly isolated cells, as well as tissue and cell culture models of gene-environment interactions to explore ...
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The Barbara Ann Karmanos Cancer Center - Case study
The Barbara Ann Karmanos Cancer Center, located in midtown Detroit, is the only National Cancer Institute (NCI)-designated comprehensive cancer center in metro Detroit and one of just 51 centers of its kind in the United States. The comprehensive cancer center designation means patients can access treatments exclusive to Karmanos, as well as clinical trials, cancer prevention programs, and ...
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CD Genomics Perspective: Bioinformatic Analysis for Microbial Metagenomics
Introduction to Bioinformatics for Microbial Metagenomics In microbial ecology, metagenomic techniques are now widely utilized to research microbial communities in greater depth, including many strains that cannot be produced in the lab. Microbial bioinformatics may now be used to mine large metagenomic datasets for broad patterns that govern microbial communities. Typical metagenomic and ...
By CD Genomics
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A synoptic survey of the bioethics of human genome research
The authors discuss the wider social and ethical consequences of recent developments in bioinformatics, "DNA fingerprinting", genetic screening, health and insurance and the patenting of life forms. They appraise the ethics of human genome research, including research conducted under the Human Genome Diversity Project (HGDP) - one type of human genome research which specifically ...
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Bioinformatics Analysis Brings Disease Genomics Research to a Crossroads
Introduction Since the completion of the Human Genome Project, genomics has played an increasingly critical role in the biomedical field. Its applications include variation and risk assessment in disease genomics, analysis of changes in transcriptomic gene expression, revealing epigenetic effects on tissue and organ development, and heterogeneity at the single-cell level, among others. We present ...
By CD Genomics
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A yeast exosome cofactor, mpp6, functions in rna surveillance and in the degradation of noncoding rna transcripts
A genome-wide screen for synthetic lethal (SL) interactions with loss of the nuclear exosome cofactors Rrp47/Lrp1 or Air1 identified 3'5' exonucleases, the THO complex required for mRNP assembly, and Ynr024w (Mpp6). SL interactions with mpp6 were confirmed for rrp47 and nuclear exosome component Rrp6. The results of bioinformatic analyses revealed homology between Mpp6 and a human exosome ...
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