Bioinformatics

Recent Advances in Bioinformatics in the Medical Research Environment and Applications to the Study of Skin Diseases

Background:

The computer has become increasingly intertwined in society for the past 30 years. Within the academic health science centre, there is an increasing need for researchers to become skilled at using the Internet as a mechanism for the retrieval of scientific results and the underlying data. The discipline of bioinformatics, which uses computer technology to provide answers to biological questions, has been expanding in scope and utility for the past decade. Increasing numbers of research groups have been investing in bioinformatics infrastructure to aid in the research process. These continuing investments have led to the establishment for the first time of a supercomputing facility within a hospital. Such computational power is being used for the mapping of genes and the study of human disease.

Objective:

A discussion of the increasing role of computational biology in the research environment of the clinician scientist is presented here.

Conclusions:

Though the investment in a supercomputer may not be possible in most research settings, several less expensive alternatives relying on existing desktop computers can provide supercomputer-like performance within nearly any environment.

Bioinformatics for cancer management in the post-genome era

Human cancer is caused by multiple factors, such as genetic predisposition, chronic persistent inflammation, environmental factors, life style, and aging. Dysregulated proliferation, dysregulated adhesion, resistance to apoptosis, resistance to senescence, and resistance to anti-cancer drugs are features of cancer cells. Accumulation of multiple epigenetic changes and genetic alterations of cancer-associated genes during multi-stage carcinogenesis results in more malignant phenotypes. Post-genome science is characterized by omics data related to genome, transcriptome, proteome, metabolome, interactome, and epigenome as well as by high-throughput technology, such as whole-genome tiling oligonucleotide array, array CGH with 32,433 overlapping BAC clones, transcriptome microarray, mass spectrometry, tissue-based expression array, and cell-based transfection array. Benchtop oncology supplies Desktop oncology with large amounts of omics data produced by high-throughput technology. Desktop oncology establishes knowledge on cancer-related biomarkers, such as predisposition markers, diagnostic markers, prognostic markers, and therapeutic markers, by using bioinformatics and human intelligence of experts for data mining and text mining. Bedside oncology applies the knowledge established by Desktop oncology to determine therapeutics for cancer patients. Antibody drugs (Trastuzumab/Herceptin, Cetuximab/Erbitux, Bevacizumab/Avastin, et cetera), small molecule inhibitors for tyrosine kinases (Gefitinib/Iressa, Erlotinib/Tarceva, Imatinib/Gleevec, et cetera), conventional cytotoxic drugs, and anti-hormonal drugs are used for cancer chemotherapy. Biomarker monitoring contributes to therapeutic optional choice and drug dosage determination for cancer patients. Knowledge on biomarkers is feedforwarded from desktop to bedside in the translational research, and then biomarker monitoring is feedbacked from bedside to desktop in the reverse translational research. Desktop oncology is indispensable for cancer research in the post-genome era. Combination of genetic screening for cancer predisposition in the general population and precise selection of therapeutic options during cancer management could contribute to the realization of personalized prevention and to dramatically improve the prognosis of cancer patients in the future.

Bioinformatics education in an MLIS program: the McGill experience

Program objective – The objective of this course (GLIS691 – Bioinformatics) was to provide formal bioinformatics education within a master of library and information studies (MLIS) program. As bioinformatics becomes increasingly integral to biomedical research, there is a need for librarians to expand their practice into the domain of bioinformatics, supporting the efficient and accurate use of these complex resources. We developed this course, the first such course offered in a Canadian library school, in response to the demand for librarians to be able to support bioinformatics information needs. Setting – The course was offered in the winter term of 2005 in the Graduate School of Library and Information Studies, McGill University. Participants – Course participants were MLIS students. Program – The course took a library and information science perspective to bioinformatics. The goal was to provide students with the skills and knowledge to provide information services in the domain of bioinformatics and to collaborate in the design and development of bioinformatics resources. This included understanding the field of bioinformatics and the range of resources, the needs and requirements of user groups, practical searching skills, the creation of resources, and the role of the librarian. Conclusions – This course represents one approach to providing formal bioinformatics education for librarians. Librarians who are knowledgeable and proficient in bioinformatics will be able to expand the role of the library into this domain; apply their knowledge, skills, and expertise in a complex, chaotic information environment; and develop the essential role of the librarian in the domain of bioinformatics.

Medical biotechnology in India

The potential of biotechnology has just began to emerge in the 20th century. After the full knowledge of human genomes is available, biotechnology is going to play a major role in shaping the concept of future drug discovery, drug delivery, diagnostic methodology, clinical trials, and to a great extent the major lifestyle of the human society. This article is a comprehensive review of the major impact of biotechnology in diagnostics, antibiotics, r-proteins, vaccines, and antibodies production. It also highlights the future aspects of gene therapy in the management of healthcare. A comprehensive list of biotech products in healthcare management has been given. Also, the growth of biotechnology throughout the world at large and in the Indian industries in particular has been highlighted. Constraints, concerns and difficulties in biotechnology in India have been addressed mainly related to human resources, training institutions in India, funding in biotechnology, patent-related issues and regulatory hurdles. Like in information technology, India has great potential in bioinformatics as well. Some of the recent information on bioinformatics centers in India has been summarized. Indian biotechnology industries have the potential to use the modern discoveries in life sciences to reach an enviable position in the world of biotechnology.

Neuroscience databases: tools for exploring brain structure-function relationships

Faster than ever, neuroscience is generating vast amounts of data that await cross-referencing, comparison, integration and interpretation in the endeavour to unravel the mechanisms of the brain. The complex, diverse and distributed nature of these data requires the development of advanced neuroinformatics methodologies for databases and associated tools that are now beginning to emerge. This paper presents an overview of current issues in the representation, integration and analysis of neuroscience data from molecular to brain systems levels, including issues of implementation, standardization, management, quality control, copyright, confidentiality and acceptance. Particular emphasis is given to integrative neuroinformatics approaches for exploring structure-function relationships in the brain.