XML in Motion from Genome to Drug

Information technology (IT) has emerged as a central to the solution of contemporary genomics and drug discovery problems. Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution. As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics tools. Organizing these data into knowledgeable databases and developing appropriate software tools for analyzing the same are going to be major challenges. XML (eXtensible Markup Language) forms the backbone of biological data representation and exchange over the internet, enabling researchers to aggregate data from various heterogeneous data resources. The present article covers a comprehensive idea of the integration of XML on particular type of biological databases mainly dealing with sequence-structure-function relationship and its application towards drug discovery. This e-medical science approach should be applied to other scientific domains and the latest trend in semantic web applications is also highlighted

Review on Proteomics Technologies and Its Application for Crop Improvement

Proteomics is the study of proteins and their interactions in a cell. Within the wide field of functional OMICS, proteomics has become a useful tool and the emphasis is shifting from genomics to the protein compliment of the human organism. Because proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. Hence the present review was to review proteomics technologies and their applications for crop improvement. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities and challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways and signalling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular and cellular biology. However, future developments may enable faster and more sensitive proteomics studies and Proteomics alone cannot provide all the information required for understanding cellular processes. Therefore Complementary approaches in genomics, metabolomics and bioinformatics will have to be used together with proteomics to permits a more holistic view of biological systems and their alterations in disease, so that the maximum benefit can be realized. Keywords: Bioinformatics, mass spectrometry, proteomics, Two-dimensional electrophoresi

Educating the educators: Incorporating bioinformatics into biological science education in Malaysia

Bioinformatics can be defined as a fusion of computational and biological sciences. The urgency to process and analyse the deluge of data created by proteomics and genomics studies has caused bioinformatics to gain prominence and importance. However, its multidisciplinary nature has created a unique demand for specialist trained in both biology and computing. In this review, we described the components that constitute the bioinformatics field and distinctive education criteria that are required to produce individuals with bioinformatics training. This paper will also provide an introduction and overview of bioinformatics in Malaysia. The existing bioinformatics scenario in Malaysia was surveyed to gauge its advancement and to plan for future bioinformatics education strategies. For comparison, we surveyed methods and strategies used in education by other countries so that lessons can be learnt to further improve the implementation of bioinformatics in Malaysia. It is believed that accurate and sufficient steerage from the academia and industry will enable Malaysia to produce quality bioinformaticians in the future

A streamlined approach to high-throughput proteomics

Proteomics has rapidly become an important tool for life science research, allowing the integrated analysis of global protein expression from a single experiment. To accommodate the complexity and dynamic nature of any proteome, researchers must use a combination of disparate protein biochemistry techniques, often a highly involved and time-consuming process. Whilst highly sophisticated, individual technologies for each step in studying a proteome are available, true high-throughput proteomics that provides a high degree of reproducibility and sensitivity has been difficult to achieve. The development of high-throughput proteomic platforms, encompassing all aspects of proteome analysis and integrated with genomics and bioinformatics technology, therefore represents a crucial step for the advancement of proteomics research. ProteomIQ™ (Proteome Systems) is the first fully integrated, start-to-finish proteomics platform to enter the market. Sample preparation and tracking, centralized data acquisition and instrument control, and direct interfacing with genomics and bioinformatics databases are combined into a single suite of integrated hardware and software tools, facilitating high reproducibility and rapid turnaround times. This review will highlight some features of ProteomIQ, with particular emphasis on the analysis of proteins separated by 2D polyacrylamide gel electrophoresis. © 2005 Future Drugs Ltd

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Bioinformatics: Computational Approaches for Genomics and Proteomics

Bioinformatics is a fast evolving field that combines biology, computer science, and statistics to analyze and comprehend enormous volumes of biological data. As a result of the introduction of high-throughput technologies like next-generation sequencing and mass spectrometry, genomic and proteomics research has generated enormous volumes of data, necessitating the development of computational tools to process and extract useful insights from these datasets. This presentation presents a survey of computational approaches in bioinformatics with a particular emphasis on their application to genomics and proteomics. The study of the entire genome is a topic covered in the discipline of genomics, which also includes genome annotation, assembly, and comparative genomics. Proteomics focuses on the investigation of proteins, including their identification, quantification, structural analysis, and functional characterization. Consequently, the importance of the area of bioinformatics has increased