13,848 research outputs found
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
Establishment of computational biology in Greece and Cyprus: Past, present, and future.
We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and sizeābased on publication counts recorded in the literatureāand predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding
Complex-based analysis of dysregulated cellular processes in cancer
Background: Differential expression analysis of (individual) genes is often
used to study their roles in diseases. However, diseases such as cancer are a
result of the combined effect of multiple genes. Gene products such as proteins
seldom act in isolation, but instead constitute stable multi-protein complexes
performing dedicated functions. Therefore, complexes aggregate the effect of
individual genes (proteins) and can be used to gain a better understanding of
cancer mechanisms. Here, we observe that complexes show considerable changes in
their expression, in turn directed by the concerted action of transcription
factors (TFs), across cancer conditions. We seek to gain novel insights into
cancer mechanisms through a systematic analysis of complexes and their
transcriptional regulation.
Results: We integrated large-scale protein-interaction (PPI) and
gene-expression datasets to identify complexes that exhibit significant changes
in their expression across different conditions in cancer. We devised a
log-linear model to relate these changes to the differential regulation of
complexes by TFs. The application of our model on two case studies involving
pancreatic and familial breast tumour conditions revealed: (i) complexes in
core cellular processes, especially those responsible for maintaining genome
stability and cell proliferation (e.g. DNA damage repair and cell cycle) show
considerable changes in expression; (ii) these changes include decrease and
countering increase for different sets of complexes indicative of compensatory
mechanisms coming into play in tumours; and (iii) TFs work in cooperative and
counteractive ways to regulate these mechanisms. Such aberrant complexes and
their regulating TFs play vital roles in the initiation and progression of
cancer.Comment: 22 pages, BMC Systems Biolog
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The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report.
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities
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