Workshop on IT in Biology and Medicine (ITBM'13)

Department of Biotechnology,

Manipal University Dubai Campus

Firdos Alam Khan, Professor, and Chairperson, Department of Biotechnology, Manipal University Dubai, UAE and over past 8 years Prof. Khan has been associated with the Manipal University Dubai. Professor Khan received his PhD degree in Neuroscience from Nagpur University, India. He has more than 19 years of research and teaching experience in various domains of biotechnology. He did his first postdoctoral research from Tata Institute of Fundamental Research, Mumbai, India and second postdoctoral research from Massachusetts Institute of Technology (MIT), Cambridge, USA. He worked with Reliance Life Sciences a multimillion dollar Biotech Company based in Mumbai, India, as a research scientist and worked on adult and embryonic stem cell projects. His area of specialty in biotechnology includes stem cell technology, neuropharmacology, and neuroscience. He has written numerous articles in various national and international journals in the areas of neuroscience, neuropharmacology and stem cell biology. He has been granted two US patents in the field of stem cell technology. He has nominated as a member of scientific advisory committee for Pharmaceutical & Biotechnology Middle East. He has written a textbook entitled “Biotechnology Fundamentals” in 2011 published by CRC Press/Francis Taylor Group, USA. He has been associated with various international scientific organizations like International Brain Research Organization, France, and Society for Neuroscience, USA.

The making of new drug molecule is a highly expensive and time-consuming process especially drug target identification is very laborious and time-consuming and it’s has been suggested that about 12-15 years of research is required in order to bring a new drug molecule in the market. Over many years drug and pharmaceutical companies were on hunt to identify a technology that can expedite the drug discovery process with cost-effective way and fortunately with advent of information technology, it has become possible to virtually design the drug molecule in the computer. The computer-aided drug design technology has given a tremendous opportunity to pharmaceutical companies to identify new potential drug targets with less-time consumption. In recent years, we have seen an explosion in the amount of biological data being generated and that enormous amount of biological databases is doubling in size every 2 years. With the help of information technology it become possible not only to analyze the biological data but also possible to completely map the genome sequences of more than 100 different species. More recently the pharmaceutical industry has incorporated genomics as a source of drug targets. It also recognizes that the field of information technology is crucial for validating these potential drug targets and for determining which ones are the most appropriate for actual drug development process. Of late, there has been a change in the way that drugs are being developed due to our amplified understanding of molecular biology of the target receptors. Though information technology has expedited the drug discovery process but still laboratory research is mandatory to evaluate drug efficacy both in animals and human trials to study the unknown or undesirable side effects of drug molecules.

Computing and Information Science

Masdar Institute

Dr. Andreas Henschel received his M.Sc. in Computational Logic at the Technische Universitaet Dresden, Germany in 2002. He then joined Scionics Computer Innovation Ltd., where he worked for the Bioinformatics service facility of the Max Planck Institute Dresden, Germany. In 2008 he received his PhD from Technische Universitaet Dresden in Bioinformatics. His PhD thesis focused on the classification of protein-protein interactions and was awarded summa cum laude. He joined Masdar Institute as a post-doctoral researcher in April 2009 and will join as faculty in August 2011. From August 2011 till August 2012 he worked at Martin Polz' lab (Massachusetts Institute of Technology, Cambridge, USA) as Visiting Scholar.

The ever decreasing cost of DNA sequencing has led to a recent deluge of Metagenomic projects and Microbial Community Profiling experiments in all kinds of environments, e.g., the Human Microbiome Projectand the Earth Microbiome project. It is clear that the current data collections require formalisms to integrate knowledge of meta data and ontolgy based knowledge management systems are in an early stage to tackle this task. Within this framework we suggest an approach of how a topology of environments can be derived from 16S rRNA profiles using phylogeny based distance measures.

On a more detailed level, microbial populations are defined as ecologically and phylogenetically coherent groups. Their dynamics with respect to their habitat is studied through time series or spacial sampling. In order to discover habitat changes and emerging sub-populations, it is necessary to relate populations from different sampling time points. This is a frequent task and it is therefore desirable to automize the process of relating populations to each other. To this end we developed a method that integrates populations associations, their assigned habitats and their combined phylogeny.

College of Engineering

Khalifa University

Paul D. Yoo is an Assistant Professor in the Department of Electrical and Computer Engineering, at Khalifa University, Science, Technology and Research (KUSTAR). He was a Research Scientist in the Centre for Distributed and High Performance Computing, at the University of Sydney from 2008 to 2009, and PhD Researcher (Quantitative Research) at the Capital Markets CRC “ initiated and administered by the Australia Federal Department for Education, Science and Training, from 2004 to 2008. Recently, he was a Principal Investigator (PI) of a e-Bioinformatics research project funded by the Emirates Foundation 2010-2011, and has been supervising a number of MSc/PhD students in the areas of bioinformatics/intelligent systems. Paul is the inventor for DomNet, SiteSeek and IGRN, well-regarded artificial intelligent systems in proteomics. He has also been awarded a number of prestigious international and national awards for his work in research and application of artificial intelligence in bio-/medical-/health-, green ICT and financial domains, notably ARC Research Network in EII Award, Emirates Foundation (EF) Research Award, Australian Postgraduate Award, and Capital Markets CRC Award.

In this talk, the following three research topics will be discussed: (1) bioinformatics – big data and computational power; (2) protein structure prediction; and (3) prediction of AIDS disease progression.