Prof. Sir Munir Pirmohamed
Professor Sir Munir Pirmohamed is currently David Weatherall Chair in Medicine at the University of Liverpool, and a Consultant Physician at the Royal Liverpool University Hospital. He is also the Associate Executive Pro Vice Chancellor for Clinical Research and Head of Department of Molecular and Clinical Pharmacology. He also holds the only NHS Chair of Pharmacogenetics in the UK, and is Director of the M.R.C. Centre for Drug Safety Sciences, and Director of the Wolfson Centre for Personalised Medicine. He is also an inaugural NIHR Senior Investigator, and Fellow of the Academy of Medical Sciences in the UK. He has authored over 350 peer-reviewed publications.
Professor Pirmohamed’s research focuses on individual variability in drug response (including anti-cancer drugs), both safety and efficacy, with a view to evaluating the mechanisms, and identifying strategies to personalise healthcare in order to optimise drug efficacy and minimise toxicity. The work spans the whole spectrum from discovery to implementation with laboratory based studies being linked translationally to patient studies, with the aim being to develop the evidence base that can move discoveries from the lab to the clinic, and from clinic to application. Professor Pirmohamed has received a number of honours including most recently, the William Withering Medal from the Royal College of Physicians. Read more
Discovering and implementing drug safety biomarkers
Munir Pirmohamed, Wolfson Centre for Personalised Medicine, Waterhouse Building, 1-5 Brownlow Street, Liverpool, L69 3GL.
Adverse drug reactions (ADRs) are a major clinical problem accounting for a great deal of morbidity, mortality and are a drain on healthcare resources. ADRs can generally be divided into on-target and off target reactions. Both types of ADRs have a genetic predisposition, but the quantitative contribution of genetic vs. non-genetic factors varies with the type of reaction, the drug implicated and the patient’s clinical co-morbidities. Genomic research in this area has progressed from discovery, using candidate gene approaches, to genome-wide approaches. The latter has met with a lot of success because the effect size of pharmacogenomic biomarkers is greater than the effect size observed for complex diseases. A notable area has been the identification of different HLA alleles predisposing to a variety of serious immune mediated adverse drug reactions. The effect size in such cases can be so high that it allows for implementation into practice, which has prevented ADRs in patients. An example of this is the use of HLA-B*57:01 to prevent abacavir hypersensitivity, and HLA-B*15:02 to prevent carbamazepine-induced Stevens-Johnson Syndrome and toxic epidermal necrolysis in South East Asian patients. Genetic predisposing loci outside the HLA region are also being discovered which is providing new insights into the mechanisms of the ADRs. Although the general framework for implementation has focused on the use of genetic tests to predict and prevent ADRs, genetic tests can be used in more novel ways to improve patient outcomes, including for diagnosis and stratification – such approaches will be discussed in the presentation.
Prof. Katsushi Tokunaga
- Human Genome Variation: Editor-in-Chief
- Journal of Human Genetics: Advisory Editor
- HLA: Advisory Editor
- International Journal of Immunogenetics: Advisory Board
- Journal of Genetics and Genomics: International Members of Editorial Board
- Genes & Genomics: Advisory Board
- DNA Polymorphism: Editorial Board
ISCB Speaker
Prof. Christine Orengo
The Orengo Group’s research focuses on how proteins function and evolve, how relatives in a family acquire new functions and how they evolve to operate in different biological contexts. Over twenty years ago, the group established the CATH evolutionary classification of protein domains which is a partner resource in InterPro and widely accessed. The Orengo Group develops methods for predicting functions for proteins and the networks they participate in. They are interested in integrating heterogenous functional genomics data to learn how protein networks rewire during evolution and under different biological conditions. To optimise and validate these methods the group collaborate with experimental groups characterising the signalling processes involved in development, neuropathic pain, ageing and cancer. Orengo has collaborated with over 30 groups worldwide and several consortia including the EU funded InteGr8, Biosapiens, EMBRACE, ENFIN, IMPACT, Europain consortia exploiting CATH tools and data, the NIH funded MCSG, SGCID consortia researching structural genomics and the CRUK funded LPC and DDIP consortia researching biological networks. The original CATH resource publication has been cited ~2600 times. Christine Orengo became a Fellow of the Royal Society of Biology in 2014, an elected member of EMBO in 2014, and a Fellow of the International Society of Computational Biology in 2016. She has been on the board of ISCB since 2011 and a Vice president of ISCB since 2013. Read more
Dr. Denis Bauer
Dr. Denis Bauer is an internationally recognised expert in machine learning, specifically in processing big genomic data to help unlock the secrets in human DNA – secrets that could change the course of human history. Her achievements include developing an open-source, artificial intelligence-based search engine in the cloud that helps researchers pinpoint the exact genes they need to study or edit to cure disease.
As CSIRO’s transformational bioinformatics leader, Denis is involved in Australian and international initiatives to integrate genomics into medical practice. She is frequently invited as a keynote at heavyweight medical and IT conferences including Amazon Web Services Summit ‘17/’18, International conference on Frontotemporal Dementia 18, Alibaba Infinity Singapore ’18 and Open Data Science Conference India ’18. Her revolutionary achievements have been featured in international press such as GenomeWeb, ZDNet, Computer World, CIO Magazine, the AWS Jeff Barr blog, and was in ComputerWeekly’s Top 10 IT stories of 2017.
Denis holds a BSc from Germany and PhD in Bioinformatics from the University of Queensland, and has completed postdoctoral research in both biological machine learning and high-throughput genetics. She has 33 peer-reviewed publications (14 as first or senior author) and an H-index 14. Read more
Genomic data is outpacing traditional Big Data disciplines, producing more information than Astronomy, twitter, and YouTube combined. As such, Genomic research has leapfrogged to the forefront of Big Data and Cloud solutions. We developed software platforms using the latest in cloud architecture, artificial intelligence and machine learning to support every aspect genome medicine; from disease gene detection through to validation and personalized medicine.
This talk outlines how we find disease genes for complex genetic diseases, such as ALS, using VariantSpark, which is a custom machine learning implementation capable of dealing with Whole Genome Sequencing data of 80 million common and rare variants. To support disease gene validation, we created GT-Scan, which is an innovative web application, which we think of it as the “search engine for the genome”. It enables researchers to identify the optimal editing spot to create animal models efficiently. The talk concludes by demonstrating a novel cloud-based architecture that enables a decision support framework capable of processing genomic and medical data at a speed fit for point-of-care application.
Prof. Stuart C. Ray
Prof. Stuart C. Ray, MD, FACP, FIDSA serves as Vice Chair of Medicine for Data Integrity and Analytics and is a Professor in the Division of Infectious Diseases within the Department of Medicine, with secondary appointments in Viral Oncology and Health Sciences Informatics. He is Scientific Director of the JHU Laboratory for Integrated NanoDiagnostics, directs the virology laboratory and is a clinical investigator in the Center for Viral Hepatitis Research in the Division of Infectious Diseases. He is a faculty member of the Graduate Immunology program, the Graduate Pharmacology program, and of the Janeway Firm of the Osler Medical Service.
Dr. Ray received his M.D. from Vanderbilt University School of Medicine in 1990. After an internship and residency at Johns Hopkins Hospital, he continued there as an Assistant Chief of Service and fellow in Infectious Diseases. During his fellowship, he studied the immunology and sequence variation of HIV in the laboratory of Dr. Robert Bollinger. During that time, he developed an interest in HIV sequence variation during antiretroviral therapy in a productive collaboration with Dr. Robert Siliciano that continues to the present.
In 1997 Dr. Ray joined the Johns Hopkins faculty, and under the mentorship of Dr. David Thomas shifted his primary research focus to hepatitis C virus (HCV). His laboratory work has focused on the sequence variation of HCV during acute and chronic infection, developing and applying computational and molecular biology tools to underlying mechanisms including stochastic variation, immune selection, and viral fitness. He continues to care for patients with HIV, HCV, and other infectious diseases.
Prof. Adrian V. S. Hill
Professor Hill is Director of the Jenner Institute, which focuses on designing and developing vaccines for infectious diseases prevalent in developing countries, such as HIV/AIDS, malaria and tuberculosis. He also heads a group at the Wellcome Trust Centre for Human Genetics which studies genetic susceptibility factors for common bacterial diseases. He is a passionate believer in the power of molecular medicine to design and deliver new health care interventions that will improve the lives of the poorest billion in sub-Saharan Africa and elsewhere. His own vaccine research programme has developed one of the most promising potential vaccines for malaria which is currently in large scale trials in infants in sub-Saharan Africa.
In 2014 his group led the first clinical trial of an Ebola virus vaccine targeting the outbreak of Ebola in West Africa.
GOBLET Speaker
Dr Eija Korpelainen
Dr. Eija Korpelainen works currently as a Product manager at CSC – IT Center for Science. Being the national supercomputing centre, CSC provides bioinformatics services for all the universities and research institutes in Finland. Eija has long experience in enabling life scientists to analyze high-throughput data. She has run over 100 training courses in Finland and abroad, and her team has established a popular YouTube channel with tutorial videos. The book “RNA-seq data analysis – practical approach” by Korpelainen et al has been one of the most popular bioinformatics books in recent years. In order to enable biologists to analyze data more efficiently, her team has developed the open source analysis software Chipster which is used worldwide. Eija has participated in several international consortia including the EU funded EMBRACE, AllBio and SeqAhead, and she is currently the national training coordinator of the European ELIXIR initiative. Eija has been involved in GOBLET from the start.
Eija holds a PhD from the Medical faculty of University of Adelaide, Australia, and she completed her post doctoral research as an EMBO long term fellow in the University of Helsinki, Finland. Eija has over 40 peer-reviewed publications and an H-index of 21.
Prof. Heru Suhartanto, PhD
Prof. Heru Suhartanto a Professor in Faculty of Computer Science, Universitas Indonesia He holds a BSc from Department of Mathematics, University of Indonesia. He holds Master of Science, from Department of Computer Science, The University of Toronto, Canada since 1990. He also holds PhD in Parallel Computing from Department of Mathematics, The University of Queensland since 1998. His main research interests are Numerical, Parallel, Cloud and Grid computing. He is also a member of reviewer of several referred international journal such as journal of Computational and Applied Mathematics, International Journal of Computer Mathematics, and Journal of Universal Computer Science. Furthermore, he has supervised some Master and PhD students; he has won some research grants; holds several software copyrights; published a number of books in Indonesian and international papers in proceeding and journal. Some of the awards that he has received include Honorary Professor, School of ITEE, The University of Queensland, (2014 – 2017); Adjunct Professor, School of ITEE, The University of Queensland, (2017-2019); Universitas Indonesia Best Researcher, 2007 and The University of Queensland Alumni Award, 2010.
HIGH PERFORMANCE COMPUTING CHALLENGES IN INSILICO DRUG DESIGN BASED ON INDONESIA MEDICAL PLANTS
Molecular Dynamics is one part of In silico drug design processes, and it is a computer simulation method for studying the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period, giving a view of the dynamic evolution of the system*. Assuming that there are N atoms in a molecule, the time complexity is O(N2). Usually, one needs to do a great number of timesteps simulation such as in 100 Nano Second (NS) and large computing time as the number of atoms (N) are huge due to the complexity of the molecule. For example, the Gromacs results in 90 NS which shows the development of veskel DPPC (dipalmitoyl phosphatidyl choline) [De Vries2008], required 3750 days of single CPU processes, or 117,2 days of 32 CPUs processes. It is becoming more challenges as not many Research institution own HPC infrastructure, and many of the users are not in Computer Science background. In this talk, the authors will present their experience in developing a feasible Cloud Computing environment for users in developing countries, such as Indonesia. Some findings on the computing aspects and some results on Indonedia medical plants simulation will be given.
