Limsoon Wong

Kwan-Im-Thong-Hood-Cho-Temple Chair Professor of Computer Science, School of Computing Acting Executive Director NUS Graduate School for Integrative Sciences and Engineering National University of Singapore

Topic: Dealing with Confounders in Omics Analysis

Abstract

The Anna Karenina effect is a manifestation of the theory–practice gap that exists when theoretical statistics are applied on real-world data. In the course of analyzing biological data for differential features such as genes or proteins, it derives from the situation where the null hypothesis is rejected for extraneous reasons (or confounders), rather than because the alternative hypothesis is relevant to the disease phenotype. The mechanics of applying statistical tests therefore must address and resolve confounders. It is inadequate to simply rely on manipulating the P-value; indeed, we show how/why this can be the wrong thing to do!) We discuss three mechanistic elements (hypothesis statement construction, null distribution appropriateness, and test-statistic construction) with real-life examples in computational biology, and suggest how they can be designed to foil the Anna Karenina effect to select phenotypically relevant biological features. (This talk is based on joint work with Wilson Wen Bin Goh.)

Biography

Limsoon Wong is Kwan-Im-Thong-Hood-Cho-Temple Chair Professor in the School of Computing at the National University of Singapore (NUS). He was also a professor (now honorary) of pathology in the Yong Loo Lin School of Medicine at NUS. Limsoon currently works mostly on knowledge discovery technologies and their application to biomedicine and data analytics. He is a Fellow of the ACM, inducted in 2013 for his many contributions to database theory and computational biology. His other recent awards include the 2003 FEER Asian Innovation Gold Award for his work on treatment optimization of childhood leukemias, and the ICDT 2014 Test of Time Award for his work on naturally embedded query languages. He co-founded Molecular Connections Pvt Ltd in India in the early 2000s and served as the company’s chairman for a decade and a half, helped helm the steady growth of the company to over 2000 engineers, scientists, and curators, and some 400x increase in value. Limsoon received his BSc(Eng) in 1988 from Imperial College London and his PhD in 1994 from University of Pennsylvania.

Olivo Miotto

Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand

Topic: Big Data for Malaria Elimination

Abstract

Malaria remains a major public health scourge, killing hundreds of thousands young children every year. Although most of the burden is in Africa, public health efforts have focused on eliminating malaria from Southeast Asia, where multi-drug resistant Plasmodium falciparum parasites have emerged, and threaten to undermine global progress made against the disease. The availability of high-throughput genome sequencing and the development of innovative techniques have made it possible to harness advanced technologies, providing new insight on the epidemiology of this disease, and on the evolution of drug resistance. Here we review some of the advances and applications that have been made possible by genome analyses of thousands of parasite samples from clinical infections.

Biography

Because of malaria, millions of African children die before their first day at school. For decades, scientists and health authorities have raised hopes of eliminating this burden on the developing world, only to have these hopes dashed, time after time, by the astonishing adaptability of Plasmodiumparasites, which seem capable of becoming tolerant to most drugs we deploy. Today, genomic technologies provide a powerful new weapon against these parasites. At the Centre for Genomics and Global Health, we have developed methods for determining the genetic code of Plasmodium parasite directly from blood samples taken from infected patients. Thanks to the falling cost of sequencing, and the reliability of our approach, we are now able to sequence literally thousands of parasites from clinical cases, and map this genomic information in geographical, ecological and historical contexts. Our goal is to determine how parasite populations change as a result of human intervention and environmental change, and observe new epidemiological trends in real time, to inform and guide public health intervention. In other words, "genomic epidemiology" will monitor Plasmodiumevolution, so that humanity can keep steps ahead of the parasite. Olivo Miotto focuses on translating the massive quantities of data produced by sequencing thousands of genomes into meaningful knowledge about the epidemiology of Plasmodium falciparum. By analyzing hundreds of thousands of genomic variations in each blood sample, he studies the genetics of parasite populations in four continents, and identifies patterns of evolution associated to responses to drug pressure and other human interventions. Based in Bangkok, Olivo collaborates with many clinical research groups in malaria endemic regions, particularly in Southeast Asia, to study relationships between  response to clinical therapy and genetics of the disease-causing parasites in the patient. In the early stages, the focus is on immediate problems, such as discovering mutations causing resistance to current drugs, such as artemisinin. However, Olivo's longer-term perspective is to create tools that will identify patterns in thousands of accumulated genomic sequences, leading to a deep understanding of parasite evolution and, ultimately, to interventions that will win the struggle against the disease. When learning about Darwin at age 12, Olivo thought evolution was the coolest thing he had heard of. It took him decades to realize that it was also the best use for his skills. In between, he studied physics and worked as a software engineer, both in the commercial and academic worlds. At various times he focussed on Web applications, graphical user  interfaces, speech synthesis, online learning, and database systems, before finally switching to bioinformatics and genomics.

Dong-Yup Lee

School of Chemical Engineering, Sungkyunkwan University, Republic of Korea Bioprocessing Technology Institute, Agency for Science and Technology Research (A*STAR), Singapore

Topic: Big data based systems and synthetic agrobiotechnology toward crop improvement

Abstract

Big Data have been rapidly generated in the modern biological science and biotechnology fields, including plant science and agrobiotechnology, due to the recent advances in high-throughput omics technology. Now, one of major challenges is to analyze and integrate these large and heterogeneous datasets in order to enhance the crop productivity and quality which are severely hampered by various biotic and abiotic stresses as well as inherent genetic limitation. Thus, it is highly required to develop various systems and data mining analytics approaches for their systematic applications. To this end, we have established the integrative framework for characterizing model crop plants such as rice by resorting to systems biology techniques which include metabolic modeling and machine learning. The information derived from the current in silico analysis of virtual plant cells in conjunction with multi-omics profiling and synthetic biology tools can potentially guide for developing new breeding and/or engineering targets for next generation crop development. In this talk, modeling of various plant systems will be introduced, and current challenges and future direction in the field, e.g., smart farming, will be discussed. [This work was supported by Next-Generation BioGreen 21 Program (SSAC, No. PJ01334605), the Rural Development Administration, Republic of Korea]

Arinthip Thamchaipenet

Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand

Topic: Transcriptomic analysis of beneficial effect of ACC-deaminase producing endophytic Streptomyces associating with indica rice under salt stress

Abstract

1-aminocyclopropane-1-carboxylate (ACC) deaminase is one of plant growth promoting (PGP) traits of endophytic Streptomyces sp. GKU 895 isolated from sugarcane. ACC deaminase reduced stress ethylene in plant under environmental stress by conversion ACC, a precursor of ethylene, into ketobutyrate and ammonia that bacteria can consume. To investigate mechanisms between plant-actinomycete interaction, Streptomyces sp. GKU 895 was inoculated into salt-susceptible indica rice cultivar IR29. RNA-seq revealed differentially expressed DEGs of (i) IR29, (ii) IR29 salt, (iii) IR29 GKU 895, (iv) IR29 salt GKU 895. Genes involved in growth (e.g. photosynthesis) were up-regulated in inoculated rice IR29. Rice IR29 GKU 895 tolerated to salt through down-regulation of genes involved in ethylene biosynthesis, transcriptional factors, and MPK5; and up-regulation of genes associated with hormones, antioxidants, ion homeostasis, compatible solutes, and transcription factors. The results strongly evidenced that Streptomyces sp. GKU 895 beneficially enhanced growth and salt tolerance in rice.

Kunihiko Fukushima

Senior Research Scientist, Fuzzy Logic Systems Institute (Iizuka, Fukuoka, Japan)

Topic: Deep CNN neocognitron for artificial vision

Abstract

Recently, deep convolutional neural networks (deep CNN) have become very popular in the field of visual pattern recognition. The neocognitron, which was first proposed by Fukushima (1979), is a network classified to this category. It is a hierarchical multi-layered network. Its architecture was suggested by neurophysiological findings on the visual systems of mammals. It acquires the ability to recognize visual patterns robustly through learning. Although the neocognitron has a long history, improvements of the network are still continuing. This talk discusses the recent neocognitron, focusing on differences from the conventional deep CNN. Some other functions of the visual system can also be realized by networks extended from the neocognitron. For example, by adding top-down connections to the neocognitron, function of selective attention can be introduced. The ability of recognizing and completing partly occluded patterns can also be realized.

Biography

Kunihiko Fukushima received a B.Eng. degree in electronics in 1958 and a PhD degree in electrical engineering in 1966 from Kyoto University, Japan. He was a professor at Osaka University from 1989 to 1999, at the University of Electro-Communications from 1999 to 2001, at Tokyo University of Technology from 2001 to 2006; and a visiting professor at Kansai University from 2006 to 2010. Prior to his Professorship, he was a Senior Research Scientist at the NHK Science and Technology Research Laboratories. He is now a Senior Research Scientist at Fuzzy Logic Systems Institute (part-time position), and usually works at his home in Tokyo. He received the Achievement Award, Distinguished Achievement and Contributions Award, and Excellent Paper Awards from IEICE; the Neural Networks Pioneer Award from IEEE; APNNA Outstanding Achievement Award; Excellent Paper Award, and Academic Award from JNNS; INNS Helmholtz Award; Pioneer Award from ELM2017; and so on. He was the founding President of JNNS (the Japanese Neural Network Society) and was a founding member on the Board of Governors of INNS (the International Neural Network Society). He is a former President of APNNA (the Asia-Pacific Neural Network Assembly). He is one of the pioneers in the field of neural networks and has been engaged in modeling neural networks of the brain since 1965. His special interests lie in modeling neural networks of the higher brain functions, especially the mechanism of the visual system. In 1979, he invented "neocognitron ", which is a deep CNN (convolutional neural network) and acquires the ability to recognize visual patterns through learning. The extension of the neocognitron is still continuing. By the introduction of top-down connections and new learning methods, various kinds of neural networks have been developed. When two or more patterns are presented simultaneously, the "Selective Attention Model " can segment and recognize individual patterns in tern by switching its attention. Even if a pattern is partially occluded by other objects, we human beings can often recognize the occluded pattern. An extended neocognitron can now have such human-like ability and can, not only recognize occluded patterns, but also restore them by completing occluded contours. He also developed neural network models for extracting visual motion and optic flow, for extracting symmetry axis, and many others. He is recently interested in new learning rules for neural networks.

Aimon Kopera

GlobalHealthSpan

Topic: Precision Medicine in Asia: What's Next?

Biography

Dr. Aimon Kopera has been among the leaders in innovative health and wellness global initiatives for more than 20 years. Born in Bangkok, Thailand she is a dual national of Thailand and the United States. She graduated from Mahidol University, Thailand, in 1986 with a major in nursing. Early in her career, she served on the United Nations International Medical team providing critical medical service for casualties of Southeast Asian conflicts. Dr. Kopera studied in the United States in the 1990s bringing her into contact with leaders in holistic health and integrative medicine which aims to combine alternative medicine, conventional evidence-based medicine, and other practices that work in wellness, such as Traditional Chinese Medicine and Ayurveda based approaches, to address wellness in multiple "dimensions" (biological, psychological, social, and spiritual). Dr. Kopera then spent nearly a decade in entrepreneurship (Rambutan Properties, LLC; Worldsites, Inc.; Qi Mountain Wellness Institute, LLC), personal pilgrimage (Tibet, Machu Picchu, Chichen Itza, Camino de Santiago) scientific exploration (Russia, USA), and medical study followed by her MD degree from American Global University, Columbus, Ohio USA, with a concentration in preventive medicine, and resident internships in the United States at Emory University, Atlanta Georgia. More recently, she has focused on commercialization of genetic science for genetics-based lifestyle intervention. In this capacity she has researched, met and, in some cases affiliated with, pioneering genetic testing and health/wellness providers worldwide including, among others: Human Longevity, Inc., LifecodeGx, myDNAhealth, DNA life, DfMedic, GeneU, Pathway Genomics, Affymetrix, and Thermo Fisher Scientific Genetic Testing Services. Dr. Kopera has founded and co-founded several commercial enterprises. Services though Dr. Kopera’s businesses include direct to consumer genetic testing, and consumer lifestyle protocols that accompany genetic results with suggestions for food, vitamins, personal care and various wellness activities and products. Client services through Dr. Kopera’s businesses include consulting on the design and development of wellness centers and, food, drink, movement and mind products, fully integrated with cloud based technology. The wellness centers can be delivered with site license options for health, beauty and fitness nutritional supplements and self-care supplies, as well as, genetic testing services. She also provides advisory services to help clients identify, validate, and bring to market genetics-based product innovations that enhance life. And, she provides product formulation for discovery, scientific analysis, and formulation of genetically relevant nutritional supplements & self-care products. Registered trademarks of Dr. Kopera’s brands include: The International Research Institute for Wellness and Prevention LP; Genomics International LLC; Genomics International USA LLC; Genomics International Asia Pacific LLC; MeGenome Limited Company (Thailand); MeGenome LLC (USA); Discover Your Code LLC; Origami Society (non-profit foundation for Asian Ethnobotany); and, co-patents: The Life Force Index; and, the Wellness Navigation Expert System, smartphone technology.

Sarawut Wongphayak

Vishuo Biomedical (Thailand) LTD

Topic: Big Data in Life Sciences and Healthcare: Changing challenges into opportunities

Abstract

Life Sciences and Healthcare have been highly affected by the rapid generation of large and complex data sets created by high-throughput devices across the globe every day. The data in life sciences and healthcare has been growing exponentially for the past few years and will be beyond the capability of the traditional methods of data analytics and management. These massive quantities of data also come with significant challenges, especially in discovering associations and understanding patterns and trends within the data. Therefore, the utilization of big data in life sciences and healthcare helps the organizations to create new growth opportunities. For example, precision medicine play an important role for improving many aspects of diagnosis, treatment, and classification of illnesses. In agriculture, it has the power to revolutionize food security and sustainable agriculture including food safety, reducing the risks from disease outbreaks and improving agriculture through effective plant and animal breeding.

Biography

Sarawut Wongphayak is currently Branch Manager at Vishuo Biomedical (Thailand) LTD. He earned his Bachelor of Science in Marine Technology at Burapha University, Thailand, in 2005, and his Master of Science in Bioinformatics at King Mongkut's University of Technology Thonburi, Thailand, in 2007. As Branch Manager, Sarawut Wongphayak leads the team with the vision of establishing the company as a national provider of genomic services and solutions with cutting edge Next Generation Sequencing technology and bioinformatics expertise that address individual customer needs in clinical and research projects. Before joining Vishuo Biomedical (Thailand) LTD, Sarawut Wongphayak was Senior Bioinformatics Scientist at Vishuo Biomedical PTE. LTD., Singapore. He was the team leader for the designing and developing the algorithms for NGS data analysis workflow for genotyping, mutation detection, clinical annotation and drug resistance interpretation of infectious disease study. Sarawut Wongphayak worked with R&D team at Vela Diagnostics in Singapore to develop software and analysis pipeline for Sentosa® SQ automated oncology and virology NGS workflow, the integrated and flexible IVD solutions for NGS. He was Bioinformatician at the Institute of Molecular and Cell Biology, A*STAR, Singapore, where he applied his expertise in Graphical User Interface (GUI) design to develop a GUI for a software to accelerate and facilitate RNAi high-throughput screening (HTS) data analysis called ScreenSifter. Sarawut Wongphayak also worked with bioinformatics team at the Center for Translational Research and Diagnostics at Cancer Science Institute of Singapore, National University of Singapore, to develop Genome Bisulfite Sequencing Analyser (GBSA), an academical and open-source software (GPL) capable of analyzing whole-genome bisulfite sequencing data. Vishuo Biomedical (Thailand) LTD is a healthcare technology company established in 2016. It is one of the pioneers in providing a complete solution for Next Generation Sequencing and Bioinformatics in Thailand. Vishuo Biomedical (Thailand) LTD delivers genomic data, data analysis solution and interpretation to research institutes, universities, and healthcare providers. It provides a wide range of bioinformatics solutions to facilitate clinical and research projects with proprietary technology and data analysis approaches by bioinformatics team who has expertise across multiple aspects of genomics and discovery encompassing all fields of life science.

Richard Wintle

Assistant Director, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
Associate Scientific Director, CP-NET Cerebral Palsy Integrated Discovery Program

Topic: Whole genome analysis in Cerebral Palsy: a neuromuscular disorder meets 21st century genomics

Workshop Topic: Detecting structural variation from whole genome sequence data: application to neurodevelopmental disorders

Biography

Dr. Wintle’s scientific interests lie in the application of genomic technologies to the understanding of individual genetic variability, with a specific focus on the neuromotor condition, Cerebral Palsy. He serves as both Associate Scientific Director of the CP-NET Cerebral Palsy Integrated Discovery Program within Ontario, Canada, and as a founding member of the Governance Council of the International Cerebral Palsy Genomics Consortium (ICPGC). His most recent work has focused on the discovery of large-scale, highly-penetrant rare variation in children with CP, and the delineation of the extent to which genetic and genomic changes contribute to this disorder.

Dr. Wintle holds a PhD in Molecular and Medical Genetics from the University of Toronto, during which he characterized the human immunoglobulin heavy chain gene cluster, as part of international efforts supporting chromosome 14 mapping for the Human Genome Project. He completed his postdoctoral training at the Centre for Addiction and Mental Health in Toronto, studying the molecular neurobiology of dopamine signalling in the model organism, the nematode C. elegans. Following this, he worked in two related biotechnology startup companies, in a variety of R&D and Operations roles, mainly focused on the complex genetics of autoimmune and inflammatory disorders. Since 2006, he has been with The Centre for Applied Genomics (TCAG), a genome centre located within the Research Institute of The Hospital for Sick Children in Toronto, Canada, where he serves as Assistant Director and a member of its Scientific Management. TCAG is a Genomics Technology Platform of Genome Canada, and a founding member of Canada’s Genomics Enterprise, a nationally-funded, pan-Canadian genome sequencing network, and is affiliated with the University of Toronto. A major focus of work at TCAG is in developing approaches to identify and interpret structural variation within whole genome sequence (WGS) data. Dr. Wintle has also acted as a consultant to a wide variety of private- and public-sector biotechnology, market research, and healthcare organizations.

Sakda Khoomrung

Faculty of Medicine Siriraj Hospital, Mahidol University Thailand

Topic: Metabolomics for the Development of Human Vaccine