Each month the IRMACS Centre is proud to feature novel research being conducted at the centre. We call this "Research Spotlights". Below are the past spotlights.
Award Month Project
October - December 2015

3D Video Coding and Transmission

3D video is a promising new media format. However, it poses challenges for the storage and transmission due to the large amount of data involved. This project will develop new and efficient algorithms for the compression and transmission of 3D video, using interdisciplinary theories from mathematics, signal processing, information theory, and communications. Compared to traditional single view video, 3D video has some unique properties, such as the availability of depth maps, view synthesis and the associated view switching. 

The project focuses on the following topics and tasks:
- Designing new 3D video coding schemes using the recently developed sparse and redundant signal representation theory, such as compressed sensing, K-SVD, and approximate message passing. The key idea is to find a sparse representation of the 3D video. 
-  Studying how to jointly optimize the encoding and decoding schemes to achieve different tradeoffs among distortion, storage cost, transmission rate, realtime computed frames, pre-computed frames, server-generated virtual views, and client-generated virtual views. 
- Exploring the impact of transmission error in the texture and depth maps on quality of the synthesized virtual view, and develop encoder-side algorithms to estimate the decoder-side distortion. This will optimize the encoding, for example, by applying smart error protection scheme at the encoder to improve the quality at the receiver.
- Studying the error propagation, the optimal concealment of depth map error, and the optimal design of error protection scheme for 3D video transmission.

About Jie Liang

Jie Liang received the B.E. and M.E. degrees from Xi'an Jiaotong University, China, the M.E. degree from National University of Singapore (NUS), and the PhD degree from the Johns Hopkins University, Baltimore, Maryland, USA, in 1992, 1995, 1998, and 2003, respectively. Between 1997-1999, he was with Hewlett-Packard Singapore and the Center for Wireless Communications (now part of the Institute for Infocomm Research), NUS. From 2003 to 2004, he worked at the Video Codec Group of Microsoft Digital Media Division. In 2012, he visited University of Erlangen-Nuremberg, Germany, as an Alexander von Humboldt Research Fellow.  

Since May 2004, he has been with the SFU School of Engineering Science. 

Professor Liang's research interests include Image and Video Coding, Multimedia Communications, Sparse Signal Processing, Computer Vision, and Machine Learning. He is currently an Associate Editor for the IEEE Transactions on Image Processing (TIP), IEEE Transactions on Circuits and Systems for Video Technology (TCSVT), IEEE Signal Processing Letters (SPL), Signal Processing: Image Communication, and EURASIP Journal on Image and Video Processing. He is a member of the IEEE Multimedia Systems and Applications (MSA) Technical Committee and Multimedia Signal Processing (MMSP) Technical Committee , and is a Professional Engineer in British Columbia. He received the 2014 IEEE TCSVT Best Associate Editor Award, 2014 SFU Dean of Graduate Studies Award for Excellence in Leadership, and 2015 Canada NSERC Discovery Accelerator Supplements (DAS) Award.

March - April 2015

iReceptor

iReceptor is a distributed data management system and scientific gateway for mining “Next Generation” sequence data from immune responses. The goal of the project is to: improve the design of vaccines and therapeutic antibodies by integrating Canadian and international data repositories of antibody and T-cell receptor gene sequences.

iReceptor will provide a technology platform that will lower the barrier to immune genetics researchers who need to federate large, distributed, immune genetics databases in order to answer complex questions about the immune response. The focus of the iReceptor project is to leverage existing capabilities and technologies to build a new scientific platform for the immune genetics research community. In order to provide such a system, the iReceptor project will develop the following components:

The iReceptor project is working closely with international partners to develop both the foundational biological and immune genetics requirements as well as to develop the technological components of the iReceptor Scientific Gateway. The iReceptor team has been working with colleagues from the international ImMunoGeneTics information system (IMGT) at the Centre national de la recherche scientifique (CNRS), Montpellier, France to determine the initial scientific requirements of the iReceptor Gateway. At the same time, iReceptor has been working with the Agave scientific gateway team from the Texas Advanced Computing Centre to design and develop the technological platform on which iReceptor will be based.

About Felix Breden and Jamie Scott

About Dr. Felix Breden

Dr. Felix Breden is a professor in the Department of Biological Sciences and the Executive Director for the IRMACS Centre. He is also Chair of the IRMACS Management Committee and the Executive Director of the Complex Systems Modelling Group (CSMG).

Dr. Breden is a population geneticist interested in behaviour, sexual selection, guppies and human immunogenetics. He has worked on toads, beetles, cornborers, and mathematical models of the evolution of social behaviour. Currently he concentrates on opsin evolution and speciation in guppies, and how variability in human immunoglobulin genes can affect susceptibility to autoimmune and infectious diseases, and response to vaccines. 

About Dr. Jamie Scott 

Dr. Jamie Scott is a Professor in the Faculty of Health Sciences with a joint appointment with MBB. 

Dr. Scott's  research interest is in understanding the molecular basis for antigen recognition by antibodies using peptide as probes of these interactions. As a molecular immunologist and physician, she has a strong interest in understanding how the peptide recognition profile of an antibody response may be applied to the development of vaccines and autoimmune diagnostics. One of Dr. Scott's most interesting projects involves her search for peptides will bind to human monoclonal antibodies that kill HIV-1. She hopes to create a vaccine that will elicit these same antibodies in uninfected people, and thus protect them from AIDS.



January - February 2014

Population Genomics of Sea Stars

We study the evolution of sex in the ocean. We use sea stars as a model system for analyzing population genetic variation and how that variation is shaped over evolutionary time by differences among species in mate selection and gene flow. New methods in this work use high-throughput sequencing methods to discover new genes expressed on sea star sperm and egg surfaces, and to analyze the pattern of molecular evolution of those genes compared to other parts of the genome. We use the IRMACS Centre's computational and bioinformatics resources in those analyses. The group uses molecular genetic methods and data in evolutionary biology. The specific research area is the analysis of population genetic variation, and comparative studies of population genetics among species that differ in demographic variables such as mate choice, population size, and gene flow.

One project I am pursuing now uses multiple ovary and testis transcriptomes to analyze both selectively neutral and adaptive molecular evolution in the context of a recently discovered zone of incipient speciation between northern and southern populations of a British Columbia sea star. The transcriptome data sets use the Illumina HiSeq platform, which generates hundreds of millions of short DNA sequence reads. A major bottleneck in my analysis of this project is the efficient processing and analysis of the sequence data and comparisons of the transcriptomes among different individual sea stars from northern and southern populations. The access to IRMACS computational resources provide resources for running Galaxy bioinformatics analyses via IRMACS's Compute Canada cluster resource allocation.

About Dr. Michael Hart

Dr. Michael Hart completed his B.Sc. in Zoology at the University of Alberta and his M.Sc. in Biology at Dalhousie University. He completed his Ph.D. in Zoology at the University of Washington. Dr. Hart is a Professor at the Department of Biological Sciences, at Simon Fraser.  He is a member in two research groups the Evolutionary and Behavioural Ecology Research Group and the Organic Evolution Group. A segment of Dr. Hart's research made the Discovery News list of 10 Sexiest Stories of 2013: http://news.discovery.com/human/10-sexiest-stories-2013-131230.htm

November - December 2013

Conservation Connections: Using Evolution to Guide Conservation Priorities

The Conservation Connections project supports Canada’s leading role in conservation biology by developing new data management and modelling techniques to help identify, organize, and track species of greatest concern in Canada. Though phylogenetic data are critical both for setting conservation priorities and for predicting species vulnerability, no current conservation database explicitly incorporates such data. Our project will harness existing taxonomic databases (ubio.org) to National Centre for Biotechnology Information (NCBI) genomic data and graft these outputs to 'known' backbone trees by adapting new methodologies, e.g., from medical genomics and supertree approaches. This dynamic phylogenetic framework will form the core of a world-wide, freely accessible conservation scientific gateway for sharks and rays. This approach will change the way phylogenies are integrated with ecological, morphological, genomic and conservation data, and to our knowledge is a unique application of phylogenetic information in a dynamic environment, extensible to all endangered Canadian species.

About Dr. Nick Dulvy

Dr. Nicholas Dulvy completed his B.Sc. in Animal Zoology at the University of Birmingham, UK before taking up a position as scientific officer for an expedition to Mafia Island, Tanzania. On his return he completed his Ph.D. in evolutionary ecology at the University of East Anglia, UK in 1999, before moving to Fiji to begin a postdoctoral fellowship on "alternate stable states of coral reefs." On his return he was a lecturer at the University of Newcastle-upon-Tyne, UK and in 2003 he became a policy advisor and research scientist at the UK government fisheries agency. Nick is a Professor in the Department of Biological Sciences after joining SFU in 2008 as an Associate Professor and CRC tier II in Marine Biodiversity and Conservation. He has been the Co-Chair of the International Union for the Conservation of Nature Shark Specialist Group - a global volunteer network of around 160 scientists and experts from 90 countries in 12 ocean regions. The SSG has a mission: "to secure the conservation, management and recovery of the world's sharks, rays and chimaeras through the mobilisation of global technical expertise". The focus of his work is to understand the nature and scale of global change using comparative analyses of populations, communities and ecosystems along temporal and spatial gradients of human impact. He has published over eighty peer-reviewed paper and book chapters on life histories, extinction risk, the ecosystem impacts of fishing and the ecological and socioeconomic impacts of climate change. In 2009 he was presented with the Zoological Society of London's Marsh Award for Marine and Freshwater Conservation which is awarded for "contributions of fundamental science and its application to the conservation in marine and/or freshwater ecosystems." The award citation was for "research on the effects of climate change on fisheries and coastal communities, as well as threat and extinction risks in the context of improving fisheries management". In 2010, he was made a Conservation Fellow of the Zoological Society of London, an award "to honour individuals who have made exceptional contributions to conservation."

August - October 2013

HIV Lab

Dr. Brumme's research project integrates molecular biology, epidemiology and computational approaches to study HIV evolution in response to selection pressures imposed by its human host. One of the greatest challenges to HIV vaccine design is the virus' capacity to evade immune recognition through rapid mutation, a process called "immune escape". Through the analysis of population-based cohorts of HIV-infected individuals in Canada and worldwide, we have created "maps" of HIV genome that systematically identify specific sites and pathways of immune escape in viral proteins. We are also interested in how human immune selection pressures have shaped HIV evolution over the course of the epidemic, how this evolution has impacted on HIV replication and protein function, and the implications of this on HIV vaccine design.

About Dr. Zabrina Brumme

Dr. Zabrina Brumme received her Ph.D. in Experimental Medicine in 2006 from the University of British Columbia. She then went on to complete a post-doctoral fellowship at the Ragon Institute of MGH, MIT and Harvard University (formerly known has the Partners AIDS Research Center), in Boston, Massachusetts. She joined the SFU Faculty of Health Science as an Assistant Professor, Molecular Epidemiology of Infectious Diseases, in September 2009. Dr. Brumme currently holds a New Investigator Award from the Canadian Institute of Health Research and a Scholar Award from the Michael Smith Foundation for Health Research. Most recently, Dr. Brumme's work has focused on assessing the consequences of immune escape mutations to HIV replication and viral protein function.

May - July 2013

Statistical Methods for Association Studies of Complex Genetic Disorders

A single gene can be solely responsible for certain genetic disorders. For example, only people who carry two defective copies of the CFTR gene develop cystic fibrosis. By contrast, complex genetic disorders such as diabetes and cancer likely involve a number of genes that increase susceptibility, and act in conjunction with lifestyle and environmental exposures to increase risk for developing disease. To tackle complex disorders, researchers have turned from studies of families to studies of populations. Among other goals, this project aims to develope improved biostatistical methods. The new techniques will reduce inaccuracies associated with the existing methods and will be applied to data from ongoing studies with collaborators. The analytic tools that are being developed should enable researchers to better evaluate genetic and environmental risks for conditions such as diabetes, cancer and asthma, and find the underlying genes. The knowledge gained can help with devising more effective treatment and prevention strategies for these conditions.

About Drs. Jinko Graham and Brad McNeney

Drs. Graham and McNeney work on problems at the interface of statistics and genetics. They have a long-standing interest in developing statistical tools that use the molecular genetic or genomic data of individuals to inform about their ancestral relationships. Another Dr. Graham's interest is exploratory visualization tools to understand how the health effect of an environmental factor can be modified by an individual's genetic background, using data from case-parent trios. In Dr. Graham's words: "As a statistician, my focus is on developing analysis tools that can uncover patterns in data while accounting for random variation. Much of the research involves complex data structures and so has a strong computational component."

March - April 2013

Sustaining Quality of Life for the Rapidly Increasing Aging Population

By 2031, more than nine million Canadians (25%) will be aged over 65, and as many as 45% of them will report some form of disability through physical or cognitive impairment, chronic disease or frailty. There is therefore a crucial need for innovative and economically sustainable approaches to meet the future social and health care needs of older people and provide services that promote independent living and positively enhance their quality of life. This project's interdisciplinary research team is uniquely qualified to address these challenges and integrates social and health sciences, engineering, computing science and applied maths, communications, policy studies, economics and business.

About Dr. Andrew Sixsmith

Dr. Andrew Sixsmith is a Professor and Director of the Gerontology Research Centre at SFU. Dr. Sixsmith has been a member of the British Society of Gerontology Executive Committee and has been the UK representative on the EU's COST-A5 Committee on Ageing and Technology. Since 2000 he has developed research and teaching links with numerous universities worldwide and commercial and government organizations.

Dr. Sixsmith's research has two main themes. Firstly, he has extensive research experience within the area of health and quality of life of older people and the role of health and social care services. Secondly, he has been particularly involved in the strategic development of research in the area of technology for independent living. Andrew has used gerontological knowledge, theories and methods to provide input into user centred design and development of community care technologies (telecare) to facilitate and deliver health and social care services for older and disabled people.

Much of Dr. Sixsmith's research has had an applied perspective, with a specific aim to transfer empirical results into policy and practice.

Dr. Sixsmith is a member of the IRMACS Management Committee and the MoCSSy Graduate Research and Training Program.

January - February, 2013

Human Evolutionary Studies Programme

Over the last 150 years biology has been transformed by the adoption of Darwinian evolutionary theory to such an extent that, as the well-known geneticist Theodosius Dobzhansky once put it, "nothing in biology makes sense except in the light of evolution". The extension of Darwin's insights to humans has been halting and controversial. This is particularly the case for human cognition and behaviour. However, we have now reached a point where the utility of such research can no longer be denied. It is now clear that Darwinian theory can be productively applied to many of the puzzles that scholars in the humanities and social sciences have long sought to explain, such as perception, thought and culture. Likewise, it has become increasingly apparent that Darwinian theory can shed new light on important social and health issues, including prejudice, interpersonal violence and schizophrenia. The purpose of the Human Evolutionary Studies Program (HESP) is to create an internationally- recognized research and training 'hub' that will simultaneously advance the integrated understanding of the body, mind, behaviour and social institutions of Homo sapiens within the framework of evolutionary theory, and maximize the contribution of SFU researchers to this important, dynamic and publicly visible field of research. HESP will accomplish these goals by fostering collaborative relationships among diverse SFU faculty, postdoctoral fellows and graduate students, and between these individuals and researchers in other institutions; by supporting novel, highly interdisciplinary research projects; by providing undergraduates, graduate students and postdoctoral fellows with world-class training that transcends traditional disciplinary boundaries; and by disseminating the results of its research to academics in other fields, policymakers and the general public both directly and through the media.

About Dr. Mark Collard

Dr. Mark Collard trained in both archaeology and biological anthropology. After obtaining a PhD in hominin palaeontology at the University of Liverpool under the supervision of Bernard Wood,  he spent three years as a Wellcome Trust Bioarchaeology Postdoctoral Fellow in the Department of Anthropology at University College London. Dr. Collard's postdoc research was supervised by Leslie Aiello.

Dr. Collard has worked in a variety of capacities in the UK, the USA, and Canada: as a lecturer (the equivalent of an assistant professor) in the Department of Anthropology at University College London,  an assistant professors at the Department of Anthropology at Washington State University-Pullman, and as an assistant professor at the Department of Anthropology at the University of British Columbia. In 2007, Dr. Collard moved to the Department of Archaeology at Simon Fraser University to become an associate professor and Canada Research Chair. He was promoted to Full Professor in September 2011.

Dr. Collard's research interests span biological anthropology and archaeological science.

September - December, 2012

Study of Automata and its Applications to Number Theory and Algebra

Finite-state automata play a fundamental role in theoretical computer science, but in recent years many advances in number theory, geometry, and algebra have been made by adopting an automaton-theoretic viewpoint. Just a few of their many applications are to noncommutative algebra, where they can often be used to find Groebner bases for finitely presented algebras; and to number theory, where they can sometimes be used to determine whether power series satisfy certain differential equations. This project involves graduate students and visitors to IRMACS, who have both done research on these areas and holded seminars. IRMACS facilities have been also used for undertaking computations.

About Dr. Jason Bell

Dr. Jason Bell is an Associate Professor in the Department Mathematics at Simon Fraser University. Dr. Bell currently works in noncommutative algebra and its connections with number theory and combinatorics. His research interests span across several mathematical areas: algebra, number theory, automata and words, combinatorics, and algebraic geometry. Well known for his readiness to share his ideas and knowledge with fellow mathematicians, Dr. Bell has collaborated with some of the most prominent mathematicians of our time including A. Frankel, D. Djokovic, and P. Cameron for example, as well as some young talented mathematicians at the beginning of their careers, M. Coons and K. Casteels, for example.

July - August, 2012

Explorations in Computational Number Theory

Number theory is one of the oldest, deepest and most vibrant branches of modern mathematics. It centrally incorporates some of the most sophisticated and profound mathematical ideas that have been developed (witness the recent proof of Fermat's Last Theorem) and yet remains broadly useful in many areas of pure and applied mathematics. It is remarkable how often number theory comes to bear both in other areas of mathematics and in applications. A notable recent example is internet security whose protocols are based on number theoretic problems. Number theory has historically been motivated by the study of properties of integers and solutions to equations in integers, but now includes many other aspects, each with its own flavour and viewpoints. Broadly speaking, these can be divided into Analytic, Algebraic, Diophantine, and Geometric aspects of Number Theory. Research in Number theory today often involves knowledge and expertise from areas such as Algebra, Algebraic Geometry, Analysis, Combinatorics, Probability Theory, Representation Theory, Topology. Connections to applicable fields include Coding Theory and Cryptography. At the IRMACS Centre, we have a strong group in Number Theory which covers the spectrum of Number Theory. Together with the groups at the University of British Columbia and the University of Washington at Seattle, we form one of the largest groups of Number Theory Researchers in North America. The IRMACS Centre has played an important role in hosting the SFU - UBC Number Theory Seminar and Pacific Northwest Number Theory Seminar. The group members are also active participants in the programs and initiatives of the PIMS and MITACS.

About Drs. Peter Borwein & Stephen Choi

Dr. Peter Borwein is a full professor in the Department of Mathematics of Simon Fraser University and the Founding Director of the IRMACS Centre. After completing a Bachelor of Science in Honours Math at the University of Western Ontario in 1974, he went on to complete an MSc and Ph.D. at the University of British Columbia. He joined the Department of Mathematics at Dalhousie University. While he was there, he, his brother Jonathan Borwein and David H. Bailey of NASA wrote the 1989 paper that showed a proof for computing one billion digits of π. They won the 1993 Chauvenet Prize and Hasse Prize.

Dr. Stephen Choi is an associate professor in the Department of Mathematics of Simon Fraser University. After completing a Bachelor of Science and Masters of Science at the University of of Hong Kong in 1991, he went on to complete a Ph.D. at the University of Texas at Austin in 1996. Dr. Choi's research interests include Diophantine approximations, Diophantine equations, Goldbach-Waring problem, polynomials with restricted coefficients and merit factors of binary sequences.