Speakers

Speakers and their biographies are listed below with our international speakers listed first.

SiLokProfessor Si Lok has 20 years experience in the bio-industrial sector and academia. At ZymoGenetics (Novo Nordisk) he helped develop technologies establishing the company as a world leader in therapeutic protein discovery. His team discovered the long sought and contested megakaryocytic-lineage growth factor, Thrombopoietin (TPO).  As principal scientist, he instigated massive scale sequencing of cDNA libraries driving the company’s pioneering use of EST mining to discover new biologic entities that contributed to the company’s successful IPO in 2002. Since 2007, he was the Chair Professor of Genomic Medicine and the Scientific Director of the Genome Research Centre of Hong Kong University and most recently as Professor of Practice in Applied Genomics at the Chinese University of Hong Kong where his small group continues to develop genomics technology and translate their use in research and discovery. His group assumes a lead role in nano-scale and strand-specific cDNA library construction to dissect regulatory pathways, and the use of targeted sequencing to identify mutations contributing to diseases. Professor Lok has also developed methods for pair-end read sequencing of up to 50-kb separation to identify genomic rearrangements that are otherwise not readily detectable.  Under his leadership, the centre has begun to apply genomics in the non-medical disciplines. Prof Lok's talk is titled "A Small Genome Centre’s Adoption of New Generation DNA Sequencing for Research and CORE Service". Abstract.

SteveWylieSteve Wylie attended Otago University in the 1980s and completed an honours degree in the botany department before moving to Western Australia to study plant viruses of pasture legumes for his PhD. The chance discovery of viruses in wild plants there sparked an ongoing interest in the roles of viruses of the indigenous flora. Currently his focus is on the threatened terrestrial orchid flora of the southwestern corner of Australia. Steve's talk is titled "Tailoring high-throughput sequencing approaches to next-generation plant virology in south-west Australia". Abstract.

HayleyBairdHayley Baird graduated from Otago University with a BSc(Hons) in microbiology. She is now a research associate for AgResearch Animal Genomics at Invermay. The majority of her time over the last few years has involved working with the Illumina iSCAN in particular the sheep 50 and 5k chips, however the area of her research thatsheI’ll be talking about is the Aquaculture industry and the process of creating a SNP chip for Chinook salmon. Hayley's talkisi titled "Using Next Generation Sequencing techniques to identify Single Nucleotide Polymorphisms in Chinook Salmon". Abstract.


ChatterjeeAniruddha Chatterjee obtained his BSc (triple major in biotechnology, biochemistry and chemistry) from Osmania University, Hyderabad and MSc in biotechnology from VIT University, Vellore, India. Aniruddha is member of Professor Ian Morison’s group and is based in the department of Pathology at the University of Otago. Aniruddha’s current research focuses on unraveling epigenetic signatures in humans. He is using the technique of reduced representation bisulphite sequencing (RRBS) to quantify human methylomes. He played a key role in establishing an analysis pipeline to analyze large-scale methylation data and further developing advanced (together with Dr. Peter Stockwell) tools which enables bench-scientists to analyze complex epigenomic data at greater ease. His methods has applicability to other species, for e.g., zebrafish and the findings will be a big step forward in understanding the role of specific epigenetic marks in normal individuals. DNA methylation analysis of human genome at this global scale is one of the first attempts made in New Zealand. Aniruddha was awarded the “AGRF Young Investigator Award” in 2011 (Melbourne, Australia) in appreciation of his work. Aniruddha's talk is titled "Reduced representation bisulphite sequencing indicates widespread epigenetic variation among normal individuals". Abstract.

JohnClearyProfessor John Cleary has 40 years experience in commercial software engineering and computer science. Originally a pure mathematician he gained a PhD in electrical engineering from Canterbury University. He spent 12 years in Calgary Canada where he did research on distributed computing systems and data compression and was co-founder of a software company that simulated systems on high performance distributed computers. For the last 10 years he has been developing new algorithms and software for high performance computing for NGS data. This has included both read mapping to genomes and variant calling. Currently he is Chief Scientist at Real Time Genomics and an Adjunct Professor of Computer Science at Waikato University. John's talk is titled "Calling variants in populations with pedigrees". Abstract.

LesleyCollinsLesley Collins has extensive experience in working with NGS data and was instrumental in getting the Illumina Genome Analyser at Massey University up and running.  Her hands-on approach has seen her tackle many NGS-focused bioinformatics demands and she will share her experience and knowledge with you in the post-conference workshop. Lesley has been course-controller for highly successful Workshops on NGS and Bioinformatic workshops run over the last few years as well as researching and teaching in RNA evolution. Recently, Lesley edited the book "RNA Infrastructure and Networks". Lesley's talk is titled "NGS project analysis on small-scale computing (aka You did WHAT on a laptop?)". Abstract.


ChrisCouldreyChristine Couldrey's career has been dominated by molecular biology, although her fields of study have varied considerably.  She completed a PhD reproductive biology at Cambridge University in the Laboratory of Nobel Laureate Sir Martin Evans.  From there she completed a postdoctoral position at the National Institutes of Health investigating the role of epithelial stem cells in breast cancer.  This stem cell work led to a second postdoctoral position with the American Red Cross identifying genes involved in hematopoietic stem cell signalling.  A short stint curating DNA sequences for GenBank provided her with a greater understanding of the intricacies of DNA, after which she headed back to New Zealand to work at AgResearch, where she has been investigating epigenetic nuclear reprogramming (in particular DNA methylation) in large animal cloning. More recentlyshe has been adapting protocols for genome wide DNA methylation analysis (reduced representation bisulfite sequencing) used in humans and mice to agricultural animals with the ultimate goal in using epigenetics to improve production efficiency and performance.  Christine's talk is titled "Development of epigenomic pipelines for use in agricultural animals ". Abstract.


BrianFritzBrian Fritz is a Senior Field Applications Scientist with Illumina.  Brian supports experimental design consulting, training, troubleshooting and a variety of other customer-support activities relating to Illumina’s genotyping and sequencing technologies and applications.  His customer support portfolio runs from single researchers up to Genome Centers and encompasses diverse applications across agricultural, plant, wildlife, infectious disease and model organisms as well as research-use only and translational human studies.  Brian’s training and research background is in genetics, cell, molecular and developmental biology applied to model organisms and human research models of development, molecular evolution and disease.  He holds a PhD from the University of Wisconsin-Madison and undertook Postdoctoral Research studies at the Fred Hutchinson Cancer Research Center in Seattle, WA (USA) before moving to Illumina in early 2008. Brian's talk is titled "Current and imminent state of the art for Illumina’s sequencing technologies". Abstract.

ChadHarlandChad Harland graduated from University of Canterbury with an MSc in Biochemistry. As a member of the LIC Bioinformatics team he has been heavily involved in analysis of the first phase of the Dairy PGP sequencing project. During which he focusing on the testing and developing the Bioinformatics pipelines that can scale from tens of sequenced individuals to hundreds of sequenced individuals while making maximal use of existing genotype and pedigree data. Chad's talk is titled "Pipelines, Pedigree & Polymorphism". Abstract.

NickHengNick Heng is currently a senior lecturer in the Department of Oral Sciences (Faculty of Dentistry), University of Otago. Over the past decade or so, he has been “moving up” in the microbiological world, starting with gastrointestinal bacteria (PhD research), rumen microbiology (postdoctoral studies) and now oral bacterial species. His primary research expertise is in prokaryotic (bacterial) genetics and his current research projects that involve the use of next-generation DNA sequencing platforms are: (i) whole-genome sequencing of oral bacteria (from any source), and (ii) surveying the oral microbiota in health and disease. Nick’s other research interests include oral immunology and oral pathology but he does not claim, in any way, to be proficient in either. Nick's talk is titled "De novo sequencing of the genome of Streptococcus trichosurus, a new oral bacterial species isolated from the New Zealand brushtail possum Trichosurus vulpecula". Abstract.

MikeKeehanMike Keehan is a Senior Bioinformaticist at LIC. He is currently involved in the LIC genomic selection project and the Primary Growth Partnership Dairy Genomics project. With a career background in applied mathematics, software development and systems administration he has undertaken a variety of bioinformatics tasks for LIC. Mike has a masters degree in Operations Research and a post graduate diploma in Science from Massey University. He is interested in obtaining genotype phase from sequence read information and in the application of population deNovo assemblers. Mike's talk is titled "An update on year two of the PGP Dairy Genomics Sequencing project". Abstract.

MartinKennedyMartin Kennedy obtained his PhD in bacterial genetics at the University of Auckland, and carried out postdoc research in leukaemia genetics at the Laboratory of Molecular Biology, Cambridge (UK) before returning to Christchurch, New Zealand in 1991.  His current research interests include the genetics of complex disease, gene by environment interactions, and pharmacogenomics. He also holds a Marsden grant to examine the role of G-quadruplex structures in DNA and their relevance to genomic imprinting. Martin's talk is titled "Earthquake induced stress cardiomyopathy: is it a Mendelian condition". Abstract.

LiaLieftingLia Liefting has many years experience in working with plant pathogens, especially bacteria-like organisms (phytoplasmas and liberibacters).  After completing her PhD at the University of Auckland, Lia spent 5 years as a postdoctoral scholar at the University of California, Davis.  During this time she sequenced the complete genome of a phytoplasma, before the era of NGS technology.  On return to New Zealand, Lia worked on a Marsden grant to sequence the genome of the phytoplasma that is killing our cabbage trees.  Lia currently works at the Plant Health and Environment Laboratory, Ministry for Primary Industries performing plant disease diagnostics. Lia's talk is titled "Diagnosis of Plant Pathogens using Next-Generation Sequencing". Abstract.

TonyLoughTony Lough is Chief Executive NZGL. Dr Lough has a research background and operations management experience in a number of technology companies. He holds a PhD in biochemistry from the University of Otago and, during the early phase of his career, he researched viral RNA movement and vascular signalling systems in plants. Over the past 10 years, he has held various operational management roles within biotechnology and start-up engineering companies – most recently at Pacific Edge Limited, where he oversaw the product development portfolio. Dr Lough has an MBA from the University of Auckland, in keeping with his interest in commercial outcomes for technology businesses. Tony will be talking in the Bioinformatics Software session. More on NZGL can be found here.

McComishBennet McComish obtained his BSc and MPhil from Massey University in the 1990s. He is currently completing his PhD in computational biology under the supervision of David Penny, also at Massey University. Bennet's PhD research covers several areas of sequence analysis, including assembly of next-generation sequence data, estimation of mutation rates, and phylogenetics. Bennet's talk is titled "Index-free de novo assembly and deconvolution of mixed mitochondrial genomes". Abstract.

AlanMcCullochAlan McCulloch is a bioinformatics software engineer at AgResearch in Dunedin who has worked on postgres and oracle sequence and gene expression database design and management, sequence clustering and assembly pipeline and method design and implementation, NGS processing and pipelines, HPC systems architecture and administration, and everything in between. Pre human-genome he was involved in helping set up a clinical trials research unit at Auckland University, including database design, implementation, management and reporting, treatment randomisation design and implementation, for several large international clinical trials. He has a Bachelors degree in Mathematics and Philosophy from Canterbury University. Alan's talk is entitled "A method for designing NGS transcriptomics experiments that includes in-silico biological replicates". Abstract.

MaryMary Morgan-Richards is an academic within the Ecology Group at Massey University, Palmerston North.  She and her research group (http://evolves.massey.ac.nz) study speciation, evolutionary ecology and conservation genetics using endemic New Zealand animals (weta, stick insects, snails).  Mary gained her PhD from Victoria University of Wellington, she then did postdoctoral fellowships at the University of St Andrews, Scotland, University of Otago NZ, the Natural History Museum London UK, and University of Canterbury NZ.  She has experience working with plants, and animals, invasive species and endangered species and is interested in using NGS datasets for testing theories in evolutionary biology. Mary's talk is titled "Hybrid origin of a parthenogenetic genus: the genomic evidence". Abstract.

 

KristinaRamstadKristina Ramstad completed a PhD in Ecological Genetics at the University of Montana, USA.  She emigrated to New Zealand in 2006 to conduct postdoctoral research with the Allan Wilson Centre at Victoria University of Wellington.  Kristina research focuses on mechanisms (genetic drift, selection, migration and mutation) and patterns of diversification within and among species. She has worked with a diverse array of taxa, including sockeye salmon, tuatara and, most recently, kiwi.   Applied species conservation is the primary goal of her work.  With her co-author Gabe Kolle, she will present a talk titled "HiSeq transcriptomics to discover genes associated with reproductive success in kiwi". Abstract.

RuchardSpenceRichard Spence has worked for the last three and a half years as a Senior Scientist at the Investigation and Diagnostic Centre, Ministry for Primary Industries. Prior to working in New Zealand Richard worked as a Clinical Scientist in the NHS running a molecular diagnostics laboratory within a clinical microbiology department. He has a PhD in molecular diagnostics from the University of Nottingham. Richard's main area of interest is the application of molecular tools for identification and characterisation of new and/or emerging pathogens. Richard's talk is titled "New Zealand Ostreid herpesvirus – application of high throughput sequencing in a biosecurity context". Abstract.

JoStantonJo Stanton trained in molecular biology and holds a PhD from the University of Western Australia. Jo is part of the Department of Anatomy and Structural Biology, University of Otago. She holds a New Economy Research Fund grant and was director of the University of Otago High Throughput DNA Sequencing Unit.

PeterStockwellPeter Stockwell started a PhD in protein chemistry at Otago University but was diverted on to numerical projects, including population genetics and early DNA sequence data handling.  Postdoctoral work at ICRF, London, established the importance of computational methods and homology comparisons as tools in the developing field of biological sequence analysis.  Subsequent work has included the development of SW tools for sequence analysis and assembly and data mining of sequence data repositories.  The size and complexity of sequence data has evolved rapidly alongside computational resources and Peter has used a variety of computer languages in order to handle data in practical time frames. Most recently, Peter has been working on the processing of data from NGS Reduced Representation Bisulphite Sequence work in association with Aniruddha Chatterjee and Professor Ian Morison and has an involvement with N.Z. Genomics Limited. Peter's talk is titled "Differential Methylation Analysis using RRBS: Challenges and New Insights". Abstract.

TraceyTracey van Stijn is a research associate working for AgResearch Animal Genomics at Invermay. Her main focus previously was on identifying genes and polymorphisms that affect meat traits in the New Zealand Sheep industry. She assisted in sequencing for the Sheep HapMap project, which led to the currently used 50K SNP Chip. Her current project is to optimise Genotyping by Sequencing methods in agricultural species. Tracey's talk is titled "High-throughput Genotyping-by Sequencing (GBS) in Sheep". Abstract.