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Bioinformatics

The Westmead Research Hub has a great amount of talented Bioinformaticians with the skills, time and enthusiasm to collaborate with you on your research project. Below is a list of some of those scientists who you can contact if you would like to strike up a partnership. If you are a bioinformatician and you would like to be added to this page, please email jlinton@wrh.org.au to get started.

Emilie Wilkie

Emilie Wilkie is passionate about facilitating many stages of biomedical research. Emilie has expertise in the experimental design and analysis of various omics data types including gene expression analysis of coding and non-coding RNA; determining DNA and RNA binding sites of proteins; assessing epigenetic modifications including DNA methylation, histone modifications and chromatin accessibility; functional enrichment analysis and interpretation; regulatory network elucidation and integration of multi-omics datasets. Additionally, she has experience with epidemiological data analysis and enjoys optimising routine tasks by developing Shiny applications.
 
My contact details are:
E: ewilkie@cmri.org.au

Erdahl Teber

Dr Erdahl Teber has a  background in computing science, biochemistry and statistics. Erdahl works on projects that attempt to use the latest and best data science practices in integrative systems biology, biostatistics, machine learning and data visualisation techniques. In his experience, some critical factors that determine the success of research outcomes involving data can be summarised as: 1) how clear your research question is; 2) how well matched the data and analytical tools are to your question; 3) how reliable the data is; 4) how well you understand the way the data was produced; 5) how well the analytical tool is used, results interpreted and communicated; and 6) whether there are controls to compare to and the level of quality assurance applied by the data scientist to ensure no errors are introduced.

My contact details are:
T: 8865 2800
E: eteber@cmri.org.au

Rosemarie Sadsad

Dr. Rosemarie Sadsad is the Informatics Services Lead at the Sydney Informatics Hub. She is a computer biomedical engineer, with a PhD in health informatics (UNSW). She also conducts research in pathogen genomics and clinical decision support at the Centre for Infectious Diseases and Microbiology - Public Health for NSW Health. Rosemarie specialises in complex systems analysis (multiscale modelling and simulation, network analyses), decision support systems, pathogen genomics, and bioinformatics. She has over 10 years experience applying these skills and knowledge across the health domain including health services, heart disease, Dementia, and largely, infectious diseases and is a member of the National Communicable Disease Genomics Network. Her interests are in utlising innovative technology and analytics to synthesise complex big health data and improve its accessibility on the ground through effective communication and visualisation.

My contact details are:
T: 8627 6286
E: rosemarie.sadsad@sydney.edu.au
 

Verlaine Timms

Dr Verlaine is a microbiologist with expertise in gastrointestinal pathogens and commensals as well as pathogen genomics for outbreak surveillance. She has worked internationally in the UK on Helicobacter pylori and her current interests include the re-emergence of pertussis and opportunistic pathogens such as Legionella pneumophila. Verlaine utilizes whole genome sequencing to investigate how pathogens evade current vaccination strategies and how opportunistic pathogens contribute to outbreaks of public health significance.
 
My contact details are:
T: +61 2 8890 9870
E: verlaine.timms@health.nsw.gov.au

Qing Zhong

Dr Qing Zhong is Group Leader for Cancer Data Science at CMRI and a conjoint Senior Lecturer at the University of Sydney. He completed his undergraduate study in computer science and a PhD in biochemistry and computer science at ETH (Swiss Federal Institute of Technology) in Zurich, Switzerland.
 
He was awarded the ProMedica Stiftung for his post-doctoral training at University of Zurich, and was then appointed as a senior data scientist at University Hospital Zurich (USZ). Prior to joining CMRI, Dr Zhong was responsible for the analysis of biomedical data at the USZ and implemented a clinical big data system for consolidating genomic, clinical and demographic information into a unified model for precision and data-driven medicine. His research interests include big cancer data analysis, machine learning, and computational biology.
 
My contact details are:
T: +61 2 8865 2993
E: qzhong@cmri.org.au

Ellis Patrick

Dr Ellis Patrick is a computational biologist and applied statistician. He is currently an Early Career Development Fellow in the School of Mathematics and Statistics and a staff member at The Westmead Institute for Medical Research. He obtained his PhD in statistical bioinformatics in the School of Mathematics and Statistics at the University of Sydney. In his postdoctoral studies, he worked as a computational biologist with joint appointments at Brigham and Women's hospital, Harvard Medical School and The Broad Institute of MIT and Harvard. He spent this time using his statistical background to investigate the molecular drivers of Alzheimer's disease and MS. As he spends most of his time analysing large biomedical datasets, his research relies on the subtlety of translating between biological and statistical concepts to form simple, suitable and targeted statistical questions.

My contact details are:
T: 8627 6286
E: ellis.patrick@sydney.edu.au

Aldo Saavedra

Dr Aldo Saavedra is a Senior Research Scientist
with expertise in the application of state of the art data analytics for understanding and improving human health as well as creating the capacity within the health system.
 
As the Lead Engineer in Health in the Sydney Informatics Hub, he has led a group of research data engineers on a vast array of data-driven health projects aimed at deriving meaningful insights from routinely collected digital health records for wide range of problems.
They range from determining factors contributing to clinical variation to facilitating clinical decision making through the visualisation of patient care plans.
 
Aldo and his team work closely with clinicians, health staff and eMR experts at the various medical institutes and hospitals that the University of Sydney is affiliated with as well as eHealth NSW to achieve translational outcomes.

My contact details are:
T: +61 2 9063 9807
E: aldo.saavedra@sydney.edu.au

Ranjeeta Menon

Dr Ranjeeta Menon is a computational biologist presently working as Research Fellow Microbial informatics in the Sydney Medical School, The University Of Sydney and CIDM-PH Westmead Hospital. She holds her PhD in Bioinformatics from Macquarie University. In her postdoctoral studies at University of New South Wales, she has worked in cancer research focussing on cancer cell lines and collaboration projects for cancer drug trial projects. Moving on, next postdoctoral studies in virus short linear motif predictions. Ranjeeta has expertise in analysis of various omics data types including RNA-seq, MBD-seq, Chip-seq, epigenetic modifications including DNA methylation, gene expression analysis, mass-spec data analysis, pipelines, Genome wide association studies, statistics. The major focus currently is on pathogen genomics projects focusing on disease transmission, outbreak and virulence of Infectious diseases using whole genome sequencing data exploring on integrating clinical and epidemiological data analysis with advanced bioinformatics analysis and looking forward to work on Nanopore sequencing data.


My contact details are:
T: +61 2 9845 5541
E: ranjeeta.menon@sydney.edu.au