Sydney Precision Data Science Centre
Sydney Data Science Insights
The University of Sydney
Edition 1, July 2023

Message from the Director - Professor Jean Yang

 
Dear Colleagues,

Welcome to the first newsletter of the Sydney Precision Data Science Centre. I’m delighted to welcome friends who have been with us for a long time, and new colleagues to share in our updates and learn about upcoming events.
It is very exciting for us to have formalised the Sydney Precision Data Science Centre with the Dean of Science launching the Centre on 5 June at a well-attended in-person event on campus.
In Semester 1, we continued to deliver the statistical bioinformatics seminar series with local, international and national speakers. The seminar series kicks off again for Semester 2 on 7 August. In October we will be hosting Professor Elaine Holmes as one of the Judith and David Coffey invited speakers. Please keep an eye on our website for details of upcoming sessions.
Our inaugural Winter Data Analysis Challenge is keeping us busy during the break between semesters. The challenge offers an opportunity for undergraduate students to showcase their innovation and creativity in data analysis, and the chance to win prizes. 

This newsletter will be a regular channel of communication for our network to get to know our researchers and stay up to date with our latest tools and methods via regular feature sections. Our network is a community of people working in data-intensive research across health, biomedicine, food science and conservation. I hope to see you at one of our events soon and everyone is welcome to join us for a BBQ hosted by our ECR committee as we start Semester 2. 

Best wishes,

Jean 

ECR Spotlight with Dr Shila Ghazanfar


To celebrate our first newsletter we chat with one of our founding members Dr Shila Ghazanfar. 
What got you interested and excited about data science?
I trained as an applied statistician and am working in bioinformatics and biomedical data science. What excites me about data science is the opportunity for creativity and to connect with other people towards solving a real problem. I am fortunate to always be learning new things and be able to use a mixture of statistics, visualisation and data wrangling to address important questions in biology and disease.
What is keeping you busy at the moment?
Together with my students, I’m working on developing new analyses for molecule-resolved spatial transcriptomics data, funded by my DECRA and CZI grants. I’m also collaborating with other scientists to analyse new data, funded by OGE and BGI. I’ve just finished lecturing DATA3888 for this Semester, and I’m excited to be organising the inaugural Winter Data Analysis Challenge geared towards undergraduate students.
What is your involvement with SPDS and how does it help you?
I’m a founding member and research leader within the SPDS and am curently establishing our scholarships and training committee. Being part of SPDS helps me provide a community for my students and trainees, which is especially important as an EMCR, where they can learn from their peers as well as other research leaders. Data science is an interdisciplinary endeavour, and it’s great to be part of a network of researchers from across the whole University.
Where could we find you when you’re not working? 
In my kitchen, cooking some traditional Afghan dishes.  
Discover Shila's research and publications

Feature method: scFeatures


We plan to highlight a tool or method in each edition of our newsletter. In this edition, we are looking at scFeatures, a novel approach that allows the creation of an interpretable multi-view representation of single-cell and spatial data at the sample level.

In recent years we have seen remarkable progress in the analytical methods for single-cell data analysis. Currently, the scrna-tools website records over 1500 methods. However, while a vast number of tools focus on individual cell analysis, there is a lack of tools that can effectively represent individual samples based on their cellular characteristics and shed light on how these properties influence disease outcomes. 

scFeatures is a method and a toolkit that generates a diverse range of 17 types of features across six feature categories from a given data. The feature categories include cell type proportions, cell type-specific gene expressions, pathway expressions, cell-cell interaction scores, aggregated gene expressions, and spatial metrics. scFeatures can be easily applied to various data types, including single-cell RNA-seq, single-cell spatial proteomics, and spatial transcriptomics.

By harnessing the power of the derived features, scFeatures empowers researchers to gain a deeper understanding of the data. With the biologically relevant and literature-driven features, we can perform various patient-level discoveries, such as uncovering hidden links to patient outcomes and identifying the most perturbed feature types. 
Check out the scFeatures paper. 
Upcoming events
  • 17 July: Unlocking single cell spatial omics analyses with scdney. Register now.
  • 21 July:  Welcome to Semester 2 BBQ. All welcome! Let us know you'll be there. 
  • 7 August: Statistical Bioinformatics Seminar series resumes.  

News and updates

  • July: Several research leaders traveled to Banff, Canada to attend the Single-Cell Plus Data Science Challenges in Single-Cell Research Conference.
  • July: The inaugural Winter Data Analysis Challenge will run for 2 weeks over the break providing a new opportunity for undergraduate students to showcase data science skills.
  • June: Dean of Science officially launched Sydney Precision Data Science Centre.
  • April: Prof Jean Yean and Dr Shila Ghazanfar receive the Chan Zuckerberg Initiative grant in the Data Insights category.
  • March: Dr Rachel Wang was awarded the Moran Medal in Statistical Sciences.
  • February: A/Prof Pengyi Yang was awarded a Sydney Research Accelerator Prize. 
Images above from the Centre launch showing Professor Stephen Bartlett and Professor Marcel Dinger (left) opening the event, Professor Jean Yang (centre) explaining the rationale for the Centre, and a diagram showing the Centre concept and research approach (right). 

Contributions
We will be sending our newsletter quarterly. Please email us with any submissions for consideration or suggestions of what you'd like included in the newsletter. 
 
 
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