Monash University, Melbourne, Australia
PhD Student (Computational Biology)
2019 - 2022
- Project title: Identification of biological signals by combining distinct categories of biological data through machine learning.
Australian National University, Canberra, Australia
Bachelor of Science (Hons. 1st Class) Bioinformatics, Molecular Biology, Plant Science.
2010 - 2013
- Honours thesis title: A novel motif discovery algorithm for discovering shared motifs in non-homologous sequences.
- Undergraduate research project: An investigation of the potential role of small RNA in maintaining genomic stability of plants.
- Summer research project: A systematic analysis of the photosynthetic properties of the land plant Hirschfeldia incana
Bioinformatics lab, School of Biological Sciences, Faculty of Science, Monash University (Dr Sonika Tyagi), Melbourne, Australia
PhD Student (Computational Biology)
2019 - Present
- Applying machine learning to integrate biological data across multiple modalities.
- Large scale data (1-10 TB) analysis.
- Contributed to writing and data analysis for peer-reviewed academic publications.
- Open source software development for biological data analysis.
Stemformatics Project, Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne (Prof. Christine Wells), Melbourne, Australia
Research Assistant (Bioinformatics)
2016 - 2019
- Curated and ran large quantities of microarray, high throughput sequencing and single cell data through pipelines on high performance compute clusters to contribute to a database of interest for both internal and external collaborators.
- Large scale data (1-10 TB) and metadata standardisation/management as well as retrieving and transmitting these in an accessible format to requesters.
- Contributed to data analysis for peer-reviewed academic publications.
- Open source software development for microarray and high throughput sequencing pipelines.
Stemformatics Project, Australian Institute for Bioengineering and Nanotechnology, University of Queensland (Prof. Christine Wells), Brisbane, Australia
Research Assistant (Bioinformatics)
2014 - 2016
- Duties and achievements are the same as previously listed role Research Assistant (Bioinformatics) at the University of Queensland.
John Curtin School of Medical Research, Australian National University (Prof. Gavin Huttley), Canberra, Australia
Honours Scholar (Bioinformatics)
- Honours project on the development of a computational motif discovery toolkit for identification of signals in biological data.
- Implemented an algorithm in python using information theory and numerical optimisation to discover contiguous and discontigous signals inbiological sequence data.
Research School of Biology, Australian National University (Prof. Murray Badger), Canberra, Australia
Summer Research Student (Plant Biology, Microscopy)
2012 - 2013
- Carried out a systematic analysis of physiology of the land plant Hirschfeldia incana to identify the principles underlying its relatively high photosynthetic rate compared to closely related plants in its family.
- Performed plant growth under controlled conditions and conducted subsequent physiological measurements including microscopy as well as associated imaging and leaf gas exchange measurement.
Research School of Biology, Australian National University (Dr. Iain Searle) Canberra, Australia
Undergraduate Research Student (Molecular Biology, Plant Biology)
- Investigated the possible effect of mutations in the small RNA silencing mechanism which might contribute to genomic instability.
- Performed sterile plant and bacterial growth, PCR, transformation and gel electrophoresis, antibiotic screens, RNAase digestion, DNA extraction and media preparation
Monash University, Melbourne, Australia.
Data Fluency Associate Instructor
2019 - present
- Running software carpentry sessions in unix shell, python, R and high performance computing cluster usage.
College of Medicine, Biology & Environment, Australian National University, Canberra, Australia
Peer Mentor for Biology Students
- Facilitated learning among undergraduate biology students by running tutoring sessions and designing exercises
TraffixGroup, Melbourne, Australia.
Supervisor (Tram Surveyor)
- Led a team to count and interview passengers across Melbourne’s tram routes.
Research School of Biology, Australian National University, Canberra, Australia.
- Maintained a molecular biology laboratory focused on non-coding RNA in plants.
Awards and honours
The full list of publications and presentations is available on ORCID:
Florian Rohart, Elizabeth A. Mason, Nicholas Matigian, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Suzanne Butcher, Jatin Patel, Kerry Atkinson, Kiarash Khosrotehrani, Nicholas M. Fisk, Kim-Anh Lê Cao, Christine A. Wells, "A molecular classification of human mesenchymal stromal cells." PeerJ, 2016, 4:e1845. DOI: https://doi.org/10.7717/peerj.1845
Mesenchymal Stromal Cells are Readily Recoverable from Lung Tissue, but not the Alveolar Space, in Healthy Humans
Kenneth A Sinclair, Stephanie T Yerkovich, Tyrone Chen, Jonathan L McQualter, Peter M-A Hopkins, Christine A Wells, Daniel C Chambers, "Mesenchymal Stromal Cells are Readily Recoverable from Lung Tissue, but not the Alveolar Space, in Healthy Humans" Stem Cells, 2016, 34: 2548-2558. DOI: https://doi.org/10.1002/stem.2419
Jarny Choi, Chris M Pacheco, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Isha Nagpal, Steve Englart, Paul W Angel, Christine A Wells, "Stemformatics: visualize and download curated stem cell data." Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D841–D846. DOI: https://doi.org/10.1093/nar/gky1064
Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids
Ali Motazedian, Freya F. Bruveris, Santhosh V. Kumar, Jacqueline V. Schiesser, Tyrone Chen, Elizabeth S. Ng, Ann P. Chidgey, Christine A. Wells, Andrew G. Elefanty, Edouard G. Stanley, "Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids." Nat Cell Biol 22, 60–73 (2020). DOI: https://doi.org/10.1038/s41556-019-0445-8
Paul W Angel, Nadia Rajab, Yidi Deng, Chris M Pacheco, Tyrone Chen, Kim-Anh Lê Cao, Jarny Choi, Christine A Wells, "A simple, scalable approach to building a cross-platform transcriptome atlas." bioRxiv, 2020.03.09.984468. DOI: https://doi.org/10.1101/2020.03.09.984468
Tyrone Chen, Sonika Tyagi, "Integrative computational epigenomics to build data-driven gene regulation hypotheses." GigaScience, Volume 9, Issue 6, June 2020, giaa064. DOI: https://doi.org/10.1093/gigascience/giaa064
- Machine learning: building and implementing machine learning models (including deep learning)
- Languages (including markup): python, R, bash, pSQL, LaTeX, restructured text, markdown
- Version control: git, mercurial
- Virtual environments: conda, virtualenv
- High performance computing clusters and associated job submissions: PBS, SGE, slurm
- Big data management: organisation, archival, retrieval and standardisation of large quantities of data and metadata (1-10TB) per dataset
- Reproducible research practices and documentation: jupyter notebooks, Rmarkdown
- Workflow languages: nextflow, snakemake
- Graphic design for posters and scientific articles: Adobe inDesign, Adobe Illustrator example poster
Bioinformatics, Mathematics, Statistics
- Data integration: sPLSDA
- Data visualisation: PCA, interactive plots, genome browsers (IGV, UCSC)
- Differential gene expression analysis
- Motif enrichment analyses
- Batch effect correction
- Specialised software: data analysis (ComBAT, deseq, edgeR, fastqc, ISMARA, limma, MEME suite, mixOmics, multiqc, pandas, pytorch, supervised normalisation, tensorflow, variance partitioning, voom), data visualisation (ggplot, glimma, matplotlib, Rcircos, seaborn)
- Microscopy: light microscopy and associated sample preparation
- Plant physiology: Leaf gas exchange measurements, Membrane inlet mass spectrometry, fieldwork, plant growth, sterile plant growth
- Molecular biology: PCR, Molecular cloning, bacterial transformation, antibiotic screens, gel electrophoresis, RNAase digestion, DNA extraction, media preparation
- Teaching and training: usage of microarray and high throughput sequencing pipelines, introduction to programming (python, R, unix shell, high performance computing clusters, deep learning, image recognition), peer mentoring for undergraduate biology students
- Time management and task organisation
- Liasing with external collaborators across disciplines to obtain experimental data and relevant metadata
- Awareness of cultural and professional diversity and clear communication
- Social media editor: Stemformatics Project, Computational biology lab
International Society for Computational Biology
2020 - present
The International Society for Computational Biology (ISCB) is a scholarly society for advancing understanding of living systems through computation and for communicating scientific advances worldwide.
2020 - present
The Carpentries teaches foundational coding and data science skills to researchers worldwide. Software Carpentry is a volunteer project dedicated to teaching basic computing skills to researchers.
Australian Bioinformatics and Computational Biology Society (ABACBS)
2018 – present
Bioinformatics and computational biology deal with the management, analysis and interpretation of biological information, especially at the molecular level. The Australian Bioinformatics And Computational Biology Society (ABACBS) is focused on the science and profession of bioinformatics and computational biology in Australia.
Australasian Genomic Technologies Association (AGTA)
2014 – 2015
The Australasian Genomic Technologies Association AGTA is an incorporated association which serves as a multi-disciplinary professional and educational forum for the use of genomic technologies in Australasia, building on generous support provided by the Australian Cancer Research Foundation (ACRF).
Institute of Electrical and Electronics Engineers (IEEE)
2013 – present
The Institute of Electrical and Electronics Engineers is a professional association headquartered in New York City that is dedicated to advancing technological innovation and excellence.
American Association for the Advancement of Science
2013 - 2015
AAAS (American Association for the Advancement of Science) is the world’s largest multidisciplinary science organization, with nearly 130,000 members and subscribers. Its mission is to work toward sound science policy, improved science education, greater international cooperation, and increased public interest in scientific discovery.
Australian Society for Medical Research (ASMR)
The Australian Society for Medical Research (ASMR) is the peak professional society representing Australian health and medical research. The Society has a long established role in public, political and scientific advocacy.
- Hosting and organising lab social events.
- Organising and participating in journal clubs.
- Workshop assistance at the Introduction to Python workshop, 28th March, 2019, Monash University, Clayton, Australia.
- Community outreach with visiting students at the University of Melbourne, 14 July 2016.
- Community outreach with visiting students at the University of Queensland, 14 September 2014.
- Community outreach with visiting students at the Australian National University, 2013.
Contributions to open source software libraries
- MONET multi-omics clustering algorithm
- Modules for use with the s4m shell framework used in the Stemformatics project
- The extra tools needed to run the Stemformatics project and add datasets into it
- Software carpentries lesson material
Conference and workshop attendance
- Conference presentation at the 28th International Conference on Intelligent Systems for Molecular Biology (ISMB), 13-16th July, 2020*
- Conference presentation at the Bioinformatics Open Source Conference (BOSC 2020), 20-23rd July, 2020*
- Conference presentation at the Australian Bioinformatics and Computational Biology Conference, 9-11th December, 2019, University of Sydney, Sydney, Australia.
- Software carpentries instructor training, 10-11th November, 2019, Monash University, Melbourne, Australia.
- Workshop attendance at the Introduction to Tensor Flow and Machine Learning workshop, 22nd March, 2019, Monash University, Melbourne, Australia.
- Workshop attendance at the Machine Learning workshop, 29th November, 2018, University of Melbourne, Melbourne, Australia.
- Workshop attendance at the BioIT workshop, 26th November, 2018, University of Melbourne, Melbourne, Australia.
- Conference presentation at the Australian Bioinformatics and Computational Biology Conference, 26-29th November, 2018, University of Melbourne, Melbourne, Australia.
- Conference presentation at the Single Cell Genomics Conference, 14-16th September, 2016, Wellcome Genome Campus Conference Centre, Cambridge, United Kingdom.
- Workshop attendance at the QFAB RNA-Sequencing workshop, 19-20th November, 2014, Queensland Biosciences Precinct, University of Queensland, Australia.
- Conference attendance at the Australian Bioinformatics Conference, 11-12th October, 2014, Royal Children’s Hospital, Melbourne, Australia.
- Conference presentation at the Australasian Genomic Technologies Association 14th Annual Conference (AGTA), 13-15th October, 2014, Crown Promenade Hotel, Melbourne, Australia.
- Seminar and discussion group attendance for relevant topics in the University of Queensland, University of Melbourne, the Walter and Eliza Hall Institute of Medical Research, Monash University, Royal Melbourne Institute of Technology.
* virtual participation due to the COVID-19 pandemic of 2020