Tyrone Chen (曾垂德)

Tyrone Chen (曾垂德)

PhD, Computational Biology and Bioinformatics, Monash University

Publications

The full list of publications and presentations is available on ORCID:

ORCID iD iconhttps://orcid.org/0000-0002-9207-0385

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria

Published in Nature Communications, 2023

The collaborative consortium took on the challenging task of producing and integrating multi-omics datasets generated from key clinical sepsis pathogens from Australia and globally, to support discovery and translational research to tackle the global challenge in the rise of antimicrobial resistance.

Recommended citation: Antibiotic Resistant Pathogens Framework Data Initiative consortium; Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria; Nature Communications 14, 1530 (2023). DOI: https://doi.org/10.1038/s41467-023-37200-w https://doi.org/10.1038/s41467-023-37200-w

Single-cell analysis of lymphatic endothelial cell fate specification and differentiation during zebrafish development

Published in The EMBO Journal, 2023

We here present a single-cell transcriptomic atlas of lymphangiogenesis in zebrafish, revealing new markers and hallmarks of LEC differentiation over four developmental stages.

Recommended citation: Lin Grimm, Elizabeth Mason, Hujun Yu, Stefanie Dudczig, Virginia Panara, Tyrone Chen, Neil I Bower, Scott Paterson, Maria Rondon Galeano, Sakurako Kobayashi, Anne Senabouth, Anne K Lagendijk, Joseph Powell, Kelly A Smith, Kazuhide S Okuda, Katarzyna Koltowska, Benjamin M Hogan; Single-cell analysis of lymphatic endothelial cell fate specification and differentiation during zebrafish development; The EMBO Journal (2023) e112590. DOI: https://doi.org/10.15252/embj.2022112590 https://doi.org/10.15252/embj.2022112590

A user-friendly multi-omics data harmonisation R pipeline

Published in f1000, 2021

We present our R multiomics pipeline as an easy to use and flexible pipeline that takes unrefined multi-omics data as input, sample information and user-specified parameters to generate a list of output plots and data tables for quality control and downstream analysis.

Recommended citation: Tyrone Chen, Al J Abadi, Kim-Anh Lê Cao, Sonika Tyagi, "multiomics: A user-friendly multi-omics data harmonisation R pipeline [version 1; peer review: awaiting peer review]" F1000Research July 2021, 10:538. DOI: https://doi.org/10.12688/f1000research.53453.1 https://doi.org/10.12688/f1000research.53453.1

A Survey of Current Resources to Study lncRNA-Protein Interactions

Published in non-coding RNA, 2021

We reviewed the current state of the art in lncRNA-protein interactions (LPI). We specifically surveyed recent computational methods and databases which researchers can exploit for LPI investigation.

Recommended citation: Melcy Philip, Tyrone Chen, Sonika Tyagi, "A Survey of Current Resources to Study lncRNA-Protein Interactions." Non-Coding RNA, June 2021, Volume 7, Issue 2. DOI: https://doi.org/10.3390/ncrna7020033 https://doi.org/10.3390/ncrna7020033

A multi-modal data harmonisation approach for discovery of COVID-19 drug targets

Published in Briefings in Bioinformatics, 2021

We demonstrate with two independent case studies that our multi-modal data harmonisation pipeline easily generates a list of pertinent biological features for downstream analyses without using algorithms specifically tailored to the datasets.

Recommended citation: Tyrone Chen, Melcy Philip, Kim-Anh Lê Cao, Sonika Tyagi, "A multi-modal data harmonisation approach for discovery of COVID-19 drug targets." Briefings in Bioinformatics, May 2021, bbab185. DOI: https://doi.org/10.1093/bib/bbab185 https://doi.org/10.1093/bib/bbab185

Integrative computational epigenomics to build data-driven gene regulation hypotheses

Published in GigaScience, 2020

In this review, we perform a critical analysis of methods with the explicit aim of harmonizing data, as opposed to case-specific integration.

Recommended citation: 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 http://dx.doi.org/10.1093/gigascience/giaa064

A simple, scalable approach to building a cross-platform transcriptome atlas

Published in PLoS computational biology, 2020

We demonstrate that it is possible to combine a large number of different profiling experiments summarised from dozens of laboratories and representing hundreds of donors, to create an integrated molecular map of human tissue.

Recommended citation: 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 https://doi.org/10.1371/journal.pcbi.1008219

Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids

Published in Nature Cell Biology, 2020

We provide evidence for a wave of human T-cell development that originates directly from haemogenic endothelium via a RAG1+ intermediate with multilineage potential.

Recommended citation: 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 https://rdcu.be/b440v

Stemformatics: visualize and download curated stem cell data

Published in Nucleic Acids Research, 2018

Stemformatics includes curated ‘collections’ of data relevant to cell reprogramming, as well as hematopoiesis and leukaemia.

Recommended citation: 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 https://doi.org/10.1093/nar/gky1064

Mesenchymal Stromal Cells are Readily Recoverable from Lung Tissue, but not the Alveolar Space, in Healthy Humans

Published in Stem Cells, 2016

This investigation comprehensively characterizes and contrasts human lung derived mesenchymal stromal cells (MSCs) from tissue and bronchoalveolar lavage.

Recommended citation: 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 https://doi.org/10.1002/stem.2419

A molecular classification of human mesenchymal stromal cells

Published in PeerJ, 2016

The Rohart MSC test is a simple in silico test that accurately discriminates MSC from fibroblasts, other adult stem/progenitor cell types or differentiated stromal cells.

Recommended citation: 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 https://doi.org/10.7717/peerj.1845