Dr Thuc Le

ARC Discovery Early Career Researcher UniSA STEM

Mawson Lakes Campus (D3-14)
tel +61 8 830 23996

City West Campus (HB8-11)
tel +61 8 830 27731

email Thuc.Le@unisa.edu.au

Alternative contact

Available for media comment
Research Degree Supervisor

About me

Data mining
Cancer research
Machine learning
Causality
Bioinformatics

I am looking for a PhD student working on Bioinformatics research, PhD scholarships

My publications: Google Scholar and go here to download the papers.

I am currently a DECRA Fellow (2020-2022), and before that, an NHMRC ECR Fellow in Bioinformatics/Computational Biology (2017-2019). Bioinformatics is an inter-disciplinary research area which uses knowledge in Computer Science, Mathematics, and Statistics to solve biological problems. My research focuses on the development of causal inference methods and their applications in Bioinformatics, particularly in gene regulatory networks, cancer drivers, non-coding RNAs, and cancer subtype discovery.

I have a diverse educational background with BSc and MSc... Read more

UniSA STEM

Harnessing connections across science, technology, engineering and mathematics, UniSA STEM creates innovative solutions and groundbreaking developments across teaching, learning and research.

Tweets by @UniversitySA

About me

In the media

Date	Title
19/05/2015	The Lead South Australia, http://www.theleadsouthaustralia.com.au/industries/health/bioinformatics-points-the-way-to-cancers-genetic-causes/

Research

Research themes

Cancer
Healthy futures

Research focus

Information and Computing Sciences
Biological Sciences
Artificial Intelligence and Image Processing
Biochemistry and Cell Biology
Mathematical Sciences

Highlights

My research focuses on the development of causal inference methods and their applications in Bioinformatics, particularly in gene regulatory networks, cancer drivers, non-coding RNAs, and cancer subtype discovery.

Research

Outputs

Research since 2008 is shown below. To see earlier years visit ORCID, ResearcherID or Scopus

Open access indicates that an output is open access.

Books

Year	Output
2015	Li, J, Liu, L & Le, TD 2015, Practical approaches to causal relationship exploration, Springer, US.

Chapters

Year	Output
2019	Le, TD, Ong, KL, Wong, S, Zhao, Y, Jin, WH, Liu, L & Williams, G 2019, 'Preface', Data mining: AusDM: Australasian Conference on Data Mining, Springer Nature, Singapore, pp. v-vi.

Journal Articles

Year	Output
2020	Li, J, Liu, L, Le, TD & Liu, J 2020, 'Accurate data-driven prediction does not mean high reproducibility', Nature Machine Intelligence, vol. 2, pp. 13-15. 1
2020	Pan, J, Cui, T, Le, TD, Li, X & Zhang, J 2020, 'Multi-group transfer learning on multiple latent spaces for text classification', IEEE Access, vol. 8, article no. 9051683, pp. 64120-64130. Open access
2020	Truong, B, Zhou, X, Shin, J, Li, J, van der Werf, JH, Le, TD & Lee, SH 2020, 'Efficient polygenic risk scores for biobank scale data by exploiting phenotypes from inferred relatives', Nature Communications, vol. 11, article no. 3074, pp. 1-11. Open access
2020	Zhang, J, Xu, T, Liu, L, Zhang, W, Zhao, C, Li, S, Li, J, Rao, N & Le, TD 2020, 'LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer', PLoS Computational Biology, vol. 16, no. 4, article no. e1007851, pp. 1-22. Open access
2019	Brown, P, Zhou, Y, Li, J, Lim, R, You, Y, Li, Y & Le, TD and 1 consortia 2019, 'Large expert-curated database for benchmarking document similarity detection in biomedical literature search', Database : The Journal of Biological Databases and Curation, article no. baz085, pp. 1-66. Open access 29
2019	Choobdar, S, Ahsen, ME, Crawford, J, Tomasoni, M, Le, TD, Li, J, Liu, L, Zhang, W & Marbach, D and 168 other authors and 1 consortia 2019, 'Assessment of network module identification across complex diseases', Nature Methods, vol. 16, no. 9, pp. 843-852. Open access 10 4 108
2019	Le, TD, Hoang, T, Li, J, Liu, L, Liu, H & Hu, S 2019, 'A fast PC algorithm for high dimensional causal discovery with multi-core PCs', IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 13, no. 9, pp. 1483-1495. Open access 9 6 3
2019	MA, S, Liu, L, LI, J & LE, TD 2019, 'Data-driven discovery of causal interactions', International Journal of Data Science and Analytics, vol. 8, pp. 285-297.
2019	Ma, S, Li, J, Liu, L & Le, TD 2019, 'Discovering context specific causal relationships', Intelligent Data Analysis, vol. 23, no. 4, pp. 917-931. Open access
2019	Pham, VV, Liu, L, Bracken, CP, Goodall, GJ, Long, Q, Li, J & Le, TD 2019, 'CBNA: A control theory based method for identifying coding and non-coding cancer drivers', PLoS Computational Biology, vol. 15, no. 12, article no. e1007538, pp. 1-12. Open access 5
2019	Pham, VV, Zhang, J, Liu, L, Truong, B, Xu, T, Nguyen, TT, Li, J & Le, TD 2019, 'Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction', BMC Bioinformatics, vol. 20, no. 1, article no. 143, pp. 1-12. Open access 2 2 5
2019	Pillman, KA, Scheer, KG, Hackett-Jones, E, Saunders, K, Bert, AG, Toubia, J, Whitfield, HJ, Sapkota, S, Sourdin, L, Pham, H, Le, TD, Cursons, J, Davis, MJ, Gregory, PA, Goodall, GJ & Bracken, CP 2019, 'Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA)', Nucleic Acids Research, vol. 47, no. 16, pp. 8606-8619. Open access 5
2019	Yu, K, Liu, L, Li, J, Ding, W & Le, TD 2019, 'Multi-source causal feature selection', IEEE Transactions on Pattern Analysis and Machine Intelligence, online. 5
2019	Zhang, J, Liu, L, Xu, T, Xie, Y, Zhao, C, Li, J & Le, TD 2019, 'MiRspongeR: An R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules', BMC Bioinformatics, vol. 20, no. 1, article no. 235, pp. 1-12. Open access 5 2 3
2019	Zhang, J, Pham, VVH, Liu, L, Xu, T, Truong, B, Li, J, Rao, N & Le, TD 2019, 'Identifying miRNA synergism using multiple-intervention causal inference', BMC Bioinformatics, vol. 20, article no. 613, pp. 1-11. Open access 1
2018	Thuyen, T, Suriyanarayanan, T, Zeng, G, Le, TD, Liu, L, Li, J, Tong, C, Wang, Y & Seneviratne, CJ 2018, 'Use of haploid model of Candida albicans to uncover mechanism of action of a novel antifungal agent', Frontiers in Cellular and Infection Microbiology, vol. 8, article no. 164, pp. 1-14. Open access 2 2
2018	Xu, T, Su, N, Liu, L, Zhang, J, Wang, H, Zhang, W, Gui, J, Yu, K, Li, J & Le, T 2018, 'miRBaseConverter: An R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase', BMC Bioinformatics, vol. 19, article no. 514, pp. 1-10. Open access 4 4 1
2018	Zhang, J, Le, TD, Liu, L & Li, J 2018, 'Inferring and analyzing module-specific lncRNA-mRNA causal regulatory networks in human cancer', Briefings in Bioinformatics, vol. 20, no. 4, pp. 1403-1419. 3 1 1
2018	Zhang, J, Liu, L, Li, J & Le, TD 2018, 'LncmiRSRN: identification and analysis of long non-coding RNA related miRNA sponge regulatory network in human cancer', Bioinformatics, vol. 34, no. 24, pp. 4232-4240. 13 6 2
2018	Zhang, W, Le, DT, Lui, L & Li, J 2018, 'Estimating heterogeneous treatment effect by balancing heterogeneity and fitness', BMC Bioinformatics, vol. 19, article no. 518, pp. 1-12. Open access 1
2017	Le, TD, Zhang, J, Liu, L & Li, J 2017, 'Computational methods for identifying miRNA sponge interactions', Briefings in Bioinformatics, vol. 18, no. 4, pp. 577-590. 37 26 2
2017	Li, J, Ma, S, Le, T, Liu, L & Liu, J 2017, 'Causal Decision Trees', IEEE Transactions on Knowledge and Data Engineering, vol. 29, no. 2, pp. 257-271. Open access 10 2 2
2017	Liu, H, Liu, L, Le, TD, Lee, I, Sun, S & Li, J 2017, 'Nonparametric sparse matrix decomposition for cross-view dimensionality reduction', IEEE Transactions on Multimedia, vol. 19, no. 8, article no. 7879190, pp. 1848-1859. 4 4
2017	Weijia Zhang , Le, TD, Liu, L, Zhou, Z-H & Li, J 2017, 'Mining heterogeneous causal effects for personalized cancer treatment', Bioinformatics, vol. 33, no. 15, pp. 2372-2378. Open access 9 5 2
2017	Xu, T, Le, TD, Liu, L, Su, N, Wang, R, Sun, B, Colaprico, A, Bontempi, G & Li, J 2017, 'CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization', Bioinformatics, vol. 33, n. 19, pp. 3131-3133. Open access 32 25 7
2017	Zhang, J, Le, TD, Liu, L & Li, J 2017, 'Identifying miRNA sponge modules using biclustering and regulatory scores', BMC Bioinformatics, vol. 18, suppl. 3, article no. 44, pp. 1-12. Open access 8 6 2
2017	Zhang, J, Le, TD, Liu, L & Li, J 2017, 'Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer', BMC Bioinformatics, vol. 18, no. 243, pp. 1-12. Open access 15 10 2
2016	Ma, S, Li, J, Liu, L & Le, TD 2016, 'Mining combined causes in large data sets', Knowledge-Based Systems, vol. 92, pp. 104-111. Open access 8 4
2016	Masud, K, Liu, L, Le, TD & Li, J 2016, 'Identification of miRNA-mRNA regulatory modules by exploring collective group relationships', BMC Genomics, vol. 17, no. S1, pp. 71-84. Open access 14 9 2
2016	Weijia Zhang , Le, TD, Liu, L, Zhou, Z-H & Li, J 2016, 'Predicting miRNA targets by integrating gene regulatory knowledge with expression profiles', PLoS One, vol. 11, no. 4, article no. e0152860, pp. 1-19. Open access 10 8 2
2016	Xu, T, Le, TD, Liu, L, Wang, R, Sun, B & Li, J 2016, 'Identifying cancer subtypes from miRNA-TFmRNA regulatory networks and expression data', PLoS One, vol. 11, no. 4, pp. 1-20. Open access 31 18 7
2016	Zhang, J, Le, TD, Liu, L, He, J & Li Jiuyong, 2016, 'A novel framework for inferring condition-specific TF and miRNA co-regulation of protein-protein interactions', Gene, vol. 557, no. 1, pp. 55-64. 8 7 1
2016	Zhang, J, Le, TD, Liu, L, He, J & Li, J 2016, 'Identifying miRNA synergistic regulatory networks in heterogeneous human data via network motifs', Molecular Biosystems, vol. 12, no. 2, pp. 454-463. 5 5 1
2015	Le, TD, Liu, L, Zhang, J, Liu, B & Li, J 2015, 'From miRNA regulation to miRNA-TF co-regulation: computational approached and challenges', Briefings in Bioinformatics, vol. 16, no. 9, pp. 475-496. Open access 21 15 2
2015	Le, TD, Zhang, J, Liu, L & Li, J 2015, 'Ensemble methods for MiRNA target prediction from expression data', PLoS One, vol. 10, no. 6, pp. 1-19. Open access 22 16 2
2015	Le, TD, Zhang, J, Liu, L, Liu, H & Li, J 2015, 'miRLAB: An R Based Dry Lab for Exploring miRNA-mRNA Regulatory Relationships', PLoS One, vol. 10, no. 12, pp.1-15. Open access 16 9 7
2015	Li, J, Le, TD, Liu, L, Liu, J, Jin, Z, Sun, B & Ma, S 2015, 'From observational studies to causal rule mining', ACM Transactions on Intelligent Systems and Technology, vol. 7, no. 2, article no. 14. Open access 19 4 1
2014	Zhang, J, Le, TD, Liu, L, Liu, B, He, J, Goodall, GJ & Li, J 2014, 'Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data', Bioinformatics, v 30, no. 21, pp. 3070-3077. Open access 13 9 3
2014	Zhang, J, Le, TD, Liu, L, Liu, B, Jianfeng, H, Goodall, GJ & Li, J 2014, 'Identifying direct miRNA-mRNA causal regulatory relationships in heterogeneous data', Journal of Biomedical Informatics, vol. 52, pp. 438-447. Open access 18 15
2013	Le, TD, Liu, L, Liu, B, Tsykin, A, Goodall, G, Satou, K & Li, J 2013, 'Inferring microRNA and transcription factor regulatory networks in heterogeneous data', BMC Bioinformatics, vol. 14, article no. 92, pp. 1-13. Open access 34 36 3
2013	Le, TD, Liu, L, Tsykin, A, Goodall, GJ, Liu, B, Sun, B-Y & Li, J 2013, 'Inferring microRNA-mRNA causal regulatory relationships from expression data', Bioinformatics, vol. 29, no. 6, pp. 765-771. Open access 48 44 4

Conferences

Year	Output
2020	Lu, S, Liu, L, Li, J, Le, TD & Liu, J 2020, 'LoPAD: A local prediction approach to anomaly detection', 24th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2020, Springer, vol. 12085, pp. 660-673.
2019	Lu, S, Liu, L, Li, J & Le, TD 2019, 'Effective outlier detection based on Bayesian Network and Proximity', International Conference on Big Data, Big Data 2018, IEEE, article no. 8622230, pp. 134-139. Open access
2018	Le, TD, Xu, T, Liu, L, Shu, H, Hoang, T & Li, J 2018, 'ParallelPC: An R package for efficient causal exploration in genomic data', 22nd Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2018, Springer Nature, pp. 207-218. 2
2017	Le, TD, Zhang, J, Liu, L, Thanh Truong, BM, Hu, S, Xu, T & Li, J 2017, 'Identifying microRNA targets in epithelial-mesenchymal transition using joint-intervention causal inference', 8th International Conference on Computational Systems-Biology and Bioinformatics, (CSBio 2017), ACM - Association for Computing Machinery, pp. 34-41. 1
2017	Li, J, Liu, J, Liu, L, Thuc, DL, Ma, S & Han, Y 2017, 'Discrimination detection by causal effect estimation', IEEE International Conference on Big Data (IEEE Big Data), IEEE, pp. 1087-1094. 3 1
2013	Li, J, Le, TD, Liu, L, Liu, J, Jin, Z & Sun, B 2013, 'Mining causal association rules', IEEE 13th International Conference on Data Mining Workshops 2013, IEEE Press, pp. 114-123. 22 15
2012	Jin, Z, Li, J, Liu, L, Le, TD, Sun, B & Wang, R 2012, 'Discovery of causal rules using partial association', 2012 IEEE 12th International Conference on Data Mining, IEEE, pp. 309-318. 14 9

Reports

Year	Output
2017	Le, TD 2017, Causal inference methods and applications in Bioinformatics: A Summary, Australia. Open access

External engagement & recognition

Collaborations

Highlights

Associate Editor:

Plos One
BMC Cancer

Conference/workshop Organiser of:

Causality Workshop 2018, 2019, 2020
BioinfoSummer 2016

Program committee chair/member of:

PC co-chair of Australasian Data Mining Conference 2019
AAAI, ICDM, PAKDD, InCOB, GIW

Paper reviewer for:

Bioinformatics
Plos Computational Biology
Nucleic Acids Research
BMC Bioinformatics
IEEE Transactions on Knowledge and Data Engineering (TKDE)
ACM Transactions on Intelligent Systems and Technology (ACM TIST)
Annals of Medicine Computers in Biology and Medicine
Plos One
Briefings in Bioinformatics

Grant reviewer for:

ARC
NHMRC

External engagement & recognition

Collaborations

Organisation	Country
Agency for Science Technology & Research (ASTAR)	UNITED STATES
Children's Cancer Institute Australia	AUSTRALIA
Chinese Academy of Sciences	CHINA
Consilium Technology Pty Ltd	AUSTRALIA
CSIRO Australia (Commonwealth Scientific Industrial Research Organisation)	AUSTRALIA
Dali University	CHINA
East China Normal University	CHINA
Griffith University	AUSTRALIA
Heifei University of Technology	CHINA
Icahn School of Medicine at Mount Sinai	UNITED STATES
Institute of Medical and Veterinary Science	AUSTRALIA
Jiangsu Normal University	CHINA
Kanazawa University	JAPAN
Kunming University of Science and Technology	CHINA
La Trobe University	AUSTRALIA
Microsoft	AUSTRALIA
Nanjing University	CHINA
Nanjing University of Science and Technology	CHINA
National University of Singapore	SINGAPORE
Pham Ngoc Thach University of Medicine	VIET NAM
SA Pathology	AUSTRALIA
Tufts University	UNITED STATES
University Libre Bruxelles	BELGIUM
University of Adelaide	AUSTRALIA
University of British Columbia	CANADA
University of Electronic Science and Technology of China	CHINA
University of Lausanne	SWITZERLAND
University of Massachusetts Boston	UNITED STATES
University of Michigan	UNITED STATES
University of New England	AUSTRALIA
University of Pennsylvania	UNITED STATES
University of Science and Technology of China	CHINA
University of South Australia	AUSTRALIA
Walter and Eliza Hall Institute of Medical Research	AUSTRALIA
Zhejiang Normal University	CHINA

External engagement & recognition

Engagement/recognition	Year
Academic Editor PLOS One	2020
ARC Grant Reviewer Australian Research Council Discovery	2020
Associate Editor BMC Cancer Journal	2020
Discovery Early Career Researcher Award Australian Research Council Discovery	2020
HDR Thesis Examiner University of Sydney	2020
HDR Thesis Examiner Deakin University	2020
Academic Editor PLOS One	2019
PC Co-chair of Australasian Data Mining Conference Australian Computer Society (ACS)	2019
Visiting Professor University of Pennsylvania	2019
Conference and Workshop Organiser ACM SIGKDD Workshop on Causal Discovery	2018
Early Career Fellowship National Health and Medical Research Council (NHMRC)	2018
Member Australian Bioinformatics Network	2018
Member The Australian Bioinformatics And Computational Biology Society (ABACBS)	2018
Member Association for Computing Machinery (ACM) SIG-Bioinformatics	2018
Professional Member Association for Computing Machinery (ACM)	2018
Professional Member Institute of Electrical and Electronics Engineers (IEEE)	2018
Early Career Fellowship National Health and Medical Research Council (NHMRC)	2017
Member Australian Bioinformatics Network	2017
Member The Australian Bioinformatics And Computational Biology Society (ABACBS)	2017
Member Association for Computing Machinery (ACM) SIG-Bioinformatics	2017
Professional Member Association for Computing Machinery (ACM)	2017
Professional Member Institute of Electrical and Electronics Engineers (IEEE)	2017
Program Committee Member International Conference on Bioinformatics InCOB	2017
Board Member BioInfoSummer, University of Adelaide	2016
Conference and Workshop Organiser BioinfoSummer	2016
Contributor Movember Foundation	2016
Early Career Fellowship National Health and Medical Research Council (NHMRC)	2016
HDR Thesis Examiner Deakin University	2016
Program Committee Member, Causality Workshop 22nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2016)	2016
Runner-up prize for DREAM challenge DREAM	2016
Cancer Research Fund Raising Campaign Movember Foundation	2015
Interviewed by The LEAD South Australia about bioinformatics research and the success in PhD research thesis The LEAD South Australia	2015
Invited by the SA Governor as an SA emerging scientist to talk to the HRH The Duke of Kent during his visit to Australia Government of South Australia	2015

Teaching & student supervision

Research degree supervision

Supervisions from 2010 shown

Thesis title	Student status
Achieving improved explainability and accuracy in explainable machine learning	Current
Causal inference methods for identification of subtypes of cancer based on multi-levelled biological data	Current
Causality based approach to outlier detection	Current
Developing causal inference methods for personalised medicine in cancer research	Current
Intervention recommendation for improvement in disability employment	Current
Predicting Protein Subcellular Location by Fusing Multi-Source Information	Current
Computational causal discovery from observational data and application in bioinformatics	Completed
Developing data mining methods for finding causal relationships involving multiple factors	Completed

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Dr Thuc Le

Alternative contact

Alternative contact details

About me

About me

UniSA STEM

About me

Professional Associations

In the media

Experience

Qualifications

Research

Research themes

Research focus

Highlights

Projects

Outputs

Books

Chapters

Journal Articles

Conferences

Reports

Current research & highlights

External engagement & recognition

Collaborations

Highlights

Collaborations

External engagement & recognition

Academic Editor

ARC Grant Reviewer

Associate Editor

Discovery Early Career Researcher Award

HDR Thesis Examiner

HDR Thesis Examiner

Academic Editor

PC Co-chair of Australasian Data Mining Conference

Visiting Professor

Conference and Workshop Organiser

Early Career Fellowship

Member

Member

Member

Professional Member

Professional Member

Early Career Fellowship

Member

Member

Member

Professional Member

Professional Member

Program Committee Member

Board Member

Conference and Workshop Organiser

Contributor

Early Career Fellowship

HDR Thesis Examiner

Program Committee Member, Causality Workshop

Runner-up prize for DREAM challenge

Cancer Research Fund Raising Campaign

Interviewed by The LEAD South Australia about bioinformatics research and the success in PhD research thesis

Invited by the SA Governor as an SA emerging scientist to talk to the HRH The Duke of Kent during his visit to Australia

Teaching & student supervision

Courses and programs

Courses I teach and/or co-ordinate

Research degree supervision

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