Mr Timothy Stephens
Higher degree by research (PhD) student
Institute for Molecular Bioscience
334 62606
334 62619
Book Chapter
Bernard, Guillaume, Stephens, Timothy G., González-Pech, Raúl A. and Chan, Cheong Xin (2021). Inferring phylogenomic relationship of microbes using scalable alignment-free methods. Bacterial pangenomics: methods and protocols. (pp. 69-76) New York, United States: Humana Press. doi: 10.1007/978-1-0716-1099-2_5
Journal Articles
Jacobus, Ana Paula, Stephens, Timothy G., Youssef, Pierre, González-Pech, Raul, Ciccotosto-Camp, Michael M., Dougan, Katherine E., Chen, Yibi, Basso, Luiz Carlos, Frazzon, Jeverson, Chan, Cheong Xin and Gross, Jeferson (2021). Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to Cachaça spirit yeasts. Frontiers in Microbiology, 12 644089, 644089. doi: 10.3389/fmicb.2021.644089
Gonzalez-Pech, Raul A., Stephens, Timothy G., Chen, Yibi, Mohamed, Amin R., Cheng, Yuanyuan, Shah, Sarah, Dougan, Katherine E., Fortuin, Michael D. A., Lagorce, Remi, Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2021). Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biology, 19 (1) 73, 73. doi: 10.1186/s12915-021-00994-6
Stephens, Timothy G., González-Pech, Raúl A., Cheng, Yuanyuan, Mohamed, Amin R., Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2020). Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biology, 18 (1) 56, 56. doi: 10.1186/s12915-020-00782-8
González-Pech, Raúl A., Stephens, Timothy G. and Chan, Cheong Xin (2018). Commonly misunderstood parameters of NCBI BLAST and important considerations for users. Bioinformatics, 35 (15) bty1018, 2697-2698. doi: 10.1093/bioinformatics/bty1018
Stephens, Timothy G., Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2018). Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports, 8 (1) 17175, 17175. doi: 10.1038/s41598-018-35620-z
Lee, JunMo, Yang, Eun Chan, Graf, Louis, Yang, Ji Hyun, Qiu, Huan, Zel Zion, Udi, Chan, Cheong Xin, Stephens, Timothy G., Weber, Andreas P. M., Boo, Ga Hun, Boo, Sung Min, Kim, Kyeong Mi, Shin, Younhee, Jung, Myunghee, Lee, Seung Jae, Yim, Hyung-Soon, Lee, Jung-Hyun, Bhattacharya, Debashish and Yoon, Hwan Su (2018). Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta. Molecular Biology and Evolution, 35 (8), 1869-1886. doi: 10.1093/molbev/msy081
Stephens, Timothy, Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2016). PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ, 4 (5) e2038, e2038.1-e2038.13. doi: 10.7717/peerj.2038
Conference Paper
Chan, Cheong Xin, Stephens, Timothy G., Ling, Edmund Y. S., Foret, Sylvain, Morrow, Kathleen, Bourne, David G., Voolstra, Christian R., Leggat, William, Miller, David J. and Ragan, Mark A. (2015). Genome Analysis of Two Symbiodinium Isolates. 6th European Phycological Congress, London, United Kingdom, 23-28 August 2015. Abingdon, Oxfordshire, United Kingdom: Taylor and Francis. doi: 10.1080/09670262.2015.1069489
Data Collection
Stephens, Timothy, Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2020). Genome assemblies and the associated annotations for Polarella glacialis CCMP1383 and CCMP2088. The University of Queensland. (Dataset) doi: 10.14264/uql.2020.222