- An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data
Vaccine and Infectious Disease Organization International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
BMC Genomics 16:359. 2015
..Few automatic software tools have yet been established to investigate large-scale RNA-seq data for bacterial transcript structure analysis...
- Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. cubense
Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
BMC Genomics 14:851. 2013
..The knowledge of global gene expression patterns influenced by infection of different Foc races will help to understand the host responses to the infection...
- Prediction of bacterial type IV secreted effectors by C-terminal features
Genomics Research Center, Harbin Medical University, Harbin, China
BMC Genomics 15:50. 2014
..Therefore, an effective inter-species T4SS effector prediction tool is urgently needed to help discover new effectors in a variety of bacterial species, especially those with few known effectors, e.g., Helicobacter pylori...
- T3DB: an integrated database for bacterial type III secretion system
School of Life Science, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
BMC Bioinformatics 13:66. 2012
..It is necessary to set up a knowledgebase integrating T3SS-related research data to facilitate the communication between different research groups interested in different bacteria...
- T3_MM: a Markov model effectively classifies bacterial type III secretion signals
Genomics Research Center, Haerbin Medical University, Harbin, China
PLoS ONE 8:e58173. 2013
..We used these comparisons to set up a statistic model to quantitatively model and effectively distinguish T3S effectors...
- Effective identification of bacterial type III secretion signals using joint element features
School of Life Sciences and the State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
PLoS ONE 8:e59754. 2013
- High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles
The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
Bioinformatics 27:777-84. 2011
..Previous computational methods for T3S protein prediction have only achieved limited accuracy, and distinct features for effective T3S protein prediction remain to be identified...
- RedoxDB--a curated database for experimentally verified protein oxidative modification
Ming An Sun
School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
Bioinformatics 28:2551-2. 2012
..Bulk download of the entire dataset is also available. We expect that RedoxDB will be useful for both experimental studies and computational analyses of protein oxidative modification...
- A model-based method for gene dependency measurement
School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
PLoS ONE 7:e40918. 2012
..To validate the new prediction, the promoter sequences of target genes regulated by the same transcription factors were analyzed and significant motifs were identified...
- Investigation of glandular trichome proteins in Artemisia annua L. using comparative proteomics
School of Life Sciences and State Kay Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, People s Republic of China
PLoS ONE 7:e41822. 2012
..Functional classification of these GSTs enriched proteins revealed that many of them participate in major plant metabolic processes such as electron transport, transcription and translation...