Pathway Analysis of Bacillus subtillis Metabolic Network Based on Genomic Information. - Hongwu Ma; Xiaofeng Guo; Xue-Ming Zhao (German Conference on Bioinformatics, 2001)

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. - Hongwu Ma; An-Ping Zeng 001 (Bioinform., 2003)

The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks. - Hongwu Ma; An-Ping Zeng 001 (Bioinform., 2003)

Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. - Hongwu Ma; Xue-Ming Zhao; Ying-Jin Yuan; An-Ping Zeng 001 (Bioinform., 2004)

Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. - Hongwu Ma; Jan Buer; An-Ping Zeng 001 (BMC Bioinform., 2004)

SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. - Tim Van den Bulcke; Koen Van Leemput; Bart Naudts; Piet van Remortel; Hongwu Ma; Alain Verschoren; Bart De Moor; Kathleen Marchal (BMC Bioinform., 2006)

Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions. - Qingzhao Wang; Yudi Yang; Hongwu Ma; Xue-Ming Zhao (Bioinform., 2007)

Modeling the arsenic biosensor system. - Yizhi Cai; Bryony Davidson; Hongwu Ma; Chris French (BMC Syst. Biol., 2007)

Arsenic biosenseor: a step further. - Chris French; Judith Nicholson; Farid Bizzari; Jelena Aleksic; Yizhi Cai; Sreemati Seshasayee; Sergii Ivakhno; Bryony Davidson; Jen Wilson; Kim de Mora; Hongwu Ma; Laszlo Kozma-Bognar; et al. (BMC Syst. Biol., 2007)

Centrality, Network Capacity, and Modularity as Parameters to Analyze the Core-Periphery Structure in Metabolic Networks. - Marcio Rosa da Silva; Hongwu Ma; An-Ping Zeng 001 (Proc. IEEE, 2008)

BioDiVinE: A Framework for Parallel Analysis of Biological Models - Jiri Barnat; Lubos Brim; Ivana Cerná; Sven Drazan; Jana Fabriková; Jan Láník; David Safránek; Hongwu Ma (COMPMOD, 2009)

Compartmentalization of the Edinburgh Human Metabolic Network. - Tong Hao; Hongwu Ma; Xue-Ming Zhao; Igor Goryanin (BMC Bioinform., 2010)

A semi-automated genome annotation comparison and integration scheme. - Zhe Liu 013; Hongwu Ma; Igor Goryanin (BMC Bioinform., 2013)

Taxonomic and functional metagenomic analysis of anodic communities in two pilot-scale microbial fuel cells treating different industrial wastewaters. - Larisa Kiseleva; Sofya K. Garushyants; Hongwu Ma; David J. W. Simpson; Viatcheslav Fedorovich; Michael F. Cohen; Igor Goryanin (J. Integr. Bioinform., 2015)

ECRECer: Enzyme Commission Number Recommendation and Benchmarking based on Multiagent Dual-core Learning. - Zhenkun Shi; Qianqian Yuan; Ruoyu Wang 025; Hoaran Li; Xiaoping Liao; Hongwu Ma (CoRR, 2022)

ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database. - Zhitao Mao; Ruoyu Wang 025; Haoran Li; Yixin Huang; Qiang Zhang; Xiaoping Liao; Hongwu Ma (Nucleic Acids Res., 2022)

AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms. - Yi Yang 001; Yufeng Mao; Ruoyu Wang 025; Haoran Li; Ye Liu; Haijiao Cheng; Zhenkun Shi; Yu Wang 159; Meng Wang 001; Ping Zheng; Xiaoping Liao; Hongwu Ma (Nucleic Acids Res., 2022)

CAVE: a cloud-based platform for analysis and visualization of metabolic pathways. - Zhitao Mao; Qianqian Yuan; Haoran Li; Yue Zhang; Yuanyuan Huang; Chunhe Yang; Ruoyu Wang 025; Yongfu Yang; Yalun Wu; Shihui Yang; Xiaoping Liao; Hongwu Ma (Nucleic Acids Res., 2023)