Hong-Yu Ou

18 papers Journal 15Unranked 3
YearRankTypeTitle / Venue / Authors
2025 — conf
FMAlign3: A Scalable and Adaptive Framework for Large-Scale Multiple Sequence Alignment.
ICIC (26)
Hong-Yu Ou, Huan Liu, Fajun Huang, JingTong Nie, Mengyuan Wang
2024 J jnl
Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor-antigen recognition.
Nat. Mac. Intell.
Yumeng Zhang, Zhikang Wang, Yunzhe Jiang, Dene R. Littler, Mark Gerstein, Anthony W. Purcell, Jamie Rossjohn, Hong-Yu Ou, Jiangning Song
2022 J jnl
T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model.
Briefings Bioinform.
Yumeng Zhang, Yangming Zhang, Yi Xiong, Hui Wang, Zixin Deng, Jiangning Song, Hong-Yu Ou
2022 J jnl
VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens.
Nucleic Acids Res.
Meng Wang, Ying-Xian Goh, Cui Tai, Hui Wang, Zixin Deng, Hong-Yu Ou
2019 — conf
ICEO: a Biological Ontology for Representing and Analyzing the Bacterial Integrative and Conjugative Element.
ICBO
Meng Liu, Hong-Yu Ou, Yongqun He
2019 J jnl
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.
Nucleic Acids Res.
Meng Liu, Xiaobin Li, Yingzhou Xie, Dexi Bi, Jingyong Sun, Jun Li, Cui Tai, Zixin Deng, Hong-Yu Ou
2019 — conf
OGG-Bac: Ontological Representation of Orthologous Bacterial Genes.
ICBO
Meng Liu, Hong-Yu Ou, Yongqun He
2018 J jnl
TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci.
Nucleic Acids Res.
Yingzhou Xie, Yiqing Wei, Yue Shen, Xiaobin Li, Hao Zhou, Cui Tai, Zixin Deng, Hong-Yu Ou
2018 J jnl
VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria.
Briefings Bioinform.
Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou
2018 J jnl
oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements.
Nucleic Acids Res.
Xiaobin Li, Yingzhou Xie, Meng Liu, Cui Tai, Jingyong Sun, Zixin Deng, Hong-Yu Ou
2013 J jnl
SecReT4: a web-based bacterial type IV secretion system resource.
Nucleic Acids Res.
Dexi Bi, Linmeng Liu, Cui Tai, Zixin Deng, Kumar Rajakumar, Hong-Yu Ou
2012 J jnl
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.
Nucleic Acids Res.
Dexi Bi, Zhen Xu, Ewan M. Harrison, Cui Tai, Yiqing Wei, Xinyi He, Shiru Jia, Zixin Deng, Kumar Rajakumar, Hong-Yu Ou
2011 J jnl
TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea.
Nucleic Acids Res.
Yucheng Shao, Ewan M. Harrison, Dexi Bi, Cui Tai, Xinyi He, Hong-Yu Ou, Kumar Rajakumar, Zixin Deng
2010 J jnl
mGenomeSubtractor: a web-based tool for parallel
Nucleic Acids Res.
Yucheng Shao, Xinyi He, Ewan M. Harrison, Cui Tai, Hong-Yu Ou, Kumar Rajakumar, Zixin Deng
2007 J jnl
MobilomeFINDER: web-based tools for
Nucleic Acids Res.
Hong-Yu Ou, Xinyi He, Ewan M. Harrison, Bridget R. Kulasekara, Ali Bin Thani, Aras Kadioglu, Stephen Lory, Jay C. D. Hinton, Michael R. Barer, Zixin Deng, Kumar Rajakumar
2004 J jnl
EG: a database of essential genes.
Nucleic Acids Res.
Ren Zhang, Hong-Yu Ou, Chun-Ting Zhang
2003 J jnl
Recognition of Translation Initiation Sites of Eukaryotic Genes Based on an EM Algorithm.
J. Comput. Biol.
Yonghong Wang, Hong-Yu Ou, Fengbiao Guo
2003 J jnl
The Z curve database: a graphic representation of genome sequences.
Bioinform.
Chun-Ting Zhang, Ren Zhang, Hong-Yu Ou