Publications

Publications



Latest journal papers Full list

#Equal contributions
*Corresponding author

1 Chia-Tzu Ho, Yu-Wei Huang, Chia-Hua Lo, Wei-Cheng Lo* (2021, Nov). Discovering the ultimate limits of protein secondary structure prediction. Biomolecules, 11(11):1627, doi: 10.3390/biom11111627.
Abstract
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2 Teng-Ruei Chen, Yen-Cheng Lin, Yu-Wei Huang, Chih-Chieh Chen, Wei-Cheng Lo* (2021, Oct). CirPred, the first structure modeling and linker design system for circularly permuted proteins. BMC Bioinformatics, 22(Suppl 10):494, doi: 10.1186/s12859-021-04403-1.
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3 Teng-Ruei Chen#, Sheng-Hung Juan#, Yu-Wei Huang, Yen-Cheng Lin, Wei-Cheng Lo* (2021, Jul). A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction. PLOS ONE, 16(7):e0255076, doi: 10.1371/journal.pone.0255076.
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4 Teng-Ruei Chen#, Chia-Hua Lo#, Sheng-Hung Juan, Wei-Cheng Lo* (2021, Jul). The influence of dataset homology and a rigorous evaluation strategy on protein secondary structure prediction. PLOS ONE, 16(7):e0254555, doi: 10.1371/journal.pone.0254555.
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5 Sheng-Hung Juan#, Teng-Ruei Chen#, Wei-Cheng Lo* (2020, Jun). A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy. PLOS ONE, 15(6):e0235153, doi: 10.1371/journal.pone.0235153.
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6 Rupesh Kumar Chikara, Wei-Cheng Lo*, Li-Wei Ko* (2020, Mar). Exploration of brain connectivity during human inhibitory control using inter-trial coherence. Sensors, 20(6):1722, doi:10.3390/s20061722.
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Patents

*指導教授

1 Wei-Cheng Lo*, Yu-Huang Chen, Shuan-Yu Chung (2019) 以機器學習為基礎之最佳化預測模型的建立與預測結果的取得系統及方法。中華民國專利, 發明第I676940號。
2 Wei-Cheng Lo*, Yu-Huang Chen, Shuan-Yu Chung (2019) 分散式運算方法與管理系統。中華民國專利, 發明第I661312號。
3 Ping-Chang Lyu*, Wei-Cheng Lo (2012) CPSARST: 高效能蛋白質環形序列重組搜尋比對工具。中華民國專利, 發明第I356103號。

 

Journal papers Full list

#Equal contributions
*Corresponding authors

1 Chia-Tzu Ho, Yu-Wei Huang, Chia-Hua Lo, Wei-Cheng Lo* (2021, Nov). Discovering the ultimate limits of protein secondary structure prediction. Biomolecules, 11(11):1627, doi: 10.3390/biom11111627.
Abstract
Full text
2 Teng-Ruei Chen, Yen-Cheng Lin, Yu-Wei Huang, Chih-Chieh Chen, Wei-Cheng Lo* (2021, Oct). CirPred, the first structure modeling and linker design system for circularly permuted proteins. BMC Bioinformatics, 22(Suppl 10):494, doi: 10.1186/s12859-021-04403-1.
Abstract
Full text
3 Teng-Ruei Chen#, Sheng-Hung Juan#, Yu-Wei Huang, Yen-Cheng Lin, Wei-Cheng Lo* (2021, Jul). A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction. PLOS ONE, 16(7):e0255076, doi: 10.1371/journal.pone.0255076.
Abstract
Full text
4 Teng-Ruei Chen#, Chia-Hua Lo#, Sheng-Hung Juan, Wei-Cheng Lo* (2021, Jul). The influence of dataset homology and a rigorous evaluation strategy on protein secondary structure prediction. PLOS ONE, 16(7):e0254555, doi: 10.1371/journal.pone.0254555.
Abstract
Full text
5 Sheng-Hung Juan#, Teng-Ruei Chen#, Wei-Cheng Lo* (2020, Jun). A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy. PLOS ONE, 15(6):e0235153, doi: 10.1371/journal.pone.0235153.
Abstract
Full text
6 Rupesh Kumar Chikara, Wei-Cheng Lo*, Li-Wei Ko* (2020, Mar). Exploration of brain connectivity during human inhibitory control using inter-trial coherence. Sensors, 20(6):1722, doi:10.3390/s20061722.
Abstract
Full text
7 Yun-Tzai Lee, Wei-Cheng Lo*, and Shih-Che Sue* (2017, Jan). Computational prediction of new intein split sites. Methods Mol Biol, 1495:259-68.
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8 Yi-Lin Hung, Hsia-Ju Lee, Ingjye Jiang, Shang-Chi Lin, Wei-Cheng Lo, Yi-Jan Lin and Shih-Che Sue* (2015, Jul). The first residue of the PWWP motif modulates HATH domain binding, stability, and protein-protein interaction. Biochemistry, 54(26):4063-74, doi: 10.1021/acs.biochem.5b00454.
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9 Chi-Ching Lee, Yi-Ping Phoebe Chen, T.J. Yao, C.Y. Ma, Wei-Cheng Lo, Ping-Chiang Lyu* and Chuan Yi Tang* (2013, Apr). GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects. Gene, 518(1):114-23.
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10 Yun-Tzai Lee, Tz-Hsiang Su, Wei-Cheng Lo, Ping-Chiang Lyu* and Shih-Che Sue* (2012, Aug). Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. PLoS ONE, 7(8):e43820.
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11 Wei-Cheng Lo, Li-Fen Wang, Yen-Yi Liu, Tian Dai, Jenn-Kang Hwang* and Ping-Chiang Lyu* (2012, Jul). CPred: a web server for predicting viable circular permutations in proteins. Nucleic Acids Research, 40:W232-7, doi:10.1093/nar/gks529.
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12 Chien-Hua Shih, Chih-Min Chang, Yeong-Shin Lin, Wei-Cheng Lo and Jenn-Kang Hwang* (2012, Jun). Evolutionary information hidden in a single protein structure. Proteins: Structure, Function, and Bioinformatics, 80(6):1647-57, doi:10.1002/prot.24058.
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13 Chi-Ching Lee#, Wei-Cheng Lo#, Szu-Ming Lai, Yi-Ping Phoebe Chen, Chuan Yi Tang and Ping-Chiang Lyu* (2012, Apr). Metabolic classification of microbial genomes using functional probes. BMC Genomics, 13:157.
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14 Nai-Jyuan Wang#, Chi-Ching Lee#, Chao-Sheng Cheng, Wei-Cheng Lo, Ya-Fen Yang, Ming-Nan Che and Ping-Chiang Lyu* (2012, Jan). Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB). BMC Genomics, 13:S9.
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15 Wei-Cheng Lo#, Tian Dai#, Yen-Yi Liu, Li-Fen Wang, Jenn-Kang Hwang* and Ping-Chiang Lyu* (2012, Feb). Deciphering the preference and predicting the viability of circular permutations in proteins. PLoS ONE, 7:e31791.
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16 Chia-Han Chu#, Wei-Cheng Lo#, Hsin-Wei Wang, Yen-Chu Hsu, Jenn-Kang Hwang, Ping-Chiang Lyu, Tun-Wen Pai* and Chuan Yi Tang* (2010, Sep). Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. PLoS ONE, 5:e13361.
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17 Wei-Cheng Lo, Che-Yu Lee, Chi-Ching Lee and Ping-Chiang Lyu* (2009, Jul). iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Research, 37:W545-51.
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18 Wei-Cheng Lo, Chi-Ching Lee, Che-Yu Lee and Ping-Chiang Lyu* (2009, Jan). CPDB a database of circular permutation in proteins. Nucleic Acids Research, 37:D328-32.
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19 Wei-Cheng Lo and Ping-Chiang Lyu* (2008, Jan). CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biology, 9:R11.
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20 Wei-Cheng Lo, Po-Jung Huang, Chih-Hung Chang and Ping-Chiang Lyu* (2007, Aug). Protein structural similarity search by Ramachandran codes. BMC Bioinformatics, 8:307.
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International conference posters (selected)

1 Wei-Cheng Lo, Li-Fen Wang, Yen-Yi Liu, Tian Dai, Jenn-Kang Hwang*, Ping-Chiang Lyu*. (2011, Aug) CPred: a Prediction System for Viable Circular Permutations in Proteins. 2011 Asian Young Researchers Conference on Computational and Omics Biology, Daejeon, Korea.
2 Wei-Cheng Lo et al. (2010, Dec) The development of a standard dataset and a precise hinge loop determination procedure for 3D domain swapping proteins. 2010 Asian Young Researchers Conference on Computational and Omics Biology, Singapore.
3 Wei-Cheng Lo et al. (2009, Jun) CPSARST - Circular Permutation Search Aided by Ramachandran Sequential Transformation. The 12th SCBA International Symposium, Taipei, Taiwan.
4 Wei-Cheng Lo et al. (2009, Nov) CPSARST & CPDB - an efficient search tool and a comprehensive database of circular permutation in proteins. Asia Pacific Bioinformatics Conference (APBC2009), Beijing, China.
5 Wei-Cheng Lo et al. (2008, Dec) CPSARST & CPDB - an efficient search tool and a comprehensive database of circular permutation in proteins. 13th Biological Sciences Graduate Congress, Singapore.
6 Wei-Cheng Lo et al. (2008, Nov) CPDB: a database of circular permutation in proteins. The 2nd Taiwan-Japan Young Researchers Conference on Computational and Systems Biology, Tokyo, Japan.