Microbe and Drug Bioinformatics
87. Ye A, Shen JN, Li Y, Lian X, Ma BG, Guo FB. (2024) Reconstruction of the genome-scale metabolic network model of Sinorhizobium fredii CCBAU45436 for free-living and symbiotic states. Front Bioeng Biotechnol. 2024 Mar 25;12:1377334. [FULL TEXT]
202386. Wang CY, Kuang X, Wang QQ, Zhang GQ, Chen ZS, Deng ZX & Guo FB. (2023) GMMAD: a comprehensive database of human gut microbial metabolite associations with diseases. BMC Genomics. 2023 Aug 24;24(1):482. doi: 10.1186/s12864-023-09599-5. [FULL TEXT]
85. Zhu SB, Jiang QH, Chen ZG, Zhou X, Jin YT, Deng ZX, Guo FB*. (2023) Mslar: Microbial synthetic lethal and rescue database. PLoS Comput Biol. 2023 Jun 8;19(6):e1011218. doi: 10.1371/journal.pcbi.1011218. [FULL TEXT]
84. Yu JF, Jiang W, Zhu SB, Liao Z, Dou XH, Liu J, Guo FB*, Dong C*. (2023) Prediction of protein-coding small ORFs in multi-species using integrated sequence-derived features and the random forest model. Methods. 2023 Feb;210:10-19. doi: 10.1016/j.ymeth.2022.12.003. [FULL TEXT]
202283. Guo HX, Zhu SB, Deng ZX, Guo FB*. (2022) EcoliGD: An Online Tool for Designing Escherichia coli Genome. ACS Synth Biol. 2022 Jul 15;11(7):2267-2274. doi: 10.1021/acssynbio.2c00165. [FULL TEXT]
82. Wang CY, Wen QF, Wang QQ, Kuang X, Dong C*, Deng ZX, Guo FB*. (2022) Discovery of Drug Candidates for Specific Human Disease Based on Natural Products of Gut Microbes. Front Microbiol. 2022 Jun 15;13:896740. doi: 10.3389/fmicb.2022.896740. [FULL TEXT]
81. Jin YT#, Pu DK, Guo HX, Deng Z, Chen LL*, Guo FB*. (2022) T-G-A Deficiency Pattern in Protein-Coding Genes and Its Potential Reason. Front Microbiol. 2022 May 4;13:847325. doi: 10.3389/fmicb.2022.847325. [FULL TEXT]
80. Dong C#, Wang X, Ma C, Zeng Z, Pu DK, Liu S, Wu CS, Chen S, Deng Z, Guo FB*. (2022) Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins. Database (Oxford). 2022 Mar 28;2022:baac010. doi: 10.1093/database/baac010. [FULL TEXT]
79. Jin YT#, Ma C, Wang X, Wang SX, Zhang KY, Zheng WX, Deng Z, Wang J*, Guo FB*. (2022) Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference. Interdiscip Sci. 2022 Jun;14(2):349-357. doi: 10.1007/s12539-021-00493-w. [FULL TEXT]
78. Wen QF#, Wei W#, Guo FB*. (2022) Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes. Methods Mol Biol. 2022;2377:423-430. doi: 10.1007/978-1-0716-1720-5_23. [FULL TEXT]
202177. Jin YT#, Jin TY#, Zhang ZL#, Ye YN, Deng Z, Wang J, Guo FB*. (2021) Quantitative elucidation of associations between nucleotide identity and physicochemical properties of amino acids and the functional insight. Comput Struct Biotechnol J. doi: 10.1016/j.csbj.2021.07.012. [FULL TEXT]
76. Wang B#*, Yang H#, Sun J#, Dou C#, Huang J, Guo FB. (2021) BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts. Front Microbiol. doi: 10.3389/fmicb.2021.593979. [FULL TEXT]
202075. Liu S#, Wang SX, Liu W, Wang C, Zhang FZ, Ye YN, Wu CS, Zheng WX, Rao N, Guo FB*. (2020) CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms. Database (Oxford). doi:10.1093/database/baaa112 [FULL TEXT]
74. Dong C#, Jin YT#, Hua HL, Wen QF, Luo S, Zheng WX, Guo FB* (2020) Comprehensive review of the identification of essential genes using computational methods: Focusing on feature implementation and assessment. Brief Bioinform. 21(1):171-181 [FULL TEXT]
201973. Tang Z#, Chen S#, Chen A, He B, Zhou Y, Chai G, Guo FB*, Huang J* (2019) CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. Database (Oxford). 2019: baz093. [FULL TEXT]
72. Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Xu H, Ning L, Guo FB, Jiang Y, Lin H, Wang D*, Huang Y*, Huang J* (2019) RIscoper: a tool for RNA-RNA interaction extraction from the literature. Bioinformatics. 35(17):3199-3202. [FULL TEXT]
71. Dong C#, Zeng Z#, Pu DK, Wen QF, Liu S, Du MZ, Sun Y, Gao YZ, Rao N, Huang J, Guo FB* (2019) CasLocusAnno: a web-based server for annotating cas loci and their corresponding (sub)types. FEBS Lett. 593(18):2646-2654 [FULL TEXT]
70. Wen QF, Liu S, Dong C, Guo HX, Gao YZ, Guo FB* (2019) Geptop 2.0: An Updated, More Precise, and Faster Geptop Server for Identification of Prokaryotic Essential Genes. Front Microbiol. 10:1236 [FULL TEXT]
69. Zhang KY#, Gao YZ#, Du MZ, Liu S, Dong C, Guo FB* (2019) Vgas: A Viral Genome Annotation System. Front Microbiol. 10:184. [FULL TEXT]
68. Lin Y#, Zhang FZ#, Xue K, Gao YZ, Guo FB* (2019) Identifying bacterial essential genes based on a feature-integrated method. IEEE/ACM Trans Comput Biol Bioinform. 16(4),1274-1279 [FULL TEXT]
201867. Du MZ, Zhang C, Wang H, Liu S, Wei W, Guo FB* (2018) The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process. Front Microbiol. 9:2948. [FULL TEXT]
66. Liu S, Du MZ, Wen QF, Kang J, Dong C, Xiong L, Huang J, Guo FB* (2018) Comprehensive exploration of the enzymes catalysing oxygen-involved reactions and COGs relevant to bacterial oxygen utilization. Environ Microbiol. 20(10):3836-3850. [FULL TEXT]
65. Wei W#, Xiong LF#, Ye YN#, Du MZ, Gao YZ, Zhang KY, Jin YT, Yang Z, Wong PC, Lau SKP, Kan B, Zhu J, Woo PCY*, Guo FB* (2018) Mutation landscape of base substitutions, duplications, and deletions in the representative current cholera pandemic strain. Genome Biol Evol. 10(8):2072-2085. [FULL TEXT]
64. Labena AA#, Guo HX#, Dong C, Li L*, Guo FB* (2018) The Topologically Associated Domains (TADs) of a chromatin correlated with isochores organization of a genome. Current Bioinformatics. 13(4), 420-425. [FULL TEXT]
63. Du MZ, Liu S, Zeng Z, Alemayehu LA, Wei W*, Guo FB* (2018) Amino acid compositions contribute to the proteins' evolution under the influence of their abundances and genomic GC content. Sci Rep. 8(1):7382. [FULL TEXT]
62. Dong C#, Hao GF#, Hua HL, Liu S, Labena AA, Chai GS, Huang J, Rao NN, Guo FB* (2018) Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins. Nucleic Acids Res. 46(D1): D393–D398. [FULL TEXT]
201761. Du MZ, Wei W, Qin L, Liu S, Zhang AY, Zhang Y, Zhou H, Guo FB* (2017) Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains. DNA Res. 24(6):623-633. [FULL TEXT]
60. Labena AA, Gao YZ, Dong C, Hua HL, Guo FB* (2017) Metabolic pathway databases and model repositories. Quantitative Biology. 6(1):30-39. [FULL TEXT]
59. Wei W#, Gao F#, Du MZ, Hua HL, Wang J, Guo FB* (2017) Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity prop erties. Brief Bioinform. 18(3):357-366. [FULL TEXT]
58. Labena AA#, Ye YN#, Dong C, Zhang FZ, Guo FB*. (2017) SSER: Species specific essential reactions database. BMC Syst Biol. 11(1):50. [FULL TEXT]
57. Guo FB#, Xiong LF#, Zhang KY, Dong C, Zhang FZ, Woo PC* (2017) Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands. BMC Microbiol. 17(1):73. [FULL TEXT]
56. Guo FB*, Dong C, Hua HL, Liu S, Luo H, Zhang HW, Jin YT, Zhang KY. (2017) Accurate prediction of human essential genes using only nucleotide composition and association information. Bioinformatics. 33 (12): 1758-1764. [FULL TEXT]
55. Xiong L, Yang Y, Ye YN, Teng JL, Chan E, Watt RM, Guo FB, Lau SK, Woo PC* (2017) Laribacter hongkongensis anaerobic adaptation mediated by arginine metabolism is controlled by the cooperation of FNR and ArgR. Environ Microbiol. 19(3):1266-1280. [FULL TEXT]
54. Ye C, Xu N, Dong C, Ye Y, Zou X, Chen X, Guo F, Liu L*. (2017) IMGMD: a platform for the integration and standardisation of in silico microbial genome-scale metabolic models. Sci Rep. 7(1):727. [FULL TEXT]
201653. Ye YN, Ma BG, Dong C, Zhang H, Chen LL, Guo FB* (2016) A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network. Sci Rep. 6:35082. [FULL TEXT]
52. Dong C, Yuan YZ, Zhang FZ, Hua HL, Ye YN, Labena AA, Lin H, Chen W, Guo FB* (2016) Combining pseudo dinucleotide composition with the Z curve method to improve the accuracy of predicting DNA elements: a case study in recombination spots. Mol Biosyst. 12(9):2893-900. [FULL TEXT]
51. Ding H*, Liang ZY, Guo FB, Huang J, Chen W*, Lin H* (2016) Predicting bacteriophage proteins located in host cell with feature selection technique. Comput Biol Med. 71:156-61. [FULL TEXT]
50. He B, Chai G, Duan Y, Yan Z, Qiu L, Zhang H, Liu Z, He Q, Han K, Ru B, Guo FB, Ding H, Lin H, Wang X, Rao N, Zhou P, Huang J* (2016) BDB: biopanning data bank. Nucleic Acids Res 44(D1):D1127-32 [FULL TEXT]
49. Liu HM, Rao N*, Yang D, Yang L, Li Y, Guo FB (2016) Modified bagging of maximal information coefficient for genome-wide identification. International Journal of Data Mining and Bioinformatics. 14(3):229-57. [FULL TEXT]
48. Hua HL, Zhang FZ, Labena AA, Dong C, Jin YT, Guo FB* (2016) An approach for predicting essential genes using multiple homology mapping and machine learning algorithms. Biomed Res Int. 2016:7639397. [FULL TEXT]
47. Wei W, Jin YT, Du MZ, Wang J, Rao N, Guo FB* (2016) Genomic complexity places less restrictions on the evolution of young coexpression networks than protein - protein interactions. Genome Biol Evol. 8(8):2624-31. [FULL TEXT]
46. Hao GF#, Jiang W#, Ye YN, Wu FX, Zhu XL, Guo FB*, Yang GF* (2016) ACFIS: a web server for fragment-based drug discovery. Nucleic Acids Res. 44(W1):W550-6. [FULL TEXT]
45. Teng JL#, Tang Y#, Huang Y, Guo FB, Wei W, Chen JH, Wong SS, Lau SK*, Woo PC* (2016) Phylogenomic analyses and reclassification of species within the genus tsukamurella: insights to species definition in the post-genomic era. Front Microbiol. 7:1137. [FULL TEXT]
201544. Hua ZG#, Lin Y#, Yuan YZ, Yang DC, Wei W, Guo FB* (2015) ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes. Nucleic Acids Res. 43(W1):W85-90. [FULL TEXT]
43. Zhao HL, Xia ZK, Zhang FZ, Ye YN*, Guo FB* (2015) Multiple factors drive replicating strand composition bias in bacterial genomes. Int J Mol Sci. 16(9):23111-26. [FULL TEXT]
42. Zheng WX, Luo CS, Deng YY, Guo FB* (2015) Essentiality drives the orientation bias of bacterial genes in a continuous manner. Sci Rep. 5:16431. [FULL TEXT]
41. Guo FB*, Ye YN, Ning LW, Wei W (2015) Three computational tools for predicting bacterial essential genes. Methods Mol Biol. 1279:205-17. [FULL TEXT]
201440. Ding H, Lin H*, Chen W*, Li ZQ, Guo FB, Huang J, Rao N. (2014) Prediction of protein structural classes based on feature selection technique. Interdiscip Sci. 6(3): 235-40. [FULL TEXT]
39. Guo FB* (2014) Thematic issue: predict various types of genes in prokaryotic and eukaryotic genomes. Current Bioinformatics. 9(2):87-8. [FULL TEXT]
38. Li Y, Rao N*, Yang F, Zhang Y, Yang Y, Liu HM, Guo F, Huang J. (2014) Biocomputional construction of a gene network under acid stress in Synechocystis sp. PCC 6803. Res Microbiol. 165(6):420-8. [FULL TEXT]
37. Ru B, 't Hoen PA, Nie F, Lin H, Guo FB, Huang J*. (2014) Phd7faster: predicting clones propagating faster from the PH.D.-7 phage display peptide library. J Bioinform Comput Biol. 12(1):1450005. [FULL TEXT]
36. Wei W, Ning LW, Ye YN, Li SJ, Zhou HQ, Huang J, Guo FB* (2014) SMAL: a resource of spontaneous mutation accumulation lines. Mol Biol Evol. 31(5):1302-8. [FULL TEXT]
35. Zhou HQ#, Ning LW#, Zhang HX, Guo FB* (2014) Analysis of the relationship between genomic GC content and patterns of base usage, codon usage and amino acid usage in prokaryotes: similar GC content adopts similar compositional frequencies regardless of the phylogenetic lineages. PLoS One. 9(9):e107319. [FULL TEXT]
34. Wei W#, Ye YN#, Luo S, Deng YY, Lin D, Guo FB* (2014) IFIM: a database of integrated fitness information for microbial genes. Database(Oxford). 2014.pii:bau052. [FULL TEXT]
33. Guo FB, Lin Y, Chen LL* (2014) Recognition of protein-coding genes based on Z-curve algorithms. Curr Genomics. 15(2): 95-103. [FULL TEXT]
32. Ning LW, Lin H, Ding H, Huang J, Rao N, Guo FB*. (2014) Predicting bacterial essential genes using only sequence composition information. Genet Mol Res. 13(2): 4564-72. [FULL TEXT]
201331. Ye YN, Hua ZG, Huang J, Rao N, Guo FB*. (2013) CEG: a database of essential gene clusters. BMC Genomics. 14: 769. [FULL TEXT]
30. Wei W, Ning LW, Ye YN, Guo FB*. (2013) Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny. PLoS One. 8(8): e72343. [FULL TEXT]
29. Wei W, Zhang T, Lin D, Yang ZJ, Guo FB*. (2013) Transcriptional abundance is not the single force driving the evolution of bacterial proteins. BMC Evol Biol. 13: 162. [FULL TEXT]
28. Lin D#, Yin X#, Wang X, Zhou P, Guo FB*. (2013) Re-annotation of protein-coding genes in the genome of Saccharomyces cerevisiae based on support vector machines. PLoS One. 8(7): e64477. [FULL TEXT]
27. Ding H*, Guo SH, Deng EZ, Yuan LF, Guo FB, Huang J, Rao N, Chen W*, Lin H*. (2013) Prediction of Golgi-resident protein types by using feature selection technique. Chemometr Intell Lab. 124: 9-13. [FULL TEXT]
26. Lin H*, Ding C, Yuan LF, Chen W*, Ding H, Li ZQ, Guo FB, Huang J, Rao N. (2013) Predicting subchloroplast locations of proteins based on the general form of Chou's pseudo amino acid composition: approached from optimal tripeptide composition. International Journal of Biomathematics 62(2): 1350003. [FULL TEXT]
25. Guo FB, Xiong L, Teng JL, Yuen KY, Lau SK*, Woo PC*. (2013) Re-annotation of protein-coding genes in 10 complete genomes of Neisseriaceae family by combining similarity-based and composition-based methods. DNA Res. 20(3): 273-76. [FULL TEXT]
201224. Guo FB*, Ye YN, Zhao HL, Lin D, Wei W. (2012) Universal pattern and diverse strengths of successive synonymous codon bias in three domains of life, particularly among prokaryotic genomes. DNA Res. 19(6): 477-85. [FULL TEXT]
23. Guo FB*. (2012) Replicating strand asymmetry in bacterial and eukaryotic genomes. Curr Genomics. 13(1): 2-3. [FULL TEXT]
22. Guo FB*, Wei W. (2012) Prediction of genomic islands in three bacterial pathogens of pneumonia. Int J Mol Sci. 13(3): 3134-44. [FULL TEXT]
21. Huang J*, Ru B, Zhu P, Nie F, Yang J, Wang X, Dai P, Lin H, Guo FB, Rao N. (2012) MimoDB 2.0: a mimotope database and beyond. Nucleic Acids Res. 40(Database issue): D271-7. [FULL TEXT]
201120. Du MZ, Guo FB*, Chen YY. (2011) Gene re-annotation in genome of the extremophile Pyrobaculum aerophilum by using bioinformatics methods. J Biomol Struct Dyn. 29(2): 391-401. [FULL TEXT]
19. Ding H, Liu L, Guo FB, Huang J, Lin H*. (2011) Identify Golgi protein types with modified Mahalanobis discriminant algorithm and pseudo amino acid composition. Protein Pept Lett. 18(1): 58-63. [FULL TEXT]
201018. Ru B, Huang J*, Dai P, Li S, Xia Z, Ding H, Lin H, Guo FB, Wang X. (2010) MimoDB: a new repository for mimotope data derived from phage display technology. Molecules. 15(11): 8279-88. [FULL TEXT]
17. Guo FB*, Ning LW, Huang J, Lin H, Zhang HX. (2010) Chromosome translocation and its consequence in the genome of Burkholderia cenocepacia AU-1054. Biochem Biophys Res Commun. 403(3-4): 375-9. [FULL TEXT]
16. Huang J*, Ru B, Li S, Lin H, Guo FB. (2010) SAROTUP: scanner and reporter of target-unrelated peptides. J Biomed Biotechnol. 2010: 101932. [FULL TEXT]
15. Lin H*, Ding H, Guo FB, Huang J. (2010) Prediction of subcellular location of mycobacterial protein using feature selection techniques. Mol Divers. 14(4): 667-71. [FULL TEXT]
200914. Guo FB*, Lin H, Huang J. (2009) A plot of G+C content against sequence length of 640 bacterial chromosomes shows the points are widely scattered in the upper triangular area. Chromosome Res. 17(3): 359-64. [FULL TEXT]
13. Guo FB* , Yuan JB. (2009) Codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in Lawsonia intracellularis. DNA Res. 16(2): 91-104. [FULL TEXT]
12. Guo FB* , Lin Y. (2009) Identify protein-coding genes in the genomes of Aeropyrum pernix K1 and Chlorobium tepidum TLS. J Biomol Struct Dyn. 26(4): 413-20. [FULL TEXT]
200811. Lin H*, Ding H*, Guo FB, Zhang AY, Huang J. (2008) Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition. Protein Pept Lett. 15(7): 739-44. [FULL TEXT]
200710. Guo FB*, Yu XJ. (2007) Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method. BMC Genomics. 8: 366. [FULL TEXT]
9. Guo FB*. (2007) The distribution patterns of bases of protein-coding genes, non-coding ORFs, and intergenic sequences in Pseudomonas aeruginosa PA01 genome and its implications. J Biomol Struct Dyn. 25(2): 127-33. [FULL TEXT]
8. Guo FB*, Yu XJ. (2007) Re-prediction of protein-coding genes in the genome of Amsacta moorei entomopoxvirus. J Virol Methods. 146(1-2): 389-92. [FULL TEXT]
Before 20067. Guo FB, Zhang CT*. (2006) ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. BMC Bioinformatics. 10: 7-9. [FULL TEXT]
6. Guo FB, Wang J, Zhang CT*. (2004) Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 11(6): 361-70. [FULL TEXT]
5. Ou HY, Guo FB, Zhang CT*. (2004) GS-Finder: a program to find bacterial gene start sites with a self-training method. Int J Biochem Cell Biol. 36(3): 535-44. [FULL TEXT]
4. Wang Y*, Ou H, Guo FB. (2003) Recognition of translation initiation sites of eukaryotic genes based on an EM algorithm. J Comput Biol. 10(5): 699-708. [FULL TEXT]
3. Ou HY, Guo FB, Zhang CT*. (2003) Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method. FEBS Lett. 540(1-3): 188-94. [FULL TEXT]
2. Guo FB, Ou HY, Zhang CT*. (2003) ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res. 31(6): 1780-9. [FULL TEXT]
1. Wang J*, Guo FB. (2002) Base frequencies at the second codon position of Vibrio cholerae genes connect with protein function. Biochem Biophys Res Commun. 290(1): 81-4. [FULL TEXT]