Publications during 2024

1. Y.T. Liang, H. Luo, Y. Lin, F. Gao (2024). Recent advances in the characterization of essential genes and development of a database of essential genes. iMeta, e157

2. X.Y. Zhao, F. Gao (2024). Novel Omicron Variants Enhance Anchored Recognition of TMEM106B: A New Pathway for SARS-CoV-2 Cellular Invasion. The Journal of Physical Chemistry Letters, 671-680.[PubMed]

3. Y.H. Zeng, Z.N. Yin, H. Luo, F. Gao (2024). DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins. Genomics, Proteomics & Bioinformatics, qzae076.[PubMed]

4. Z.N. Yin, F.L. Lai, F. Gao (2024). Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis. Briefings in Bioinformatics, 25(1):bbad432.[PubMed]

5. Y.Q. Geng, F.L. Lai, H. Luo, F. Gao (2024). Nmix: A hybrid deep learning model for precise prediction of 2'-O-methylation sites based on multi-feature fusion and ensemble learning. Briefings in Bioinformatics, -

Publications during 2023

1. M. J. Dong^#, H. Luo^#, F. Gao (2023). DoriC 12.0, an updated database of replication origins in both complete and draft prokaryotic genomes. Nucleic Acid Research, 51(D1): D117–D120.[PubMed]

2. F. Gao*, K. Huang*, Y. Xing* (2023). Artificial Intelligence in Omics. Genomics, Proteomics & Bioinformatics, 20(5):811–813..[PubMed]

3. F.L. Lai, F. Gao (2023). Auto-Kla: a novel web server to discriminate lysine lactylation sites using automated machine learning. Briefings in Bioinformatics, 24(20):bbad070.[PubMed]

4. H.S. Zhong, M.J. Dong, F. Gao (2023). G4Bank: A database of experimentally identified DNA G-quadruplex sequences. Interdisciplinary Sciences: Computational Life Sciences, 15, 515–523.[PubMed]

5. E. Perez-Rueda*, F. Gao* (2023). Insights in evolutionary & genomic microbiology: 2022. Frontiers in Microbiology, 14, 1269933.[PubMed]

6. B. Sun, F. Gao (2023). Investigation of escape mechanisms of SARS-CoV-2 Omicron sub-lineages and exploration of potential antibodies for XBB. 1. Journal of Infection, 87 (4), 354-357.[PubMed]

7. F.L Lai, F. Gao (2023). LSA-ac4C: A hybrid neural network incorporating double-layer LSTM and self-attention mechanism for the prediction of N4-acetylcytidine sites in human mRNA. International Journal of Biological Macromolecules, 253, 126837.[PubMed]

Publications during 2022

1. F.F. Yan, F. Gao (2022). Mutant EK1 with Q1004E/N1006I: a promising fusion inhibitor for the HR1 domain of SARS-CoV-2. Journal of Infection, 84(4):579-613.[PubMed]

2. F.L. Lai, F. Gao (2022). GC-Profile 2.0: an extended web server for the prediction and visualization of CpG islands. Bioinformatics, 38(6): 1738-1740.[PubMed]

3. H. Luo, F. Gao as co-author in CNCB-NGDC Members and Partners (2022). Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research, 50(D1):D27-D38.[PubMed]

4. P. Li, J. Zhang, Z. Deng, F. Gao, H.Y. Ou (2022). Identification and characterization of a central replication origin of the mega-plasmid pSCATT of Streptomyces cattleya. Microbiological Research, 126975.[PubMed]

5. T. Yang, F. Gao (2022). High-quality pan-genome of Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands. Briefings in Bioinformatics, 23(4):bbac283.[PubMed]

6. F.F. Yan, F. Gao (2022). RBD-ACE2 binding properties in five SARS-CoV-2 variants of concern with new perspectives in the design of pan-coronavirus peptide inhibitors. Journal of Infection, 86(2):e51-e54.[PubMed]

7. M. J. Dong^#, H. Luo^#, F. Gao (2022). Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins. Genomics, Proteomics & Bioinformatics, 20(6): 1207-1213.[PubMed]

Publications during 2021

1. H. Luo, Y. Lin, T. Liu, F.L. Lai, C.T. Zhang, F. Gao, R. Zhang (2021). DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. Nucleic Acids Research, 49(D1), D677-D686.[PubMed]

2. H. Luo, F. Gao as co-author in CNCB-NGDC Members and Partners (2021). Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Research, D1 (2021): D18-D28.[PubMed]

3. H. Wu, D. Wang, F. Gao (2021). Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains. Briefings in Bioinformatics, 22(2):1951-1971.[PubMed]

4. F.F. Yan, F. Gao (2021). Comparison of the binding characteristics of SARS-CoV and SARS-CoV-2 RBDs to ACE2 at different temperatures by MD simulations. Briefings in Bioinformatics, 22(2):1122-1136.[PubMed]

5. T. Liu, H. Luo, F. Gao (2021). Position preference of essential genes in prokaryotic operons. PLoS ONE, 16(4): e0250380.[PubMed]

6. D. Wang, F.L. Lai, F. Gao (2021). Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae. Briefings in Bioinformatics, 22(3): bbaa182.[PubMed]

7. S. Pelliciari, M.J. Dong, F. Gao* and H. Murray* (2021). Evidence for a chromosome origin unwinding system broadly conserved in bacteria. Nucleic Acid Research, 49(13), 7525-7536.[PubMed]

8. Z.K. Yang, L.Y. Pan, Y.M. Zhang, H. Luo and F. Gao (2021). Data-driven identification of SARS-CoV-2 subpopulations using PhenoGraph and binary-coded genomic data, Briefings in Bioinformatics. Briefings in Bioinformatics, 22(6): bbab307.[PubMed]

9. F.F. Yan, F. Gao (2021). An overview of potential inhibitors targeting non-structural proteins 3 (PLpro and Mac1) and 5 (3CLpro/Mpro) of SARS-CoV-2. Computational and Structural Biotechnology Journal, 19:4868-4883.[PubMed]

10. H. Wu, Z.K. Yang, T. Yang, D. Wang, H. Luo, F. Gao (2021). An Effective Preprocessing Method for High-Quality Pan-Genome Analysis of Bacillus subtilis and Escherichia coli. Methods in Molecular Biology, 2377: 371-390.[PubMed]

Publications during 2020

1. H. Luo, F. Gao as co-author in National Genomics Data Center Members and Partners (2020). Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research, D1 (2020): D24-D33.[PubMed]

2. F.F. Yan, F. Gao (2020). A systematic strategy for the investigation of vaccines and drugs targeting bacteria. Computational and Structural Biotechnology Journal, 18: 1525-1538.[PubMed]

3. L. Bai, S.C. Zhang, Y. Deng, C.C. Song, G.B. Kang, Y. Dong, Y. Wang, F. Gao, H. Huang (2020). Comparative genomics analysis of Acinetobacter haemolyticus isolates from sputum samples of respiratory patients. Genomics, 2020, 112(4):2784-2793.[PubMed]

Publications during 2019

1. H. Luo, C.L. Quan, C. Peng, F. Gao (2019). Recent development of Ori-Finder system and DoriC database for microbial replication origins. Briefings in Bioinformatics, 20(4): 1114–1124.[PubMed]

2. H. Luo, F. Gao as co-author in BIG Data Center Members (2019). Database Resources of the BIG Data Center in 2019. Nucleic Acids Res, 47(D1):D8-D14.[PubMed]

3. H. Luo, F. Gao (2019). DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Research, 47(D1):D74-D77.[PubMed]

4. C.L. Quan, F. Gao (2019). Quantitative analysis and assessment of base composition asymmetry and gene orientation bias in bacterial genomes. FEBS Letters, 593(9):918-925.[PubMed]

5. Z.K. Yang, H. Luo, Y. Zhang, B. Wang, F. Gao (2019). Pan-genomic analysis provides novel insights into the association of E. coli with human host and its minimal genome. Bioinformatics, 35(12):1987-1991.[PubMed]

6. F.Gao (2019). Recent developments of software and database in microbial genomics and functional genomics. Briefings in Bioinformatics, 20(2):732-734.[PubMed]

7. D. Wang, F. Gao (2019). Comprehensive Analysis of Replication Origins in Saccharomyces cerevisiae Genomes. Frontiers in Microbiology, 10:2122.[PubMed]

8. X.L. Wu, Y.H. Bi, F. Gao, Z.X. Xie, X. Li, X. Zhou, D.J. Zhou, B.Z. Li (2019). The effect of autonomously replicating sequences on gene expression in Saccharomyces cerevisiae. Biochemical Engineering Journal, 149, 107250

Publications during 2018

1. H. Luo, F. Gao as co-author in BIG Data Center Members (2018). Database Resources of the BIG Data Center in 2018. Nucleic Acids Res, 46(Database issue):D14–D20.[PubMed]

2. Z.K. Yang , F. Gao (2018). The systematic analysis of ultraconserved genomic regions in the budding yeast. Bioinformatics, 34(3):361-366.[PubMed]

3. Z.K. Yang, H. Luo, Y. Zhang, B. Wang, F. Gao (2018). Recombinational DSBs-intersected genes converge on specific disease- and adaptability-related pathways. Bioinformatics, 34(20):3421-3426.[PubMed]

Publications during 2017

1. W. Wei^#, F. Gao^#, M.Z. Du, H.L. Hua, J. Wang, F.B. Guo (2017). Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties. Brief Bioinform, 18(3):357-366.[PubMed]

2. G. Zhang, F. Gao (2017). Quantitative analysis of correlation between AT and GC biases among bacterial genomes. PLoS One, 12(2): e0171408.[PubMed]

3. Y. Lin, F.Z. Zhang, K. Xue, Y.Z. Gao, F.B. Guo (2017). Identifying bacterial essential genes based on a feature-integrated method. IEEE/ACM Trans Comput Biol Bioinform, 16(4), 1274-1279.[PubMed]

4. N. Jia, M.Z. Ding, Y. Zou, F. Gao, Y.J. Yuan (2017). Comparative genomics and metabolomics analyses of the adaptation mechanism in Ketogulonicigenium vulgare-Bacillus thuringiensis consortium. Sci Rep, 7:46759.[PubMed]

5. Xie, Z.X., Li, B.Z., Mitchell, L.A., Wu, Y., Qi, X., Jin, Z., Jia, B., Wang, X., Zeng, B.X., Liu, H.M., Wu, X.L., Feng, Q., Zhang, W.Z., Liu, W., Ding, M.Z., Li, X., Zhao, G.R., Qiao, J.J., Cheng, J.S., Zhao, M., Kuang, Z., Wang, X., Martin, J.A., Stracquadanio, G., Yang, K., Bai, X., Zhao, J., Hu, M.L., Lin, Q.H., Zhang, W.Q., Shen, M.H., Chen, S., Su, W., Wang, E.X., Guo, R., Zhai, F., Guo, X.J., Du, H.X., Zhu, J.Q., Song, T.Q., Dai, J.J., Li, F.F., Jiang, G.Z., Han, S.L., Liu, S.Y., Yu, Z.C., Yang, X.N., Chen, K., Hu, C., Li, D.S., Jia, N., Liu, Y., Wang, L.T., Wang, S., Wei, X.T., Fu, M.Q., Qu, L.M., Xin, S.Y., Liu, T., Tian, K.R., Li, X.N., Zhang, J.H., Song, L.X., Liu, J.G., Lv, J.F., Xu, H., Tao, R., Wang, Y., Zhang, T.T., Deng, Y.X., Wang, Y.R., Li, T., Ye, G.X., Xu, X.R., Xia, Z.B., Zhang, W., Yang, S.L., Liu, Y.L., Ding, W.Q., Liu, Z.N., Zhu, J.Q., Liu, N.Z., Walker, R., Luo, Y., Wang, Y., Shen, Y., Yang, H., Cai, Y., Ma, P.S., Zhang, C.T., Bader, J.S., Boeke, J.D., and Yuan, Y.J. (2017). "Perfect" designer chromosome V and behavior of a ring derivative. Science, 355(6329).[PubMed]

6. Wu, Y., Li, B.Z., Zhao, M., Mitchell, L.A., Xie, Z.X., Lin, Q.H., Wang, X., Xiao, W.H., Wang, Y., Zhou, X., Liu, H., Li, X., Ding, M.Z., Liu, D., Zhang, L., Liu, B.L., Wu, X.L., Li, F.F., Dong, X.T., Jia, B., Zhang, W.Z., Jiang, G.Z., Liu, Y., Bai, X., Song, T.Q., Chen, Y., Zhou, S.J., Zhu, R.Y., Gao, F., Kuang, Z., Wang, X., Shen, M., Yang, K., Stracquadanio, G., Richardson, S.M., Lin, Y., Wang, L., Walker, R., Luo, Y., Ma, P.S., Yang, H., Cai, Y., Dai, J., Bader, J.S., Boeke, J.D., and Yuan, Y.J. (2017). Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 355(6329).[PubMed]

7. N. Jia, M.Z. Ding, H. Luo, F. Gao, Y.J. Yuan (2017). Complete genome sequencing and antibiotics biosynthesis pathways analysis of Streptomyces lydicus 103. Sci Rep, 7:44786.[PubMed]

8. F.B. Guo, C. Dong, H.L. Hua, S. Liu, H. Luo, H.W. Zhang, Y.T. Jin, K.Y. Zhang (2017). Accurate prediction of human essential genes using only nucleotide composition and association information. Bioinformatics, 33(12):1758-1764.[PubMed]

9. C. Peng, Y. Lin, H. Luo, F. Gao (2017). A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes. Front Microbiol, 8:2331.[PubMed]

Publications during 2016

1. F. Gao, ed. (2016). DNA Replication Origins in Microbial Genomes. Lausanne: Frontiers Media, ISBN: 978-2-88919-779-8.[PubMed]

2. N. Jia, M.Z. Ding, J. Du, C.H. Pan, G. Tian, J.D. Lang, J.H. Fang, F. Gao, Y.J. Yuan (2016). Insights into mutualism mechanism and versatile metabolism of Ketogulonicigenium vulgare Hbe602 based on comparative genomics and metabolomics studies. Sci Rep, 6:23068.[PubMed]

3. N. Jia, M.Z. Ding, F. Gao, Y.J. Yuan (2016). Comparative genomics analysis of the companion mechanisms of Bacillus thuringiensis Bc601 and Bacillus endophyticus Hbe603 in bacterial consortium. Sci Rep, 6:28794.[PubMed]

4. F. Gao (2016). Editorial: DNA Replication Origins in Microbial Genomes. Front Microbiol, 6: 1545.[PubMed]

5. N. Jia, M.Z. Ding, Y.Z. Du, S. Feng, F. Gao, Y.J. Yuan (2016). Complete Genome Sequence of the Industrial Bacterium Ketogulonicigenium vulgare SKV. Genome Announc, 4(6), e01426-16.[PubMed]

Publications during 2015

1. F. Gao, H. Luo, C.T. Zhang, R. Zhang (2015). Book chapter: "Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes.". Methods in Molecular Biology, 1279:219-33.[PubMed]

2. C. Peng, H. Luo, X. Zhang, F. Gao (2015). Recent advances in the genome-wide study of DNA replication origins in yeast. Front Microbiol, 6:117.[PubMed]

3. C.T. Zhang (2015). Editorial: Z-curve Applications in Genome Analysis. Curr Genomics, 15(2):77.[PubMed]

4. F. Gao (2015). Bacteria may have multiple replication origins. Front Microbiol, 6, 324.[PubMed]

5. C. Zhang, H. Luo, F. Gao, C.T. Zhang, R. Zhang (2015). A reduction in both visceral and subcutaneous fats contributes to increased adiponectin by lifestyle intervention in the Diabetes Prevention Program. Acta Diabetol, 52(3):625-8.[PubMed]

6. F. Gao, H. Luo, Z. Fu, C. T. Zhang, R. Zhang (2015). Exome sequencing identifies novel ApoB loss-of-function mutations causing hypobetalipoproteinemia in type 1 diabetes. Acta Diabetol, 52(3), 531-537.[PubMed]

7. C. Zhang, F. Gao, H. Luo, C.T. Zhang, R. Zhang (2015). Differential response in levels of high-density lipoprotein cholesterol to one-year metformin treatment in prediabetic patients by race/ethnicity. Cardiovasc Diabetol, 14:79.[PubMed]

8. Z.G. Hua, Y. Lin, Y.Z. Yuan, D.C. Yang, W. Wei, F.B. Guo (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.[PubMed]

9. X. Zhang,C. Peng, G. Zhang, F. Gao (2015). Comparative analysis of essential genes in prokaryotic genomic islands. Sci Rep, 5:12561.[PubMed]

10. N. Jia, J. Du, M. Z. Ding, F. Gao, Y. J. Yuan (2015). Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium. PLoS One, 6;10(8):e0135104.[PubMed]

11. C. Peng, F. Gao (2015). Protein localization analysis of essential genes in prokaryotes. Sci Rep, 4:6001.[PubMed]

12. H. Luo, F. Fao, Y. Lin (2015). Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes. Sc. Rep, 5, 13210.[PubMed]

13. H. Huang, C.C. Song, Z. Yang, Y. Dong, Y. Hu, F. Gao (2015). Identification of the replication origins from Cyanothece ATCC 51142 and their interactions with the DnaA protein: from in silico to in vitro studies. Front Microbiol, 6, 1370.[PubMed]

Publications during 2014

1. H. Luo, Y. Lin, F. Gao, C.T. Zhang, R. Zhang (2014). DEG 10, an update of the Database of Essential Genes that includes both protein-coding genes and non-coding genomic elements. Nucleic Acids Res, 42(Database issue):D574-80.[PubMed]

2. R. Zhang, C.T. Zhang (2014). A Brief Review: The Z-curve Theory and its Application in Genome Analysis. Curr Genomics, 15(2):78-94.[PubMed]

3. F.B. Guo, Y. Lin, L.L. Chen (2014). Recognition of Protein-coding Genes Based on Z-curve Algorithms. Curr Genomics, 15(2):95-103.[PubMed]

4. F. Gao (2014). Recent Advances in the Identification of Replication Origins Based on the Z-curve Method. Curr Genomics, 15(2), 104-112.[PubMed]

5. R. Zhang, H.Y. Ou, F. Gao, H. Luo (2014). Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method. Curr Genomics, 15(2):113-21.[PubMed]

6. H. Huang, Y. Dong, Z.L. Yang, H. Luo, X. Zhang, F. Gao (2014). Complete Sequence of pABTJ2, a Plasmid from A. baumannii MDR-TJ, Carrying Many Phage-like Elements. Genomics Proteomics Bioinformatics, 12(4):172-7.[PubMed]

7. H. Luo, C.T. Zhang, F. Gao (2014). Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes. Front Microbiol, 5:482.[PubMed]

Publications during 2013

1. F. Gao, H. Luo, C.T. Zhang (2013). DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Res, 41(Database issue):D90-3.[PubMed]

2. C.T. Zhang (2013). A novel triangle mapping technique to study the h-index based citation distribution. Sci Rep, 3:1023.[PubMed]

3. C.T. Zhang (2013). The h'-index, effectively improving the h-index based on the citation distribution. PLoS One, 8(4):e59912.[PubMed]

4. Z.G. Yang, C.T. Zhang (2013). A proposal for a novel impact factor as an alternative to the JCR impact factor. Sci Rep, 3:3410.[PubMed]

5. B.L. Hao, C.T Zhang, Y.X. Li, H. Li, L.P. Wei, M. Kanehisa, L.H Lai, R.S Chen, N. Rajewsky, M.Q. Zhang, J.D. Han, R. Jiang, X.G. Zhang, Y.D Li (2013). Advanced topics in bioinformatics and computational biology. Basics of Bioinformatics, 369-95

Publications during 2012

1. F. Gao#, Y. Lin#, R.R. Zhang (2012). RNA-DNA differences are rarer in proto-oncogenes than in tumor suppressor genes. Sci Rep, 2:245.[PubMed]

2. F. Gao, H. Luo, C.T. Zhang (2012). DeOri: a database of eukaryotic DNA replication origins. Bioinformatics, 28(11):1551-2.[PubMed]

3. Z.G. Yang, F. Gao, C.T. Zhang (2012). Comparison of journal self-citation rates between some Chinese and non-Chinese international journals. PLoS ONE, 7(11):e49001.[PubMed]

4. H. Huang, Z.L. Yang, X.M. Wu, Y. Wang, Y.J. Liu, H. Luo, X. Lv, Y.R. Gan, S.D. Song, F. Gao (2012). Complete genome sequence of Acinetobacter baumannii MDR-TJ and insights into its mechanism of antibiotic resistance. J Antimicrob Chemother, 67, 2825-2832.[PubMed]

Publications before 2012

1. F. Gao, Y. Wang, Y.J. Liu, X.M. Wu, X. Lv, Y.R. Gan, S.D. Song, H. Huang (2011). Genome sequence of Acinetobacter baumannii MDR-TJ. J Bacteriol, 193(9):2365-6.[PubMed]

2. F. Gao, R. Zhang (2011). Enzymes are enriched in bacterial essential genes. PLoS One, 6(6):e21683.[PubMed]

3. Y. Lin, R. Zhang (2011). Putative essential and core-essential genes in Mycoplasma genomes. Sci Rep, 1:53.[PubMed]

4. Y. Lin, F. Gao, C.T. Zhang (2010). Functionality of essential genes drives gene strand-bias in bacterial genomes. Biochem Biophys Res Commun, 396(2):472-6.[PubMed]

5. R. Zhang, Y. Lin (2009). DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res, 37(Database issue):D455-8.[PubMed]

6. C.T. Zhang (2009). A proposal for calculating weighted citations based on author rank. EMBO Rep, 10(5):416-7.[PubMed]

7. C.T. Zhang (2009). The e-index, complementing the h-index for excess citations. PLoS One, 4(5):e5429.[PubMed]

8. C.T. Zhang (2009). Relationship of the h-index, g-index, and e-index. J Am Soc Inf Sci Tech, 61(3), 625-8

9. C.T. Zhang, R. Zhang (2008). Gene essentiality analysis based on DEG, a database of essential genes. Methods Mol Biol, 416:391-400.[PubMed]

10. R. Zhang, Y. Lin, C.T. Zhang (2008). Greglist, a database listing potential G-quadruplex regulated genes. Nucleic Acids Res, 36(Database issue):D372-6.[PubMed]

11. R. Zhang, C.T. Zhang (2008). Accurate localization of the integration sites of two genomic islands at single-nucleotide resolution in the genome of Bacillus cereus ATCC 10987. Comp Funct Genomics, 451930.[PubMed]

12. F. Gao, C.T. Zhang (2008). Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics, 9:79.[PubMed]

13. W.X. Zheng, C.T. Zhang (2008). Biological Implications of Isochore Boundaries in the Human Genome. J Biomol Struct Dyn, 25(4):327-36.[PubMed]

14. F. Gao, C.T. Zhang (2008). Origins of replication in Sorangium cellulosum and Microcystis aeruginosa. DNA Res, 15(3):169-71.[PubMed]

15. F. Gao, C.T. Zhang (2008). Prediction of replication time zones at single nucleotide resolution in the human genome. FEBS Lett, 582(16):2441-4.[PubMed]

16. W.X. Zheng, C.T. Zhang (2008). Ultraconserved Elements Between the Genomes of the Plants Arabidopsis thaliana and Rice. J Biomol Struct Dyn, 26(1):1-8.[PubMed]

17. F. Gao, C.T. Zhang (2008). Origins of replication in Cyanothece 51142. Proc Natl Acad Sci U S A, 105(52):E125.[PubMed]

18. F. Gao, C.T. Zhang (2007). DoriC: a database of oriC regions in bacterial genomes. Bioinformatics, 23(14):1866-7.[PubMed]

19. F. B. Guo, C.T. Zhang (2006). ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. BMC Bioinformatics, 7:9.[PubMed]

20. R. Zhang, C.T. Zhang (2006). The impact of comparative genomics on infectious disease research. Microbes Infect, 8(6):1613-22.[PubMed]

21. F. Gao, C.T. Zhang (2006). Isochore structures in the chicken genome. FEBS J, 273(8):1637-48.[PubMed]

22. F. Gao, C.T. Zhang (2006). GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res, 34(Web Server issue):W686-91.[PubMed]

23. R. Zhang, C.T. Zhang (2005). Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea, 1(5):335-46.[PubMed]

24. R. Zhang, C.T. Zhang (2005). Genomic islands in the Corynebacterium efficiens genome. Appl Environ Microbiol, 71(6):3126-30.[PubMed]

25. W.X. Zheng, L.L. Chen, H.Y. Ou, F. Gao, C.T. Zhang (2005). Coronavirus phylogeny based on a geometric approach. Mol Phylogenet Evol, 36(2):224-32.[PubMed]

26. C. T. Zhang, F. Gao and R. Zhang (2005). Segmentation algorithm for DNA sequences. Phys Rev E, 72(4 Pt 1):041917.[PubMed]

27. R. Zhang, H.Y. Ou, C.T. Zhang (2004). DEG: a database of essential genes. Nucleic Acids Res, 32(Database issue):D271-2.[PubMed]

28. C.T. Zhang, R. Zhang (2004). Isochore structures in the mouse genome. Genomics, 83(3):384-94.[PubMed]

29. H.Y. Ou, F.B. Guo, C.T. Zhang (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.[PubMed]

30. R. Zhang, C.T. Zhang (2004). A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I. Bioinformatics, 20(5):612-22.[PubMed]

31. F. Gao, C.T. Zhang (2004). Comparison of various algorithms for recognizing short coding sequences of human genes. Bioinformatics, 20(5):673-81.[PubMed]

32. C.T. Zhang, R. Zhang (2004). A nucleotide composition constraint of genome sequences. Comput Biol Chem, 28(2):149-53.[PubMed]

33. R. Zhang, C.T. Zhang (2004). Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii. Extremophiles, 8(3):253-8.[PubMed]

34. R. Zhang, C.T. Zhang (2004). Isochore structures in the genome of the plant Arabidopsis thaliana. J Mol Evol, 59(2):227-38.[PubMed]

35. C.T. Zhang, R. Zhang (2004). Genomic islands in Rhodopseudomonas palustris. Nat Biotechnol, 22(9):1078-9.[PubMed]

36. F.B. Guo, J. Wang, C.T. Zhang (2004). Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res, 11(6):361-70.[PubMed]

37. F.B. Guo, H.Y. Ou, CT Zhang (2003). ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res, 31(6):1780-9.[PubMed]

38. H.Y. Ou, F.B. Guo, C.T. Zhang (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.[PubMed]

39. R. Zhang, C.T. Zhang (2003). Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem Biophys Res Commun, 302(4):728-34.[PubMed]

40. C.T. Zhang, R. Zhang, H.Y. Ou (2003). The Z curve database: a graphic representation of genome sequences. Bioinformatics, 19(5):593-9.[PubMed]

41. L.L. Chen, C.T. Zhang (2003). Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages. Biochem Biophys Res Commun, 306(1):310-7.[PubMed]

42. L.L. Chen, H.Y. Ou, R. Zhang, C.T. Zhang (2003). ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem Biophys Res Commun, 307(2):382-8.[PubMed]

43. C.T. Zhang, R. Zhang (2003). Q9, a content-balancing accuracy index to evaluate algorithms of protein secondary structure prediction. Int J Biochem Cell Biol, 35(8):1256-62.[PubMed]

44. L.L. Chen, C.T. Zhang (2003). Gene recognition from questionable ORFs in bacterial and archaeal genomes. J Biomol Struct Dyn, 21(1):99-109.[PubMed]

45. F. Gao, H.Y. Ou, L.L. Chen, W.X. Zheng, C.T. Zhang (2003). Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS‐CoV genomes. FEBS Lett, 553(3):451-6.[PubMed]

46. C.T. Zhang, R. Zhang (2003). An isochore map of the human genome based on the Z curve method. Gene, 317(1-2):127-35.[PubMed]

47. S.Y. Wen, C.T. Zhang (2003). Identification of isochore boundaries in the human genome using the technique of wavelet multiresolution analysis. Biochem Biophys Res Commun, 311(1):215-22.[PubMed]

48. R. Zhang, C.T. Zhang (2003). Identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis. Physiol Genomics, 16(1):19-23.[PubMed]

49. C.T. Zhang, J. Wang, R. Zhang (2002). Using a Euclid distance discriminant method to find protein coding genes in the yeast genome. Comput Chem, 26(3):195-206.[PubMed]

50. Y.H. Wang, C.T. Zhang, P.X. Dong (2002). Recognizing shorter coding regions of human genes based on the statistics of stop codons. Biopolymers, 63(3):207-16.[PubMed]

51. Z.P. Feng, C.T. Zhang (2002). A graphic representation of protein sequence and predicting the subcellular locations of prokaryotic proteins. Int J Biochem Cell Biol, 34(3):298-307.[PubMed]

52. C.T. Zhang, R. Zhang (2002). Evaluation of gene-finding algorithms by a content-balancing accuracy index. J Biomol Struct Dyn, 19(6):1045-52.[PubMed]

53. R. Zhang, C.T. Zhang (2002). Single replication origin of the archaeon Methanosarcina mazei revealed by the Z curve method. Biochem Biophys Res Commun, 297(2):396-400.[PubMed]

54. Z.D. Zhang, Z.R. Sun, C.T. Zhang (2001). A new approach to predict the helix/strand content of globular proteins. J Theor Biol, 208(1):65-78.[PubMed]

55. Z.P. Feng, C.T. Zhang (2001). Prediction of the subcellular location of prokaryotic proteins based on the hydrophobicity index of amino acids. Int J Biol Macromol, 28(3):255-61.[PubMed]

56. C.T. Zhang, R. Zhang (2001). A refined accuracy index to evaluate algorithms of protein secondary structure prediction. Proteins, 43(4):520-2.[PubMed]

57. J. Wang, C.T. Zhang (2001). Analysis of the codon usage pattern in the Vibrio cholerae genome. J Biomol Struct Dyn, 18(6):872-80.[PubMed]

58. J. Wang, C.T. Zhang (2001). Identification of protein‐coding genes in the genome of Vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotides. Eur J Biochem, 268(15):4261-8.[PubMed]

59. C.T. Zhang, J. Wang, R. Zhang (2001). A novel method to calculate the G+ C content of genomic DNA sequences. J Biomol Struct Dyn, 19(2):333-41.[PubMed]

60. Z.P. Feng, C.T. Zhang (2000). Prediction of membrane protein types based on the hydrophobic index of amino acids. J Protein Chem, 19(4):269-75.[PubMed]

61. C.T. Zhang, R. Zhang (2000). S curve, a graphic representation of protein secondary structure sequence and its applications. Biopolymers, 53(7):539-49.[PubMed]

62. C.T. Zhang, J. Wang (2000). Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve. Nucleic Acids Res, 28(14):2804-14.[PubMed]

63. C.T. Zhang, R. Zhang (1999). Skewed distribution of protein secondary structure contents over the conformational triangle. Protein Eng, 12(10):807-10.[PubMed]

64. W.S. Bu, Z.P. Feng, Z.D. Zhang, C.T. Zhang (1999). Prediction of protein (domain) structural classes based on amino‐acid index. Eur J Biochem, 266(3):1043-9.[PubMed]

65. C.T. Zhang, R. Zhang (1999). A quadratic discriminant analysis of protein structure classification based on the Helix/Strand content. J Theor Biol, 201(3):189-99.[PubMed]

66. C.T. Zhang, Z.S. Lin, Z.D. Zhang, M. Yan (1998). Prediction of the helix/strand content of globular proteins based on their primary sequences.. Protein Eng, 11(11):971-9.[PubMed]

67. M. Yan, Z.S. Lin, C.T. Zhang (1998). A new fourier transform approach for protein coding measure based on the format of the Z curve.. Bioinformatics, 14(8):685-90.[PubMed]

68. C.T. Zhang, R. Zhang (1998). A new criterion to classify globular proteins based on their secondary structure contents. Bioinformatics, 14(10):857-865.[PubMed]

69. K.C. Chou, W.M. Liu, G.M. Maggiora, C.T. Zhang (1998). Prediction and classification of domain structural classes. Proteins, 31(1):97-103.[PubMed]

70. C.T. Zhang, Z.S. Lin, M. Yan, R. Zhang (1998). A novel approach to distinguish between intron-containing and intronless genes based on the format of Z curves. J Theor Biol, 192(4):467-73.[PubMed]

71. C.T. Zhang, Z.D. Zhang, Z.M. He (1998). Prediction of the secondary structure contents of globular proteins based on three structural classes. J Protein Chem, 17(3):261-72.[PubMed]

72. C.T. Zhang, R. Zhang (1998). A new quantitative criterion to distinguish between α/β and α+ β proteins (domains). FEBS Lett, 440(1-2):153-7.[PubMed]

73. C.T. Zhang, K.C. Chou (1997). Prediction of β-turns in proteins by 1-4 and 2-3 correlation model. Biopolymers, 41(6), 673-702

74. K.C. Chou, C.T. Zhang, G.M. Maggiora (1997). Disposition of amphiphilic helices in heteropolar environments. Proteins, 28(1):99-108.[PubMed]

75. C.T. Zhang (1997). Relations of the numbers of protein sequences, families and folds. Protein Eng, 10(7):757-61.[PubMed]

76. C.T. Zhang (1997). A symmetrical theory of DNA sequences and its applications. J Theor Biol, 187(3):297-306.[PubMed]

77. K.C. Chou, C.T. Zhang, D.W. Elrod (1996). Do “antisense proteins” exist?. J Protein Chem, 15(1):59-61.[PubMed]

78. C.T. Zhang, K.C. Chou (1996). Beat motion in DNA double helix and a mechanism of energy exchange between its two strands with microwave frequency. Chemical physics, 206(3), 271-277

79. Z.R. Sun, C.T. Zhang, F.H. Wu, L.W. Peng (1996). A vector projection method for predicting supersecondary motifs. J Protein Chem, 15(8):721-9.[PubMed]

80. C.T. Zhang, Z. Zhang, Z. He (1996). Prediction of the secondary structure content of globular proteins based on structural classes. J Protein Chem, 15(8):775-86.[PubMed]

81. K.C. Chou, C.T. Zhang (1995). Prediction of protein structural classes. Crit Rev Biochem Mol Biol, 30(4):275-349.[PubMed]

82. C.T. Zhang (1995). Diagrammatic representation of base composition in DNA sequences. Visualizing Biological Information, 84-95

83. K.C. Chou, C.T. Zhang, F.J. Kézdy, R.A. Poorman (1995). A vector projection method for predicting the specificity of GalNAc‐transferase. Proteins, 21(2), 118-126.[PubMed]

84. C.T. Zhang, K.C. Chou (1995). The nonlinear stretching model of hydrogen bonds and local self-fluctuation of base rotation in DNA. Chemical Physics, 191(1-3), 17-23

85. C.T. Zhang, K.C. Chou (1995). Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. II. Correlative effect. J Protein Chem, 14(4):251-8.[PubMed]

86. C.T. Zhang, K.C. Chou, G.M. Maggiora (1995). Predicting protein structural classes from amino acid composition: application of fuzzy clustering. Protein Eng, 8(5):425-35.[PubMed]

87. C.T. Zhang, K.C. Chou (1995). An eigenvalue-eigenvector approach to predicting protein folding types. J Protein Chem, 14(5):309-26.[PubMed]

88. C.T. Zhang, K.C. Chou (1995). An analysis of protein folding type prediction by seed-propagated sampling and jackknife test. J Protein Chem, 14(7):583-93.[PubMed]

89. K.C. Chou, C.T. Zhang, G.M. Maggiora (1994). Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth. Biopolymers, 34(1):143-53.[PubMed]

90. C.T. Zhang, K.C. Chou (1994). An alternate-subsite-coupled model for predicting HIV protease cleavage sites in proteins. Protein Eng, 7(1):65-73.[PubMed]

91. R. Zhang, C.T. Zhang (1994). Z curves, an intutive tool for visualizing and analyzing the DNA sequences. J Biomol Struct Dyn, 11(4):767-82.[PubMed]

92. B. Mao, K.C. Chou, C.T. Zhang (1994). Protein folding classes: a geometric interpretation of the amino acid composition of globular proteins. Protein Eng, 7(3):319-30.[PubMed]

93. C.T. Zhang, Y. Zhan (1994). Analysis on the distribution of bases in 1487 human protein coding sequences. J Theor Biol, 167(2):161-6.[PubMed]

94. C.T. Zhang, K.C. Chou (1994). A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences. J Mol Biol, 238(1):1-8.[PubMed]

95. K.C. Chou, C.T. Zhang (1994). Predicting protein folding types by distance functions that make allowances for amino acid interactions. J Biol Chem, 269(35):22014-20.[PubMed]

96. J.J. Chou, C.T. Zhang (1993). A joint prediction of the folding types of 1490 human proteins from their genetic codons. J Theor Biol, 161(2):251-62.[PubMed]

97. K.C. Chou, C.T. Zhang (1993). A new approach to predicting protein folding types. J Protein Chem, 12(2):169-78.[PubMed]

98. C.T. Zhang, K.C. Chou (1993). Graphic analysis of codon usage strategy in 1490 human proteins. J Protein Chem, 12(3):329-35.[PubMed]

99. K.C. Chou, C.T. Zhang, F.J. Kézdy (1993). A vector projection approach to predicting HIV protease cleavage sites in proteins. Proteins, 16(2):195-204.[PubMed]

100. K.C. Chou, C.T. Zhang (1993). Studies on the specificity of HIV protease: an application of Markov chain theory. J Protein Chem, 12(6):709-24.[PubMed]

101. C.T. Zhang, K.C. Chou (1992). Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. Biophys J, 63(6):1523-9.[PubMed]

102. C.T. Zhang, K.C. Chou (1992). An optimization approach to predicting protein structural class from amino acid composition. Protein Sci, 1(3), 401-408.[PubMed]

103. K.C. Chou, C.T. Zhang (1992). A correlation‐coefficient method to predicting protein‐structural classes from amino acid compositions. Eur J Biochem, 207(2):429-3.[PubMed]

104. K.C. Chou, C.T. Zhang (1992). Diagrammatization of codon usage in 339 human immunodeficiency virus proteins and its biological implication. AIDS Res Hum Retroviruses, 8(12):1967-76.[PubMed]

105. W.G. Han, C.T. Zhang (1991). A theory of non-linear stretch vibrations of hydrogen bonds. Journal of Physics: Condensed Matter, 3(1), 27

106. G.F. Zhou, C.T. Zhang (1991). A short review on the nonlinear motion in DNA. Physica Scripta, 43(3), 347-352

107. C.T. Zhang, R. Zhang (1991). Diagrammatic representation of the distribution of DNA bases and its applications. Int J Biol Macromol, 13(1):45-9.[PubMed]

108. C.T. Zhang, Z.X. Shang (1991). The study of stacking energy for natural DNA sequences. J Theor Biol, 149(2):257-63.[PubMed]

109. C.T. Zhang, R. Zhang (1991). Analysis of distribution of bases in the coding sequences by a digrammatic technique. Nucleic Acids Res, 19(22):6313-7.[PubMed]

110. C.T. Zhang (1990). Equations between frequencies of amino acids in organisms. J Theor Biol, 142(2):281-4.[PubMed]

111. C.T. Zhang (1990). Solitary-wave excitation of hydrogen-bond stretching in deoxyribonucleic acid. Journal of Physics, 8259-8268

112. C.T. Zhang, G.F. Zhou (1990). Analysis of patterns of twist angles in DNA double helix. Int J Biol Macromol, 12(4):226-32.[PubMed]

113. C.T. Zhang, G.T. Ying (1989). Upper limit for the variances of some helical parameters in DNA double helix. Int J Biol Macromol, 11(1):9-12.[PubMed]

114. C.T. Zhang, G.F. Zhou (1989). Analysis of sequences of twist angles in DNA double helix. Int J Biol Macromol, 11(3):165-8.[PubMed]

115. C.T. Zhang, Y.Q. Cen (1989). The study of DNA sequences by their sequences of twist angles. J Theor Biol, 138(4):457-65.[PubMed]

116. C.T. Zhang (1989). Harmonic and subharmonic resonances of microwave absorption in DNA. Phys Rev A Gen Phys, 40(4):2148-2153.[PubMed]

117. C.T. Zhang (1987). Soliton excitations in deoxyribonucleic acid (DNA) double helices. Phys Rev A Gen Phys, 35(2):886-891.[PubMed]

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