Research Topics
| Chun Ting ZhangSummaryAffiliation: Tianjin University Country: China Publications
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Detail Information
Publications
A novel triangle mapping technique to study the h-index based citation distributionChun Ting Zhang
Department of Physics, Tianjin University, Tianjin 300072, China
Sci Rep 3:1023. 2013..By viewing the distribution of mapping points, shapes of the citation functions can be studied in a perceivable form. As an example, the distribution of the mapping points for 100 most prolific economists is studied by this technique...
Using a Euclid distance discriminant method to find protein coding genes in the yeast genomeChun Ting Zhang
Department of Physics, Tianjin University, China
Comput Chem 26:195-206. 2002..This fact constitutes the basis of the algorithm to distinguish between coding and non-coding ORFs in the yeast genome. The names of putative non-coding ORFs are listed here in detail...- Evaluation of gene-finding algorithms by a content-balancing accuracy indexChun Ting Zhang
Department of Physics, Tianjin University, Tianjin 300072, China
J Biomol Struct Dyn 19:1045-52. 2002..Additionally, the new accuracy index q(9) may be applied to evaluate the performance of weather forecast, clinical diagnosis, psychological examination and protein secondary structure prediction etc... - The Z curve database: a graphic representation of genome sequencesChun Ting Zhang
Department of Physics, Tianjin University, Tianjin 300072, People s Republic of China
Bioinformatics 19:593-9. 2003..are presented in detail. The Z curve database reported here is a treasure trove in which biologists could find useful biological knowledge... - Q9, a content-balancing accuracy index to evaluate algorithms of protein secondary structure predictionChun Ting Zhang
Department of Physics, Tianjin University, PR China
Int J Biochem Cell Biol 35:1256-62. 2003..Rather than Q(3), we believe that Q(9) should be used to evaluate algorithms of protein secondary structure prediction in future studies in order to improve prediction quality... - An isochore map of the human genome based on the Z curve methodChun Ting Zhang
Department of Physics, Tianjin University, Nankai District, Tianjin 300072, China
Gene 317:127-35. 2003..Due to the relevance to many important biological functions, the clarification of isochore structures will provide much insight into the understanding of the human genome... - Isochore structures in the mouse genomeChun Ting Zhang
Department of Physics, Tianjin University, Tianjin 300072, China
Genomics 83:384-94. 2004..In addition, the analysis of a segment of the rat genome shows that the rat genome also has clear isochore structures... - A nucleotide composition constraint of genome sequencesChun Ting Zhang
Department of Physics, Tianjin University, Tianjin 300072, China
Comput Biol Chem 28:149-53. 2004..211 and 0.789... - Segmentation algorithm for DNA sequencesChun Ting Zhang
Department of Physics, Tianjin University, Tianjin 300072, China
Phys Rev E Stat Nonlin Soft Matter Phys 72:041917. 2005..Particularly, it is much simpler and faster than the entropy-based method. Therefore, the new algorithm is more suitable for analyzing long genome sequences, such as human and other newly sequenced eukaryotic genome sequences... - The e-index, complementing the h-index for excess citationsChun Ting Zhang
Department of Physics, Tianjin University, Tianjin, China
PLoS ONE 4:e5429. 2009.... - A novel method to calculate the G+C content of genomic DNA sequencesC T Zhang
Department of Physics, Tianjin University, China
J Biomol Struct Dyn 19:333-41. 2001..Especially, the position and size of the large integron island on the smaller chromosome was precisely predicted. This method would be a useful tool for analyzing genomic sequences... - A new quantitative criterion to distinguish between alpha/beta and alpha+beta proteins (domains)C T Zhang
Department of Physics, Tianjin University, China
FEBS Lett 440:153-7. 1998..Applying the new criterion to reclassify the alpha/beta and alpha+beta proteins (domains) in SCOP is also discussed. It is hoped that the new quantitative criterion will be useful for the development of protein classification databases... - A quadratic discriminant analysis of protein structure classification based on the Helix/Strand contentC T Zhang
Department of Physics, Tianjin University, Tianjin, 300072, China
J Theor Biol 201:189-99. 1999..Further complete automated classification scheme should consider both structures and evolutionary relationship. The methodology presented provides an appropriate mathematical format to reach this goal... - S curve, a graphic representation of protein secondary structure sequence and its applicationsC T Zhang
Department of Physics, Tianjin University, Tianjin 300072, China
Biopolymers 53:539-49. 2000..This is particularly useful in the cases in which longer sequences are involved and structures of proteins are unknown... - A graphic approach to evaluate algorithms of secondary structure predictionC T Zhang
Department of Physics, Tianjin University, China
J Biomol Struct Dyn 17:829-42. 2000..It is pointed out that the accuracy for predicting either the alpha-helix or beta-strand in proteins with higher alpha-helix or beta-strand content, respectively, should be greatly improved for both algorithms... - Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curveC T Zhang
Department of Physics, Tianjin University, Tianjin 300072, China
Nucleic Acids Res 28:2804-14. 2000..5 or YZ < 0.5, respectively. The YZ scores for all the ORFs annotated in the MIPS database have been calculated and are available on request by sending e-mail to the corresponding author... - A new criterion to classify globular proteins based on their secondary structure contentsC T Zhang
Department of Physics, Tianjin University, Tianjin 300072, China and Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, China
Bioinformatics 14:857-65. 1998..The Fisher linear discriminant algorithm is used to derive the new classification criterion... - DoriC: a database of oriC regions in bacterial genomesFeng Gao
Department of Physics, Tianjin University, Tianjin 300072, China
Bioinformatics 23:1866-7. 2007..AVAILABILITY: DoriC can be accessed from http://tubic.tju.edu.cn/doric/. SUPPLEMENTARY INFORMATION: Supplementary data are available at http://tubic.tju.edu.cn/doric/supplementary.htm... - Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomesFeng Gao
Department of Physics, Tianjin University, Tianjin 300072, China
BMC Bioinformatics 9:79. 2008..Therefore, the increasing availability of genome sequences calls for improved software to identify oriCs in newly sequenced and unannotated bacterial genomes... - ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomesFeng Biao Guo
Department of Physics, Tianjin University, Tianjin 300072, China
BMC Bioinformatics 7:9. 2006..This paper puts forward an alternative approach for viral and phage gene-finding to improve the quality of annotations, particularly for newly sequenced genomes... 
Prediction of replication time zones at single nucleotide resolution in the human genomeFeng Gao
Department of Physics, Tianjin University, Tianjin 300072, China
FEBS Lett 582:2441-4. 2008..1, 6p21.32, 17q11.2 and 22q12.1 nearly all coincide with the determined isochore boundaries. The precise boundaries of the 3198 isochores are available via the website: http://tubic.tju.edu.cn/isomap/...- Functionality of essential genes drives gene strand-bias in bacterial genomesYan Lin
Department of Physics, Tianjin University, Tianjin 300072, China
Biochem Biophys Res Commun 396:472-6. 2010.... - Gene essentiality analysis based on DEG, a database of essential genesChun Ting Zhang
Department of Physics, Tianjin University, Tianjin, China
Methods Mol Biol 416:391-400. 2008..Finally, some potential pitfalls for analyzing gene essentiality based on DEG are discussed... - Biological implications of isochore boundaries in the human genomeWen Xin Zheng
Department of Physics, Tianjin University, Tianjin 300072, China
J Biomol Struct Dyn 25:327-36. 2008..These results suggest possible key roles of the isochore boundaries and may further our understanding of the human genome organization... - Analysis of the codon usage pattern in the Vibrio cholerae genomeJ Wang
Department of Physics, Tianjin University, China
J Biomol Struct Dyn 18:872-80. 2001..The encoding products of these genes have significant bias in amino acids composition as compared with other genes. The codon usage patterns for the 1,836 function unknown ORFs are also analyzed, which is useful to study their functions... - DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomesFeng Gao
Department of Physics, Tianjin University, Tianjin 300072, China
Nucleic Acids Res 41:D90-3. 2013..Consequently, the latest release of DoriC contains oriCs for >1500 bacterial genomes and 81 archaeal genomes, respectively... - Origins of replication in Sorangium cellulosum and Microcystis aeruginosaFeng Gao
Department of Physics, Tianjin University, Tianjin 300072, People s Republic of China
DNA Res 15:169-71. 2008.... - Greglist: a database listing potential G-quadruplex regulated genesRen Zhang
Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, China
Nucleic Acids Res 36:D372-6. 2008..Greglist therefore provides candidates for further studying G-quadruplex functions and is freely available at http://tubic.tju.edu.cn/greglist... - Identification of protein-coding genes in the genome of Vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotidesJ Wang
Department of Physics, Tianjin University, Tianjin 300072, China
Eur J Biochem 268:4261-8. 2001..A computer program was written to calculate a coding score called VCZ for gene identification in the genome. Coding/noncoding is simply determined by VCZ > 0/VCZ < 0. The program is freely available on request for academic use... - DeOri: a database of eukaryotic DNA replication originsFeng Gao
Department of Physics, Tianjin University, Tianjin, China
Bioinformatics 28:1551-2. 2012..AVAILABILITY: Database of Eukaryotic ORIs (DeOri) can be accessed from http://tubic.tju.edu.cn/deori/.. - Skewed distribution of protein secondary structure contents over the conformational triangleC T Zhang
Department of Physics, Tianjin University, Tianjin 300072, China
Protein Eng 12:807-10. 1999..223. It is hoped that the skewed distribution observed here could be used to test the secondary structure and threading predictions... - Comparison of journal self-citation rates between some Chinese and non-Chinese international journalsZu Guo Yang
Library, Tianjin University, Tianjin, China
PLoS ONE 7:e49001. 2012..This study aimed to evaluate these journals by calculating various journal self-citation rates, which are important parameters influencing a journal impact factor... - A new approach to predict the helix/strand content of globular proteinsZ Zhang
Chemical Engineering Research Center, Tianjin University, Tianjin 300072, China
J Theor Biol 208:65-78. 2001..Both tests indicate the self-consistency and the extrapolating effectiveness of the new method. The high prediction accuracy means that the method is suitable for practical applications... - Prediction of the subcellular location of prokaryotic proteins based on the hydrophobicity index of amino acidsZ P Feng
Department of Physics, Tianjin University, 300072, Tianjin, PR China
Int J Biol Macromol 28:255-61. 2001..This work would be useful for a systematic analysis of the great amounts of prokaryotic genome sequences. The computer programs used in this paper are available on request via email... - A refined accuracy index to evaluate algorithms of protein secondary structure predictionC T Zhang
Department of Physics, Tianjin University, Tianjin, China
Proteins 43:520-2. 2001..Of the five algorithms, PHD turned out to be the unique algorithm, with Q8 accuracy better than 70%. It is suggested that Q3 should be replaced by Q8 in evaluating secondary structure prediction in future studies...