The publications of the CUCKOO Workgroup

Dr. Yu Xue's publications and citations can be available at below:

    

 

2016

77. Deng W, Wang Y, Ma L, Zhang Y, Ullah S, Xue Y**. (2016) Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins. Brief Bioinform. 2016 May 30. pii: bbw041. [Epub ahead of print] [Pubmed][PDF][Supplemental Data]

76. Xie Y, Zheng Y, Li H, Luo X, He Z, Cao S, Shi Y, Zhao Q, Xue Y, Zuo Z, Ren J. (2016) GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites. Sci Rep. 6:28249. [Pubmed][PDF][Supplemental Data]

75. Xue Y**, Wang Y, Shen H. (2016) Ray Wu, fifth business or father of DNA sequencing? Protein Cell. 7(7):467-70. [Pubmed][PDF]
This paper is my first essay on public science in English. Besides PTM Bioinformatics, I am also an active blogger on ScienceNet in China. The Chinese version of this essay can be available at: "DNA֮".

74. Zhang J, Tian Y, Yan L, Zhang G, Wang X, Zeng Y, Zhang J, Ma X, Tan Y, Long N, Wang Y, Ma Y, He Y, Xue Y, Hao S, Yang S, Wang W, Zhang L, Dong Y, Chen W, Sheng J. (2016) Genome of Plant Maca (Lepidium meyenii) Illuminates Genomic Basis for High-Altitude Adaptation in the Central Andes. Mol Plant. 9(7):1066-77. [Pubmed][PDF][Supplemental Data]

73. Guo X, Lv X, Fang C, Lv X, Wang F, Wang D, Zhao J, Ma Y, Xue Y, Bai Q, Yao X, Chen Y. (2016) Dysbindin as a novel biomarker for pancreatic ductal adenocarcinoma identified by proteomic profiling. Int J Cancer. 2016 Oct 15;139(8):1821-9. [Pubmed][PDF]

72. Ullah S, Lin S, Xu Y, Deng W, Ma L, Zhang Y, Liu Z#, Xue Y#. (2016) dbPAF: an integrative database of protein phosphorylation in animals and fungi. Sci Rep. 6:23534. [Pubmed][PDF][Supplemental Data]

71. He CL, Bian YY, Xue Y, Liu ZX, Zhou KQ, Yao CF, Lin Y, Zou HF, Luo FX, Qu YY, Zhao JY, Ye ML, Zhao SM, Xu W. (2016) Pyruvate Kinase M2 Activates mTORC1 by Phosphorylating AKT1S1. Sci Rep. 6:21524. [Pubmed][PDF][Supplemental Data]

70. Klionsky DJ, ..., Xue Y, ..., Zughaier SM. (2016) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 12(1):1-222. [Pubmed][PDF]
I am very pleased to be an authorship of this super paper on autophagy. We established a yeast model to analyze functional PTM events in autophagy, using both computational and experimental approaches. Also, our database, THANATOS (THe Apoptosis, Necrosis, AuTophagy OrchestratorS, http://thanatos.biocuckoo.org/) was introduced and recommended in this guideline.

69. Zhong Z, Yang L, Zhang YE, Xue Y, He S. (2015) Correlated expression of retrocopies and parental genes in zebrafish. Mol Genet Genomics. 291(2):723-37. [Pubmed][PDF][Supplemental Data]

68. Gao Y, Li Y, Zhang C, Zhao M, Deng C, Lan Q, Liu Z, Su N, Wang J, Xu F, Xu Y, Ping L, Chang L, Gao H, Wu J, Xue Y, Deng Z, Peng J, Xu P. (2016) Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs). Mol Cell Proteomics. 2016 Apr;15(4):1381-96. [Pubmed][PDF]

67. IC4R Project Consortium, Hao L, Zhang H, Zhang Z, Hu S, Xue Y. (2016) Information Commons for Rice (IC4R). Nucleic Acids Res. 44(D1):D1172-80. [Pubmed][PDF]

2015

66. Feng W, Zhang W, Wang H, Ma L, Miao D, Liu Z, Xue Y, Deng H, Yu L. (2015) Analysis of phosphorylation sites on autophagy proteins. Protein Cell. 6(9):698-701. [Pubmed][PDF][Supplemental Data]

65. Cheng H, Wang Y, Liu Z, Xue Y**. (2015) Computational identification of protein kinases and kinase-specific substrates in plants. Methods Mol Biol. 2015;1306:195-205. [Pubmed][PDF]

64. Wang Y, Cheng H, Pan Z, Ren J, Liu Z#, Xue Y#. (2015) Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility. J Mol Cell Biol. 7(3):187-202. [Pubmed][PDF][Supplemental Data]
This paper is the first article of the JMCB Special Issue "Bio-network Medicine". Two Guest Editors, Dr. Luonan Chen and Dr. Jiarui Wu, wrote an editorial to highlight the importance of network medicine. I also wrote a blog on it, in Chinese.

63. Liu W, Xie Y, Ma J, Luo X, Nie P, Zuo Z, Lahrmann U, Zhao Q, Zheng Y, Zhao Y, Xue Y#, Ren J#. (2015) IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics. 2015 Jun 10. pii: btv362. [Pubmed][PDF][Supplemental Data]
This is a small but cute tool for preparing and visualizing biological sequences. I wrote a blog on it, in Chinese.

62. Liu Z, Cai Y, Guo X, Li A, Li T, Qiu J, Ren J, Shi S, Song J, Wang M, Xie L, Xue Y#, Zhang Z, Zhao X. (2015) Post-translational modification (PTM) bioinformatics in China: progresses and perspectives. DHEREDITAS(Beijing), 2015, 37(7): 621-634. [PDF, in Chinese][Weblink][CNKI]
This review was a consensus from a small conference of "Proteome-based Bioinformatics Symposium-2014". Up to 12 groups of Chinese Bioinformaticians who were working in the field of PTMs took a serious discussion, and highlighted the PTM research in the near future. The review was written in Chinese.

61. Pan Z, Wang B, Zhang Y, Wang Y, Ullah S, Jian R, Liu Z#, Xue Y#. (2015) dbPSP: a curated database for protein phosphorylation sites in prokaryotes. Database (Oxford). 2015:bav031. [Pubmed][PDF]

60. Tian M, Cheng H, Wang Z, Su N, Liu Z, Sun C, Zhen B, Hong X, Xue Y, Xu P. (2015) Phosphoproteomic analysis of the highly-metastatic hepatocellular carcinoma cell line, MHCC97-H. Int J Mol Sci. 16(2):4209-25. [Pubmed][PDF][Supplemental Data]

59. Zhang HM, Liu T, Liu CJ, Song S, Zhang X, Liu W, Jia H, Xue Y, Guo AY. (2015) AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. Nucleic Acids Res. 43:D76-81. [Pubmed][PDF][Supplemental Data]

58. Huang Z, Ma L, Wang Y, Pan Z, Ren J, Liu Z#, Xue Y#. (2015) MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. Nucleic Acids Res. 43:D328-34. [Pubmed][PDF][Supplemental Data]

2014

57. Cheng H, Deng W, Wang Y, Ren J, Liu Z#, Xue Y#. (2014) dbPPT: a comprehensive database of protein phosphorylation in plants. Database (Oxford). 2014:bau121. [Pubmed][PDF][Supplemental Data]

56. Pan Z, Liu Z, Cheng H, Wang Y, Gao T, Ullah S, Ren J, Xue Y**. (2014) Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. Sci Rep. 4:7331. [Pubmed][PDF][Supplemental Data]

55. Deng W, Wang Y, Liu Z, Cheng H, Xue Y**. (2014) HemI: A Toolkit for Illustrating Heatmaps. PLoS One. 9(11):e111988. [Pubmed][PDF]

54. Qi L, Liu Z, Wang J, Cui Y, Guo Y, Zhou T, Zhou Z, Guo X#, Xue Y#, Sha J. (2014) Systematic Analysis of the Phosphoproteome and Kinase-substrate Networks in the Mouse Testis. Mol Cell Proteomics. 13(12):3626-38. [Pubmed][PDF][Supplemental Data]

53. Zhao Q, Xie Y, Zheng Y, Jiang S, Liu W, Mu W, Liu Z, Zhao Y, Xue Y#, Ren J#. (2014) GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. Nucleic Acids Res. 42:W325-30. [Pubmed][PDF][Supplemental Data]

52. Yao Y, Ma L, Jia Q, Deng W, Liu Z, Zhang Y, Ren J, Xue Y, Jia H, Yang Q. (2014) Systematic characterization of small RNAome during zebrafish early developmental stages. BMC Genomics. 2014, 15:117. [Pubmed][PDF][Supplemental Data]

51. Liu Z, Wang Y, Zhou C, Xue Y, Zhao W, Liu H. (2014) Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins. Biochim Biophys Acta. 1844(1 Pt B):171-80. [Pubmed][PDF].

50. Wang Y, Liu Z, Cheng H, Gao T, Pan Z, Yang Q, Guo A, Xue Y**. (2014) EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. Nucleic Acids Res. 42(1):D496-502. [Pubmed][PDF][Supplemental Data]

49. Liu Z, Wang Y, Gao T, Pan Z, Cheng H, Yang Q, Cheng Z, Guo A, Ren J, Xue Y**. (2014) CPLM: a database of protein lysine modifications. Nucleic Acids Res. 42(1): D531-6. [Pubmed][PDF][Supplemental Data]

2013

48. Gao T, Liu Z, Wang Y, Xue Y**. (2013) Ubiquitin and Ubiquitin-Like Conjugations in Complex Diseases: A Computational Perspective. Translational Bioinformatics, Volume 4 2013, "Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases", Editors: Bairong Shen. ISBN: 978-94-007-7974-7 (Print), 978-94-007-7975-4 (Online) (Book Chapter 9) [PDF]
http://link.springer.com/book/10.1007%2F978-94-007-7975-4
For whom are interested in the relation of Ubiquitin and diseases

47. Yang Z, Guo G, Zhang M, Liu CY, Hu Q, Lam H, Cheng H, Xue Y, Li J, Li N. (2013) Stable isotope metabolic labeling-based quantitative phosphoproteomic analysis of Arabidopsis mutants reveals ethylene-regulated time-dependent phosphoproteins and putative substrates of constitutive triple response 1 kinase. Mol Cell Proteomics. 12(12):3559-82. [Pubmed][PDF][Supplemental Data]

46. Liu Z, Wang Y, Xue Y**. (2013) Phosphoproteomics-based network medicine. FEBS J, 280(22):5696-704. (Invited review) [Pubmed][PDF]

45. Liu Z, Ren J, Cao J, He J, Yao X, Jin C#, Xue Y#. (2013) Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. Brief Bioinform. 14(3):344-60. [Pubmed][PDF][Supplemental Data]

44. Wang Y, Dai Z, Cheng H, Liu Z, Pan Z, Deng W, Gao T, Li X, Yao Y, Ren J, Xue Y**. (2013) Towards a better understanding of the novel avian-origin H7N9 influenza A virus in China. Sci Rep. 2013;3:2318. [Pubmed][PDF][Supplemental Data]

43. Gao T, Liu Z, Wang Y, Cheng H, Yang Q, Guo A, Ren J, Xue Y**. (2013) UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. Nucleic Acids Res. 41(D1):D445-51. [Pubmed][PDF][Supplemental Data]

2012

42. Song C, Ye M, Liu Z, Cheng H, Jiang X, Han G, Songyang Z, Tan Y, Wang H, Ren J#, Xue Y#, Zou H#. (2012) Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Mol Cell Proteomics. 11(10):1070-83. [Pubmed][PDF][Supplemental Data]

41. Zhang Y, Xu B, Yang Y, Ban R, Zhang H, Jiang X, Cooke HJ, Xue Y#, Shi Q#. (2012) CPSS: a computational platform for the analysis of small RNA deep sequencing data. Bioinformatics. 2012, 28(14):1925-7. [Pubmed][PDF][Supplemental Data]

40. Liu Z, Yuan F, Ren J, Cao J, Zhou Y, Yang Q#, Xue Y#. (2012) GPS-ARM: computational analysis of the APC/C recognition motif by predicting D-boxes and KEN-boxes. PLoS One. 2012;7(3):e34370. [Pubmed][PDF][Supplemental Data]

39. Cai R, Liu Z, Ren J, Ma C, Gao T, Zhou Y, Yang Q#, Xue Y#. (2012) GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes. PLoS One. 2012;7(3):e33884. [Pubmed][PDF][Supplemental Data]

2011

38. Xue Y, Liu Z, Cao J, Jian Ren. (2011) Computational Prediction of Post-Translational Modification Sites in Proteins. Systems and Computational Biology - Molecular and Cellular Experimental Systems, InTech - Open Access Publisher, ISBN: 978-953-307-280-7. (Book Chapter 6) [PDF] (Has been viewed 1,967 and downloaded 1,149 times on Feb., 13, 2014; the 2nd of "Most downloaded chapters")
For whom are interested in the GPS algorithms

37. Liu Z, Ma Q, Cao J, Gao X, Ren J#, Xue Y#. (2011) GPS-PUP: computational prediction of pupylation sites in prokaryotic proteins. Mol Biosyst., 7(10):2737-40. [Pubmed][PDF][Supplemental Data]

36. Ren J, Gao X, Liu Z, Cao J, Ma Q, Xue Y**. (2011) Computational Analysis of Phosphoproteomics: Progresses and Perspectives. Current Protein and Peptide Science, 2011 Nov;12(7):591-601. [Pubmed] [PDF]

35. Liu Z, Cao J, Ma Q, Gao X, Ren J#, Xue Y#. (2011) GPS-YNO2: computational prediction of tyrosine nitration sites in proteins. Mol Biosyst., 7(4):1197-204. [Pubmed][PDF][Supplemental Data]
This paper was highlighted as "Top ten accessed articles in August" of Molecular BioSystems, and ranked as 7th.

34. Liu Z, Cao J, Gao X, Ma Q, Ren J#, Xue Y#. (2011) GPS-CCD: a novel computational program for the prediction of calpain cleavage sites. PLoS One., 6(4):e19001. [Pubmed][PDF][Supplemental Data]

33. Zhang Y, Yang Y, Zhang H, Jiang X, Xu B, Xue Y, Cao Y, Zhai Q, Zhai Y, Xu M, Cooke HJ, Shi Q. (2011) Prediction of novel pre-microRNAs with high accuracy through boosting and SVM. Bioinformatics, 27(10):1436-7.[Pubmed][PDF][Supplemental Data]

32. Xue Y#, Liu Z, Cao J, Ma Q, Gao X, Wang Q, Jin C, Zhou Y, Wen L, Ren J#. (2011) GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Eng Des Sel., 24(3):255-60. [Pubmed][PDF][Supplemental Data]

31. Liu Z, Cao J, Gao X, Zhou Y, Wen L, Yang X, Yao X, Ren J#, Xue Y#. (2011) CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Res., 39:D1029-34. [Pubmed][PDF][Supplemental Data]

2010

30. Xue Y#, Liu Z, Gao X, Jin C, Wen L, Yao X, Jian Ren#. (2010) GPS-SNO: Computational prediction of protein S-nitrosylation sites with a modified GPS algorithm. PLoS ONE, 5(6):e11290. [Pubmed][PDF][Supplemental Data]

29. Xue Y#, Gao X, Cao J, Liu Z, Jin C, Wen L, Yao X, Ren J#. (2010) A summary of computational resources for protein phosphorylation. Current Protein and Peptide Science, 11(6):485-96. (Review) [Pubmed][PDF]

28. Ren J, Jiang C, Gao X, Liu Z, Yuan Z, Jin C, Wen L, Zhang Z#, Xue Y#, Yao X#. (2010) PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. Molecular & Cellular Proteomics, 9:623-34. [Pubmed][PDF][Supplemental Data]

27. Ren J, Liu Z, Gao X, Jin C, Ye M, Zou H, Wen L, Zhang Z, Xue Y#, Yao X#. (2010) MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Research, 38:D155-160. [Pubmed][PDF]

2009

26. Han G, Ye M, Jiang X, Chen R, Ren J, Xue Y, Wang F, Song C, Yao X, Zou H. (2009) Comprehensive and reliable phosphorylation site mapping of individual phosphoproteins by combination of multiple stage mass spectrometric analysis with a target-decoy database search. Analytical Chemistry, 81:5794-805. [Pubmed][PDF][Supplemental Data]

25. Ren J, Gao X, Jin C, Zhu M, Wang X, Shaw A, Wen L, Yao X#, Xue Y#. (2009) Systematic study of protein sumoylation: development of a site-specific predictor of SUMOsp 2.0. Proteomics. 9:3409-3412. [Pubmed][PDF][Supplemental Data]

24. Ren J, Wen L, Gao X, Jin C, Xue Y#, Yao X#. (2009) DOG 1.0: Illustrator of Protein Domain Structures. Cell Research. 19:271-273. [Pubmed][PDF][Supplemental Data]

23. Xu Y#, Wang Z, Lei Y, Zhao Y, Xue Y#. (2009) MBA: a literature Mining system for extracting Biomedical abbreviations. BMC Bioinformatics. 10:14. [Pubmed][PDF]

2008

22. Zhao Y, Xu Y, Wang Z, Jin C, Gao X, Xue Y#, Yao X#. (2008) Proteome-Wide Analysis of Amino Acid Absence in Composition and Plasticity. ICIC 2008, LNCS 5226, 167-178. [PDF]

21. Xu Y#, Wang Z#, Zhao Y#, Xue Y#. (2008) A New Alignment Algorithm to Identify Definitions Corresponding to Abbreviations in Biomedical Text. WKDD 2008, 118-124. [PDF]

20. Gao X, Jin C, Ren J, Yao X, Xue Y**. (2008) Proteome-wide prediction of PKA phosphorylation sites in eukaryotic kingdom. Genomics. 92(6):457-63. [Pubmed][PDF][Supplemental Data]

19. Ren J, Wen L, Gao X, Jin C, Xue Y#, Yao X#. (2008) CSS-Palm 2.0: an updated software for palmitoylation sites prediction. Protein Eng Des Sel. 21(11):639-44. [Pubmed][PDF] (Included in "50 Most Frequently Cited Articles", ranked as 35th on Feb., 2014)

18. Xue Y*, Ren J*, Gao X, Jin C, Wen L, Yao X. (2008) GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics. 7(9):1598-608. [Pubmed][PDF][Supplemental Data]

17. Gao X, Jin C, Xue Y#, Yao X#. (2008) Computational analyses of TBC protein family in eukaryotes. Protein Pept Lett. 15:505-9. [Pubmed][PDF]

16. Yu J, Lan J, Zhu Y, Li X, Lai X, Xue Y, Jin C, Huang H. (2008) The E3 ubiquitin ligase HECTD3 regulates ubiquitination and degradation of Tara. Biochem Biophys Res Commun. 367(4):805-12. [Pubmed][PDF]

15. Cheng Z, Ke Y, Ding X, Wang F, Wang H, Ahmed K, Liu Z, Xu Y, Aikhionbare F, Yan H, Liu J, Xue Y, Powell M, Liang S, Reddy SE, Hu R, Huang H, Jin C, Yao X. (2008) Functional characterization of TIP60 sumoylation in UV-irradiated DNA damage response. Oncogene. 27(7):931-41. [Pubmed][PDF][Supplemental Data]

2007

14. Xue Y , Zhou F, Xu Y, Yao X. (2007) GPS: A computational protocol for kinase-specific phosphorylation site prediction. Nature Protocol, DOI: 10.1038/nprot.2007.219. (Invited) [Protocols Network] (Not peer reviewed)

13. Jin C, Cai X, Ma H, Xue Y, Yao J, Yao X. (2007) An efficient site-directed mutagenesis method for ColE1-type ori plasmid. Analytical Biochemistry, 363 (1), 151-153. [Pubmed][PDF]

2006

12. Xue Y*, Chen H*, Jin C, Sun Z, Yao X. (2006) NBA-Palm: prediction of palmitoylation site implemented in Naive Bayes algorithm. BMC Bioinformatics, 7, 458. [Pubmed][PDF]

11. Li A*, Xue Y*, Jin C, Wang M, Yao X. (2006) Prediction of Nε-acetylation on internal lysines implemented in Bayesian Discriminant Method. Biochem. Biophys. Res. Commun., 350(4), 818-824. [Pubmed][PDF]

10. Xue Y, Jin C, Yao X. (2006) HSPPIP: An Online tool for prediction of protein-protein interactions in humans. ICIC 2006, LNBI 4115, 603-611. [PDF]

9. Zhou F*, Xue Y*, Yao X, Xu Y. (2006) A general user interface for prediction servers of proteins' post-translational modification sites. Nature Protocols, 1(3), 1318-1321. [Pubmed][PDF]

8. Xue Y*, Liu D*, Fu C, Dou Z, Zhou Q, Tang X, Yao X. (2006) A novel genome-wide full-length kinesin prediction analysis reveals additional mammalian kinesins. Chinese Science Bulletin, 51(15), 1836- 1847. (PDF, Chinese version,790kb; English version, 959kb)

7. Chen H*, Xue Y*, Huang N, Yao X, Sun Z. (2006) MeMo: a web tool for prediction of protein methylation modifications. Nucleic. Acids Res., 34, W249-W253. [Pubmed][PDF][Supplemental Data]

6. Xue Y*, Zhou F*, Fu C, Xu Y, Yao X. (2006) SUMOsp: a web server for sumoylation site prediction. Nucleic. Acids Res., 34, W254-W257. [Pubmed][PDF][Supplemental Data]

5. Xue Y*, Li A*, Wang L, Feng H, Yao X. (2006) PPSP: Prediction of PK-Specific Phosphorylation Site with Bayesian Decision Theory. BMC Bioinformatics, 7, 163. [Pubmed][PDF][Supplemental Data]
This paper was highlighed as "Top 100 protein kinase publications" in 2006 by Ion Channel Media Group, and ranked as 89th. (Highly accessed)

4. Zhou F*, Xue Y*, Yao X, Xu Y. (2006) CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). Bioinformatics, 22, 894-896. [Pubmed][PDF][Supplemental Data]

2005

3. Xue Y*, Zhou F*, Zhu M, Ahmed K, Chen G, Yao X. (2005) GPS: a comprehensive www server for phosphorylation sites prediction. Nucleic. Acids Res., 33, W184-W187. [Pubmed][PDF]

2. Zhou F*, Xue Y*, Lu H, Chen G, Yao X. (2005) A genome-wide analysis of sumoylation-related biological processes and functions in human nucleus. FEBS Lett., 579, 3369-3375. [Pubmed][PDF]

2004

1. Zhou F*, Xue Y*, Chen G, Yao X. (2004) GPS: a novel group-based phosphorylation predicting and scoring method. Biochem. Biophys. Res. Commun., 325, 1443-1448. [Pubmed][PDF]

(*Co-first author, #Co-corresponding author, **Corresponding author)