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For publication of results please cite the following articles:

DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning..
Yubin Xie, Xiaotong Luo, Yupeng Li, Li Chen, Wenbin Ma, Junjiu Huang,Yong Zhao, Yu Xue,Zhixiang Zuo,and Jian Ren. Genomics, Proteomics & Bioinformatics .2018; 16(4): 294-306.

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1.         Bachi A, et al. Chemical Reviews.2013;113(1):596-698.[PMID: 23181411]

2.         Hu J, et al. Molecular Cell.2017;67(4):702-710.[PMID: 28757206]

3.         Nakamura T, et al. Neuron.2013;78(4):596-614.[PMID: 23719160]

4.         Faccenda A, et al. Journal of the American Chemical Society.2010;132(33):11392-11394.[PMID: 20677743]

5.         Cao Y, et al. Journal of Clinical Investigation.2015;125(4):1679-1691.[PMID: 25798618]

6.         Feng J, et al. Nature Communications.2013;4.[PMID: 23443557]

7.         Wang Y, et al. Nucleic Acids Research.2014;42(D1):D496-D502.[PMID: 24214991]

8.         Zhao Q, et al. Nucleic Acids Research.2014;42(W1):W325-W330.[PMID: 24880689]

9.         Seth D, et al. Current Opinion in Chemical Biology.2011;15(1):129-136.[PMID: 21087893]

10.         Smith BC, et al. Current Opinion in Chemical Biology.2012;16(5-6):498-506.[PMID: 23127359]

11.       Gao X-H, et al. Elife.2015;4.[PMID: 26595448]

12.       Yu M, et al. Current Opinion in Plant Biology.2012;15(4):424-430.[PMID: 22464350]

13.       Kovacs I, et al. New Phytologist.2015;208(3):860-872.[PMID: 26096525]

14.       Yu M, et al. New Phytologist.2014;202(4):1142-1156.[PMID: 24611485]

15.       Doctor A, et al. Comprehensive Physiology.2011;1(1):541-568.[PMID: 23737185]

16.       Saito A, et al. Cerebral Cortex.2017;27(8):3918-3929.[PMID: 27371763]

17.       Song C, et al. Molecular & Cellular Proteomics.2012;11(10):1070-1083.[PMID: 22798277]

18.       Yang H, et al. Plant Physiology.2015;167(4):1604-U1753.[PMID: 25667317]

19.       Evangelista AM, et al. Antioxidants & Redox Signaling.2013;19(11):1209-1219.[PMID: 23157187]

20.       Morisse S, et al. Antioxidants & Redox Signaling.2014;21(9):1271-1284.[PMID: 24328795]

21.       Salanova M, et al. Redox Biology.2013;1(1):514-526.[PMID: 24251120]

22.       Zhao Q-F, et al. Molecular Neurobiology.2015;51(1):268-280.

23.       Zhao F, et al. Plant Cell and Environment.2016;39(1):147-164.[PMID: 26177592]

24.       Gutierrez DA, et al. Cardiovascular Research.2013;100(3):392-401.[PMID: 23963842]

25.       Hichri I, et al. Journal of Experimental Botany.2015;66(10):2877-2887.[PMID: 25732535]

26.       Ortega-Galisteo AP, et al. Journal of Experimental Botany.2012;63(5):2089-2103.[PMID: 22213812]

27.       Sanz-Luque E, et al. Journal of Experimental Botany.2013;64(11):3373-3383.[PMID: 23918969]

28.       Murphy E, et al. Journal of Molecular and Cellular Cardiology.2012;52(3):568-577.[PMID: 21907718]

29.       Deng W, et al. Briefings in Bioinformatics.2017;18(4):647-658.[PMID: 27241573]

30.       Reaves DK, et al. Molecular Cancer Research.2017;15(2):165-178.[PMID: 27856957]

31.       Tamplenizza M, et al. Journal of Nanobiotechnology.2013;11.[PMID: 24119372]

32.       Gong B, et al. Plant and Cell Physiology.2015;56(4):790-802.[PMID: 25634962]

33.       Yun B-W, et al. Biochimica Et Biophysica Acta-General Subjects.2012;1820(6):770-776.[PMID: 21723374]

34.       Boscari A, et al. Frontiers in Plant Science.2013;4.[PMID: 24130563]

35.       Kovacs I, et al. Frontiers in Plant Science.2013;4.[PMID: 23717319]

36.       Salmi ML, et al. Frontiers in Plant Science.2013;4.[PMID: 24298275]

37.       Sehrawat A, et al. Journal of Proteome Research.2014;13(5):2599-2619.[PMID: 24684139]

38.       Trost B, et al. Journal of Proteome Research.2016;15(8):2760-2767.[PMID: 27367363]

39.       Pan Z, et al. Scientific Reports.2014;4.[PMID: 25476580]

40.       Xu Y, et al. Scientific Reports.2015;5.[PMID: 26084794]

41.       Castella C, et al. Nitric Oxide-Biology and Chemistry.2017;68:125-136.[PMID: 28193486]

42.       Jose Jimenez-Quesada M, et al. Nitric Oxide-Biology and Chemistry.2017;68:23-37.[PMID: 28645873]

43.       Uehara T, et al. Nitric Oxide-Biology and Chemistry.2011;25(2):108-111.[PMID: 21111056]

44.       Qian J, et al. Frontiers in Physiology.2013;4.[PMID: 24379783]

45.       Liu Z, et al. Journal of Biological Chemistry.2015;290(31):19011-19017.[PMID: 26070564]

46.       Lamotte O, et al. Frontiers in Chemistry.2015;2.[PMID: 25750911]

47.       Begara-Morales JC, et al. Bmc Plant Biology.2013;13.[PMID: 23586608]

48.       Ulrich C, et al. Molecular Pharmacology.2012;81(2):143-153.[PMID: 22027755]

49.       Camejo D, et al. Journal of Proteomics.2013;79:87-99.[PMID: 23238061]

50.       Li B-Q, et al. Journal of Proteomics.2012;75(5):1654-1665.[PMID: 22178444]

51.       Lopez-Sanchez LM, et al. Expert Review of Proteomics.2012;9(1):59-69.[PMID: 22292824]

52.       Sun M-a, et al. Bmc Genomics.2017;18.[PMID: 28376774]

53.       Yao Y, et al. Bmc Genomics.2014;15.[PMID: 24507755]

54.       Kolodziejczyk-Czepas J, et al. International Journal of Biological Macromolecules.2015;81:212-219.[PMID: 26234576]

55.       Ponczek MB. International Journal of Biological Macromolecules.2016;91:589-597.[PMID: 27268383]

56.       Davies HA, et al. Biophysical Journal.2015;109(11):2363-2370.[PMID: 26636947]

57.       Siddiqui NN, et al. Tumor Biology.2016;37(8):10487-10497.[PMID: 26850594]

58.       Abunimer A, et al. Genes.2014;5(2):254-269.[PMID: 24705329]

59.       Tu M, et al. Toxicology.2012;299(1):60-68.[PMID: 22627297]

60.       Stoyanovsky DA, et al. Organic & Biomolecular Chemistry.2013;11(27):4433-4437.[PMID: 23743503]

61.       Chand V, et al. Open Biology.2016;6(9).[PMID: 27605378]

62.       Ng JY, et al. Open Biology.2013;3.[PMID: 23389939]

63.       Sharma P, et al. Open Biology.2014;4(2).[PMID: 24522884]

64.       Astier J, et al. Plant Science.2011;181(5):527-533.[PMID: 21893248]

65.       Chaki M, et al. Plant Science.2015;238:115-126.[PMID: 26259180]

66.       Gong B, et al. Physiologia Plantarum.2017;160(4):396-409.[PMID: 28464254]

67.       Li J, et al. Database-the Journal of Biological Databases and Curation.2014.[PMID: 24705204]

68.       Zahid S, et al. Neuroscience.2014;256:126-136.[PMID: 24157928]

69.       Tian M, et al. International Journal of Molecular Sciences.2015;16(2):4209-4225.[PMID: 25690035]

70.       Zhang J, et al. International Journal of Molecular Sciences.2014;15(7):11204-11219.[PMID: 24968264]

71.       Jarmula A, et al. Journal of Computer-Aided Molecular Design.2013;27(1):45-66.[PMID: 23239172]

72.       Guerra D, et al. Biochemistry.2016;55(17):2452-2464.[PMID: 27064847]

73.       Miles S, et al. Infection Genetics and Evolution.2017;54:338-346.[PMID: 28728879]

74.       Ju Y, et al. Molecules.2017;22(8).[PMID: 28800080]

75.       Cai R, et al. Plos One.2012;7(3).[PMID: 22479466]

76.       Chaki M, et al. Plos One.2014;9(10).[PMID: 25333472]

77.       Karle AC, et al. Plos One.2012;7(2).[PMID: 22348091]

78.       Lee T-Y, et al. Plos One.2011;6(7).[PMID: 21789187]

79.       Liu Z, et al. Plos One.2012;7(3).[PMID: 22479614]

80.       Vanzo E, et al. Plos One.2014;9(9).[PMID: 25192423]

81.       Xu Y, et al. Plos One.2013;8(2).[PMID: 23409062]

82.       Xu Y, et al. Plos One.2014;9(8).[PMID: 25121969]

83.       Zhao X, et al. Plos One.2012;7(10).[PMID: 23110047]

84.       Cheng S, et al. Molecular Biosystems.2013;9(11):2860-2868.[PMID: 24056708]

85.       Cheng S, et al. Molecular Biosystems.2014;10(10):2597-2606.[PMID: 25030274]

86.       Jones LH, et al. Molecular Biosystems.2014;10(5):952-969.[PMID: 24623162]

87.       Liu Z, et al. Molecular Biosystems.2011;7(4):1197-1204.[PMID: 21258675]

88.       Liu Z, et al. Molecular Biosystems.2011;7(10):2737-2740.[PMID: 21850344]

89.       Liu Z, et al. Biochimica Et Biophysica Acta-Proteins and Proteomics.2014;1844(1):171-180.[PMID: 23499845]

90.       Miglio G, et al. Biochimica Et Biophysica Acta-Proteins and Proteomics.2016;1864(2):211-218.[PMID: 26589354]

91.       Kolbert Z. Plant Physiology and Biochemistry.2016;101:149-161.[PMID: 26895428]

92.       Kolbert Z, et al. Plant Physiology and Biochemistry.2017;113:56-63.[PMID: 28187345]

93.       Mohabatkar H, et al. Current Topics in Medicinal Chemistry.2017;17(21):2381-2392.[PMID: 28356000]

94.       Xu Y, et al. Current Topics in Medicinal Chemistry.2016;16(6):591-603.[PMID: 26286211]

95.       Biojone C, et al. Cns & Neurological Disorders-Drug Targets.2015;14(8):979-987.[PMID: 26350341]

96.       Huang G, et al. Biomed Research International.2014.[PMID: 25184139]

97.       Fares A, et al. Biochemical and Biophysical Research Communications.2011;416(3-4):331-336.[PMID: 22115780]

98.       Livaja M, et al. Molecular Breeding.2016;36(2).

99.       Livaja M, et al. Molecular Breeding.2016;36(2):1-19.

100.       Xu Y, et al. Gene.2017;602:1-7.[PMID: 27845204]

101.     Yu B, et al. Chemometrics and Intelligent Laboratory Systems.2017;167:102-112.

102.     Gasier HG, et al. Neuroscience Letters.2017;653:283-287.[PMID: 28579483]

103.     Wang B, et al. Peerj.2017;5.[PMID: 28462053]

104.     Xu Y, et al. Peerj.2013;1.[PMID: 24109555]

105.     Xu Y, et al. Journal of Theoretical Biology.2015;379:10-15.[PMID: 25913879]

106.     Zhao X, et al. Journal of Theoretical Biology.2015;374:60-65.[PMID: 25843215]

107.     Slowinska M, et al. Theriogenology.2015;84(3):425-436.[PMID: 25930730]

108.     Prokop JW, et al. Journal of Molecular Modeling.2017;23(3).[PMID: 28204942]

109.     Huang G, et al. Mini-Reviews in Organic Chemistry.2015;12(6):468-480.

110.     Li Y-X, et al. Protein and Peptide Letters.2011;18(6):573-587.[PMID: 21271979]

111.     Wasti AZ, et al. Current Proteomics.2017;14(1):53-57.

112.     Hichri I, et al. In Wendehenne.2016;77:193-218.

113.     Jose Jimenez-Quesada M, et al. Bioinformatics and Biomedical Engineering.2015;9043:450-459.

114.     Liu Z, et al. Hereditas(Beijing).2015;37(7):621-634.[PMID: 26351162]

115.     Wang D, et al. Plant Physiology Journal.2014;50(8):1079-1088.

116.     Wen L-S, et al. 2015 International Conference on Intelligent Transportation, Big Data and Smart City (Icitbs).2016:805-808.