Xiao Y, Zhang Y*. (2025) deep-Sep: a deep learning-based method for fast and accurate prediction of selenoprotein genes in bacteria. mSystems 10:e0125824.
Zhang Y*, Zhang Z, Li H, Xiao Y, Ying H. (2025) Recent advancements in the application of multi-elemental profiling and ionomics in cardiovascular diseases. J Trace Elem Med Biol 88:127616.
Huang B, Xiao Y, Zhang Y*. (2024) Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery. ISME J 18(1):wrae111.
Zhang Y*, Huang B, Jin J, Xiao Y and Ying H. (2023) Recent advances in the application of ionomics in metabolic diseases. Front Nutr 9:1111933.
Zhang Y*, Jin J, Huang B, Ying H, He J, Jiang L. (2022) Selenium metabolism and selenoproteins in prokaryotes: a bioinformatics perspective. Biomolecules (7):917.
Zhang Y*, He J, Jin J, Ren C. (2022) Recent advances in the application of metallomics in diagnosis and prognosis of human cancer. Metallomics (7):mfac037.
He Z, Zheng L, Zhao X, Li X, Xue H, Zhao Q, Ren B, Li N, Ni J, Zhang Y*, Liu Q*. (2022) An Adequate Supply of Bis(ethylmaltolato)oxidovanadium(IV) Remarkably Reversed the Pathological Hallmarks of Alzheimer's Disease in Triple-Transgenic Middle-Aged Mice. Biol Trace Elem Res. (7):3248-3264.
Xu Y, Cao J, Jiang L, Zhang Y*. (2021) Biogeographic and evolutionary patterns of trace element utilization in marine microbial world. Genomics Proteomics Bioinformatics 19:958-972.
Yao F, Yan C, Zhang Y, Shen L, Zhou D, Ni J. (2021) Identification of blood protein biomarkers for breast cancer staging by integrative transcriptome and proteome analyses. J Proteomics 230:103991.
Zhang Y*, Xu Y, Zheng L. (2020) Disease ionomics: understanding the role of ions in complex disease. J Mol Sci. 21(22):8646.
Jiang L*, Lu Y, Zheng L, Li G, Chen L, Zhang M, Ni J, Liu Q, Zhang Y*. (2020) The algal selenoproteomes. BMC Genomics 21(1):699.
Zhang Y*, Zheng J. (2020) Bioinformatics of metalloproteins and metalloproteomes. Molecules 25(15):3366.
Chen D, Li G, Ji C, Lu Q, Qi Y, Tang C, Xiong J, Hu J, Yasar FBA, Zhang Y*, Hoon DSB, Yao Y*, Zhou L. (2020) Enhanced B7-H4 expression in gliomas with low PD-L1 expression identifies super-cold tumors. J ImmunoTher Cancer 8(1):e000154.
Shen Z, Lin J, Teng J, Zhuang Y, Zhang H, Wang C, Zhang Y*, Ding X*, Zhang X*. (2020) Association of Urinary Ionomic Profiles and Acute Kidney Injury and Mortality in Patients after Cardiac Surgery. J Thorac Cardiovasc Surg. 159(3):918-926.
Ying H, Zhang Y*. (2019) Systems biology of selenium and complex disease. Biol Trace Elem Res. 192(1):38-50.
Zhang Y*, Ying H, Xu Y. (2019) Comparative genomics and metagenomics of the metallomes. Metallomics 11(6):1026-1043.
Li Q, Hu C, Lin J, Yang Z, Zhou Q, Yang R, Yuan H, Zhu X, Lv Y, Liang Q, Lv Z, Sun L, Zhang Y*. (2019) Urinary ionomic analysis reveals new relationship between minerals and longevity in a Han Chinese population. J Trace Elem Med Biol. 53:69-75.
Lin J, Wu YJ, Liang X, Ji M, Ying HM, Wang XY, Sun X, Shao CH, Zhan LX, Zhang Y*. (2019) Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer. Mol Carcinog. 58(2):206-218.
Yao F, Zhang K, Zhang Y, Guo Y, Li A, Xiao S, Liu Q, Shen L, Ni J. (2019) Identification of Blood Biomarkers for Alzheimer's Disease Through Computational Prediction and Experimental Validation. Front Neurol. 9:1158.
Li F, Liu CF, Xu YZ, Guo YL, Xue SW, Kong XD, Zhang HB, Zhang Y, Kang JS. (2019) Neonatal lethality and recycling defect of transferrin receptor in mice with Syntaxin12/13 disruption. Protein Cell 10(1):67-71.
Lin S, Liu Y, Goldin LR, Lyu C, Kong X, Zhang Y, Caporaso NE, Xiang S, Gao Y. (2019) Sex-related DNA methylation differences in B cell chronic lymphocytic leukemia. Biol Sex Differ. 10(1):2.
Peng T, Xu Y, Zhang Y*. (2018) Comparative genomics of molybdenum utilization in prokaryotes and eukaryotes. BMC Genomics 19(1):691.
Yao F, Hong X, Li S, Zhang Y, Zhao Q, Du W, Wang Y, Ni J. (2018) Urine-Based Biomarkers for Alzheimer's Disease Identified Through Coupling Computational and Experimental Methods. J Alzheimers Dis. 65(2):421-431.
Xie Y, Liu Q, Zheng L, Wang B, Qu X, Ni J, Zhang Y, Du X. (2018) Se-Methylselenocysteine Ameliorates Neuropathology and Cognitive Deficits by Attenuating Oxidative Stress and Metal Dyshomeostasis in Alzheimer Model Mice. Mol Nutr Food Res. 62(12):e1800107
Zhang F, Hu Z, Li G, Huo S, Ma F, Cui A, Xue Y, Han Y, Gong Q, Gao J, Bian H, Meng Z, Wu H, Long G, Tan Y, Zhang Y, Lin X, Gao X, Xu A, Li Y. (2018) Hepatic CREBZF couples insulin to lipogenesis by inhibiting insig activity and contributes to hepatic steatosis in diet-induced insulin-resistant mice. Hepatology 68(4):1361-1375.
Ying HM, Zhang Y*. (2018) Progress on ionomics of complex disease. Acta physiol Sin. 70(4):413-423.
Zhang Y*. (2017) Trace Elements and Healthcare: A Bioinformatics Perspective. Adv Exp Med Biol. 1005:63-98.
张茂娜, 姜亮*, 张焱*. (2017) 硒代谢网络与硒蛋白质组的生物信息学研究进展. 生物技术进展 7(5):537-544.
Zheng L, Zhu HZ, Wang BT, Zhao QH, Du XB, Zheng Y, Jiang L, Ni JZ, Zhang Y*, Liu Q*. (2016) Sodium selenate regulates the brain ionome in a transgenic mouse model of Alzheimer's disease. Sci Rep. 6:39290.
Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y. (2016) Selenoprotein Gene Nomenclature. J Biol Chem. 291(46):24036-24040.
Li GP, Liu L, Li P, Chen L, Song H, Zhang Y*. (2016) Gene expression profiling of selenophosphate synthetase 2 knockdown in Drosophila melanogaster. Metallomics 8(3):354-365.
Peng T, Lin J, Xu YZ, Zhang Y*. (2016) Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria. ISME J. 10(8):2048-2059.
Yang Z, Zhang Y*, Chen L*. (2015) Single amino acid changes in naked mole rat may reveal new anti-cancer mechanisms in mammals. Gene 572(1):101-107.
Lin J, Peng T, Jiang L, Ni JZ, Liu Q, Chen L, Zhang Y*. (2015) Comparative genomics reveals new candidate genes involved in selenium metabolism in prokaryotes. Genome Biol Evol. 7(3):664-676.
Li GP, Jiang L, Ni JZ, Liu Q, Zhang Y*. (2014) Computational identification of a new SelD-like family that may participate in sulfur metabolism in hyperthermophilic sulfur-reducing archaea. BMC Genomics 15:908.
Yu T, Tao Y, Yang M, Chen P, Gao X, Zhang Y, Zhang T, Chen Z, Hou J, Zhang Y, Ruan K, Wang H, Hu R. (2014) Profiling human protein degradome delineates cellular responses to proteasomal inhibition and reveals a feedback mechanism in regulating proteasome homeostasis. Cell Res. 24(10):1214-1230.
Sun L, Lin J, Du H, Hu C, Huang Z, Lv Z, Zheng C, Shi X, Zhang Y*, Yang Z*. (2014) Gender-specific DNA methylome analysis of a Han Chinese longevity population. Biomed Res Int. 2014:396727.
Malinouski M, Hasan NM, Zhang Y, Seravalli J, Lin J, Avanesov A, Lutsenko S, Gladyshev VN. (2014) Genome-wide RNAi ionomics screen reveals new genes and regulation of human trace element metabolism. Nat Commun. 5:3301
Zhao HW, Lin J, Wang XB, Cheng X, Wang JY, Hu BL, Zhang Y*, Zhang X*, Zhu JH*. (2013) Assessing plasma levels of selenium, copper, iron and zinc in patients of Parkinson's disease. PLoS One 8(12):e83060.
Jiang L, Zhu HZ, Xu YZ, Ni JZ, Zhang Y*, Liu Q*. (2013) Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes. PeerJ 1:e202.
Gobler CJ, Lobanov AV, Tang YZ, Turanov AA, Zhang Y, Doblin M, Taylor GT, Sañudo-Wilhelmy SA, Grigoriev IV, Gladyshev VN. (2013) The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens. ISME J. 7(7):1333-1343.
Li G, Zhang Y*. (2013) Progress in bioinformatics studies on essential metals. Prog Chem. 25(4):446-456.
Yu Y, Wu A, Zhang Z, Yan G, Zhang F, Hu R, Zhang Y*, Zhang K*, Wang F*. (2013) Characterization of the GufA Subfamily Member SLC39A11/Zip11 as a Zinc Transporter. J Nutr Biochem. 24(10):1697-1708.
Yang XL, Li QR, Ning ZB, Zhang Y*, Zeng R*, Wu JR*. (2013) Identification of complex relationship among protein kinases and substrates during the cell cycle of HeLa cells by phosphoproteomic analysis. Proteomics 13(8):1233-1246.
Wen Z, Liu ZP, Liu Z, Zhang Y, Chen L. (2013) An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. J Am Med Inform Assoc. 20(4):659-667.
Liang X, Kaya A, Zhang Y, Le DT, Hua D, Gladyshev VN. (2012) Characterization of methionine oxidation and methionine sulfoxide reduction using methionine-rich cysteine-free proteins. BMC Biochem. 13:21.
Liu K, Chen K, Zhang Y*. (2012) Comparative genomics of trace element-dependent proteomes. Chinese Bulletin of Life Sciences 24(8):948-965.
Zhang Y*, Lin J, Gao Y. (2012) In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria. BMC Syst Biol. 6 Suppl 1:S20.
Mariotti M#, Ridge PG#, Zhang Y#, Lobanov AV, Pringle TH, Guigo R, Hatfield DL, Gladyshev VN. (2012) Composition and evolution of the vertebrate and mammalian selenoproteomes. PLoS One 7(3):e33066. (#: co-first authors)
Shchedrina VA, Everley RA, Zhang Y, Gygi SP, Hatfield DL, Gladyshev VN. (2011) Selenoprotein K binds multiprotein complexes and is involved in the regulation of endoplasmic reticulum homeostasis. J Biol Chem. 286(50):42937-42948.
Yim SH, Kim YJ, Oh SY, Fujii J, Zhang Y, Gladyshev VN, Rhee SG. (2011) Identification and characterization of alternatively transcribed form of peroxiredoxin IV gene that Is specifically expressed in spermatids of postpubertal mouse testis. J Biol Chem. 286(45):39002-39012.
Zhang Y, Rump S, Gladyshev VN. (2011) Comparative genomics and evolution of molybdenum utilization. Coord Chem Rev. 255(9-10):1206-1217.
Zhang Y, Gladyshev VN. (2011) Comparative genomics of trace element dependence in biology. J Biol Chem. 286(27):23623-23629.
Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL, Wurch LL, Kustka AB, et al. (2011) Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc Natl Acad Sci USA. 108(11):4352-4357.
Zhang Y, Gladyshev VN. (2010) dbTEU: a protein database of trace element utilization. Bioinformatics 26(5):700-702.
Zhang Y, Gladyshev VN. (2010) General trends in trace element utilization revealed by comparative genomic analyses of Co, Cu, Mo, Ni, and Se. J Biol Chem. 285(5):3393-3405.
Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV. (2010) Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res. 38(Database issue):D69-74.
Shchedrina VA, Zhang Y, Labunskyy VM, Hatfield DL, Gladyshev VN. (2010) Structure-function relations, physiological roles, and evolution of mammalian ER-resident selenoproteins. Antioxid Redox Signal. 12(7):839-849.
Zhang Y, Gladyshev VN. (2009) Comparative genomics of trace elements: emerging dynamic view of trace element utilization and function. Chem Rev. 109(10):4828-4861.
Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN. (2009) Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics 10:78.
Le DT, Lee BC, Marino SM, Zhang Y, Fomenko DE, Kaya A, Hacioglu E, Kwak GH, Koc A, Kim HY, Gladyshev VN. (2009) Functional analysis of free methionine-R-sulfoxide reductase from Saccharomyces cerevisiae. J Biol Chem. 284(7):4354-4364.
Hirosawa-Takamori M, Ossipov D, Novoselov SV, Turanov AA, Zhang Y, Gladyshev VN, Krol A, Vorbrüggen G, Jäckle H. (2009) A novel stem loop control element-dependent UGA read-through system without translational selenocysteine incorporation in Drosophila. FASEB J. 23(1):107-113.
Kim HY, Zhang Y, Lee BC, Kim JR, Gladyshev VN. (2009) The selenoproteome of Clostridium sp. OhILAs: characterization of anaerobic bacterial selenoprotein methionine sulfoxide reductase A. Proteins 74(4):1008-1017.
Zhang Y, Gladyshev VN. (2008) Trends in selenium utilization in marine microbial world revealed through the analysis of the global ocean sampling (GOS) project. PLoS Genet. 4(6):e1000095.
Papp LV, Wang J, Kennedy D, Boucher D, Zhang Y, Gladyshev VN, Singh RN, Khanna KK. Functional characterization of alternatively spliced human SECISBP2 transcript variants. (2008) Nucleic Acids Res. 36(22):7192-7206.
Zhang Y, Turanov AA, Hatfield DL, Gladyshev VN. (2008) In silico identification of genes involved in selenium metabolism: evidence for a third selenium utilization trait. BMC Genomics 9:251.
Zhang Y, Gladyshev VN. (2008) Molybdoproteomes and evolution of molybdenum utilization. J Mol Biol. 379(4):881-899.
Ridge PG, Zhang Y, Gladyshev VN. (2008) Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen. PLoS One 3(1):e1378.
Glass RS, Berry MJ, Block E, Boakye HT, Carlson BA, Gailer J, George GN, Gladyshev VN, Hatfield DL, Jacobsen NE, Johnson S, Kahakachchi C, Kamiński R, Manley SA, Mix H, Pickering IJ, Prenner EJ, Saira K, Skowrońska A, Tyson JF, Uden PC, Wu Q, Xu XM, Yamdagni R, Zhang Y. (2008) Insights into the Chemical Biology of Selenium. Phosphorus Sulfur Silicon Relat Elem 183:924–930.
Zhang Y, Zhou Y, Schweizer U, Savaskan NE, Hua D, Kipnis J, Hatfield DL, Gladyshev VN. (2008) Comparative analysis of selenocysteine machinery and selenoproteome gene expression in mouse brain identifies neurons as key functional sites of selenium in mammals. J Biol Chem. 283(4):2427-2438.
Zhang Y, Gladyshev VN. (2007) High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis. Nucleic Acids Res. 35(15):4952-4963.
Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL. (2007) Biosynthesis of selenocysteine on its tRNA in eukaryotes. PLoS Biol. 5(1):e4.
Lobanov AV, Fomenko DE, Zhang Y, Sengupta A, Hatfield DL, Gladyshev VN. (2007) Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol. 8(9):R198.
Xu XM, Carlson BA, Zhang Y, Mix H, Kryukov GV, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL. (2007) New developments in selenium biochemistry: selenocysteine biosynthesis in eukaryotes and archaea. Biol Trace Elem Res. 119(3):234-241.
Zhang Y, Romero H, Salinas G, Gladyshev VN. (2006) Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues. Genome Biol. 7(10):R94.
Zhang Y, Baranov PV, Atkins JF, Gladyshev VN. (2005) Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies. J Biol Chem. 280(21):20740-20751.
Zhang Y, Fomenko DE, Gladyshev VN. (2005) The microbial selenoproteome of the Sargasso Sea. Genome Biol. 6(4):R37.
Zhang Y, Gladyshev VN. (2005) An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes. Bioinformatics 21(11):2580-2589.
Romero H, Zhang Y, Gladyshev VN, Salinas G. (2005) Evolution of selenium utilization traits. Genome Biol. 6(8):R66.
International Human Genome Sequencing Consortium (included in the author list). (2004) Finishing the euchromatic sequence of the human genome. Nature 431(7011):931-945.
Zhang Y, Ma F, Yan M, Zhu L, Zhang Z. (2002) Three dimensional structure prediction of a human differentiational antigen 5C5 protein. Basic and Clinical Medicine 22:92-96.
Zhang Y, Mei P, Lou R, Zhang MQ, Wu G, Qiang B, Zhang Z, Shen Y. (2002) Gene expression profiling in developing human hippocampus. J Neurosci Res. 70(2):200-208.
Pan H, Wang YP, Bao XH, Meng HD, Zhang Y, Wu XR, Shen Y. (2002) MECP2 gene mutation analysis in Chinese patients with Rett syndrome. Eur J Hum Genet. 10(8):484-486.
Ding K, Sun X, Zhou M, Cai J, Cai T, Zhang Y, Zhu T, Zhang Z, Qiang B, Shen Y. (2002) Identification of novel protein-coding genes from human fetal hippocampus ESTs database. Neurosci Res Commun. 31:93-99.
Pan H, Wang YP, Meng HD, Bao XH, Zhang Y, Shen Y, Wu XR. (2002) Mutational analysis of MECP2 gene in Rett syndrome. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 19:276-280.
Zhang Y, Zhang Z. (2001) A new network-based biologic database system. Stud Health Technol Inform. 84:988-991.
Lin L, Xu Q, Zhang Y, Yin B, Fan Y, Luo Y, Han S, Zhang Z, Wu G, Shen Y. (2000) Alternative Splicing of de novo Methyltransferase Gene 3b in Adult and Newborn Mice. Zhongguo Yi Xue Ke Xue Yuan Xue Bao 22:312-316.