Publications
研究成果

Zhang G *, Zhang Y, Jin J *
The Ultrafast and Accurate Mapping Algorithm FANSe3: Mapping a Human Whole-Genome Sequencing Dataset Within 30 min
Phenomics (2021) 1, 22–30 .

Ou J, Zhou Z, Dai R, Zhang J, Zhao S, Wu X, Lan W, Ren Y, Cui L, Lan Q, Lu L, Seto D, Chodosh J, Wu J, Zhang G *, Zhang Q *
V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity
Journal of Virology (2021) 95(16):e0061721.

Man Zhang, Jing Zhao, Wanying Li, Shuqi Wen, Huiling Huang, Jie Dong, Bing Liu, Gong Zhang, Hong-Bin Wang, Yanting Shen *, Hong-Lei Jin *
Increased photosystem II translation efficiency as an important photoprotective mechanism in an Arabidopsis thaliana ecotype (Tibet-0) adapted to high light environments
Environmental and Experimental Botany (2021) 183:104350.

Yixi Li, Dehua Li, Yang Chen, Yongping Lu, Fangbin Zhou, Chunhong Li, Zhipeng Zeng, Wanxia Cai, Liewen Lin, Qiang Li, Mingjun Ye, Jingjing Dong, Lianghong Yin *, Donge Tang *, Gong Zhang *, Yong Dai *
Robust Glycogene-Based Prognostic Signature for Proficient Mismatch Repair Colorectal Adenocarcinoma
Frontiers in Oncology (2021) 11:727752.

Xin Cao, Zhong Guo, Hualong Wang, Yuelei Dong, Songhui Lu, Qing-Yu He*, Xuesong Sun*, Gong Zhang*
Autoactivation of Translation Causes the Bloom of Prorocentrum donghaiense in Harmful Algal Blooms
J. Proteome Res. (2021) 20, 6, 3179–3187.

Zhou Z #, Yang Z #, Ou J #, Zhang H, Zhang Q *, Dong M *, Zhang G *
Temperature Dependence of the SARS-CoV-2 affinity to human ACE2 determines COVID-19 progression and clinical outcome
Computational and Structural Biotechnology Journal (2020) 19:161-167.

Lin H #, Zhang G #, Zhang XC #, Lian X, Su J, Chen SL, Wu YL *
Germline Variation Networks in the PI3K/AKT Pathway Corresponding to Familial High-incidence Lung Cancer Pedigrees
BMC Cancer (2020) 9;20(1):1209.

Li D *, Liu B, Zheng H, Xiao X, Li Z, Luan E, Li W, Wang Y, Yang Y, Long Q, Song J, Zhang G *
XY-Meta: A high-efficiency search engine for large scale metabolome annotation with accurate FDR estimation
Analytical Chemistry (2020) 92:8, 5701-5707.

Lu S, Wang T, Zhang G, He QY *
Understanding the proteome encoded by “non-coding RNAs”: New insights into human genome
Science China Life Sciences (2020) 1-10.

Lu S, Zhang J, Lian XL, Sun L, Meng K, Chen Y, Sun Z, Yin X, Li Y, Zhao J, Wang T *, Zhang G *, He QY *
A Hidden Human Proteome Encoded by “Non-Coding” Genes
Nucleic Acids Research (2019) 47 (15), 8111-8125.

Mai Z, Liu W, Ding W, Zhang G *
Misassembly of long reads undermines de novo assembled ethnicity-specific genomes: Validation in a Chinese Han Population
Human Genetics (2019) https://doi.org/10.1007/s00439-019-02032-6.

Zhao J, Zhang H, Qin B, Nikolay R, He QY, Spahn CMT *, Zhang G *
Multifaceted stoichiometry control of bacterial operons revealed by data-independent acquisition mass spectrometry
Frontiers in Genetics (2019) 10:473.

Shi T, Wei Q, Wang Z, Zhang G *, Sun X *, He QY *
Photocatalytic protein damage by silver nanoparticles circumvents bacterial stress response and multidrug resistance
mSphere (2019) 4(3), e00175-19.

Sun Y, Cai M, Zhong J, Jin F, Xiao J, Yang L, Wang Y, Zhang Q, Wang Z *, Zhang G *, Wang X *
A long noncoding RNA lnc-ob1 facilitates bone formation by upregulating Osterix in osteoblasts
Nature Metabolism (2019) 1, 485–496 (2019).

Gao L, Hu Y, et al.
Lung Cancer Deficient in the Tumor Suppressor GATA4 are Sensitive To TGFBR1 Inhibition
Nature Communications (2019) 10:1665.

Liao X, Zhao J, Liang S, Jin J, Li C, Xiao R, Li L, Guo M, Zhang G *, Lin Y *.
Enhancing co-translational folding of heterologous protein by deleting non-essential ribosomal proteins in Pichia pastoris
Biotechnology and Biofuels (2019) 12:38.

Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G *.
Translatomics: The Global View of Translation
International Journal of Molecular Sciences (2019) 20(1), 212.

完整获取植物组织中核糖体新生肽链复合物的方法与应用
国家发明专利（已授权），201510332732.5，发明人：赵晶、张弓

Zhang M, Zhao K, Xu X, Yang Y, Yan S, Wei P, Liu H, Xu J, Xiao F, Yang X, Huang N, Zhou H, Liu J, He K, Xie K, Zhang G, Huang S, Zhang N *.
A Peptide Encoded by Circular Form of LINC-PINT Suppresses Oncogenic Transcriptional Elongation in Glioblastoma
Nature Communications (2018) 9, 4475.

Li D, Lu S, Liu W, Zhao X, Mai Z, Zhang G *.
Optimal settings of mass spectrometry open search strategy for higher confidence
Journal of Proteome Research (2018) 17(11), 3719-3729.

Wu Q, Tian Y, et al.
In vivo CRISPR screening unveils histone demethylase UTX as an important epigenetic regulator in lung tumorigenesis.
PNAS (2018) 115 (17), E3978-E3986.

Cao K, Wang H, Li N, Cao X, He J, Zhang B, He QY *, Zhang G *, Sun X *.
Two zinc-binding domains in the transporter AdcA from Streptococcus pyogenes facilitate high-affinity binding and fast transport of zinc.
Journal of Biological Chemistry (2018) 293 (16), 6075-6089.

Bao X, Guo X, et al.
Capturing the Interactome of Newly Transcribed RNA.
Nature Methods (2018) 15, 213-220.

Huang W, Liu W, Jin J, Xiao Q, Lu R, Chen W, Xiong S *, Zhang G *.
Steady-state structural fluctuation is a predictor of the necessity of pausing-mediated co-translational folding for small proteins.
Biochem Biophys Res Commun (2018) 498(1), 186-192.

Liu W, Xiang L, Zheng T, Jin J, Zhang G *.
TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.
Nucleic Acids Research (2018) 46(D1), D206-212.

Zhao P, Zhong J, Liu W, Zhao J, Zhang G *.
Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage.
Journal of Proteome Research (2017) 16(12), 4446–4454.

完整获取组织内核糖体新生肽链复合物的方法
国家发明专利（已授权），201410452522.5，发明人：孙黎、张弓、王通、金静洁

曹欣，张弓 *
超高精度大规模测序mapping算法FANSe在非模式生物中的应用 【综述】
中国科学·生命科学 (2017), 47. doi: 10.1360/N052016-00280
Cao X, Zhang G *.
Application of the hyper-accurate mapping algorithm FANSe for next-generation sequencing in non-model organisms
Sci Sin Vitae, 2017, 47, doi: 10.1360/N052016-00280

曹欣，刘婉婷，张弓 *
非模式细菌功能基因组获取策略比较
基因组学与应用生物学 (2017), 36(7): 1-8.

Wang C, Chen K, Liao S, Gu W, Lian X, Zhang J, Gao X, Liu X, Wang T, He QY *, Zhang G *, Liu L *.
The flightless I protein interacts with RNA-binding proteins and is involved in the genome-wide mRNA post-transcriptional regulation in lung carcinoma cells.
International Journal of Oncology (2017) doi: 10.3892/ijo.2017.3995.

Mai Z, Xiao C, Jin J, Zhang G *.
Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing.
Scientific Reports (2017) 7:1053.

赵晶，张弓 *
翻译组学：方法及应用 【综述】
生命的化学 (2017), 37(1): 70-79. doi: 10.13488/j.smhx.20170111

Jia HL, Liu CW, Zhang L, Xu WJ, Gao XJ, Bai J, Xu YF, Xu M *, Zhang G *.
Sets of serum exosomal microRNAs as candidate diagnostic biomarkers for Kawasaki disease.
Scientific Reports (2017) 7:44706.

Chen Z, Yang L, Cui Y, Zhou Y, Yin X, Guo J, Zhang G *, Wang T *, He QY *.
Cytoskeleton-centric protein transportation by exosomes transforms tumor-favorable macrophages.
Oncotarget (2016) doi: 10.18632/oncotarget.11794.

Guo J, Cui Y, Yan Z, Luo Y, Zhang W, Deng S, Tang S, Zhang G, He QY *, Wang T *.
Phosphoproteome Characterization of Human Colorectal Cancer SW620 Cell-Derived Exosomes and New Phosphosite Discovery for C-HPP.
Journal of Proteome Research (2016) doi: 10.1021/acs.jproteome.6b00391

完整冷冻保存及解冻细胞内核糖体新生肽链复合物的方法
国家发明专利（已授权），201410387213.4，发明人：孙黎、张弓、王通、金静洁

Lian X, Guo J, Gu W, Cui Y, Zhong J, Jin J, He QY *, Wang T *, Zhang G *.
Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells.
PLoS Genetics (2016) 12(2): e1005901.

Bartholomäus A, Fedyunin I, Feist P, Sin C, Zhang G, Valleriani A, Ignatova Z *.
Bacteria differently regulate mRNA abundance to specifically respond to various stresses.
Phil. Trans. R. Soc. A (2016) 374:20150069.

Yang XY, He K, Du G, Wu X, Yu G, Pan Y, Zhang G *, Sun X *, He QY *.
Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae.
Front. Microbiol. (2016) 7:78.

Fan X, Xiong H, Wei J, Gao X, Feng Y, Liu X, Zhang G, He QY * Xu J *, Liu L *.
Cytoplasmic hnRNPK interacts with GSK3β and is essential for the osteoclast differentiation .
Scientific Reports (2015) 5:17732.

Luo B, Gu W, Zhong J, Wang Y *, Zhang G *.
Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis.
Scientific Reports (2015) 5:15407.

Yang L, Lian X, Zhang W, Guo J, Wang Q, Li Y, Chen Y, Yin X, Yang P, Lan F *, He QY *, Zhang G *, Wang T *.
Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria.
Journal of Proteome Research (2015) 14(9):3645-57

Chen Y, Li Y, Zhong J, Zhang J, Chen Z, Yang L, Cao X, He QY *, Zhang G *, Wang T *.
Identification of missing proteins defined by chromosome-centric proteome project in the cytoplasmic detergent-insoluble proteins.
Journal of Proteome Research (2015) 14(9):3693-709

Zhong J, Xiao C, Gu W, Du G, Sun X, He QY *, Zhang G *.
Transfer RNAs Mediate the Rapid Adaptation of Escherichia coli to Oxidative Stress.
PLoS Genetics (2015) 11(6):e1005302

通过翻译暂停序列理性重设计改善蛋白质可溶性表达的方法
国家发明专利（已授权），201310164454.8，发明人：张弓、陈伟、熊盛、金静洁

Guo J, Lian X, Zhong J, Wang T *, Zhang G *.
Length-dependent translation initiation benefits the functional proteome of human cells.
Molecular BioSystems (2015) 11, 370-378

表达量高和活性强的CVN突变体的编码序列及其应用
国家发明专利（已授权），201310164451.4，发明人：陈伟、张弓、熊盛、金静洁

Chen W, Jin J, Gu W, Wei B, Lei Y, Xiong S *, Zhang G *.
Rational design of translational pausing without altering the amino acid sequence dramatically promotes soluble protein expression: A strategic demonstration.
Journal of Biotechnology (2014), 189(10), 104-113

Puri P, Wetzel C, Saffert P, Gaston KW, Russell SP, Varela JA, van der Vlies P, Zhang G, Limbach PA, Ignatova Z, Poolman B *,
Systematic identification of tRNAome and its dynamics in Lactococcus lactis.
Molecular Microbiology (2014), 93(5), 944-956

Chen M, Liu T, Xu L, Gao X, Liu X, Wang C, He Q, Zhang G, Liu L *,
Direct Interaction of 14-3-3ζ with Ezrin Promotes Cell Migration by Regulating the Formation of Membrane Ruffle.
Journal of Molecular Biology (2014), 426(18), 3118-3133

X Wu, L Xu, W Gu, Q Xu, QY He *, X Sun *, G Zhang *
Iterative Genome Correction Largely Improves Proteomic Analysis of Nonmodel Organisms.
Journal of proteome research (2014), 13 (6), 2724–2734

CL Xiao, ZB Mai, XL Lian, JY Zhong, JJ Jin, QY He *, G Zhang *,
FANSe2: A Robust and Cost-Efficient Alignment Tool for Quantitative Next-Generation Sequencing Applications,
PLoS One (2014), 9(4):e94250

L Zhang, HL Jia, et al.,
Monitoring of the serum proteome in Kawasaki disease patients before and after immunoglobulin therapy,
Biochemical and Biophysical Research Communications (2014), 447(1), 19-25

G Zhang *, T Wang *, QY He *,
How to discover new proteins—translatome profiling, （中文版: 怎样发现未知蛋白质——翻译组测序）
Science China Life Sciences (2014) 57 (3), 358-360

C Chang, L Li, et al.,
Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP,
Journal of proteome research (2014) 13 (1), 38-49

Q Wang, B Wen, et al.,
Omics Evidence: Single Nucleotide Variants Transmissions on Chromosome 20 in Liver Cancer Cell Lines,
Journal of proteome research (2014) 13 (1), 200-211

Y Liu, W Ying, et al,
Chromosome-8-Coded Proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with Partial Immunohistochemical Verifications,
Journal of proteome research (2014) 13 (1), 126-136

C Zhang, N Li, et al.,
Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1,
Journal of proteome research (2014) 13 (1), 114-125

J Zhong, Y Cui, J Guo, Z Chen, L Yang, QY He, G Zhang *, T Wang *,
Resolving Chromosome-Centric Human Proteome with Translating mRNA Analysis: A Strategic Demonstration,
Journal of proteome research (2014) 13 (1), 50-59

CL Xiao, XZ Chen, YL Du, ZF Li, L Wei, G Zhang *, QY He *,
Dispec: A Novel Peptide Scoring Algorithm Based on Peptide Matching Discriminability,
PLoS One (2013) 8 (5), e62724

Wang T *, Cui Y, Jin J, Guo J, Wang G, Yin X, He QY *, Zhang G * ,
Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific.
Nucleic Acids Res. (2013) 41(9):4743-54

Xiao CL, Chen XZ, Du YL, Sun X, Zhang G*, He QY.*
Binomial Probability Distribution Model-Based Protein Identification Algorithm for Tandem Mass Spectrometry Utilizing Peak Intensity Information.
J. Proteome Res. (2013) 12 (1), 328–335

Fedyunin I, Lehnhardt L, Böhmer N, Kaufmann P, Zhang G, Ignatova Z*,
tRNA concentration fine tunes protein solubility.
FEBS Lett. (2012)

Zhang, G.*, Fedyunin, I., Kirchner, S., Xiao, C., Valleriani, A. & Ignatova, Z.*,
FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.
Nucleic Acid Res. (2012) 40(11):e83.

Hinz J., Lehnhardt L., Zakrzewski S., Zhang G., Ignatova Z.*,
Polyglutamine expansion alters the dynamics and molecular architecture of aggregates in dentatorubropallidoluysian atrophy,
J Biol Chem. (2012) 13;287(3):2068-78.

Valleriani, A.*, Zhang, G., Nagar, A., Ignatova, Z.,
Length dependent translation of messenger RNA by ribosomes,
Physical Review E, 83(4 Pt 1):042903 (2011)

Borwankar, T., Rötlein, C., Zhang, G., Techen, A., Dosche, C. & Ignatova, Z.*,
Natural osmolytes remodel the aggregation pathway of mutant Huntingtin exon 1.
Biochem. 29;50(12):2048-60 (2011).

Zhang, G., Lukoszek, R., Mueller-Roeber, B., Ignatova, Z.*,
Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.
Nucleic Acid Res. (2011) 39(8):3331-9

Zhang, G. & Ignatova, Z.*,
Folding at the birth of the nascent chain: Coordinating translation with co-translational folding.
Current Opinion of Structural Biology, (2011) 21:25-31.

Czech, A., Fedyunin, I., Zhang, G. & Ignatova, Z.*,
Silent mutations in sight: Co-variations in tRNA abundance as key to unravel consequences of silent mutations.
Molecular Biosystems. 2010 Oct 1;6(10):1767-72

Zhang, G., Fedyunin, I., Miekley, O., Valleriani, A., Moura A. & Ignatova, Z.*,
Global and local depletion of ternary complex limits translational elongation.
Nucleic Acid Res, (2010) 38(14):4778-87

Zhang, G., & Ignatova, Z.*,
A generic algorithm to predict the speed of translational elongation: implications for protein biogenesis.
PLoS One, 4(4):e5036 (2009).

Zhang, G., & Ignatova, Z.*,
Isolation of homogenous ribosome-nascent-chain complexes from coupled cell-free transcription-translation system.
Nature Protocols doi:10.1038/nprot.2009.47 (2009).

Zhang, G., Hubalewska, M., & Ignatova, Z.*,
Transient ribosomal attenuation coordinates protein synthesis and co-translational folding.
Nat Struct Mol Biol, 16(3):274-80 (2009).