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发表文章一览

2011及以前201220132014201520162017

2017

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.

2016

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.
研究意义简述(专业媒体报道)

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.

2015

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.
研究意义简述(云南日报报道)

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
研究意义简述(专业媒体报道)

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
研究意义简述(专业媒体报道)

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
当期封面文章

2014

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
研究意义简述

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
研究意义简述

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
研究意义简述

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
研究意义简述

2013

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
研究意义简述  专业媒体报道

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

2012

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.

2011年及以前

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).
当期封面文章  研究意义简述