arXiv preprint arXiv:1906.11196

2019

Ju, Fusong; Zhu, Jianwei; Wei, Guozheng; Zhang, Qi; Sun, Shiwei; Bu, Dongbo; 

Seq-SetNet: Exploring Sequence Sets for Inferring Structures

Carbohydrate Polymers

2019

Huang, Chuncui; Sun, Shiwei; Yan, Jingyu; Wang, Hui; Zhou, Jinyu; Gao, Huanyu; Xie, Wenchun; Li, Yan; Chai, Wengang; 

Identification of carbohydrate peripheral epitopes important for recognition by positive-ion MALDI multistage mass spectrometry

115528

BMC bioinformatics

2019

Wang, Chao; Wei, Yi; Zhang, Haicang; Kong, Lupeng; Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo; 

Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling

20

3

135

Computational biology and chemistry

2019

Ju, Fusong; Zhang, Jingwei; Bu, Dongbo; Li, Yan; Zhou, Jinyu; Wang, Hui; Wang, Yaojun; Huang, Chuncui; Sun, Shiwei; 

De novo glycan structural identification from mass spectra using tree merging strategy

80

217-224

Bioinformatics

2019

Wang, Yaojun; Bu, Dongbo; Huang, Chuncui; Wang, Hui; Zhou, Jinyu; Dong, Junchuan; Pan, Weiyi; Zhang, Jingwei; Zhang, Qi; Li, Yan; Shiwei Sun;

Best-first search guided multistage mass spectrometry-based glycan identification

BMC bioinformatics

2019

Zhang, Haicang; Zhang, Qi; Ju, Fusong; Zhu, Jianwei; Gao, Yujuan; Xie, Ziwei; Deng, Minghua; Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo; 

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning

20

1

537

Molecular Cellular&Proteomics

2019

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods

Analytical chemistry

2018

Sun, Shiwei; Huang, Chuncui; Wang, Yaojun; Liu, Yaming; Zhang, Jingwei; Zhou, Jinyu; Gao, Feng; Yang, Fei; Chen, Runsheng; Mulloy, Barbara; 

Toward automated identification of glycan branching patterns using multistage mass spectrometry with intelligent precursor selection

90

24

14412-14422

Current Bioinformatics

2018

Wang, Yaojun; Zhang, Jingwei; Bu, Dongbo; Sun, Shiwei; 

TagDict: Prediction of Theoretical Spectra of Peptides Based on A Tag Dictionary

13

5

444-449

2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2018

Hao, Yu; Han, Renmin; Wan, Xiaohua; Zhang, Fa; Sun, Shiwei; 

Fiducial marker detection via deep learning approach for electron tomography

642-645

Bioinformatics

2018

Zhu, Jianwei; Wang, Sheng; Bu, Dongbo; Xu, Jinbo; 

Protein threading using residue co-variation and deep learning

34

13

i263-i273

Bioinformatics

2017

Zhu, Jianwei; Zhang, Haicang; Li, Shuai Cheng; Wang, Chao; Kong, Lupeng; Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo; 

Improving protein fold recognition by extracting fold-specific features from predicted residue–residue contacts

33

23

3749-3757

BMC bioinformatics

2017

Zhang, Haicang; Zhu, Jianwei; Wang, Chao; Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo; 

Improving prediction of burial state of residues by exploiting correlation among residues

18

3

70

Progress in Biochemistry and Biophysics

2017

王耀君; 黄纯翠; 高枫; 张敬玮; 李岩; 卜东波; 孙世伟; 

串联质谱寡糖结构解析方法评介

44

10

830-847

第三届全国质谱分析学术报告会摘要集

2017

黄纯翠; 孙世伟; 王耀君; 刘亚名; 张敬玮; 周巾煜; 高枫; 杨飞; 陈润生; 柴文刚; 

基于多级质谱技术高通量鉴定糖链分支结构

Scientific reports

2016

Huang, Chunlin; Liu, Xingwu; Sun, Shiwei; Li, Shuai Cheng; Deng, Minghua; He, Guangxue; Zhang, Haicang; Wang, Chao; Zhou, Yang; Zhao, Yanlin; 

Insights into the transmission of respiratory infectious diseases through empirical human contact networks

6

31484

Bioinformatics

2015

Wang, Chao; Zhang, Haicang; Zheng, Wei-Mou; Xu, Dong; Zhu, Jianwei; Wang, Bing; Ning, Kang; Sun, Shiwei; Li, Shuai Cheng; Bu, Dongbo; 

FALCON@ home: a high-throughput protein structure prediction server based on remote homologue recognition

32

3

462-464

BMC bioinformatics

2015

Sun, Shiwei; Wang, Xuetao; Gao, Xin; Ren, Lihui; Su, Xiaoquan; Bu, Dongbo; Ning, Kang; 

Condensing Raman spectrum for single-cell phenotype analysis

16

18

S15

BMC bioinformatics

2015

Wang, Yaojun; Yang, Fei; Wu, Peng; Bu, Dongbo; Sun, Shiwei; 

OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction

16

1

110

arXiv preprint arXiv:1507.03197

2015

Zhu, Jianwei; Zhang, Haicang; Wang, Chao; Ling, Bin; Zheng, Wei-Mou; Bu, Dongbo; 

Topo: Improving remote homologue recognition via identifying common protein structure framework

arXiv preprint arXiv:1509.03434

2015

Zhang, Haicang; Shao, Mingfu; Wang, Chao; Zhu, Jianwei; Zheng, Wei-Mou; Bu, Dongbo; 

Improving protein threading accuracy via combining local and global potential using treecrf model

Journal of proteome research

2012

Sun, Shiwei; Yang, Fuquan; Yang, Qing; Zhang, Hong; Wang, Yaojun; Bu, Dongbo; Ma, Bin; 

MS-simulator: predicting y-ion intensities for peptides with two charges based on the intensity ratio of neighboring ions

11

9

4509-4516

计算机工程

2012

王耀君; 孙世伟; 卜东波; 刘金刚; 

串联质谱谱库搜索鉴定技术综述

2012 年 07

269-272

BMC bioinformatics

2011

Qiao, Yantao; Zhang, Hong; Bu, Dongbo; Sun, Shiwei; 

PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum

12

1

234

BMC bioinformatics

2011

Zhang, Shenghui; Wang, Yaojun; Bu, Dongbo; Zhang, Hong; Sun, Shiwei; 

ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity

12

1

346

计算机科学与探索

2010

乔彦涛; 缪佳铮; 孙世伟; 刘金刚; 卜东波; 

串联质谱的蛋白质序列鉴定技术综述

4

2

97-107

Annual International Conference on Research in Computational Molecular Biology

2008

Lin, Yu; Qiao, Yantao; Sun, Shiwei; Yu, Chungong; Dong, Gongjin; Bu, Dongbo; 

A fragmentation event model for peptide identification by mass spectrometry

154-166

Trends in Genetics

2008

Zhao, Yi; He, Shunmin; Liu, Changning; Ru, Songwei; Zhao, Haitao; Yang, Zhen; Yang, Pengcheng; Yuan, Xiongyin; Sun, Shiwei; Bu, Dongbo; 

MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control

24

7

323-327

Research in Computational Molecular Biology: 12th Annual International Conference, RECOMB 2008, Singapore, March 30-April 2, 2008, Proceedings

2008

Bu, Dongbo; 

A Fragmentation Event Model for Peptide Identification by Mass Spectrometry

4955

154

Journal of bioinformatics and computational biology

2007

Yu, Chungong; Lin, Yu; Sun, Shiwei; Cai, Jinjin; Zhang, Jingfen; Bu, Dongbo; Zhang, Zhuo; Chen, Runsheng; 

An iterative algorithm to quantify factors influencing peptide fragmentation during tandem mass spectrometry

5

02a

297-311

Journal of proteome research

2007

Sun, Shiwei; Yu, Chungong; Qiao, Yantao; Lin, Yu; Dong, Gongjin; Liu, Changning; Zhang, Jingfen; Zhang, Zhuo; Cai, Jinjin; Zhang, Hong; 

Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra

7

1

202-208

FEBS letters

2006

Sun, Shiwei; Zhao, Yi; Jiao, Yishan; Yin, Yifei; Cai, Lun; Zhang, Yong; Lu, Hongchao; Chen, Runsheng; Bu, Dongbo; 

Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm

580

7

1891-1896

BMC bioinformatics

2006

Zhang, Yong; Li, Shaojuan; Skogerbø, Geir; Zhang, Zhihua; Zhu, Xiaopeng; Zhang, Zefeng; Sun, Shiwei; Lu, Hongchao; Shi, Baochen; Chen, Runsheng; 

Phylophenetic properties of metabolic pathway topologies as revealed by global analysis

7

1

252

Journal of theoretical biology

2006

Zhang, Zhihua; Sun, Hong; Zhang, Yong; Zhao, Yi; Shi, Baochen; Sun, Shiwei; Lu, Hongchao; Bu, Dongbo; Ling, Lunjiang; Chen, Runsheng; 

Genome-wide analysis of mammalian DNA segment fusion/fission

240

2

200-208

Computational Systems Bioinformatics: CSB2006 Conference Proceedings, Stanford CA, 14-18 August 2006

2006

Yir, Chungong; Lhv, Yu; Sun, Shiwei; Cai, Jinjin; Zhang, Jingfen; Zhang, Zhuo; Chen, Runsheng; Bu, Dongbo; 

AN ITERATIVE ALGORITHM TO QUANTIFY THE FACTORS INFLUENCING PEPTIDE FRAGMENTATION FOR MS/MS SPECTRUM

4

353

Genome research

2006

Deng, Wei; Zhu, Xiaopeng; Skogerbø, Geir; Zhao, Yi; Fu, Zhuo; Wang, Yudong; He, Housheng; Cai, Lun; Sun, Hong; Liu, Changning; 

Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression

16

1

20-29

Computational Systems Bioinformatics

2006

Yu, Chungong; Lin, Yu; Sun, Shiwei; Cai, Jinjin; Zhang, Jingfen; Zhang, Zhuo; Chen, Runsheng; Bu, Dongbo; 

An iterative algorithm to quantify the factors influencing peptide fragmentation for MS/MS spectrum

353-360

BMC bioinformatics

2006

Zhang, Zhuo; Sun, Shiwei; Zhu, Xiaopeng; Chang, Suhua; Liu, Xiaofei; Yu, Chungong; Bu, Dongbo; Chen, Runsheng; 

A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data

7

1

222

Biochemical and biophysical research communications

2006

Zhang, Yong; Sun, Shiwei; Wu, Tao; Wang, Jie; Liu, Changning; Chen, Lan; Zhu, Xiaopeng; Zhao, Yi; Zhang, Zhihua; Shi, Baochen; 

Identifying Hfq-binding small RNA targets in Escherichia coli

343

3

950-955

BMC Infectious Diseases

2004

Lu, Hongchao; Zhao, Yi; Zhang, Jingfen; Wang, Yuelan; Li, Wei; Zhu, Xiaopeng; Sun, Shiwei; Xu, Jingyi; Ling, Lunjiang; Cai, Lun; 

Date of origin of the SARS coronavirus strains

4

1

3

Nucleic acids research

2004

Lu, Hongchao; Zhu, Xiaopeng; Liu, Haifeng; Skogerbø, Geir; Zhang, Jingfen; Zhang, Yong; Cai, Lun; Zhao, Yi; Sun, Shiwei; Xu, Jingyi; 

The interactome as a tree—an attempt to visualize the protein–protein interaction network in yeast

32

16

4804-4811

Nucleic acids research

2003

Bu, Dongbo; Zhao, Yi; Cai, Lun; Xue, Hong; Zhu, Xiaopeng; Lu, Hongchao; Zhang, Jingfen; Sun, Shiwei; Ling, Lunjiang; Zhang, Nan; 

Topological structure analysis of the protein–protein interaction network in budding yeast

31

9

2443-2450

Chinese Science Bulletin

2003

Qi, Zhen; Hu, Yu; Li, Wei; Chen, Yanjun; Zhang, Zhihua; Sun, Shiwei; Lu, Hongchao; Zhang, Jingfen; Bu, Dongbo; Ling, Lunjiang; 

Phylogeny of SARS-CoV as inferred from complete genome comparison

48

12

1175-1178

高等学校化学学报

2001

唐祥海; 温新; 孙世伟; 蒋海燕; 陈铁红; 

高钛含量钛硅中孔材料的合成及理化性质研究

z1

200-203

燃料化学学报

2001

唐祥海; 孙世伟; 蒋海燕; 陈铁红; 王敬中; 

高钛含量钛硅 mcmr41 中孔结构材料的合成及表征

29

52

Sun, Shiwei; Yu, Chungong; Zhang, Jingfen; Lin, Yu; Zhang, Zhuo; Cai, Jinjin; Bu, Dongbo; 

An EM Method to Learn the Probability of Neutral Losses from Ions during Low-energy CID

Zhao, Yi; He, Shunmin; Liu, Changning; Ru, Songwei; Zhao, Haitao; Yang, Zhen; Yang, Pengcheng; Yuan, Xiongyin; Sun, Shiwei; Bu, Dongbo; 

Online Supplementary material MicroRNA regulation of messenger-like non-coding RNAs––a network of mutual microRNA control