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1

Date of origin of the SARS coronavirus strains

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

Journal:

BMC Infectious Diseases

Year:

2004

Language:

english

File:

PDF, 885 KB

english, 2004

2

Parameterized BLOSUM Matrices for Protein Alignment

Song, Dandan, Chen, Jiaxing, Chen, Guang, Li, Ning, Li, Jin, Fan, Jun, Bu, Dongbo, Li, Shuai Cheng

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.13 MB

english, 2015

3

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

Yantao Qiao, Hong Zhang, Dongbo Bu, Shiwei Sun

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 815 KB

english, 2011

4

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

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

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 507 KB

english, 2011

5

IncorporatingAb Initioenergy into threading approaches for protein structure prediction

Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Cheng Li, Weimou Zheng, Dongbo Bu

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.67 MB

english, 2011

6

Improving consensus contact prediction via server correlation reduction

Xin Gao, Dongbo Bu, Jinbo Xu, Ming Li

Journal:

BMC Structural Biology

Year:

2009

Language:

english

File:

PDF, 1.03 MB

english, 2009

7

Analysis of correlations between protein complex and protein-protein interaction and mRNA expression

Lun Cai, Hong Xue, Hongchao Lu, Yi Zhao, Xiaopeng Zhu, Dongbo Bu, Lunjiang Ling, Runsheng Chen

Journal:

Chinese Science Bulletin

Year:

2003

Language:

english

File:

PDF, 134 KB

english, 2003

8

Phylogeny of SARS-CoV as inferred from complete genome comparison

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

Journal:

Chinese Science Bulletin

Year:

2003

Language:

english

File:

PDF, 325 KB

english, 2003

9

Genome-wide analysis of mammalian DNA segment fusion/fission

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

Journal:

Journal of Theoretical Biology

Year:

2006

Language:

english

File:

PDF, 361 KB

english, 2006

10

Finding compact structural motifs

Dongbo Bu, Ming Li, Shuai Cheng Li, Jianbo Qian, Jinbo Xu

Journal:

Theoretical Computer Science

Year:

2009

Language:

english

File:

PDF, 447 KB

english, 2009

11

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

Yi Zhao, Shunmin He, Changning Liu, Songwei Ru, Haitao Zhao, Zhen Yang, Pengcheng Yang, Xiongyin Yuan, Shiwei Sun, Dongbo Bu, Jiefu Huang, Geir Skogerbø, Runsheng Chen

Journal:

Trends in Genetics

Year:

2008

Language:

english

File:

PDF, 582 KB

english, 2008

12

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

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

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 392 KB

english, 2006

13

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

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

Journal:

Year:

2006

Language:

english

File:

PDF, 201 KB

english, 2006

14

Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations

Shuai Cheng Li, Dongbo Bu, Ming Li

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.26 MB

english, 2012

15

Fragment-HMM: A new approach to protein structure prediction

Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li

Journal:

Protein Science

Year:

2008

Language:

english

File:

PDF, 320 KB

english, 2008

16

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?

Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi…

Journal:

Algorithms for Molecular Biology

Year:

2013

Language:

english

File:

PDF, 372 KB

english, 2013

17

Multilevel structural characteristics for the natural substrate proteins of bacterial small heat shock proteins

Fu, Xinmiao, Chang, Zengyi, Shi, Xiaodong, Bu, Dongbo, Wang, Chao

Journal:

Protein Science

Year:

2014

Language:

english

File:

PDF, 709 KB

english, 2014

18

Deriving the Probabilities of Water Loss and Ammonia Loss for Amino Acids from Tandem Mass Spectra

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

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 905 KB

english, 2008

19

MS-Simulator: Predicting Y -Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions

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

Journal:

Journal of Proteome Research

Year:

2012

Language:

english

File:

PDF, 1.27 MB

english, 2012

20

[IEEE 2011 IEEE/ACM International Conference on Green Computing and Communications (GreenCom) - Chengdu, China (2011.08.4-2011.08.5)] 2011 IEEE/ACM International Conference on Green Computing and Communications - PEARL: Probing Entity Aggregation in Real Life

Liu, Xingwu, Bai, Yunfei, Huang, Chunlin, Wang, Xiaoyan, Bu, Dongbo

Year:

2011

Language:

english

File:

PDF, 529 KB

english, 2011

21

[IEEE Eighth International Conference on High-Performance Computing in Asia-Pacific Region (HPCASIA'05) - Beijing, China (2005.07.1-2005.07.1)] Eighth International Conference on High-Performance Computing in Asia-Pacific Region (HPCASIA'05) - To accelerate multiple sequence alignment using FPGAs

Xu Lin,, Zhang Peiheng,, Bu Dongbo,, Feng Shengzhong,, Sun Ninghui,

Year:

2005

Language:

english

File:

PDF, 185 KB

english, 2005

22

[IEEE 11th International Conference on Parallel and Distributed Systems (ICPADS'05) - Fukuoka, Japan (20-22 July 2005)] 11th International Conference on Parallel and Distributed Systems (ICPADS'05) - An Optimized Algorithm of High Spatial-temporal Efficiency for MegaBlast

Guangming Tan,, Lin Xu,, Yishan Jiao,, Shengzhong Feng,, Dongbo Bu,, Ninghui Sun,

Year:

2005

Language:

english

File:

PDF, 203 KB

english, 2005

23

Finding Nearly Optimal GDT Scores

Li, Shuai Cheng, Bu, Dongbo, Xu, Jinbo, Li, Ming

Journal:

Journal of Computational Biology

Year:

2011

Language:

english

File:

PDF, 720 KB

english, 2011

24

[IEEE Proceedings 20th IEEE International Parallel & Distributed Processing Symposium - Rhodes Island, Greece (2006.04.25-2006.04.29)] Proceedings 20th IEEE International Parallel & Distributed Processing Symposium - Improving locality of nonserial polyadic dynamic programming

Guangming Tan,, Ninghui Sun,, Dongbo Bu,

Year:

2006

Language:

english

File:

PDF, 415 KB

english, 2006

25

Clustering 100,000 Protein Structure Decoys in Minutes

Shuai Cheng Li,, Dongbo Bu,, Ming Li,

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.93 MB

english, 2012

26

LEX-SVM: EXPLORING THE POTENTIAL OF EXON EXPRESSION PROFILING FOR DISEASE CLASSIFICATION

YUAN, XIONGYING, ZHAO, YI, LIU, CHANGNING, BU, DONGBO

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2011

Language:

english

File:

PDF, 802 KB

english, 2011

27

AN ITERATIVE ALGORITHM TO QUANTIFY FACTORS INFLUENCING PEPTIDE FRAGMENTATION DURING TANDEM MASS SPECTROMETRY

YU, CHUNGONG, LIN, YU, SUN, SHIWEI, CAI, JINJIN, ZHANG, JINGFEN, BU, DONGBO, ZHANG, ZHUO, CHEN, RUNSHENG

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2007

Language:

english

File:

PDF, 523 KB

english, 2007

28

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

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

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.47 MB

english, 2015

29

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

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

Journal:

Year:

2015

File:

PDF, 61 KB

2015

30

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

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

Journal:

Year:

2015

Language:

english

File:

PDF, 61 KB

english, 2015

31

Improving residue–residue contact prediction via low-rank and sparse decomposition of residue correlation matrix

Zhang, Haicang, Gao, Yujuan, Deng, Minghua, Wang, Chao, Zhu, Jianwei, Li, Shuai Cheng, Zheng, Wei-Mou, Bu, Dongbo

Journal:

Biochemical and Biophysical Research Communications

Year:

2016

Language:

english

File:

PDF, 1.29 MB

english, 2016

32

Condensing Raman spectrum for single-cell phenotype analysis

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

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 500 KB

english, 2015

33

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

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

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 853 KB

english, 2016

34

[IEEE 2017 Seventh International Conference on Information Science and Technology (ICIST) - Da Nang, Vietnam (2017.4.16-2017.4.19)] 2017 Seventh International Conference on Information Science and Technology (ICIST) - Modelling close-proximity contact networks among college students

Huang, Chunlin, Lu, Gongcheng, Bu, Dongbo

Year:

2017

Language:

english

File:

PDF, 273 KB

english, 2017

35

Improving Protein Fold Recognition by Extracting Fold-specific Features from Predicted Residue-residue Contacts

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

Journal:

Year:

2017

Language:

english

File:

PDF, 1.44 MB

english, 2017

36

Biological data processing based on bio-processor unit (BPU), a new concept for next generation computational biology

Liu, Di, Bu, Dongbo, Shi, Tieliu, Quan, Jianxiao, Wang, Depeng, Shi, Yongyong, Bo, Xiao-Chen, Han, Wenbao

Journal:

SCIENCE CHINA Life Sciences

Year:

2018

Language:

english

File:

PDF, 214 KB

english, 2018

37

Protein threading using residue co-variation and deep learning

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

Journal:

Year:

2018

Language:

english

File:

PDF, 1.04 MB

english, 2018

38

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

Sun, Shiwei, Huang, Chuncui, Wang, Yaojun, Liu, Yaming, Zhang, Jingwei, Zhou, Jinyu, Gao, Feng, Yang, Fei, Chen, Runsheng, Mulloy, Barbara, Chai, Wengang, Li, Yan, Bu, Dongbo

Journal:

Analytical Chemistry

Year:

2018

Language:

english

File:

PDF, 1.31 MB

english, 2018

39

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

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

Journal:

Year:

2019

File:

PDF, 459 KB

2019

40

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

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

Journal:

BMC Bioinformatics

Year:

2019

Language:

english

File:

PDF, 1.58 MB

english, 2019

41

Constrained maximum weighted bipartite matching: a novel approach to radio broadcast scheduling

Wang, Shaojiang, Wu, Tianyong, Yao, Yuan, Bu, Dongbo, Cai, Shaowei

Journal:

SCIENCE CHINA Information Sciences

Year:

2019

Language:

english

File:

PDF, 338 KB

english, 2019

42

DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning

Chen, Hao, Shaw, Dipan, Zeng, Jianyang, Bu, Dongbo, Jiang, Tao

Journal:

Year:

2019

Language:

english

File:

PDF, 3.51 MB

english, 2019

43

Predicting human contacts through alternating direction method of multipliers

Huang, Chunlin, Bu, Dongbo

Journal:

International Journal of Modern Physics C

Year:

2019

Language:

english

File:

PDF, 2.73 MB

english, 2019

44

Identification of glycan branching patterns using multistage mass spectrometry with spectra tree analysis

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

Journal:

Journal of Proteomics

Year:

2020

Language:

english

File:

PDF, 3.89 MB

english, 2020

45

Multistage mass spectrometry with intelligent precursor selection for N-glycan branching pattern analysis

Huang, Chuncui, Wang, Hui, Bu, Dongbo, Zhou, Jinyu, Dong, Junchuan, Zhang, Jingwei, Gao, Huanyu, Wang, Yaojun, Chai, Wengang, Sun, Shiwei, Li, Yan

Journal:

Carbohydrate Polymers

Year:

2020

Language:

english

File:

PDF, 2.95 MB

english, 2020

46

ISSEC: inferring contacts among protein secondary structure elements using deep object detection

Zhang, Qi, Zhu, Jianwei, Ju, Fusong, Kong, Lupeng, Sun, Shiwei, Zheng, Wei-Mou, Bu, Dongbo

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.86 MB

2020

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