D. Bu

发表

Topological structure analysis of the protein-protein interaction network in budding yeast.

D. Bu, Yi Zhao, Lun Cai, 2003, Nucleic acids research.

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

Baoyan Bai, D. Bu, Yi Zhao, 2005, Genome research.

the protein–protein interaction network

D. Bu, Yi Zhao, Lun Cai, 2004 .

The Genomes of Oryza sativa: A History of Duplications

Dawei Li, Huanming Yang, Jun Wang, 2005, PLoS biology.

Phylogeny of SARS-CoV as inferred from complete genome comparison

Dongbo Bu, Shiwei Sun, Runsheng Chen, 2003, Chinese science bulletin = Kexue tongbao.

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

Dongbo Bu, Shiwei Sun, Qing Yang, 2012, Journal of proteome research.

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

Changning Liu, Dongbo Bu, Shiwei Sun, 2008, Journal of proteome research.

ProALIGN: Directly learning alignments for protein structure prediction via exploiting context-specific alignment motifs

Jinbo Xu, D. Bu, Shiwei Sun, 2020, bioRxiv.

Toward Automated Identification of Glycan Branching Patterns Using Multistage Mass Spectrometry with Intelligent Precursor Selection.

D. Bu, Shiwei Sun, Runsheng Chen, 2018, Analytical chemistry.

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

Chao Wang, Dongbo Bu, Mingfu Shao, 2015 .

Microrna Regulation of Messenger-like Noncoding Rnas: a Network of Mutual Microrna Control

Haitao Zhao, Changning Liu, Dongbo Bu, 2022 .

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

Shuai Cheng Li, Dongbo Bu, Minghua Deng, 2016, Biochemical and biophysical research communications.

A Fragmentation Event Model for Peptide Identification by Mass Spectrometry

Yu Lin, Dongbo Bu, Shiwei Sun, 2008, RECOMB.

BMC Infectious Diseases BioMed Central Research article Date of origin of the SARS coronavirus strains

Dongbo Bu, Shiwei Sun, Runsheng Chen, 2004 .

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

Baoyan Bai, D. Bu, Yi Zhao, 2006 .

Genome-wide analysis of mammalian DNA segment fusion/fission.

D. Bu, Yi Zhao, Hongchao Lu, 2006, Journal of theoretical biology.

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

Shuai Cheng Li, Dongbo Bu, Yang Zhou, 2016, Scientific Reports.

Bi-clustering interpretation and prediction of correlation between gene expression and protein abundance

D. Bu, Xinqi Gong, Xiaoquan Su, 2018, bioRxiv.

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

D. Bu, Shiwei Sun, Yaojun Wang, 2020, Journal of proteomics.

Resilience of human gut microbial communities for the long stay with multiple dietary shifts

Shuai Cheng Li, Kang Ning, Dongbo Bu, 2018, Gut.

A Local-stem-search Algorithm to Predict The RNA Secondary Structure*: A Local-stem-search Algorithm to Predict The RNA Secondary Structure*

Xiang Chen, Wen Gao, Fa Zhang, 2009 .

Optimizing weights of protein energy function to improve ab initio protein structure prediction

Chao Ching Wang, D. Bu, Weinan Zheng, 2013, 1312.6960.

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

D. Bu, Yi Zhao, Lun Cai, 2003 .

Consensus Approaches to Protein Structure Prediction

Shuai Cheng Li, Ming Li, Jinbo Xu, 2008 .

Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials

D. Bu, Fusong Ju, Tiansu Gong, 2022, bioRxiv.

BIOINFORMATICS Designing succinct structural alphabets

Jinbo Xu, D. Cheriton, D. Bu, 2008 .

The Genomes of Oryza sativa

Huanming Yang, Jun Wang, Wei-Mou Zheng, 2005 .

Parameterized BLOSUM Matrices for Protein Alignment

Shuai Cheng Li, Jun Fan, Jin Li, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

NONCODE: an integrated knowledge database of non-coding RNAs

Yi Zhao, Changning Liu, Wei Deng, 2004, Nucleic Acids Res..

Microbiome Resilience and Health Implications for People in Half-Year Travel

Jing Wu, D. Bu, Shiwei Sun, 2022, Frontiers in Immunology.

Comparison of transcription regulatory interactions inferred from high-throughput methods : what do they reveal ?

D. Bu, Yi Zhao, Shiwei Sun, 2008 .

FALCON2: a web server for high-quality prediction of protein tertiary structures

Dongbo Bu, Shiwei Sun, Fusong Ju, 2021, BMC Bioinformatics.

Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

Dongbo Bu, Shiwei Sun, Fusong Ju, 2021, BMC Bioinform..

TREC-10 Experiments at CAS-ICT: Filtering, Web and QA

Yue Liu, Hongbo Xu, Xueqi Cheng, 2001, TREC.

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

Hong Zhang, Dongbo Bu, Shenghui Zhang, 2011, BMC Bioinformatics.

Lex-SVM: Exploring the Potential of exon Expression Profiling for Disease Classification

Yi Zhao, Changning Liu, Dongbo Bu, 2011, J. Bioinform. Comput. Biol..

HepParser: An Intelligent Software Program for Deciphering Low-Molecular-Weight Heparin Based on Mass Spectrometry

D. Bu, Shiwei Sun, Yaojun Wang, 2021, Frontiers in Chemistry.

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

Shuai Cheng Li, Babak Alipanahi, Ming Li, 2013, Algorithms for Molecular Biology.

Improving consensus contact prediction via server correlation reduction

Jinbo Xu, Dongbo Bu, Ming Li, 2009, BMC Structural Biology.

Designing succinct structural alphabets

Shuai Cheng Li, Xin Gao, Ming Li, 2008, ISMB.

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

D. Bu, Xiaodong Shi, Xinmiao Fu, 2014, Protein science : a publication of the Protein Society.

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

Fei Yang, Peng Wu, Dongbo Bu, 2015, BMC Bioinformatics.

Fragment‐HMM: A new approach to protein structure prediction

Shuai Cheng Li, Ming Li, Dongbo Bu, 2008, Protein science : a publication of the Protein Society.

GIPS-Mix for Accurate Identification of Isomeric Components in Glycan Mixtures Using Intelligent Group-Opting Strategy

D. Bu, Shiwei Sun, Y. Zheng, 2022, Analytical chemistry.

The effect of N-glycosylation of SARS-CoV-2 spike protein on the virus interaction with the host cell ACE2 receptor

D. Bu, Shiwei Sun, Chuncui Huang, 2021, iScience.

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

Dongbo Bu, Jianyang Zeng, Hao Chen, 2019, Bioinform..

FragQA: predicting local fragment quality of a sequence-structure alignment.

Shuai Cheng Li, Ming Li, Dongbo Bu, 2007, Genome informatics. International Conference on Genome Informatics.

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

Suhua Chang, Zhuo Zhang, Dongbo Bu, 2006, BMC Bioinformatics.

Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment

Lin Xu, Shengzhong Feng, Dongbo Bu, 2006, Journal of Computer Science and Technology.

Protein threading using residue co-variation and deep learning

Sheng Wang, Jinbo Xu, Dongbo Bu, 2018, Bioinform..

PEARL: Probing Entity Aggregation in Real Life

Chunlin Huang, Xiaoyan Wang, Xingwu Liu, 2011, 2011 IEEE/ACM International Conference on Green Computing and Communications.

FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks

D. Bu, Tao Jiang, D. Shaw, 2021, NAR genomics and bioinformatics.

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space

Zhiyong Wang, Xiang Chen, Wen Gao, 2008, Bioinform..

Mut-Detecter: An EGFR activating mutation type classification method with a deep convolutional neural network

Yu Wang, Xingce Wang, Dongbo Bu, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Accurate and efficient protein sequence design through learning concise local environment of residues

D. Bu, Shiwei Sun, Weinan Zheng, 2022, bioRxiv.

Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms

D. Bu, Weinan Zheng, Haicang Zhang, 2023, Genomics, proteomics & bioinformatics.

SASA-Net: A spatial-aware self-attention mechanism for building protein 3D structure directly from inter-residue distances

D. Bu, Shiwei Sun, Fusong Ju, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction

Tie-Yan Liu, Dongbo Bu, Jianwei Zhu, 2020, Nature Communications.

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

Yan Li, Dongbo Bu, Jingwei Zhang, 2020, Carbohydrate polymers.

Predicting human contacts through alternating direction method of multipliers

Chunlin Huang, Dongbo Bu, D. Bu, 2019, International Journal of Modern Physics C.

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

D. Bu, Shiwei Sun, Weinan Zheng, 2017, BMC Bioinformatics.

Date of origin of the SARS coronavirus strains

Wei Li, D. Bu, Yi Zhao, 2004 .

Improving consensus contact prediction via server correlation reduction

Ming Li, Jinbo Xu, D. Bu, 2009, BMC Structural Biology.

An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry

CHUNGONG YU, YU LIN, SHIWEI SUN, 2007, J. Bioinform. Comput. Biol..

Seq-SetNet: Exploring Sequence Sets for Inferring Structures pdf

Dongbo Bu, Qi Zhang, Jianwei Zhu, 2019, ArXiv.

Clustering 100,000 Protein Structure Decoys in Minutes

Shuai Cheng Li, Ming Li, Dongbo Bu, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast.

D. Bu, Yi Zhao, Lun Cai, 2004 .

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

D. Bu, Yi Zhao, Shiwei Sun, 2008 .

Towards Reliable Automatic Protein Structure Alignment

Shuai Cheng Li, Ming Li, Xuefeng Cui, 2013, WABI.

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

Chao Wang, Shuai Cheng Li, Dongbo Bu, 2017, Bioinform..

How Accurately Can We Model Protein Structures with Dihedral Angles?

Shuai Cheng Li, Babak Alipanahi, Ming Li, 2012, WABI.

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

Qi Zhang, Dongbo Bu, Jianwei Zhu, 2018, BMC Bioinformatics.

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

Dong Xu, D. Bu, Shiwei Sun, 2016, Bioinform..

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

D. Bu, Xiaodong Shi, Xinmiao Fu, 2014, Protein science : a publication of the Protein Society.

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots

Xiang Chen, Wen Gao, Simin He, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

An optimized algorithm of high spatial-temporal efficiency for Megablast

Yishan Jiao, Lin Xu, Shengzhong Feng, 2005, 11th International Conference on Parallel and Distributed Systems (ICPADS'05).

Revisiting Multiple Pattern Matching Algorithms for Multi-Core Architecture

Yanbing Liu, Ping Liu, Dongbo Bu, 2011, Journal of Computer Science and Technology.

SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances

D. Bu, Shiwei Sun, Fusong Ju, 2023, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Condensing Raman spectrum for single-cell phenotype analysis

Xin Gao, Lihui Ren, Kang Ning, 2015, BMC Bioinformatics.

FragQA: predicting local fragment quality of a sequence-structure alignment.

D. Bu, Xin Gao, Shuai Cheng Li, 2007, Genome informatics. International Conference on Genome Informatics.

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

Dongbo Bu, Jingwei Zhang, Hui Wang, 2019, Comput. Biol. Chem..

EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction

D. Bu, Shiwei Sun, Yaojun Wang, 2023, Bioinform..

Designing Succinct Structural Alphabets Shuai

Ming Li, Jinbo Xu, D. Cheriton, 2007 .