Dongbo Bu

According to our database1, Dongbo Bu authored at least 33 papers between 2001 and 2018.

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Bibliography

2018
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.
CoRR, 2018

Protein threading using residue co-variation and deep learning.
Bioinformatics, 2018

2017
Improving prediction of burial state of residues by exploiting correlation among residues.
BMC Bioinformatics, 2017

Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.
Bioinformatics, 2017

2016
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
Bioinformatics, 2016

2015
Parameterized BLOSUM Matrices for Protein Alignment.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction.
BMC Bioinformatics, 2015

2013
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?
Algorithms for Molecular Biology, 2013

Towards Reliable Automatic Protein Structure Alignment.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

2012
Clustering 100, 000 Protein Structure Decoys in Minutes.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

How Accurately Can We Model Protein Structures with Dihedral Angles?
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

2011
Finding Nearly Optimal GDT Scores.
Journal of Computational Biology, 2011

Lex-SVM: Exploring the Potential of exon Expression Profiling for Disease Classification.
J. Bioinformatics and Computational Biology, 2011

ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity.
BMC Bioinformatics, 2011

Incorporating Ab Initio energy into threading approaches for protein structure prediction.
BMC Bioinformatics, 2011

PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum.
BMC Bioinformatics, 2011

PEARL: Probing Entity Aggregation in Real Life.
Proceedings of the 2011 IEEE/ACM International Conference on Green Computing and Communications (GreenCom), 2011

2009
Finding compact structural motifs.
Theor. Comput. Sci., 2009

2008
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.
Bioinformatics, 2008

A Fragmentation Event Model for Peptide Identification by Mass Spectrometry.
Proceedings of the Research in Computational Molecular Biology, 2008

Designing succinct structural alphabets.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Finding Largest Well-Predicted Subset of Protein Structure Models.
Proceedings of the Combinatorial Pattern Matching, 19th Annual Symposium, 2008

2007
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry.
J. Bioinformatics and Computational Biology, 2007

Finding Compact Structural Motifs.
Proceedings of the Combinatorial Pattern Matching, 18th Annual Symposium, 2007

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006
Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment.
J. Comput. Sci. Technol., 2006

A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data.
BMC Bioinformatics, 2006

Improving locality of nonserial polyadic dynamic programming.
Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

2005
NONCODE: an integrated knowledge database of non-coding RNAs.
Nucleic Acids Research, 2005

An Optimized Algorithm of High Spatial-temporal Efficiency for MegaBlast.
Proceedings of the 11th International Conference on Parallel and Distributed Systems, 2005

2004
A Note on the Single Genotype Resolution Problem.
J. Comput. Sci. Technol., 2004

2001
TREC-10 Experiments at CAS-ICT: Filtering, Web and QA.
Proceedings of The Tenth Text REtrieval Conference, 2001


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