2023
GM(1,1)-Based Weighted K-Nearest Neighbor Algorithm for Indoor Localization.
Remote. Sens., August, 2023
Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer.
Genom. Proteom. Bioinform., 2023
Cancer is a Survival Process under Persistent Microenvironmental and Cellular Stresses.
Genom. Proteom. Bioinform., 2023
2022
A Novel Flexure Piezomotor With Minimized Backward and Nonlinear Motion Effect.
IEEE Trans. Ind. Electron., 2022
Smartphone-Based Unconstrained Step Detection Fusing a Variable Sliding Window and an Adaptive Threshold.
Remote. Sens., 2022
Spatial-Temporal Relationship Study between NWP PWV and Precipitation: A Case Study of 'July 20' Heavy Rainstorm in Zhengzhou.
Remote. Sens., 2022
2020
Corrections to "IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads".
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
Identification of Cancer Development Related Pathways Based on Co-Expression Analyses.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020
2019
A Stable Autoregressive Moving Average Hysteresis Model in Flexure Fast Tool Servo Control.
IEEE Trans Autom. Sci. Eng., 2019
Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name.
Genom. Proteom. Bioinform., 2019
DTA-SiST: de novo transcriptome assembly by using simplified suffix trees.
BMC Bioinform., 2019
Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes.
Briefings Bioinform., 2019
DOOR: a prokaryotic operon database for genome analyses and functional inference.
Briefings Bioinform., 2019
Modified Edge-Weighted Centroidal Voronoi Tessellation for Image Segmentation.
Proceedings of the Third International Symposium on Image Computing and Digital Medicine, 2019
Multi-Classification of Cancer Samples Based on Co-Expression Analyses.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
2018
DTAST: A Novel Radical Framework for de Novo Transcriptome Assembly Based on Suffix Trees.
Proceedings of the Intelligent Computing Theories and Application, 2018
High Dynamic Control of a Flexure Fast Tool Servo Using On-line Sequential Extreme Learning Machine.
Proceedings of the 2018 IEEE/ASME International Conference on Advanced Intelligent Mechatronics, 2018
2017
Transcription regulation by DNA methylation under stressful conditions in human cancer.
Quant. Biol., 2017
IsoTree: De Novo Transcriptome Assembly from RNA-Seq Reads - (Extended Abstract).
Proceedings of the Bioinformatics Research and Applications - 13th International Symposium, 2017
2016
A New Graph Theoretic Approach for Protein Threading.
Fundam. Informaticae, 2016
PUEPro: A Computational Pipeline for Prediction of Urine Excretory Proteins.
Proceedings of the Advanced Data Mining and Applications - 12th International Conference, 2016
2015
Carrying out Phylogenetic Analyses through Computational Model Checking.
Computer, 2015
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.
BMC Bioinform., 2015
2014
Reviewer Appreciation Editorial.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014
Editorial from the Editor-in-Chief.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014
Population dynamics inside cancer biomass driven by repeated hypoxia-reoxygenation cycles.
Quant. Biol., 2014
DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Nucleic Acids Res., 2014
DMINDA: an integrated web server for DNA motif identification and analyses.
Nucleic Acids Res., 2014
Functional Understanding of the Diverse exon-intron Structures of Human GPCR genes.
J. Bioinform. Comput. Biol., 2014
Reconsideration of <i>in silico</i> siRNA design from a perspective of heterogeneous data integration: problems and solutions.
Briefings Bioinform., 2014
Springer, ISBN: 978-1-4939-1381-7, 2014
2013
Editorial from the New Editor-in-Chief.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency.
Genom. Proteom. Bioinform., 2013
An integrated toolkit for accurate prediction and analysis of <i>cis-</i>regulatory motifs at a genome scale.
Bioinform., 2013
Elucidation of drivers for cancer initiation and metastasis: A data-mining approach.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
2012
dbCAN: a web resource for automated carbohydrate-active enzyme annotation.
Nucleic Acids Res., 2012
Quartet decomposition server: a platform for analyzing phylogenetic trees.
BMC Bioinform., 2012
2011
Genome-wide discovery of missing genes in biological pathways of prokaryotes.
BMC Bioinform., 2011
2010
Sorting Genomes by Reciprocal Translocations, Insertions, and Deletions.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010
Foreword: Advances in Computational Systems Bioinformatics.
J. Bioinform. Comput. Biol., 2010
<i>In-silico </i>prediction of blood-secretory human proteins using a ranking algorithm.
BMC Bioinform., 2010
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.
Bioinform., 2010
2009
Parallel Clustering Algorithm for Large Data Sets with Applications in Bioinformatics.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009
A polynomial-time approximation scheme for embedding hypergraph in a cycle.
ACM Trans. Algorithms, 2009
DOOR: a database for prokaryotic operons.
Nucleic Acids Res., 2009
J. Comput. Sci. Technol., 2009
Computational Challenges in Deciphering Genomic Structures of Bacteria.
J. Comput. Sci. Technol., 2009
A Universal operon Predictor for prokaryotic genomes.
J. Bioinform. Comput. Biol., 2009
Large-Scale Analyses of Glycosylation in Cellulases.
Genom. Proteom. Bioinform., 2009
Analyses of domains and domain fusions in human proto-oncogenes.
BMC Bioinform., 2009
<i>De novo</i> computational prediction of non-coding RNA genes in prokaryotic genomes.
Bioinform., 2009
Detect the Different Isoforms Using GeneChip Human Exon 1.0 ST Arrays.
Proceedings of the 2nd International Conference on BioMedical Engineering and Informatics, 2009
2008
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
J. Comput. Chem., 2008
Improving the Performance of protein Threading Using Insertion/Deletion Frequency Arrays.
J. Bioinform. Comput. Biol., 2008
On application of directons to functional classification of genes in prokaryotes.
Comput. Biol. Chem., 2008
Barcodes for genomes and applications.
BMC Bioinform., 2008
Computational prediction of human proteins that can be secreted into the bloodstream.
Bioinform., 2008
PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes.
Proceedings of the Bioinformatics Research and Applications, 2008
2007
Prediction of <i>cis</i>-Regulatory Elements: from High-Information Content Analysis to Motif Identification.
J. Bioinform. Comput. Biol., 2007
An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing.
Algorithmica, 2007
An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes.
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007
Operon Prediction in Microbial Genomes Using Decision Tree Approach.
Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2007
2006
Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006
Mapping of orthologous genes in the context of biological pathways: An application of integer programming.
Proc. Natl. Acad. Sci. USA, 2006
SUMOsp: a web server for sumoylation site prediction.
Nucleic Acids Res., 2006
Gene Expression Data Analysis in Subtypes of Ovarian Cancer Using Covariance Analysis.
J. Bioinform. Comput. Biol., 2006
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS).
Bioinform., 2006
A Point-Process Model for Rapid Identification of Post-Translational Modifications.
Proceedings of the Biocomputing 2006, 2006
Fast De novo Peptide Sequencing and Spectral Alignment via Tree Decomposition.
Proceedings of the Biocomputing 2006, 2006
Peptide sequence tag-based blind identification of post-translational modifications with point process model.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006
DigitalTree: A Tool for Displaying Biological Data in Tree Structure.
Proceedings of the Computational Science, 2006
Understanding microbial genomic structures and applications to biological pathway inference.
Proceedings of the 2006 IEEE International Conference on Granular Computing, 2006
2005
PRIME: A Mass Spectrum Data Mining Tool for <i>De Nova</i> Sequencing and PTMs Identification.
J. Comput. Sci. Technol., 2005
J. Comput. Sci. Technol., 2005
More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling.
J. Comput. Biol., 2005
The Probability Distribution for a Random Match between an Experimental-theoretical Spectral Pair in Tandem Mass Spectrometry.
J. Bioinform. Comput. Biol., 2005
On Connected [<i>g, f</i> +1]-Factors in Graphs.
Comb., 2005
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra.
Bioinform., 2005
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment.
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005
Accurate Prediction of Orthologous Gene Groups in Microbes.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
PROMOCO: a New Program for Prediction of cis Regulatory Elements: From High-Information Content Analysis to Clique Identification.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
Improving Operon Prediction in E. coli.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
Computational Reconstruction of the carbon fixation pathway in Synechococcus SP. Wh 8102.
Proceedings of the Advances in Bioinformatics and Its Applications, 2005
2004
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction.
Nucleic Acids Res., 2004
Protein Threading by Linear Programming: Theoretical Analysis and Computational Results.
J. Comb. Optim., 2004
Protein Fold Recognition Through Application of Residual Dipolar Coupling Data.
Proceedings of the Biocomputing 2004, 2004
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation - A Graph-Theoretic Approach.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
A Knowledge Base for Computational Pathway Reconstruction.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Computational Construction of Nitrogen Assimilation Pathway in Cyanobacteria Synechococcus sp. WH8102.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
CUBIC: Search for Binding Sites.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Pathway Mapping with Operon Information: An Integer-Programming Method.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Molecular Modeling of Full-Length OxyR from Shewanella oneidensis MR-1 and Molecular Dynamics Studies of the Activation Domain.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
In Silico Construction of the Carbon Fixation Pathway in Synechococcus sp. WH8102.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Computational Inference of Transcription Regulation and Response Networks in Synechococcus sp. WH8102.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004
2003
Approximation algorithms for NMR spectral peak assignment.
Theor. Comput. Sci., 2003
Raptor: Optimal Protein Threading by Linear Programming.
J. Bioinform. Comput. Biol., 2003
Cubic: Identification of Regulatory Binding Sites through Data Clustering.
J. Bioinform. Comput. Biol., 2003
Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering.
J. Bioinform. Comput. Biol., 2003
MOLVIE: an interactive visualization environment for molecular structures.
Comput. Methods Programs Biomed., 2003
A computational pipeline for protein structure prediction and analysis at genome scale.
Bioinform., 2003
Protein Threading by Linear Programming.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Identification of Regulatory Binding Sites Using Minimum Spanning Trees.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Computational Inference of Regulatory Pathways in Microbes.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data.
Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003
2002
Automated assignment of backbone NMR peaks using constrained bipartite matching.
Comput. Sci. Eng., 2002
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.
Bioinform., 2002
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.
Bioinform., 2002
Improved Approximation Algorithms for NMR Spectral Peak Assignment.
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002
An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks.
Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002
2000
A Computational Method for NMR-Constrained Protein Threading.
J. Comput. Biol., 2000
Protein domain decomposition using a graph-theoretic approach.
Bioinform., 2000
Sequence-structure specificity of a knowledge based energy function at the secondary structure level.
Bioinform., 2000
Protein structure determination using protein threading and sparse NMR data (extended abstract).
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000
1998
A segmentation algorithm for noisy images: Design and evaluation.
Pattern Recognit. Lett., 1998
An Efficient Computational Method for Globally Optimal Threading.
J. Comput. Biol., 1998
A new method for modeling and solving the protein fold recognition problem (extended abstract).
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998
1997
Automated Gene Identification in Large-Scale Genomic Sequences.
J. Comput. Biol., 1997
2D image segmentation using minimum spanning trees.
Image Vis. Comput., 1997
Reference-based gene model prediction on DNA contigs (extended abstract).
Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997
Inferring Gene Structures in Genomic Sequences Using Pattern Recognition and Expressed Sequence Tags.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997
1996
GRAIL: a multi-agent neural network system for gene identification.
Proc. IEEE, 1996
Efficient Theoretic and Practical Algorithms for Linear Matroid Intersection Problems.
J. Comput. Syst. Sci., 1996
An Iterative Algorithm for Correcting Sequencing Errors in DNA Coding Regions.
J. Comput. Biol., 1996
Detection of RNA Polymerase II Promoters and Polyadenylation Sites in Human DNA Sequence.
Comput. Chem., 1996
A polynomial-time algorithm for a class of protein threading problems.
Comput. Appl. Biosci., 1996
Gene Prediction by Pattern Recognition and Homology Search.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996
1995
Correcting sequencing errors in DNA coding regions using a dynamic programming approach.
Comput. Appl. Biosci., 1995
1994
Constructing gene models from accurately predicted exons: an application of dynamic programming.
Comput. Appl. Biosci., 1994
Fast Algorithms for Transversal Matroid Intersection Problems
Proceedings of the Algorithms and Computation, 5th International Symposium, 1994
1989
Efficient Algorithms for Independent Assignments on Graphic and Linear Matroids
Proceedings of the 30th Annual Symposium on Foundations of Computer Science, Research Triangle Park, North Carolina, USA, 30 October, 1989