Browsing by Author Do, Duc Dong

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  • 228-1-979-5-10-20190624.pdf.jpg
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  • Authors: Vu, Thi Ngoc Anh; Nguyen, Trong Dong; Nguyen, Vu Hoang Vuong; Dang, Thanh Hai; Do, Duc Dong (2019)

  • Aligning protein-protein interaction networks from different species is a useful mechanism for figuring out orthologous proteins, predicting/verifying protein unknown functions or constructing evolutionary relationships. The network alignment problem is proved to be NP-hard, requiring exponential-time algorithms, which is not feasible for the fast growth of biological data. In this paper, we present a novel global protein-protein interaction network alignment algorithm, which is enhanced with an extended large neighborhood search heuristics. Evaluated on benchmark datasets of yeast, fly, human and worm, the proposed algorithm outperforms state-of-the-art algorithms. Furthermore,...

  • 170-1-688-2-10-20180311.pdf.jpg
  • Article


  • Authors: Vu, Thi Ngoc Anh; Dinh, Phuc Thai; Nguyen, Hoang Duc; Dang, Thanh Hai; Do, Duc Dong (2018)

  • Reconstruction of a set of genetic sequences (founders) that can combine together to form given genetic sequences (e.g. DNA) of individuals of a population is an important problem in evolutionary biology. Such reconstruction can be modeled as a combinatorial optimization problem, in which we have to find a set of founders upon that genetic sequences of the population can be generated using a smallest number of recombinations. In this paper we propose an ant colony optimization algorithm (ACO) based method, equipped with some important improvements, for the founder DNA sequence reconstruction problem. The proposed method yields excellent performance when validating on 108 test sets fro...

  • Preliminary Results on the Whole Genome Analysis.pdf.jpg
  • Article


  • Authors: Dang, Thanh Hai; Nguyen, Dai Thanh; Pham, Thi Minh Trang; Dang, Cao Cuong; Hoang, Kim Phuc; Pham, Bao Son; Le, Sy Vinh; Le, Si Quang; Phan, Thi Thu Hang; Do, Duc Dong; Nguyen, Huu Duc (2014)

  • We present preliminary results on the whole genome analysis of an anonymous Vietnamese individual of the Kinh ethnic group (KHV) that was deeply sequenced to 30-fold using the Illumina sequencing machines. The sequenced genome covered 99.8% of the human reference genome (GRCh37). We discovered (1) 3.4 million single polymorphism nucleotides (SNPs) of which 41,396 (1.2%) were novel, (2) 654 thousand short indels of which 35,263 (5.4%) were novel (i.e., not present in the dbSNP and the 1000 genomes project databases). We also detected 10,611 large structural variants (length ≥100 bp). This study is our initial step toward large-scale genome projects on Vietnamese population.

Browsing by Author Do, Duc Dong

Jump to: 0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
or enter first few letters:  
Showing results 1 to 3 of 3
  • 228-1-979-5-10-20190624.pdf.jpg
  • Article


  • Authors: Vu, Thi Ngoc Anh; Nguyen, Trong Dong; Nguyen, Vu Hoang Vuong; Dang, Thanh Hai; Do, Duc Dong (2019)

  • Aligning protein-protein interaction networks from different species is a useful mechanism for figuring out orthologous proteins, predicting/verifying protein unknown functions or constructing evolutionary relationships. The network alignment problem is proved to be NP-hard, requiring exponential-time algorithms, which is not feasible for the fast growth of biological data. In this paper, we present a novel global protein-protein interaction network alignment algorithm, which is enhanced with an extended large neighborhood search heuristics. Evaluated on benchmark datasets of yeast, fly, human and worm, the proposed algorithm outperforms state-of-the-art algorithms. Furthermore,...

  • 170-1-688-2-10-20180311.pdf.jpg
  • Article


  • Authors: Vu, Thi Ngoc Anh; Dinh, Phuc Thai; Nguyen, Hoang Duc; Dang, Thanh Hai; Do, Duc Dong (2018)

  • Reconstruction of a set of genetic sequences (founders) that can combine together to form given genetic sequences (e.g. DNA) of individuals of a population is an important problem in evolutionary biology. Such reconstruction can be modeled as a combinatorial optimization problem, in which we have to find a set of founders upon that genetic sequences of the population can be generated using a smallest number of recombinations. In this paper we propose an ant colony optimization algorithm (ACO) based method, equipped with some important improvements, for the founder DNA sequence reconstruction problem. The proposed method yields excellent performance when validating on 108 test sets fro...

  • Preliminary Results on the Whole Genome Analysis.pdf.jpg
  • Article


  • Authors: Dang, Thanh Hai; Nguyen, Dai Thanh; Pham, Thi Minh Trang; Dang, Cao Cuong; Hoang, Kim Phuc; Pham, Bao Son; Le, Sy Vinh; Le, Si Quang; Phan, Thi Thu Hang; Do, Duc Dong; Nguyen, Huu Duc (2014)

  • We present preliminary results on the whole genome analysis of an anonymous Vietnamese individual of the Kinh ethnic group (KHV) that was deeply sequenced to 30-fold using the Illumina sequencing machines. The sequenced genome covered 99.8% of the human reference genome (GRCh37). We discovered (1) 3.4 million single polymorphism nucleotides (SNPs) of which 41,396 (1.2%) were novel, (2) 654 thousand short indels of which 35,263 (5.4%) were novel (i.e., not present in the dbSNP and the 1000 genomes project databases). We also detected 10,611 large structural variants (length ≥100 bp). This study is our initial step toward large-scale genome projects on Vietnamese population.