Zhuozhi Wang

University Health Network, Toronto, Ontario, Canada

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Publications (7)3.69 Total impact

  • Zhuozhi Wang · Elisabeth R.M. Tillier ·
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    ABSTRACT: RNA sequences can form structures which are conserved throughout evolution and the question of aligning two RNA secondary structures has been extensively studied. Most of the previous alignment algorithms require the input of gap opening and gap extension penalty parameters. The choice of appropriate parameter values is controversial as there is little biological information to guide their assignment. In this paper, we present an algorithm which circumvents this problem. Instead of finding an optimal alignment with predefined gap opening penalty, the algorithm finds the optimal alignment with exact number of aligned blocks.
    Biomolecular Engineering 10/2007; 24(3):321-6. DOI:10.1016/j.bioeng.2007.02.004 · 3.17 Impact Factor
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    Zhuozhi Wang · Elisabeth R. M. Tillier ·
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    ABSTRACT: In solving the question of alignment of two RNA secondary structures, it is not clear how to choose parameters for the introduction of gaps in the alignment. We introduce a Bayesian approach for aligning two RNA secondary structures. The algorithm can not only compute the optimal alignment itself but also some interesting posteriors such as posteriors of substitution matrix and gap opening penalties. The running time of this algorithm is O(p<sub>1</sub> p<sub>2 </sub>nm), where p<sub>1</sub> and p<sub>2</sub> are the number of base pairs in RNA structures A and B, and n and m are the lengths of the two RNA secondary structures respectively
    Computational Intelligence and Bioinformatics and Computational Biology, 2006. CIBCB '06. 2006 IEEE Symposium on; 10/2006
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    Zhuozhi Wang · Kaizhong Zhang ·
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    ABSTRACT: RNA structures can be viewed as a kind of special strings with some characters bonded with each other. The question of aligning two RNA structures has been studied for a while, and there are several successful algorithms that are based upon different models. In this paper, by adopting the model introduced in [18], we propose two algorithms to attack the question of aligning multiple RNA structures. We reduce the multiple RNA structure alignment problem to the problem of aligning two RNA structure alignments.
    Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 02/2004; 03(03):246-54. DOI:10.1109/CSB.2004.119
  • Bin Ma · Zhuozhi Wang · Kaizhong Zhang ·
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    ABSTRACT: Alignment of two multiple alignments arises naturally when constructing approximate multiple sequence alignments progressively. In this paper, we consider the problem of alignment of two multiple alignments with SP-score and linear gap costs. When there is no gap opening cost, this problem can be solved using the well-known dynamic programming algorithm for two sequences by viewing each column in the multiple alignments as an element. However if there are gap opening costs (sometimes referred as affine gap costs) then the problem becomes non-trivial. Gotoh [4] suggested a procedure for this problem and stated that “the total arithmetic operations used is close to (quadratic) in typical cases”. Kececioglu and Zhang [7] gave heuristic algorithms based on optimistic and pessimistic gap counts and conjectured that this problem is NP-complete. In this paper we prove that this problem is indeed NP-complete and therefore settle this open problem. We then propose another heuristic algorithm for this problem.
    Combinatorial Pattern Matching, 14th Annual Symposium, CPM 2003, Morelia, Michocán, Mexico, June 25-27, 2003, Proceedings; 01/2003
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    Shihyen Chen · Zhuozhi Wang · Kaizhong Zhang ·
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    ABSTRACT: The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between A-U and G-C. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing. This paper considers pattern matching as well as local alignment between two RNA structures. For pattern matching, we present two algorithms, one for obtaining an exact match, the other for approximate match. We then present an algorithm for RNA local structural alignment.
    International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS); 06/2002
  • Zhuozhi Wang · Kaizhong Zhang ·
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    ABSTRACT: The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the four-letter alphabet {A,C, G, U}. The RNA secondary and tertiary structures can be represented as a set of nested base pairs and a set of crossing base pairs, respectively. These base pairs form bonds between A–U,–C–G, and G–U. This paper considers alignment with affine gap penalty between two RNA molecule structures. In general this problem is Max SNP-hard for tertiary structures. We present an algorithm for the case where aligned base pairs are non-crossing. Experimental results show that this algorithm can be used for practical application of RNA structure alignment.
    Mathematical Foundations of Computer Science 2001, 26th International Symposium, MFCS 2001 Marianske Lazne, Czech Republic, August 27-31, 2001, Proceedings; 01/2001
  • Zhuozhi Wang · Kaizhong Zhang ·
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    ABSTRACT: RNAs (Ribonucleic Acids) play an important role when organisms reproduce themselves. RNAs are single-stranded, however they tend to form higher order structures such as secondary or tertiary structures by folding onto themselves. It is the RNA structures that determine the functions of RNA sequences. Since it is very difficult to crystallize and/or get nuclear magnetic resonance spectrum data for large RNA molecules, reliable methods to determine RNA structures from the primary sequences is important. An important step toward the deter- mination of RNA structure is the prediction of RNA secondary structures. Based on a reliable RNA secondary structure, possible tertiary interactions that occur between secondary structural elements and between these elements and single- stranded region can be characterized. Thermodynamic stability methods have been developed [5] to fold a single RNA into secondary structures with minimum or near minimum energy with some success. Phylogenetic comparative methods are more successful which try to determine the common secondary structures from a set of RNA sequences by checking a large number of possible base pair- ings for their possible conservation. However this method is very tedious since it is basically performed manually. In this abstract, we propose an algorithm using dynamic programming trying to automate the phylogenetic comparative pro- cess. Given three RNA sequences, we first apply the folding algorithms for each sequence to determine the frequently recurring stems which are considered to be thermodynamically favourable. We then apply our algorithm to the three stem lists generated from the folding algorithm to determine the common secondary structures.We have applied our method to three viruses: cocksackievirus, human rhinovirus (type 14), and poliovirus (type 3). Our method successfully produced the main components of the common secondary structures of these viruses.
    Combinatorial Pattern Matching, 10th Annual Symposium, CPM 99, Warwick University, UK, July 22-24, 1999, Proceedings; 01/1999

Publication Stats

45 Citations
3.69 Total Impact Points


  • 2004-2007
    • University Health Network
      • Division of Experimental Therapeutics
      Toronto, Ontario, Canada
  • 2003
    • The University of Western Ontario
      • Department of Computer Science
      London, Ontario, Canada