2009:

Y. Cheng^{*},
D.Z. Du,
K.I. Ko, and
——.
On the parameterized complexity of pooling design.
Journal of Computational Biology.
16(11)(2009), 15291537.

Z. Cai,
Z.Z. Chen, and
——^{*}.
A 3.4713approximation algorithm for the capacitated multicast tree routing problem.
Theoretical Computer Science.
410(52)(2009), 54155424.
(An extended abstract of an earlier version with performance ratio 3.5375,
by Z. Cai, Z.Z. Chen, ——^{*}, and L. Wang, appears in COCOA 2008, LNCS 5165, pages 286295.)
 Z. Cai, Z.Z. Chen, ——, and L. Wang.
An improved approximation algorithm for the capacitated multicast tree routing problem.
In Proceedings of the 2nd Annual International Conference on Combinatorial Optimization and Applications (COCOA'08).
LNCS 5165, Pages 286295.

J. Zhang,
D. Xu,
W. Gao,
——^{*}, and
S. He^{*}.
Isotope pattern vector based MS/MS data calibration for improving peptide and protein identification.
Rapid Communications in Mass Spectrometry.
23(21)(2009), 34483456.
Abstract: Tandem mass spectra contain noisy peaks which make peak picking for peptide identification difficult.
Moreover, all spectral peaks can be shifted due to systematic measurement errors.
In this paper, a novel use of an isotope pattern vector (IPV) is proposed for denoising and systematic measurement error prediction.
By matching the experimental IPVs with the theoretical IPVs of candidate fragment ions, true ionic peaks can be identified.
Furthermore, these identified experimental IPVs and their corresponding theoretical IPVs are used in an optimization process
to predict the systematic measurement error associated with the target spectrum.
In return, the subsequent spectral data calibration based on the predicted systematic measurement error enhances the data quality.
We show that such an integrated denoising and calibration process leads to significantly improved peptide and protein identification.
Different from the commonly employed chemical calibration methods,
our IPVbased method is a purely computational method for individual spectra analysis and globally optimizes the use of spectral data.

M. Berjanskii,
P. Tang,
J. Liang,
J. A. Cruz,
J. Zhou,
Y. Zhu,
E. Bassett,
C. MacDonell,
P. Lu,
——, and
D. S. Wishart^{*}.
GeNMR: a web server for rapid NMRbased protein structure determination.
Nucleic Acids Research.
37(Web Server issue)(2009): W670W677.

Y. Cheng,
H. Sabaa,
Z. Cai,
R. Goebel, and
——^{*}.
Efficient haplotype inference algorithms in one whole genome scan for pedigree data with nongenotyped founders.
Acta Mathematicae Applicatae Sinica (English Series).
25(3)(2009), 477488.
(SI dedicated to the 30th Anniversary of the Institute of Applied Mathematics within the Chinese Academy of Sciences.)


 Presented at The Seventh AsiaPacific Bioinformatics Conference (APBC'09).

Y. Cheng^{*},
D.Z. Du, and
——.
On the upper bounds of the minimum number of rows of disjunct matrices.
Optimization Letters.
3(2)(2009), 297302.
2008:

M. E. J. Amaral ^{*},
J. R. Grant,
P. K. Riggs,
N. B. Stafuzza,
E. A. R. Filho,
T. Goldammer,
R. Weikard,
R. M. Brunner,
K. J. Kochan,
A. J. Greco,
J. Jeong,
Z. Cai,
——,
A. Prasad,
S. Kumar,
G. P. Saradhi,
B. Mathew,
M. A. Kumar,
M. N. Miziara,
P. Mariani,
A. R. Caetano,
S. R. Galvão,
M. S. Tantia,
R. K. Vijh,
B. Mishra,
S. T. B. Kumar,
V. A. Pelai,
A. M. Santana,
L. C. Fornitano,
B. C. Jones,
H. Tonhati,
S. Moore,
P. Stothard, and
J. E. Womack.
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle.
BMC Genomics.
9(2008), 631 (December 24, 2008).

X.F. Wan^{*},
M. Ozden, and
——.
Ubiquitous reassortments in influenza A viruses.
Journal of Bioinformatics and Computational Biology.
6(5)(2008), 981999.

D. S. Wishart^{*},
D. Arndt,
M. Berjanskii,
P. Tang,
J. Zhou, and
——.
CS23D:
a web server for rapid protein structure generation using NMR chemical shifts and sequence data.
Nucleic Acids Research.
36(Web Server Issue)(2008), W496W502.
(A poster by Wishart, Arndt, Berjanskii, Tang, Zhou, Shi, and Lin, presented in
PrP Canada'08.)

 X. Wu and ——.
Selected string representation for whole genomes.
In Proceedings of 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB'05).
Pages 105112.




2007:

(A preliminary version on HIV1 pure subtyping, by Wu, Goebel, Wan, and Lin, appears in
LSS CSB'06, pages 179190.
)
 X. Wu, R. Goebel, X.F. Wan, and ——^{*}.
Whole genome composition distance for HIV1 genotyping.
In Proceedings of the 2006 LSS Computational Systems Bioinformatics Conference (LSS CSB'06). Pages 179190.

X. Wan and
——^{*}.
CISA: combined NMR resonance connectivity information determination and sequential assignment.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
4(3)(2007), 336348.

X. Wan and
——^{*}.
GASA: a graphbased automated NMR backbone resonance sequential assignment program.
Journal of Bioinformatics and Computational Biology.
5(2A)(2007), 313333.
(SI for LSS CSB'06: a preliminary version, by the same authors, appears in
LSS CSB'06, pages 5566.
)
 X. Wan and ——^{*}.
A graphbased automated NMR backbone resonance sequential assignment.
In Proceedings of the 2006 LSS Computational Systems Bioinformatics Conference (LSS CSB'06). Pages 5566.

(Preliminary versions, by Cai, Goebel, Salavatipour, Shi, Xu, and Lin, appears in
APBC'07, pages 8190;
and by Cai, Xu, Shi, Salavatipour, Goebel, and Lin, appears in
IEEE BIBE'06, pages 235242.)
 Z. Cai, R. Goebel, M. Salavatipour, Y. Shi, L. Xu, and ——^{*}.
Selecting genes with dissimilar discrimination strength for sample class prediction.
In Proceedings of the Fifth AsiaPacific Bioinformatics Conference (APBC'07). Pages 8190.
 Z. Cai, L. Xu, Y. Shi, M. Salavatipour, R. Goebel, and ——^{*}.
Using gene clustering to identify discriminatory genes with higher classification accuracy.
In Proceedings of IEEE The 6th Symposium on Bioinformatics and Bioengineering (IEEE BIBE'06). Pages 235242.

X.F. Wan^{†*},
X. Wu^{†},
——,
S. B. Holton,
R. A. Desmone,
C.R. Shyu,
Y. Guan, and
M. Emch.
Computational identification of reassortments in avian influenza viruses.
Avian Diseases.
51(s1)(2007), 434439.
(SI for ISAI'06: an abstract, by Wu, Holton, Shyu, Lin, and Wan, presented as a poster in
ISAI'06, 2006.)

G. Wu,
J. You, and
——^{*}.
Quartet based phylogeny reconstruction with answer set programming.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
4(1)(2007), 139152.
(Preliminary versions of several parts, by Wu, You, and Lin, appears in
LPNMR'05, LNCS/LNAI 3663, pages 369373;
and by Wu, Lin, You, and Wu, appears in
APBC'05, pages 329338;
and by Wu, Lin, and You, appears in
IEEE ICTAI'04, pages 612619.)
 G. Wu, J. You^{*}, and ——.
Application of Smodels in quartet based phylogeny construction.
In Proceedings of the 8th International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR'05).
LNCS/LNAI 3662, Pages 369373.
 G. Wu, ——^{*}, J. You, and X. Wu.
Faster solution to the maximum quartet consistency problem with constrained programming.
In Proceedings of the 3rd AsiaPacific Bioinformatics Conference (APBC'05). Pages 329338.
 G. Wu, ——^{*}, and J. You.
Quartet based phylogeny reconstruction with answer set programming.
In Proceedings of The 16th IEEE International Conference on Tools with Artificial Intelligence (ICTAI'04). Pages 612619.

J. Zhou,
J. Sander, and
——^{*}.
Efficient composite pattern finding from monad patterns.
International Journal on Bioinformatics Research and Applications.
3(1)(2007), 8699.
2006:

Z. Cai,
M. Heydari, and
——^{*}.
Iterated local least squares imputation for microarray missing values.
Journal of Bioinformatics and Computational Biology.
4(5)(2006), 935957.
(A preliminary version, by the same authors, appears in
APBC'06, pages 159168.)
 Z. Cai, M. Heydari, and ——^{*}.
Microarray missing value imputation by iterated local least squares.
In Proceedings of the Fourth AsiaPacific Bioinformatics Conference (APBC'06). Pages 159168.

X.F. Wan,
——, and
D. Xu^{*}.
Rnall: an efficient algorithm for predicting RNA local secondary structural landscape in genomes.
Journal of Bioinformatics and Computational Biology.
4(5)(2006), 10151031.

W. Kennedy,
——^{*}, and
G. Y. Yan.
Strictly chordal graphs are leaf powers.
Journal of Discrete Algorithms.
4(4)(2006), 511525.

G. Wu,
J. You, and
——^{*}.
A polynomial time algorithm for the minimum quartet inconsistency problem with O(n) quartet errors.
Information Processing Letters.
100(4)(2006), 167171.
(An extended abstract, by the same authors, appears in Posters in
IEEE CSB'05, pages 5556.)

X. Wu,
X.F. Wan,
G. Wu,
D. Xu, and
——^{*}.
Phylogenetic analysis using complete signature information of whole genomes and clustered NeighborJoining method.
International Journal on Bioinformatics Research and Applications.
2(3)(2006), 219248.

(A preliminary version, by Yang, Li, Cai, and Lin, appears in
IEEE BIBE'05, pages 310.)
 K. Yang, Z. Cai, J. Li and ——^{*}.
A modelfree and stable gene selection in microarray data analysis.
In Proceedings of IEEE The 5th Symposium on Bioinformatics and Bioengineering (IEEE BIBE'05). Pages 310.

——^{*},
X. Wan,
T. Tegos, and
Y. Li.
Statistical evaluation of NMR backbone resonance assignment.
International Journal of Bioinformatics Research and Applications.
2(2)(2006), 147160.

——^{*},
Z. Cai, and
D. Lin.
Path covering on trees with its applications in machine translation.
Information Processing Letters.
97(2)(2006), 7381.
2005:

T. Tegos,
Z.Z. Chen, and
——^{*}.
Heuristic search in constrained bipartite matching with applications to protein NMR backbone resonance assignment.
Journal of Bioinformatics and Computational Biology.
3(6)(2005), 13311350.

——.
An improved approximation algorithm for multicast ktree routing.
Journal of Combinatorial Optimization.
9(4)(2005), 349356.

Z. Cai,
M. Heydari, and
——^{*}.
Clustering binary oligonucleotide fingerprint vectors for DNA clone classification analysis.
Journal of Combinatorial Optimization.
9(2)(2005), 199211.

Z.Z. Chen,
——,
R. Rizzi,
J.J. Wen,
D. Xu,
Y. Xu, and
T. Jiang^{*}.
More reliable protein NMR peak assignment via improved 2interval scheduling.
Journal of Computational Biology.
12(2)(2005), 129146.
(An extended abstract, by Chen, Jiang, Lin, Rizzi, Wen, Xu, and Xu, appears in
ESA'03, LNCS 2832, pages 580592.)
 Z.Z. Chen^{*}, T. Jiang, ——, R. Rizzi, J. J. Wen, D. Xu, and Y. Xu.
More reliable protein NMR peak assignment via improved 2interval scheduling.
In Proceedings of the 11th Annual European Symposium on Algorithms (ESA'03). LNCS 2832, Pages 580592.
2004:

X. Wan,
T. Tegos, and
——^{*}.
Histogrambased scoring schemes for protein NMR resonance assignment.
Journal of Bioinformatics and Computational Biology.
2(4)(2004), 747764.
(A preliminary version of one part, by Wan, Xu, Slupsky, and Lin, appears in
IEEE CSB'03, pages 197208.
)
 X. Wan, D. Xu, C. M. Slupsky, and ——^{*}.
Automated protein NMR resonance assignments.
In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB'03). Pages 197208.

Z.Z. Chen,
Y. Gao,
——^{*},
R. Niewiadomski,
Y. Wang, and
J. Wu.
A spaceefficient algorithm for sequence alignment with inversions and reversals.
Theoretical Computer Science.
325(3)(2004), 361372.
(SI for COCOON'03: A preliminary version, by Gao, Wu, Niewiadomski, Wang, Chen, and Lin, appears in
COCOON'03, LNCS 2697, pages 5767.)
 Y. Gao, J. Wu, R. Niewiadomski, Y. Wang, Z.Z. Chen, and ——^{*}.
A space efficient algorithm for sequence alignment with inversions.
In Proceedings of the Ninth International Computing and Combinatorics Conference (COCOON'03). LNCS 2697, Pages 5767.

——^{*} and
T. Jiang.
A further improved approximation algorithm for breakpoint graph decomposition.
Journal of Combinatorial Optimization.
8(2)(2004), 183194.

T. Jiang,
——^{*},
B. Ma, and
K. Zhang.
The longest common subsequence problem for arcannotated sequences.
Journal of Discrete Algorithms.
2(2)(2004), 257270.
(SI for CPM'00: An extended abstract, by the same authors, appears in
CPM'00, LNCS 1848, pages 154165.)
 T. Jiang, ——^{*}, B. Ma, and K. Zhang.
The longest common subsequence problem for arcannotated sequences.
In Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM'00). LNCS 1848, Pages 154165.
2003:

——^{*},
D. Xu,
Z.Z. Chen,
T. Jiang,
J.J. Wen, and
Y. Xu.
Computational assignment of protein backbone NMR peaks by efficient bounding and filtering.
Journal of Bioinformatics and Computational Biology.
1(2)(2003), 387410.
(SI for IEEE CSB'02: A preliminary version of one part, by Lin, Xu, Chen, Jiang, Wen, and Xu, appears in
IEEE CSB'02, pages 165174.
)
 ——^{*}, D. Xu, Z.Z. Chen, T. Jiang, and Y. Xu.
An efficient branchandbound algorithm for the assignment of protein backbone NMR peaks.
In Proceedings of the IEEE Computer Society Bioinformatics Conference 2002 (CSB'02). Pages 165174.

Z.Z. Chen,
T. Jiang^{*}, and
——.
Computing phylogenetic roots with bounded degrees and errors.
SIAM Journal on Computing.
32(2003), 864879.
(An extended abstract, by the same authors, appears in
WADS'01, LNCS 2125, pages 377388.)
 Z.Z. Chen, T. Jiang^{*}, and ——.
Computing phylogenetic roots with bounded degrees and errors.
In Proceedings of the 7th International Workshop on Algorithms and Data Structures (WADS'01). LNCS 2125, Pages 377388.

E. Bach,
J. Boyar,
L. Epstein,
L. M. Favrholdt,
T. Jiang,
K. S. Larsen,
——^{*}, and
R. van Stee.
Tight bounds on the competitive ratio on accommodating sequences for the seat reservation problem.
Journal of Scheduling.
6(2)(2003), 131147.
(An extended abstract, by Bach, Boyar, Jiang, Larsen, and Lin, appears in
COCOON'00, LNCS 1858, pages 221231.)
 E. Bach, J. Boyar, T. Jiang, K. S. Larsen, and ——^{*}.
Better bounds on the accommodating ratio for seat reservation problem.
In Proceedings of the 6th Annual International Computing and Combinatorics Conference (COCOON'00). LNCS 1858, Pages 221231.

Z.Z. Chen,
T. Jiang,
——^{*},
J.J. Wen,
D. Xu,
J. Xu, and
Y. Xu.
Approximation algorithms for NMR spectral peak assignment.
Theoretical Computer Science.
299(13)(2003), 211229.
(A preliminary version, by Chen, Jiang, Lin, Wen, Xu, and Xu, appears in
WABI'02, LNCS 2452, pages 8296.)
 Z.Z. Chen, T. Jiang, ——^{*}, J. J. Wen, D. Xu, and Y. Xu.
Better approximation algorithms for NMR spectral peak assignment.
In Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI'02). LNCS 2452, Pages 8296.
2002:

——^{*},
Z.Z. Chen,
T. Jiang, and
J.J. Wen.
The longest common subsequence problem for sequences with nested arc annotations.
Journal of Computer and System Sciences.
65(3)(2002), 465480.
(An extended abstract, by the same authors, appears in
ICALP'01, LNCS 2076, pages 444455.)
 ——, Z.Z. Chen, T. Jiang^{*}, and J.J. Wen.
The longest common subsequence problem for sequences with nested arc annotations.
In Proceedings of the 28th International Colloquium on Automata, Languages and Programming (ICALP'01). LNCS 2076, Pages 444455.

D. Jaitly,
P.E. Kearney,
——, and
B. Ma^{*}.
Methods for reconstructing the history of tandem repeats and their application to the human genome.
Journal of Computer and System Sciences.
65(3)(2002), 494507.

^{[citations]}
—— and G.L. Xue^{*}.
On the terminal Steiner tree problem.
Information Processing Letters.
84(2)(2002), 103107.

T. Jiang,
——,
B. Ma^{*}, and
K. Zhang.
A general edit distance between RNA structures.
Journal of Computational Biology.
9(2)(2002), 371388.
(An extended abstract, by Lin, Ma, and Zhang, appears in
ACM RECOMB'01, pages 211220.)
 ——, B. Ma^{*}, and K. Zhang.
Edit distance between two RNA structures.
In Proceedings of the 5th ACM Annual International Conference on Computational Molecular Biology (RECOMB'01). Pages 200209.

S. P. Chen,
Y. He, and
——^{*}.
3partitioning problems for maximizing the minimum load.
Journal of Combinatorial Optimization.
6(1)(2002), 6780.
(A preliminary version, by Lin and Chen, appears in
CORSC'96, pages 161166.)
 ——^{*} and S. P. Chen.
On worstcase performance of MLPT applying to 3partitioning problem.
In Proceedings of the Fifth Conference of Operations Research Society of China (CORSC'96). Pages 161166.
2001:

G. L. Xue^{*},
—— and
D. Z. Du.
Grade of service Steiner minimum trees in the Euclidean plane.
Algorithmica.
31(4)(2001), 479500.
(An extended abstract, by the same authors, appears in
IEEE ISCAS'99, pages VI:182185.)
 G. L. Xue^{*}, ——, and D. Z. Du.
Grade of service Steiner minimum trees in the euclidean plane.
In Proceedings of IEEE International Symposium on Circuits and Systems (ISCAS'99). Vol. VI, 182185.

—— and
G. L. Xue^{*}.
Signed genome rearrangements by reversals and transpositions: models and approximations.
Theoretical Computer Science.
259(12)(2001), 513531.
(An extended abstract, by the same authors, appears in
COCOON'99, LNCS 1627, pages 7180.)
 —— and G. L. Xue^{*}.
Signed genome rearrangements by reversals and transpositions: models and approximations.
In Proceedings of the Fifth Annual International Computing and Combinatorics Conference (COCOON'99). LNCS 1627, Pages 7180.
2000:

D. H. Chen,
D. Z. Du,
X. D. Hu,
——,
L. S. Wang, and
G. L. Xue^{*}.
Approximations for Steiner trees with minimum number of Steiner points.
Journal of Global Optimization.
18(1)(2000), 1733.

——,
D. S. Kim, and
D. Z. Du^{*}.
Strictly nonblocking multirate broadcasting Clos networks.
Information.
3(3)(2000), 403413.
(An extended abstract, by the same authors, appears in
PDCS'98, pages 7180.)
 —— D. S. Kim, and D. Z. Du^{*}.
Strictly nonblocking multirate multicast Clos networks.
In Proceedings of the 10th International Conference on Parallel and Distributed Computing and Systems (PDCS'98)). Pages 417420.

S.X. Gao^{*} and
——.
Decision tree complexity of graph properties with dimension at most 5.
Journal of Computer Science and Technology.
15(5)(2000), 416422.

D. F. Hsu,
X. D. Hu^{*}, and
——.
On minimumweight kedge connected Steiner networks on metric spaces.
Graphs and Combinatorics.
16(3)(2000), 275284.
(A preliminary version, by Cui, Hsu, Hu, and Lin, appears in
ISORA'96, pages 159164.)
 H. Q. Cui, D. F. Hsu, X. D. Hu^{*}, and ——.
Algorithms for constructing kconnected spanning networks.
In Proceedings of the Second International Symposium on Operations Research and its Applications (ISORA'96). Pages 159164.

—— and
G. L. Xue^{*}.
Reducing the Steiner problem in four uniform orientations.
Networks.
35(4)(2000), 287301.
(A preliminary version, by the same authors, appears in
ISAAC'98, LNCS 1533, pages 327336.)
 —— and G. L. Xue^{*}.
The Steiner tree problem in λ_{4}geometry.
In Proceedings of the Ninth Annual International Symposium on Algorithms and Computation (ISAAC'98). LNCS 1533, Pages 327336.
1999:

——,
D. Z. Du^{*},
X. D. Hu, and
G. L. Xue.
On rearrangeability of multirate Clos networks.
SIAM Journal on Computing.
28(4)(1999), 12251231.

—— and
G. L. Xue^{*}.
Steiner tree problem with minimum number of Steiner points and bounded edgelength.
Information Processing Letters.
69(2)(1999), 5357.
1998:

—— and
G. L. Xue^{*}.
Kcenter and kmedian problems in graded distances.
Theoretical Computer Science.
207(1)(1998), 181192.

——.
The exact bound of Lee's MLPT.
Discrete Applied Mathematics.
85(3)(1998), 251254.

——^{*},
E. Y. Yao, and
Y. He.
Parallel machines scheduling to maximize the minimum load with nonsimultaneous machine available times.
Operations Research Letters.
22(23)(1998), 7581.
1997:

Y. He^{*} and
——.
Two worstcase performance bounds of LPT algorithm.
Journal of Zhejiang University.
31(2)(1997), 135141.

——^{*},
Y. He,
H. Y. Lu, and
Y. J. Yao.
Exact bounds of the modified LPT algorithms applying to parallel machines scheduling with nonsimultaneous machine available times.
Applied Mathematics  A Journal of Chinese Universities.
12B(1)(1997), 109116.
