State-Space Search: Algorithms, Complexity, Extensions and Applications, Springer, 1999. ISBN 0-387-98832-7
Journal and conference publications: 2009, 2008, 2007, 2006, 2005, 2004, 2003, 2002, 2001, 2000, selected before 2000
(drop me a message (email to zhang AT cse DOT wustl DOT edu) if you want a copy of a paper which is not available here.)
Computational biology/genomics - Small noncoding RNAs
X. Zhou, R. Sunkar, H. Jin, J-K. Zhu and W. Zhang, Genome-wide identification and
analysis of small RNAs originated from natural antisense
transcripts in Oryza sativa,
Genome Research, 19:70-8, 2009. 
G. Jagadeeswaran, Y. Zheng, Y-f. Li, L.I. Shukla, J. Matts, P. Hoyt, S.L. Macmil, G.B. Wiley, B.A. Roe, W. Zhang, R. Sunkar, Cloning and characterization of small RNAs from Medicago truncatula reveals novel legume-specific and candidate microRNAs, New Phytologist, 184(1):85-98, 2009.
A.M. Reddy, Y. Zheng, G. Jagadeeswaran, S.L. Macmil, G.B. Wiley,
B.A. Roe, U. Desilva, W. Zhang and R. Sunkar, Cloning, characterization and expression
analysis of porcine microRNAs, BMC
Genomics, 10:65,
2009.
Computational biology/genomics - Transcriptome analysis
J.A. Webster, J.R. Cibbs, J. Clarke, M. Ray, W. Zhang, P. Holmans, K. Rohrer, A. Zhao, L. Marlowe, M. Kaleem, D.S. McCorquodale III, C. Cuello, D. Leung, L. Bryden, P. Nath, V.L. Zisman, K. Joshipura, M.J. Huentelman, D. H Lince, K.D. Coon, D.W. Craig, J.V. Pearson, C.B. Heward, E.M. Reiman, D. Stephan, J. Hardy, A.J. Myers, Genetic control of human brain transcript expression in Alzheimer's disease, American J. of Human Genetics, 84:445-458, 2009.
J. Ruan, Y Deng, E.J. Perkins and W. Zhang, An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series expression data, BMC Genomics, Suppl 1:S8, 2009.
M. Ray and W. Zhang, Integrating
genetic and phenotypic information to analyze Alzheimer's disease,
J. of Alzheimer's Disease,
16(1):73-84, 2009. 
Computational
biology/genomics
- Haplotype inferencing
S. Climer, G. Jaegerg, A. Templeton and W. Zhang, How frugal is mother nature with haplotypes?
Bioinformatics, 25(1):68-74, 2009. 
G. Jaeger, S. Climer and W. Zhang. Complete parsimony haplotype inference problem and algorithms, Proc. 17th Annual European Symposium on Algorithms (ESA-09), Copenhagen, Sept, 7-9, 2009, to appear.
Search, planning and combinatorial optimization
Y. Chen, R. Huang, Z. Xing and W. Zhang, Long-distance mutual exclusion for planning,
Artificial Intelligence, 173:365-91,
2009. 
Computational biology/genomics - Small noncoding RNAs
R. Sunkar, X. Zhou, Y. Zheng, W. Zhang and J-K. Zhu, Identification
of novel and candidate miRNAs in
rice by high throughput sequencing, BMC
Plant Biology, 8:25,
2008.
Y. Xu, X. Zhou and W. Zhang, MicroRNA
prediction with a novel ranking
algorithm based on random walks, Bioinformatics 24:i50-i58, 2008, (Proc. 16th
Annual Intern. Conf. on Intelligent Systems for Molecular Biology
(ISMB-2008)).
X. Zhou, G. Wang, K. Sutoh, J-K. Zhu and W. Zhang, Identification of cold inducible microRNAs
in plants by transcriptome analysis, Biochim Biophys Acta, 1779(11):780-8, 2008. (special issue
on
microRNAs) doi:10.1016/j.bbagrm.2008.04.005. 
Computational biology/genomics - Transcriptome analysis
M. Ray, J. Ruan and W. Zhang, Variations
in the transcriptome of Alzheimer's disease reveal modular networks
involved in cardiovascular diseases, Genome Biology, 9(10):R148, 2008.
J.E. McDunn, K. Husain, A.D. Polpitiya, A. Burykin, J.
Ruan, Q. Li, W. Schierding, N. Lin, D. Dixon, W. Zhang, C.M.
Coopersmith, W.M.
Dunne, M. Colonna, B.K. Ghosh and J.P. Cobb, Plasticity of the systemic inflammatory
reponse to acute infection during critical illness: Development of the
riboleukogram, PLoS ONE,
3(2):e1564, 2008.
J. Ruan and W. Zhang, Identifying
network communities with a high resolution, Physical
Review E, 77:016104,
2008. 
Search, planning and combinatorial optimization
Y. Chen, R. Huang and W. Zhang, Fast
planning by search in domain transition graphs, Proc. 23rd AAAI Conference on Artificial
Intelligence (AAAI-08),
Chicago, IL, USA, July 13-17, 2008. 
R. Huang, Y. Chen and W. Zhang, DTG-Plan:
Fast planning by search in domain transition graphs, Proc. 6th International Planning
Competition, International Conf. on Automated Planning and Scheduling, 2008.

Computational molecular biology, Machine Learning and Datamining
X. Zhou, J. Ruan, G. Wang and W. Zhang, Characterization and identification of
microRNA
core promoters in four model species, PLoS
Computational
Biology, 3(3):e37, 2007.
. [Supplemental
materials]
X. Zhou, G. Wang and W. Zhang, UV-B
light responsive microRNA genes in Arabidopsis
thaliana, Molecular
Systems Biology, 3:103,
2007.
M. Ray, S. Dharmarajan, J. Freudenberg, W. Zhang and G.A.
Patterson, Expression
profiling of human
donor lungs to understand primary graft dysfunction after lung
transplantation, American
J. of Transplantation, 7:2396-405,
2007.
H. Zeng, L. Luo, W. Zhang, J. Zhou, Z. Li, H. Liu, T.
Zhu, X. Feng and Y. Zhong, PlantQTL-GE:
A database for searching candidate genes by gene
expression and QTL information, Nucleic
Acids Research, 35:D879-82,
2007.
X. Zhou and W. Zhang, Combinatory circuits of miRNAs and transcription factors for plant gene regulation, RECOMB Satellite Conference on Systems Biology, San Diego, Nov. 30 - Dec. 1, 2007.
J. Ruan and W. Zhang, An
efficient
spectral algorithm for network community discovery and its applications
to biological and social networks, Proc. IEEE Intern. Conf. on Data Mining,
ICDM-07, Omaha, NE, USA, Oct. 28-31, 2007.
M. Ray, S. Dharmarajan, J. Freudenberg, G.A. Patterson and W. Zhang, Gene expression profiling and machine learning to understand and predict primary graft dysfunction, Proc. IEEE 7-th Intern. Conf. on BioInfornatics & BioEngineering, Boson, MA, Oct. 14-17, 2007.
R. Souvenir, J. Buhler, G. Stormo and W. Zhang, An iterative method for selecting
degenerate multiplex PCR primers, Methods in Molecular
Biology, 402:245-68, 2007.
[software]
M. Ray, J. Freudenberg and W. Zhang, A
comprehensive analysis
of the effect of microarray data preprocessing methods on
differentially expressed transcript selection, in Normalization Concepts for Microarray
Technologies, Phillip Stafford (editor), Taylor and Francis
Publications, 2007. 
Search, planning and combinatorial optimization
Z. Xing, Y. Chen and W. Zhang, Long-distance
mutual exclusions for propositional planning, Proc. 20th Intern. Joint Conf. on Artificial
Intelligence (IJCAI-07),
Hyderabad, India, Jan. 9-12, 2007.
Computational molecular biology, Machine Learning and Datamining
G. Wang and W. Zhang, A
steganalysis-based approach to
comprehensive
identification and characterization of functional regulatory elements,
Genome
Biology, 7(6):R49,
2006. [software]

S. Climer and W. Zhang, Rearrangement
clustering: Pitfalls, remedies and applications, J.
Machine
Learning Research, 7:919-43,
2006. [software] 
J. Ruan and W. Zhang, A
bi-dimensional regression tree approach to the modeling of gene
expression regulation, Bioinformatics, 22(3):332-40, 2006. 
J. Ruan and W. Zhang, Identification
and evaluation of weak community structures in networks, Proc.
21st National Conf. on Artificial Intelligence, (AAAI-06), Boston,
Massachusetts, July
16-20, 2006, pp.470-5. 
J. Ruan and W. Zhang, Identification and evaluation of functional modules in gene co-expression networks, RECOMB Satellite Conference on Systems Biology, San Diego, Dec. 1-3, 2006, (oral presentation).
X. Zhou, G. Wang and W. Zhang, UV-B light responsive microRNA genes in Arabidopsis thaliana, RECOMB Satellite Conference on Systems Biology, San Diego, Dec. 1-3, 2006, (oral presentation).
Search, planning and combinatorial optimization
S. Climer and W. Zhang, Cut-and-solve:
A linear search strategy for combinatorial optimization problems,
Artificial Intelligence, 170(8-9):714-38,
2006.
[software]
Z. Xing, Y. Chen and W. Zhang, An
efficient hybrid strategy for temporal planning, Proc. 3rd Intern. Conf. on Integration of
AI and OR Techniques for Constraint Programming for Combinatorial
Optimization Problems (CP-AI-OR 2006), Cork, Ireland, May
30-June 2, 2006. 
Z. Xing, Y. Chen and W. Zhang, Optimal
STRIPS planning by maximum satisfiability and accumulative learning,
Proc. Intern. Conf. on Automated Planning and Scheduling
(ICAPS-06), Cumbia, UK, June 6-10, 2006, pp.442-7.
Z. Xing and Y. Chen and W. Zhang, MaxPlan:
Optimal planning by decomposed satisfiability and backward reduction,
Proc. 5th International Planning Competition, Intern. Conf. on
Automated Planning and Scheduling
(ICAPS-06), Cumbia, UK, June 6-10, 2006, pp.53-6. (First Place Award, Optimal Planning
Track) 
Computational molecular biology, Machine Learning and Datamining
W. Zhang, J. Ruan, T-h. D. Ho, Y. You, T. Yu and R.S.
Quatrano, Cis-regulatory
element based targeted gene finding: Genome-wide identification of ABA-
and abiotic stress-responsive genes in Arabidopsis thaliana,
Bioinformatics, 21(14):3074-81, 2005. 
G. Wang, T. Yu and W. Zhang, WordSpy:
Identify transcription
factor
binding motifs by building a dictionary and learning a grammar, Nucleic
Acids Research, 33:W412-6, 2005. [web server] 
J. Ruan and W. Zhang, CAGER:
Classification analysis of gene
expression
regulation using multiple information sources, BMC
Bioinformatics, 6:114, 2005. 
G. Wang and W. Zhang, Genome-wide identification of cis-regulatory elements: A steganalysis approach, Proc. of First Annual RECOMB Satellite Workshop on Systems Biology and the Second Annual RECOMB Satellite Workshop on Regulatory Genomics, San Diego, CA, Dec. 2-4, 2005. (Oral presentation. The final version appeared in Genome Biology in 2006.)
X. Zhou, J. Ruan, G. Wang and W. Zhang, Characterization of the promoters of microRNA genes: A genome-scale analysis on C. elegans, A. thaliana and H. sapiens, Proc. of First Annual RECOMB Satellite Workshop on Systems Biology and the Second Annual RECOMB Satellite Workshop on Regulatory Genomics, San Diego, CA, Dec. 2-4, 2005. (Poster presentation. The final version will appear in PLoS Computational Biology.
Heuristic search and combinatorial optimization
R. Korf, W. Zhang, I. Thayer and H. Hohwald, Frontier search, J.
ACM, 52(5):715-48, 2005.
Z. Xing and W. Zhang, MaxSolver:
An
efficient exact algorithm
for
(weighted) maximum satisfiability, Artificial Intelligence,
164(1-2):47-80,
2005. [software]

W. Zhang, G. Wang, Z. Xing and L. Wittenberg, Distributed
stochastic
search and distributed breakout: Properties, comparison and
applications to constraint optimization problems in sensor networks,
Artificial
Intelligence, 161(1-2):55-87, 2005. 
W. Zhang and M. Looks A novel
local
search algorithm for the
Traveling
Salesman Problem that exploits backbones, Proc. 19th
Intern. Joint
Conf. on Artificial Intelligence (IJCAI-05).
Computational molecular biology and Machine Learning
J. Ruan, G. Stormo and W. Zhang, ILM:
A web server for
predicting
RNA secondary structures with pseudoknots, Nucleic Acids
Research, 32:W146-9, 2004. [web server] 
J. Ruan, G. Stormo and W. Zhang, An
iterated loop matching
approach
to the prediction of RNA secondary structures with pseudoknots, Bioinformatics,
20(1)58-66, 2004. [softare and web server]

S. Climer and W. Zhang, Take a
walk
and cluster genes: A
TSP-based
approach to optimal rearrangement clustering, Proc. Intern.
Conf.
on Machine Learning (ICML-04), Alberta, Canada, July 4-8,
2004. [software]

J. Buhler, R. Souvenir, W. Zhang and R.
Mitra, Design of a
high-throughput assay for alternative splicing using polymerase
colonies, Proc. Pacific Symposium on Biocomputing (PSB-04),
9:5-16,
2004. 
Heuristic search and combinatorial optimization
W. Zhang, Configuartion
landscape
analysis and backbone guided
local
search: Part I: Satisfiability and maximum satisfiability, Artificial
Intelligence, 158(1):1-26, 2004. 
A. K. Sen, A. Bagchi and W. Zhang, Average
case analysis of
best-first search in two representative directed acyclic graphs,
Artificial
Intelligence, 155(1-2):183-206, 2004. 
W. Zhang, Phase transitions
and backbones
of the asymmetric
Traveling
Salesman Problem, J. Artificial Intelligence Research,
20:471-97, 2004.
Z. Xing and W. Zhang, Efficient strategies for (weighted) maximum satisfiability, Proc. 10th Intern. Conf. on Principles and Practice of Constraint Programming (CP-04), Toronto, Canada, Sept. 27 - Oct. 1, 2004, pp.690-705.
S. Climer and W. Zhang, A linear search strategy with bounds, Proc. 14th Intern. Conf. on Automated Planning and Scheduling (ICAPS-04), British Columbia, Canada, June 3-7, 2004.
W. Zhang and X. Zhang, An improved integer local search for complex scheduling problems, Proc. 14th Intern. Conf. on Automated Planning and Scheduling (ICAPS-04), British Columbia, Canada, June 3-7, 2004.
R. Souvenir, J. Buhler, G. Stormo and W. Zhang, Selecting
degenerate
multiplex PCR primers, in Proc. Workshop on Algorithms in
Bioinformatics (WABI-03), September 15-20, 2003, Budapest,
Hungary. [software]

W. Zhang, Phase transitions of
the
asymmetric Traveling
Salesman, Proc.
18th Intern. Joint Conf. on AI (IJCAI-03), Acapulco, Mexico, Aug.
9-15, 2003, pages 1202-7. 
W. Zhang, A. Rangan and M. Looks, Backbone
guided local
search for
maximum satisfiability, Proc. 18th Intern. Joint Conf. on
Artificial Intelligence
(IJCAI-03), Acapulco, Mexico, Aug. 9-15, 2003, pages
1179-84. [software]

W. Zhang, Z. Xing, G. Wang and L. Wittenburg, An analysis and
application of distributed constraint satisfaction and optimization
algorithms in sensor networks, Proc. 2nd Intern. Joint
Conf. on
Autonomous Agents & Multi Agent Systems (AAMAS-03), Melbourne,
Australia, July 14-18, 2003, pages 185-92. 
W. Zhang and L. Wittenburg, Distributed breakout algorithm for distributed constraint optimization problems - DBArelax, Proc. 2nd Intern. Joint Conf. on Autonomous Agents & Multi Agent Systems (AAMAS-03), Melbourne, Australia, July 14-18, 2003, (poster).
G. Wang, W. Zhang, R. Mailler and V. Lesser, Analysis of negotiation protocols by distributed search, in Distributed Sensor Networks: A Multiagent Systems Approach, V. Lesser, C. Ortiz, and M. Tambe (eds.), Kluwer, 2003, pages 339-62.
W. Zhang, G. Wang, Z. Xing and L. Wittenburg, A comparative study of distributed constraint algorithms with applications to problems in sensor networks, in Distributed Sensor Networks: A Multiagent Systems Approach, V. Lesser, C. Ortiz, and M. Tambe (eds.), Kluwer, 2003, pages 319-38.
D. S. Johnson, G. Gutin, L. A. McGeoch, A. Yeo, W. Zhang and
A.
Zverovich, Experimental analysis of
heuristics for the ATSP, in The
Traveling Salesman Problem and its
Variations, G. Gutin and A. Punnen, Editors, Kluwer Academic
Publishers, 2002, pp.445-88. 
W. Zhang, Search techniques, to appear as Chapter 8 of Handbook of Data Mining and Knowledge Discovery, Oxford University Press, 2002.
Z. Deng and W. Zhang, Localization and dynamic tracking using wireless-networked sensors and multi-agent technology: First steps, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E85-A(11) 2002 (invited paper).
W. Zhang and L. Wittenburg, Distributed
breakout revisited, in Proc.
18-th National Conf. on Artificial
Intelligence (AAAI-2002), Edmonton, Canada, July 28-August 1,
2002, pp.352-7. 
S. Climer and W. Zhang, Searching
for
backbones and fat: A
limit-crossing approach with applications, in Proc. 18-th
National
Conf. on Artificial Intelligence (AAAI-2002), Edmonton, Canada,
July 28-August 1, 2002, pp.707-12. 
A. K. Sen, A. Bagchi and W. Zhang, An
average-case analysis
of graph
search, in Proc. 18-th
National
Conf. on Artificial Intelligence (AAAI-2002), Edmonton, Canada,
July 28-August 1, 2002, pp.757-62. 
W. Zhang, Phase transitions, backbones, measurement accuracy, and phase aware approximations: The ATSP as a case study, Proc. 4th Intern. Workshop on Integration of AI and OR techniques in Constraint Programming for Combinatorial Optimization Problems (AI-OR-CP-02), 2002.
W. Zhang, G. Wang and L. Wittenburg, Distributed stochastic
search
for constraint satisfaction and optimization: Parallelism, phase
transitions and performance, in Proc. AAAI Workshop
on
Probabilistic Approaches in Search, Edmonton, Canada, July 28,
2002,
pp.53-9. 
W. Zhang and Z. Xing, Distributed
breakout vs. distributed
stochastic:
A comparative evaluation on scan scheduling, in Proc. AAMAS-02 Third International
Workshop on
Distributed Constraint Reasoning, July 16, 2002, Bologna, Italy,
pp.192-201. 
W. Zhang, Z. Deng, G. Wang, L. Wittenburg and Z. Xing, Distributed
problem solving in sensor networks, in Proc. 1st Intern. Joint
Conf. on
Autonomous Agents & Multi Agent Systems (AAMAS-02), July 15-19,
Bologna, Italy, poster paper.
W. Zhang, Iterative
state-space reduction
for flexible computation, Artificial
Intelligence, 126(1-2):109-138,
2001. 
W. Zhang, Phase transitions
and backbones
of 3-SAT and Maximum
3-SAT, Proc. 7th Intern.
Conf. on
Principles and
Practice of Consstraint Programming (CP-2001), Paphos, Cyprus,
Nov. 26 - Dec. 1, 2001. 
J. Cirasella, D.S. Johnson, L. A. McGeoch and W. Zhang, The
asymmetric
Traveling Salesman Problem: Algorithms, instance generators, and tests,
in Proc. of ALENEX 2001.

M. Tambe and W. Zhang, Towards flexible teamwork in persistent teams: Extended report, Autonomous Agents and Multi-Agent Systems, 3(2):159-83, 2000. (selected from the Best of ICMAS-98)
R. E. Korf and W. Zhang, Divided-and-conquer frontier search applied to optimal sequence alignment, Proc. 17-th National Conf. on Artificial Intelligence (AAAI-2000), Austin, Texas, July 30-August 3, 2000, pp.910-6.
W. Zhang, Depth-first
branch-and-bound
vs. local search: A case
study, Proc. 17-th
National
Conf. on
Artificial Intelligence (AAAI-2000), Austin, Texas, July
30-August 3, 2000, pp.930-5.
W. Zhang and R. Hill, A
template-based and pattern-driven
approach to
situation awareness and assessment in virtual humans, Proc. of 4th Intern. Conf. on Autonomous
Agents (Agents 2000), Barcelona, Catalonia, Spain, June 3-7,
2000. 
W. Zhang and R. Hill, Situation awareness and assessment: Issues and computational approaches, Proc. 9th Conference on Computer Generated Forces and Behavioral Representation, May 16-18, 2000.
W. Zhang, Association-based multiple imputation in multivariate datasets: A summary, Proc. 16-th Intern. Conf. on Data Engineering (ICDE-2000), San Diego, CA, Feb. 29-March 3, 2000.
W. Zhang and R.E. Korf, A
study of
complexity transitions on the
asymmetric traveling salesman problem, Artificial Intelligence, 81(1-2):223-39,
1996.
J.C. Pemberton and W. Zhang, Epsilon-transformation:
Exploiting
Phase
Transitions to solve combinatorial optimization problems, Artificial Intelligence, 81(1-2):297-325,
1996.
W. Zhang, A note on the complexity of the asymmetric Traveling Salesman Problem, Operations Research Letters, 20:31-8, 1997.
W. Zhang and R.E. Korf, Performance
of linear-space search
algorithms, Artificial
Intelligence, 79(2):241-92,
1995.
W. Zhang and R.E. Korf, Parallel Heap Operations on EREW PRAM, J. Parallel and Distributed Computing, 20(2):248-55, 1994.
W. Zhang and N.S.V. Rao, Heuristic tree search with nonparametric statistical inference methods, J. Computer Mathematics, 39(1+2):133-52, 1991.
S. Olariu, Z. Wen and W. Zhang, A faster optimal algorithm for the measure problem, Parallel Computing, 17, 1991, pp.683-7.
W. Zhang, Representation of assembly and automatic robot planning by Petri net, IEEE Trans. on Systems, Man and Cybernetics, 19(2):418-22, 1989.
W. Zhang, Flexible and approximate computation through state-space reduction, Proc. 14-th Annual Conference on Uncertainty in Artificial Intelligence (UAI-98), Madison, Wisconsin, July 24-26, 1998, pp.531-38.
W. Zhang, Complete Anytime Beam Search, Proc. 15-th National Conf. on Artificial Intelligence (AAAI-98), Madison, Wisconsin, July 26-30, 1998, pp.425-30.
W. Zhang, Forward estimation for game-tree search, Proc. 13-th National Conf. on Artificial Intelligence (AAAI-96), Portland, OR, 1996, pp.240-5
W. Zhang and J. C. Pemberton, Epsilon-transformation: Exploiting complexity transitions to solve combinatorial optimization problems - Initial results, Proc. 12-th National Conf. on Artificial Intelligence (AAAI-94), Seattle, WA, July 31-Aug. 4, 1994, pp.895-900.
W. Zhang and R.E. Korf, Depth-first vs. best-first search: New results, Proc. 11-th National Conf. on Artificial Intelligence (AAAI-93), Washington, DC, July 11-15, 1993, pp.769-75.
W. Zhang, Truncated branch-and-bound: A case study on the asymmetric traveling salesman problem, Proc. of AAAI 1993 Spring Symposium on AI and NP-Hard Problems, Stanford, CA, March 23-25, 1993, pp.160-6. [ps file]
W. Zhang and R.E. Korf, An average-case analysis of branch-and-bound with applications: Summary of results, Proc. 10-th National Conf. on Artificial Intelligence (AAAI-92), San Jose, CA, July 12-17, 1992, pp.545-50.
Weixiong Zhang and Volker Sorge, Distributed Constraint Problem Solving and Reasoning in Multi-agent Systems, editers, IOS Press, 2004.
Weixiong Zhang, Rina Dechter
and Richard E. Korf, Artificial
Intelligence, vol. 129, no 1-2, special issue on Heuristic Search;
Editorial: Heuristic
search in artificial intelligence
Weixiong Zhang, Computational biology: Perspective and approaches based on feature extraction and selection, National Conference on Artificial Intelligence (AAAI-06).
Weixiong Zhang and Sharlee Climer, Techniques for computing and using bounds for combinatorial optimization problems, 19th International Joint Conference on Artificial Intelligence (IJCAI-05).
Weixiong Zhang and Sharlee Climer, Systematic bounding techniques for combinatorial optimization, 12th National Conf. on Artificial Intelligence (AAAI-05).