Publications from the Genomics in Healthcare Lab

Book

State-Space Search: Algorithms, Complexity, Extensions and Applications, Springer, 1999. ISBN 0-387-98832-7

2025

C. Huo, D. He, Y. Li, D. Jin, J. Dang, W. Pedrycz, L. Wu, and W. Zhang, Heterogeneous Graph Neural Networks using Self-supervised Reciprocally Contrastive Learning, ACM Trans. Intell. Syst. Technol, 2025, 16(1):1-21.
H. Guo, Y. Xiao, S. Dong, J. Yang, P. Zhao, T. Zhao, A. Cai, L. Tang, J. Liu, H. Wang, R. Hua, R. Liu, Y. Wei, D. Sun, Z. Liu, M. Xia, Y. He, Y. Wu, T. Si, F. Womer, F. Xu, Y. Tang, J. Wang, W. Zhang, X. Zhang & F. Wang, Bridging animal models and humans: neuroimaging as intermediate phenotypes linking genetic or stress factors to anhedonia, BMC medicine, 23(1):38, 2025.
Q. Zhao, C. Zhang, W. Zhang, dnaGrinder: a lightweight and high-capacity genomic foundation model, arXiv, 2024, https://arxiv.org/abs/2409.15697.

2024

D. He, C. Liang, C. Huo, Z. Feng, D. Jin, L. Yang, and W. Zhang, Analyzing heterogeneous networks with missing attributes by unsupervised contrastive learning, IEEE Transactions on Neural Networks and Learning Systems, 35(4):4438-50, 2024.
D. He, L. Shan, J. Zhao, H. Zhang, Z. Wang, W. Zhang, Exploitation of a latent mechanism in graph contrastive learning: Representation scattering, Proc 38-th Conference on Neural Information Processing Systems (NeurIPS 2024).
Y. Zhou, D. Jin, J. Wei, D. He, Z. Yu, and W. Zhang, Generalized taxonomy-guided graph neural networks, Proc 33-rd Intern. Joint Conf. on AI (IJCAI-24).

2023

D. He, J. Zhao, R. Guo, Z. Feng, D. Jin, Y. Huang, Z. Wang and W. Zhang, Contrastive learning meets homophily: Two birds with one stone, Conference on Machine Learning (ICML-2023).
X. Wei, C. Pan, X. Zhang*, W. Zhang*, Total network controllability analysis discovers explainable drugs for Covid-19 treatment, Biology Direct, 18(1):55, 2023.
X. Zhang*, C. Pan, X. Wei, M. Yu, S. Liu, J. An, J. Yang, B. Wei, W. Hao, Y. Yao*, Y. Zhu*, and W. Zhang*, Cancer-keeper genes as therapeutic targets, iScience, 26(8):107296, 2023.
D. Jin, Z. Yu, P. Jiao, S. Pan, D. He, J. Wu, P. Yu, W. Zhang, A survey of community detection approaches: From statistical modeling to deep learning, IEEE Transactions on Knowledge and Data Engineering, 35(2):1149-90, 2023.
Y. Xiao, FY. Womer, S. Dong, R.Zhu, R. Zhang, J. Yang, L. Zhang, J. Liu, W. Zhang, Z. Liu, X. Zhang, F. Wang*, A neuroimaging-based precision medicine framework for depression, Asian Journal of Psychiatry, 91:103803, 2023.
S. He, S. Qiu, M.Pan, J. P Palavicini, H. Wang, X. Li, A. Bhattacharjee, S. Barannikov, K. F Bieniek, J. L Dupree and X. Han, Marked reduction of spinal cord lipids causes neurogenic bladder in late Alzheimer's disease, Clinical and Translational Medicine, 2023.
S. Qiu, S. He, J. Wang, H. Wang, A. Bhattacharjee, X. Li, M. Saeed, J. L. Dupree, X. Han, Adult-onset CNS sulfatide deficiency causes sex-dependent metabolic disruption in aging, International Journal of Molecular Sciences, 24(13), 2023.
S. Qiu, J. P. Palavicini, X. Han, Myelin lipid deficiency: a new key driver of Alzheimer's disease, Neural Regeneration Research, 18:121-122, 2023.
Dustin, E., E. Suarez-Pozos, C. Stotesberry, S. Qiu, J. P. Palavicini, X. Han and J. L. Dupree, Compromised Myelin and Axonal Molecular Organization Following Adult-Onset Sulfatide Depletion, Biomedicines, 11(5), 2023.

2022

D. Jin, R. Wang, M. Ge, H. He, X. Li, W. Lin and W. Zhang, RAW-GNN: Random Walk Aggregation based graph neural network, Proc 31-st Intern. Joint Conf. on AI (IJCAI-22).
D. He, C. Liang, C. Huo, Z. Feng, D. Jin, L. Yang, and W. Zhang, Analyzing heterogeneous networks with missing attributes by unsupervised contrastive learning, IEEE Transactions on Neural Networks and Learning Systems, published online March 2022.
P. Xuan*, L. Zhan, H. Cui, T. Zhang, T. Nakaguchi, W. Zhang, Graph Triple-Attention Network for Disease-Related LncRNA Prediction, IEEE Journal of Biomedical and Health Informatics, 26(6):2839-49, 2022.
Palavicini, J. P., L. Ding, M. Pan, S. Qiu, H. Wang, Q. Shen, J. L. Dupree and X. Han, Sulfatide Deficiency, an Early Alzheimer's Lipidomic Signature, Causes Brain Ventricular Enlargement in the Absence of Classical Neuropathological Hallmarks, International Journal of Molecular Sciences, 24(1), 2022.

S. He, S. Qiu, M.Pan, J. P Palavicini, H. Wang, X. Li, A. Bhattacharjee, S. Barannikov, K. F Bieniek, J. L Dupree and X. Han, Marked reduction of spinal cord lipids causes neurogenic bladder in late Alzheimer's disease, Clinical and Translational Medicine, 2023.
S. Qiu, S. He, J. Wang, H. Wang, A. Bhattacharjee, X. Li, M. Saeed, J. L. Dupree, X. Han, Adult-onset CNS sulfatide deficiency causes sex-dependent metabolic disruption in aging, International Journal of Molecular Sciences, 24(13), 2023.
S. Qiu, J. P. Palavicini, X. Han, Myelin lipid deficiency: a new key driver of Alzheimer's disease, Neural Regeneration Research, 18:121-122, 2023.
Dustin, E., E. Suarez-Pozos, C. Stotesberry, S. Qiu, J. P. Palavicini, X. Han and J. L. Dupree, Compromised Myelin and Axonal Molecular Organization Following Adult-Onset Sulfatide Depletion, Biomedicines, 11(5), 2023.

2021

M. Chang, F. Womer, X. Gong, X. Chen, L. Tang, R. Feng, S. Dong, J. Duan, Y. Chen, R. Zhang, Y. Wang, S. Ren, Y. Wang, J. Kang, Z. Yin, Y. Wei, S. Wei, X. Jian, K. Xu, B. Cao, Y. Zhang, W. Zhang, Y. Tang, X. Zhang, F. Wang, Identifying and validating subtypes within major psychiatric disorders based on frontal-posterior functional imbalance via deep learning, Molecular Psychiatry, available online..
X. Liu, J. Frost, A. Bowcock, W. Zhang*, Canonical and interior circular RNAs function as competing endogenous RNAs in psoriatic skin, Intern. J. Molecular Sciences, 22(10):5182, 2021..
L. Chen, J. Zhou, T. Li, Z. Fang, L. Li, G. Huang, L. Gao, X. Zhu, X. Zhou, H. Xiao, J. Zhang, Q. Xiong, J. Zhang, A. Ma, W. Zhai, W. Zhang*, and H. Peng*, GmoDetector: An accurate and efficient GMO identification approach and its application, Food Research International, 149:110662, 2021.

D. Jin, Z. Yu, P. Jiao, S. Pan, D. He, J. Wu, P. Yu, and W. Zhang, A survey of community detection approaches: From statistical modeling to deep learning, IEEE Trans. on Knowledge and Data Engineering, available online..

Z. Zhang, T. Zhao, H. Gay, W. Zhang*, B. Sun*, Weaving attention U-net: A novel hybrid CNN and attention-based method for organs-at-risk segmentation in head and neck CT images, Medical Physics, in press.

Z. Zhang, T. Zhao, H. Gay, W. Zhang*, B. Sun*, ARPM-net: A novel CNN-based adversarial method with Markov Random Field enhancement for prostate and organs at risk segmentation in pelvic CT images, Medical Physics, 48(1):227-37, 2021.
Z. Zhang, T. Zhao, H. Gay, W. Zhang*, B. Sun*, Semi-supervised semantic segmentation of prostate and organs-at-risk on 3D pelvic CT images, Biomedical Physics & Engineering Express, in press.

2020

X. Liu, Z. Hu, J. Zhou, C. Tian, G. Tian, M. He, L. Gao, L. Chen, T. Li, H. Peng, and W. Zhang*, Interior circular RNA, RNA Biology, 17(1):87-97, 2020. News about our discovery

P. Xuan, T. Shen, X. Wang, T. Zhang and W. Zhang, Inferring disease-associated microRNAs in heterogeneous networks with node attributes, IEEE/ACM Trans. Computational Biology and Bioinformatics, 17(3):1019-31, 2020.
S. Climer*, A.R. Templeton, M. Garvin, D. Jacobson, M. Lane, S. Hulver, B. Scheid, and W. Zhang*, Syncronized genetic activities in Alzheimer's brains revealed by heterogeneity-capturing network analysis, bioRxiv.
S. Zhang, Z. Xia, W. Zhang, C. Li, X. Wang, X. Lu, X. Zhao, H. Ma, W. Zhang, X. Zhou, T. Zhu, P. Liu, G. Liu, H. Yang, J. Arango, M. Peters, W. Wang*, and T. Xia*, Chromosome-scale genome assembly provides insights into speciation of allotetraploid and massive biomass accumulation of elephant grass (Pennisetum purpureum Schum.), bioRxiv.

M. Li, D. Jin, D. He, and W. Zhang, Modeling with node popularities for autonomous overlapping community detection, ACM Transactions on Information Systems, 11(3):27, 2020.
X. Zhang, J. Gao, Y. Lv and W. Zhang, Early and efficient identification of useless constraint propagation for alldifferent constraints, Proc 29-th Intern. Joint Conf. on AI (IJCAI-20)
D. He, Y. Song, D. Jin, Z. Feng, B. Zhang, Z. Yu and W. Zhang, Community-centric graph Convolutional Network for unsupervised community detection, Proc 29-th Intern. Joint Conf. on AI (IJCAI-20)

2019

L. Li, H. Peng, S. Tan, J. Zhou, Z. Fang, Z. Hu, L. Gao, T. Li, W. Zhang*, and L. Chen*, Effects of early cold stress on gene expression in Chlamydomonas reinhardtii, Genomics, 2019, doi: 10.1016/j.ygeno.2019.06.027.

D. Lam, X. Zhang, H. Li, Y. Deshan, B. Schott, T. Zhao, W. Zhang, S. Mutic, and B. Sun*, Predicting gamma passing rates for portal dosimetry-based IMRT QA using machine learning, Medical Physics, doi: 10.1002/mp.13752, 2019.
X. Wang, D. Jin, D. He, and W. Zhang, Robust detection of link communities with summary description in social networks, IEEE Transactions on Knowledge Discovery and Engineering, accepted.

L. Yang, Y. Wang, J. Gu, X. Cao, X. Wang, D. Jin, G. Ding, J. Han, and W. Zhang, Autonomous semantic community detection via adaptively weighted low-rank approximation, ACM Transactions on Multimedia Computing, Communications, and Applications (TOMM), 15(3s), 2019.
D. Jin, Z. Liu, W. Li, D. He, and W. Zhang, Graph Convolutional Networks meet Markov Random Fields: Semi-supervised community detection in attribute networks, Proc 33-rd AAAI Conf on AI (AAAI-19).
D. Jin, B. Li, P. Jiao, D. He, and W. Zhang, Network-specific variational auto-encoder for embedding of attributed networks, Proc 28-th IJCAI (IJCAI-19).

2018

L. Li, G. Tian, H. Peng, D. Meng, L. Wang, X. Hu, C. Tian, M. He, J. Zhou, L. Chen, C. Fu, W. Zhang* and Z. Hu*, New class of transcription factors controls flagellar assembly by recruiting RNA polymerase II in Chlamydomonas, Proceedings of National Academy of Sciences of the USA (PNAS), 115(17):4435-40, 2018.
L. Gao, Z. Fang, J. Zhou, L. Li, L. Lu, L. Li, L. Chen, W. Zhang, W. Zhai, and H. Peng*, Transcriptional insights into the pyramided resistance to rice bacterial blight, Scientific Reports, 8(1):12358, 2018, doi:10.1038/s41598-018-29899-1.
Y. Zhong, P. Xuan*, X. Wang, T. Zhang, J. Li, Y. Liu and W. Zhang, A non-negative matrix factorization based method for predicting disease-associated miRNAs in miRNA-disease bilayer network, Bioinformatics, 34(2):267-77, 2018. .

X. Zhang and W. Zhang, A fast algorithm for generalized arc consistency of the alldifferent constraint, Proc 27-th Intern. Joint Conf. on AI (IJCAI-18).
G. Meng, D. Jin and W. Zhang, Integrative network embedding via deep joint reconstruction, Proc 27-th Intern. Joint Conf. on AI (IJCAI-18).
D. He, X. You, Z. Feng, D. Jin, X. Yang and W. Zhang, A network-specific Markov Random Field approach to community detection, Proc 32-nd AAAI Conf on A I (AAAI-18).
D. Jin, X. Wang, R. He, D. He and W. Zhang, Robust detection of link communities in large social networks by exploiting link semantics, Proc 32-nd AAAI Conf on AI (AAAI-18).

2017

L. Li, Z. Fang, J. Zhou, H. Chen, Z. Hu, L. Gao, L. Chen, S. Ren, H. Ma, L. Lu, W. Zhang* and H. Peng*, An accurate and efficient method for large-scale SSR genotyping and applications, Nucleic Acids Research, 45(10):e88, 2017, doi:10.1093/nar/gkx093.
J. Xia, L. Li, T. Li, Z. Fang, K. Zhang, J. Zhou, H. Peng, and W. Zhang*, Detecting and characterizing microRNAs of diverse genomic origins via miRvial, Nucleic Acids Research, 45(21):e176, 2017.
C. Zeng, J. Xia, X. Chen, Y. Zhou, M. Peng* and W. Zhang*, MicroRNA-like RNAs from the same miRNA precursors play a role in cassava chilling responses, Scientific Reports, 7(1):17135, 2017.

TP Michael, D. Bryant, R. Gutierrez, N. Borisjuk, P. Chu, H. Zhang, J. Xia, J. Zhou, H. Peng, M.E. Baidouri, B. ten Hallers, AR. Hastie, T. Liang, K. Acosta, S. Gilbert, C. McEntee, SA. Jackson, TC. Mockler, W. Zhang and E. Lam*, Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies, The Plant Journal, 89(3):617-35, 2017.
D. He, D. Jin and W. Zhang, Joint identification of network communities and semantics via integrative modeling of network topologies and node contents, Proc 31-st AAAI Conf on AI (AAAI-17).
J. Fu, W. Zhang and J. Wu, Identification of leader and self-organizing communities in complex networks, Scientific Reports, 7(1):704, 2017.

X. Zhang, J. Han and W. Zhang, An efficient algorithm for finding all possible input nodes for controlling complex networks, Scientific Reports, 7(1):10677, 2017.

2016

D. Tiosano, L. Audi, S. Climer, W. Zhang, A.R. Templeton*, M. Fernandez-Cancio, R. Gershoni-Baruch, J.M. Sanchez-Muro, M.E. Kholy, Z. Hochberg, Latitudinal Clines of the human Vitamin D receptor and skin color-genes, Genes, Genomes, Genetics, 6(5):1251-66, 2016. doi: 10.1534/g3.115.026773.
J. Xia, X. Wang, P-F. Perroud, Y. He, R. Quatrano and W. Zhang*, Endogenous small-noncoding RNAs and potential functions in desiccation tolerance in Physcomitrella patens, Scientific Reports, 6:30118, 2016.
Z-Y. Li, J. Xia, Z. Chen, Y. Yu, Q-F. Li, Y-C. Zhang, J-P. Zhang, C-Y. Wang, X-Y. Zhu, W. Zhang* and Y-Q. Chen*, Large-scale rewiring of innate immunity circuitry and microRNA regulation during initial rice blast infection, Scientific Reports, 6:25493, 2016.
L. Chen, J. Han, X. Deng, S. Tan, L. Li, L. Li, J. Zhou, H. Peng, G. Yang*, W. Zhang*, Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon, Scientific Reports, 6:21623, 2016.

G. Jager, S. Climer and W. Zhang. Complete Parsimony Haplotype Inference Problem and Algorithms Based on Integer Programming, Branch-and-Bound and Boolean Satisfiability, J. Discrete Algorithms, 37:68-83, 2016.
L. Yang, X. Cao, D. He, W. Zhang, Modularity based community detection with deep learning, Proc 25-th Intern. Joint Conf. on AI (IJCAI-16), to appear.
D. Jin, H. Wang, J. Dang, D. He and W. Zhang, Detect overlapping communities via ranking node popularities, Proc 30-th AAAI Conf on AI (AAAI-16), to appear.
X. Wang, D. Jin, X. Cao, L. Yang and W. Zhang, Semantic community identification in large attribute networks, Proc 30-th AAAI Conf on AI (AAAI-16), to appear.

2015

S. Climer*, A. Templeton and W. Zhang*, Human gephyrin is encompassed within giant functional noncoding yin-yang sequences, Nature Communications, 6:6534, 2015, doi: 10.1038/ncomms7534. [Software] [News]

H. Peng, Z. Chen, Z. Fang, J. Zhou, Z. Xia, L. Gao, L. Chen, L. Li, T. Li, W. Zhai, and W. Zhang*, Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection, Scientific Reports, 5:12165, 2015
X. Chen, J. Xia, Z. Xia, H. Zhang, C. Zeng, C. Lu, W. Zhang and W. Wang*, Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor, BMC Plant Biology, 15(1):33, 2015.
D. Nie, J. Xia, C. Jiang, B. Qi, X. Ling, S. Lin, W. Zhang, J. Guo, H. Jin and H. Zhao, Bacillus cereus AR156 primes induced systemic resistance by suppressing miR825/825* and activating defense related genes in Arabidopsis, J Integrative Plant Biol., doi: 10.1111/jipb.12446.

D. He, D. Jin, Z. Chen and W. Zhang, Identification of hybrid node and link communities in complex networks, Scientific Reports, 5:8638, 2015.
Z. Chen, M. Chen, K. Weinberger and W. Zhang, Marginalized denoising for link prediction and multi-label learning, Proc 29-th AAAI Conf on AI (AAAI-15), Jan 25-30, Austin, Texas, USA.
D. Jin, Z. Chen, D. He and W. Zhang, Modeling with node degree preservation can accurately find communities, Proc 29-th AAAI Conf on AI (AAAI-15), Jan 25-30, Austin, Texas, USA.

D. He, D. Liu, D. Jin and W. Zhang, stochastic model for the detection of heterogeneous link communities in complex networks, Proc 29-th AAAI Conf on AI (AAAI-15), Jan 25-30, Austin, Texas, USA.

2014

W. Zhang, Ten simple rules for writing research papers, PLOS Computational Biology, 10(1):e1003453, 2014.

W. Wang, B. Feng, J. Xiao, Z. Xia, X. Zhou, P. Li, W. Zhang, et al., Cassava genome from a wild ancestor to cultivated varieties, Nature Communications, 5:5110, 2014.

S. Climer*, A. Templeton and W. Zhang*, Allele-specific network reveals combinatorial interactions that transcends small effects in psoriasis GWAS, PLOS Computational Biology, 10(9):e1003766. [Software]

J. Xia and W. Zhang*, MicroRNAs in normal and psoriatic skin, Physiological Genomics, 46(4):113-22, 2014. Invited review.

J. Xia and W. Zhang*, A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5'-isoforms in four model species, Nucleic Acids Research, 42(3):1427-41, 2014.
J. Xia, C. Zeng, Z. Chen, K. Zhang, X. Chen, Y. Zhou, S. Song, C. Lu, R. Yang, Z. Yang, J. Zhou, H. Peng, W. Wang, M. Peng*, W. Zhang*, Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in cassava, BMC Genomics, 15:634, 2014.
W. Goettel, Z. Liu, J. Xia, W. Zhang, P.X. Zhao and Y-Q. An*, Systems and evolutionary characterization of microRNAs and their underlying regulatory networks in soybean cotyledons, PLOS ONE, 9(1):e86153, 2014.

C. Zeng, Z. Chen, J. Xia, K. Zhang, X. Chen, Y. Zhou, W. Bo, S. Song, D. Deng, X. Guo, B. Wang, J. Zhou, H. Peng, W. Wang, M. Peng*, W. Zhang*, Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in cassava, BMC Plant Biology, 14(1):207, 2014.

Z. Chen and W. Zhang, A marginalized denoising method for link prediction in relational data,Proc. SIAM Intern. Conf. on Data Mining, April 24-26, 2014, Philadelphia, USA. (Full paper, oral presentation)
Y. Gan, J. Guan, S. Zhou and W. Zhang*, Identifying cis-regulatory elements and modules using Conditional Random Fields, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(1):73-82, 2014.

2013

J. Xia, C.E. Joyce, A.M. Bowcock* and W. Zhang*, Noncanonical microRNAs and endogenous siRNAs in normal and psoriatic human skin, Human Molecular Genetics, 22(4):737-48, 2013.

Z. Chen and W. Zhang*, Integrative analysis using module-guided Random Forests reveals correlated genetic factors related to mouse weight, PLOS Computational Biology, 9(3):e1002956, 2013. [Software]
L. Gao, Y. Cao, Z. Xia, G. Jiang, G. Liu, W. Zhang* and W. Zhai*, Do transgenesis and backcross breeding produce substantially equivalent plants? - A comparative study of transgenic and backcross rice with disease resistant gene Xa21, BMC Genomics, 14(1):738, 2013.
H. Peng, G. Jiang, J. Zhang, W. Zhang and W. Zhai*, DNA methylation polymorphism and stability in Chinese indica hybrid rice, Sci. China Life Sci., 56(12):1097-106, 2013.
Z. Chen and W. Zhang, Domain adaptation with topical correspondence learning, Proc. 23rd Intern. Joint Conf. on Artificial Intelligence (IJCAI-13), Aug. 3-9, 2013, Beijing, China, to appear. (Oral presentation, acceptance rate: ~28%.)

Q. Lu, R. Huang, Y. Chen, Y. Xu, W. Zhang, G. Sun and G. Chen, A SAT-based approach to cost sensitive temporally expressive planning, ACM Transactions on Intelligent Systems and Technology, 5(1):18, 2013.

2012

X. Zhang, J. Xia, Y. Lii, B.E. Barrera-Figueroa, X. Zhou, S. Gao, L. Lu, D. Nie, Z. Chen, C. Leung, T. Wong, H. Zhang, J. Guo, Y. Li, R. Liu, W. Liang, J-K. Zhu, W. Zhang*, H. Jin*, Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function, Genome Biology, 13:R20, 2012.
Y. Zheng, Y-F. Li, R. Sunkar and W. Zhang, SeqTar: An effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants, Nucleic Acids Research, 40(4):e28, 2012.
J. Xia and W. Zhang*, Noncanonical microRNAs and endogenous siRNAs in lytic infection of murine gammaherpesvirus, PLOS ONE, 7(10):e47863, 2012.
J.K. Greenberg, J. Xia, X. Zhou, S.R. Thatcher, X. Gu, S.A. Ament, T.C. Newman, P.J. Green, W. Zhang, G.E. Robinson and Y. Ben-Shahar*, Behavioral plasticity in honey bees is associated with major differences in brain microRNA transcriptome. Genes, Brain and Behavior, 11(6):660-70, 2012.

W. Zhang*, X. Zhou, J. Xia and X. Zhou, Identification of microRNAs and natural antisense transcript-originated endogenous siRNAs from small-RNA deep sequencing data, in Methods in Molecular Biology, 883:221-7, 2012.

D. He, D. Liu, W. Zhang, B. Yang and D. Jin, Discovering link communities in complex networks by exploiting link dynamics, J. Statistical Mechanics, P10015, 2012.
Y. Gan, J. Guan*, S. Zhou and W. Zhang*, Structural features based genome-wide characterization and prediction of nucleosome organization, BMC Bioinformatics, 13:49, 2012.

R. Huang, Y. Chen and W. Zhang, SAS+ planning as Satisfiability, J. Artificial Intelligence Research, 43:293-328, 2012. AAAI 2010 Outstanding Paper Award.

2011

C.E. Joyce, X. Zhou, J. Xia, C. Ryan, B. Thrash, A. Menter, W. Zhang* and A.M. Bowcock*, Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome, Human Molecular Genetics, 20(20):4025-40, 2011.
W. Zhang*, S. Gao, X. Zhou, P. Chellappan, Z. Chen, X. Zhou, X. Zhang, N. Fromuth, G. Coutino, M. Coffey, H. Jin*, Bacterial-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks, Plant Molecular Biology, 75(1-2):93-105, 2011.

2010

W. Zhang*, S. Guo, J. Xia, X. Zhou, P. Chellappan, X. Zhou, X. Zhang and H. Jin*, Multiple distinct small RNAs originate from the same microRNA precursors, Genome Biology, 11:R81, 2010.
T.A. Reese, J. Xia, L.S. Johnson, X. Zhou, W. Zhang* and H.W. Virgin*, Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts, J. Virology, 84(19):10344-53, 2010.
P. Chellappan, J. Xia, X. Zhou, S. Gao, X. Zhang, G. Coutino, F. Vazquez, W. Zhang* and H. Jin*, siRNAs from miRNA sites mediate DNA methylation of target genes, Nucleic Acids Research, 38(20):6883-94, 2010.
C. Zeng, W. Wang, Y. Zheng, X. Chen, X. Bo, S. Song, W. Zhang* and M. Peng*, Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants, Nucleic Acids Research, 38(3):981-95, 2010.
Y-F. Li, Y. Zheng, C. Addo-Quaye, L. Zhang, A. Saini, G. Jagadeeswaran, M. Axtell, W. Zhang and R. Sunkar*, Transcriptome-wide identification of microRNA targets in rice, The Plant Journal, 62(5):742-59, 2010.
G. Jagadeeswaran, Y. Zheng, N. Sumathipala, H. Jiang, E. Arese, J.L. Soulages, W. Zhang and R. Sunkar*, Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development, BMC Genomics, 11:52, 2010.
Y. Zheng* and W. Zhang*, Animal microRNA target prediction using diverse sequence-specific determinants, J. Bioinformatics and Computational Biology, 8(4):763-88, 2010.

M. Ray and W. Zhang*, Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks, BMC Systems Biology, 4:136, 2010.
J. Ruan*, A.K. Dean and W. Zhang*, A general co-expression network-based approach to gene expression analysis: Comparison and applications, BMC Systems Biology, 4:8, 2010. [Software]

S. Pinaki, W. Zhang, P. Cobb and A. Nehorai*, Gene reachability using Page Ranking on gene co-expression networks, Chapter 21, in Link Mining: Models, Algorithms and Applications, Springer, pp.557-68, 2010.

X. Zhou, J. Ruan and W. Zhang, Promoter prediction based on a multiple instance learning scheme, ACM Intern. Conf. on Bioinformatics and Computational Biology, Aug. 2-4, 2010, Niagara Falls, NY, USA, accepted as a full paper.

S. Climer, A. Templeton and W. Zhang, SplittingHeirs: Inferring haplotypes by optimizing resultant dense graphs, ACM Intern. Conf. on Bioinformatics and Computational Biology, Aug. 2-4, 2010, Niagara Falls, NY, USA, accepted as a full paper.

G. Jaeger and W. Zhang, Phase transitions of and an efficient algorithm for the directed Hamiltonian cycle problem, J. Artificial Intelligence Research, 39:663-87, 2010.

R. Huang, Y. Chen and W. Zhang, A novel transition based encoding scheme for planning as Satisfiability, Proc. 24th AAAI Conference on Artificial Intelligence (AAAI-10), Atlanta, Georgia, USA, July 11-15, 2010; Winner of the Outstanding Paper Award of AAAI-10. (source code)

G. Jaeger and W. Zhang, A SAT based effective algorithm for the directed Hamiltonian cycle problem, Proc. of CSR-2010, 216-27.

2009

X. Zhou, R. Sunkar, H. Jin, J-K. Zhu and W. Zhang*, Genome-wide identification and analysis of small RNAs originate 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.

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.
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.
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.

S. Climer, G. Jaeger, 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.

Y. Chen, R. Huang, Z. Xing and W. Zhang, Long-distance mutual exclusion for planning, Artificial Intelligence, 173:365-91, 2009.
R. Huang, Y. Chen and W. Zhang, An optimal temporally expressive planner: Initial results and application to P2P network optimization, Proc. 19th Intern. Conf. on Automated Planning and Scheduling (ICAPS-09), Thessaloniki, Greece, Sept. 19-23, 2009.

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)).
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.
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.

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.

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.

2007

X. Zhou, G. Wang and W. Zhang*, UV-B light responsive microRNA genes in Arabidopsis thaliana, Molecular Systems Biology, 3:103, 2007.
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]
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.

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.

2006

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).

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)

2005

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.

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).

2004

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.

2003

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.

2002

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.

2001

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.

2000

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.

selected papers before 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.

Edited volumes

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 and Sven Koenig, Search Techniques for Problem Solving Under Uncertainty and Incomplete Information, Papers from 1999 AAAI Spring Symposium. ISBN 1-57735-106-1

Tutorials

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).
Carla Gomes, Tad Hogg, Toby Walsh and Weixiong Zhang, Phase Transitions and Structure in Combinatorial Problems, 17th International Joint Conference on Artificial Intelligence (IJCAI-01).