I have now "officially" given up in maintaining this list, as DBLP does such a good job
that requires no work on my part, so just got to
my DBLP entry.
DBLP does miss a few, but in general it is pretty complete.

Below is an old very partial list: most journal papers no longer appear here,
due to a rumor that someone was sued by a journal for putting copyrighted
material on the web... Where appropriate, I've made available
a technical report version of the paper.

R. Brafman, C. Domshlak, S. E. Shimony, and Y. Silver,
``Preferences Over Sets'', Proceedings of the 20th National Conference
on Artificial Intelligence, Boston, MA, AAAI Press, 2006.

G. Shani, R. Brafman, and S. E. Shimony,
``Prioritized Value Iteration for POMDPs'',
Proceedings of the ECML/PKDD 2006 conference,
Berlin, Germany.

A. Berler and S. E. Shimony,
``Multi-Agent Handling of Opportunism - AWOL Meets Discretized Unreal Tournament'',
Proceedings of the IEEE-SMC 2006 conference, Taipei, Taiwan.

Y. Radovilsky, G. Shattah, and S. E. Shimony,
``Efficient Deterministic Approximation Algorithms
for Nonmyopic Value of Information in Graphical Models'',
Proceedings of the IEEE-SMC 2006 conference, Taipei, Taiwan.

Ronen I. Brafman, C. Domshlak, and Solomon E. Shimony
``On graphical modelling of preference and importance'',
Journal of Artificial Intelligence Research,
Volume 25, pages 389-424, January-April 2006.

N. Vanetik, S. E. Shimony, and E. Gudes,
``Support Measures for Graph Data'', Data Mining and Knowledge Discovery,
Volume 13, Number 2, pages 243-260. Springer, September, 2006.

N. Vanetik, S. E. Shimony, and E. Gudes, ``Discovering Frequent Graph
Patterns Using Disjoint Paths'', Accepted for publication in
IEEE Transactions on Knowledge and
Data Engineering, 2006.

I. Rosen, S. E. Shimony, and E. Santos Jr.,
``Reasoning with BKBs - Algorithms and Complexity'',
Annals of Mathematics and Artificial Intelligence 40 (3-4) 403-425,
March 2004.

C. Domshlak and S. E. Shimony,
``Efficient Probabilistic Reasoning in Bayes Nets with
Mutual Exclusion and Context Specific Independence'',
International Journal of Intelligent Systems, 19(8) 703-725, August 2004,
Special Issue on Uncertain Reasoning (Part 1).

R. Brafman, C. Domshlak, and S. E. Shimony,
``Qualitative Decision Making in Adaptive Presentation
of Structured Information'', ACM Transactions on Information Systems,
22(4):503-539, October 2004.

S. E. Shimony and C. Domshlak,
Complexity of Probabilistic Reasoning in Directed-Path Singly Connected
Bayes Networks, Artificial Intelligence 151 (2003) 213-225.

E. Santos Jr. and S. E. Shimony,
Implicitly Preserving Semantics During Incremental Knowledge Base
Acquisition Under Uncertainty,
International Journal of Approximate Reasoning, 33 (1) 71-94, April 2003.

R. Ben-Eliyahu-Zohary, C. Domshlak, E. Gudes, N. Liusternik, A. Meisels,
T. Rosen, and S. E. Shimony,
FlexiMine - A Flexible Platform for KDD Research and Application
Development'', Annals of Mathematics and
Artificial Intelligence 39 (1-2) 175-204, September 2003, (Special Issue
on Foundations of
Artificial Intelligence VI).

S. E. Shimony, E. Santos Jr., and I. Rosen,
``Independence Semantics for BKBs'', Proceedings of the Thirteenth
FLAIRS Conference, 308-312, AAAI Press, 2000.

N. Vanetik, E. Gudes, and S. E. Shimony,
``Computing frequent graph patterns from Semi-structured data'', Proceedings
of the 2002 IEEE International Conference on Data Mining, Maebashi City, Japan.

S. E. Shimony and E. Nissan, Kappa Calculus and Evidential
Strength: A note on Aqvist's Logical Theory of Legal Evidence,
Journal of Artificial Intelligence and Law,
9(2-3):153-163, 2001.

C. Domshlak, R. Brafman, and S. E. Shimony,
``Preference-Based Configuration of Web Page Content'',
Proceedings of the International Joint Conference on Artificial
Intelligence 2001, 1451-1456, AAAI Press, 2001.

A. Meisels, S. E. Shimony, and G. Solotorevsky,
``Bayes Networks for Estimating the Number of Solutions to a CSP'',
Annals of Mathematics and Artificial
Intelligence 28(1-4) (2000), 169-186.

E. Santos Jr., S. E. Shimony, and E. Williams,
``Solving Hard Computational Problems through Collections (Portfolios)
of Cooperative Heterogeneous Algorithms'', Proceedings of the 12th
FLAIRS Conference, 356-360, AAAI Press, 1999.

E. Santos Jr. and S. E. Shimony, Deterministic
Approximation of Marginal Probabilities in Bayes Nets,
IEEE Transactions on Systems, Man, and Cybernetics
28(4) 377-393, July 1998.

Berler, A. and Shimony, S. E.
Bayes Networks for Sonar Sensor Fusion,
Proceedings of the 13th Conference on Uncertainty in AI, 1997.
(Nearly same as: Technical report FC-96-01: "Bayes Networks for Sensor
Fusion in Occupancy Grids".)

Santos Jr. E., Shimony, S. E., and Williams, E.
Sample-and-Accumulate Algorithms
for Belief Updating in Bayes Networks,
Proceedings of the 12th Conference on Uncertainty in AI, 1996.
Extended version appeared as:
``Hybrid Algorithms
for Approximate Belief Updating in Bayes Nets'',
International Journal of Approximate Reasoning 17(2-3), 191-216,
1997.

Avraham A. Melkman and Shimony, S. E.,
A note on approximate inclusion-exclusion,
Discrete Applied Mathematics 73 (1997) 23-26.
Technical report version.

A. A. Melkman and S. E. Shimony,
Algorithms for Finding Parsimonious
Complete Sets in Directed Graphs'',
Information Processing Letters 59(6):335-339, 1996.
(Technical report version - 8 pages:
manuscript.ps)

Shimony S. E., Finding MAPs for belief Networks is NP-Hard,
Artificial Intelligence Journal 68 (1994), 399-410.
Technical report version:
Ben Gurion University, Dept. of Math. and Computer Science, TR FC 93-09.

Shimony S. E., The Role of Relevance in Explanation I: Irrelevance as
Statistical Independence, International Journal of Approximate Reasoning
8(4) (1993) 281-324.

Shimony S. E., The Role of Relevance in Explanation II: Disjunctive
Assignments and Approximate Independence,
International Journal of Approximate Reasoning,
14(1):25-54, January 1996.

Kornatzky Y. and Shimony S. E.,
A Probabilistic Spatial
Data Model, 4th International Conference
on Database and Expert Systems Applications,
Prague, 1993. Extended version in Information Sciences
90(1-4):51-74, April 1996.