Alessandro Dal Palù Papers, etc...

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Papers 2006-2008 (preprints).

Publications 2012

• A. Dal Palù, F. Spyrakis and P. Cozzini A new approach for investigating protein flexibility based on Constraint Logic Programming. The first application in the case of the Estrogen Receptor. . European Journal of Medicinal Chemistry. DOI: dx.doi.org/10.1016/j.ejmech.2012.01.003

Publications 2011

• Michael R. Best, Ferdinando Fioretto, Alessandro Dal Palu', Enrico Pontelli, Tran Son, TuShun R. Powers, Elba E. Serrano. . The role of secondary and tertiary structure prediction in determining the function of novel genes found in Xenopus Leavis. Neuroscience 2011, (518.20/ZZ45).

• A. Dal Palù, A. Dovier, F. Fogolari, and E. Pontelli CLP-based protein fragment assembly . Proceedings of IJCAI 2011.

• M. Best, K. Bhattarai, F. Campeotto, A. Dal Palù, H. Dang, A. Dovier, F. Fioretto, F. Fogolari, T. Le and E. Pontelli. Introducing FIASCO: Fragment-based Interactive Assembly for protein Structure prediction with COnstraints . WCB 2011 colocated to CP2011.

Publications 2010

• A. Dal Palù, M. Moehl, S. Will and B. Berger. CARNA: Alignment of RNA with Structures of Unlimited Complexity . RECOMB 2010

• A. Dal Palù, M. Moehl, and S. Will. A Propagator for Maximum Weight String Matching with Arbitrary Pairwise Dependencies . Proceedings of CP 2010, LNCS 6308, 167-175, DOI: 10.1007/978-3-642-15396-9_16

• A. Dal Palù, M. Moehl, and S. Will. Alignnment of RNA with Structures of Unlimited Complexity . WCB 2010

• Martin Mann and A. Dal Palù. Lattice model refinement of protein structures . WCB 2010

• A. Dal Palù, A. Dovier, F. Fogolari, and E. Pontelli CLP-based protein fragment assembly . Theory and Practice of Logic Programming, special issue dedicated to ICLP 2010. 10(4-6): pp 709-724, July 2010, doi:10.1017/S1471068410000372

• A. Dal Palù, A. Dovier, F. Fogolari, and E. Pontelli CLP-based protein fragment assembly . CILC 2010 (Rende CS, Italy).

• A. Dal Palù, and P. Torroni 25 Years of Applications of Logic Programming in Italy . Book chapter in 25 Years of Logic Programming in Italy, LNCS 6125, 300-328, 2010 .

• A. Dal Palù, A. Dovier, E. Pontelli. Computing Approximate Solutions of the Protein Structure Determination Problem using Global Constraints on Discrete Crystal Lattices (preprint). In International Journal of Data Mining and Bioinformatics, 4(1), 1-20, 2010, DOI: 10.1504/IJDMB.2010.030964

Publications 2009

• A. Dal Palù, A. Dovier, E. Pontelli, G. Rossi. GASP: Answer Set Programming with Lazy Grounding. Fundamenta Informaticae, 96 (2009) DOI 10.3233/FI-2009-180, 297-322, IOS Press.

• F. Bergenti, A. Dal Palù, G. Rossi. Integrating Finite Domain and Set Constraints into a Set-based Constraint Language. Fundamenta Informaticae 96 (2009) DOI 10.3233/FI-2009-177, 227-252, IOS Press

• A. Dal Palù, A. Dovier, E. Pontelli, G. Rossi. Answer Set Programming with Constraints using Lazy Grounding. In ICLP 09 International Conference of Logic Programming.

• A. Dal Palù, A. Dovier, E. Pontelli. Logic Programming Techniques in Protein Structure Determination: Methodologies and Results. In LPNMR 09 International Conference on Logic Programming and Nonmonotonic Reasoning, 560-566 LNCS 5753 Springer 2009

• A. Dal Palù, A. Dovier, F. Fogolari, and E. Pontelli CLP-based protein fragment assembly . Bio-Logical Workshop, AI*IA, 12th Dec 2009, Reggio Emilia.

Publications 2008

• A. Dal Palù, A. Dovier, S. Will. Introduction to the Special Issue on Bioinformatics and Constraints, Constraints Journal, Special Issue on Constraint based methods for Bioinformatics 13(1):1-2.

• A. Dal Palù, A. Dovier, E. Pontelli, G. Rossi. GASP: Answer Set Programming with Lazy Grounding. In Lash 08 International Workshop on Logic and Search.

• A. Dal Palù, A. Dovier, E. Pontelli, G. Rossi. GASP: Answer Set Programming with Lazy Grounding. In CILC 08 Convegno Italiano di Logica Computazionale.

• F. Bergenti, A. Dal Palù, G. Rossi. Generalizing Finite Domain Constraint Solving. In CILC 08 Convegno Italiano di Logica Computazionale.

Publications 2007

• A. Dal Palù, A. Dovier, E. Pontelli. Enhancing the Computation of Approximate Solutions of the Protein Structure Determination Problem Through Global Constraints for Discrete Crystal Lattices. In proceedings of Computational Structural Bioinformatics Workshop (BIBM 07) November 4, 2007, San Jose, CA. (vol. 1, pp. 38-44). ISBN/ISSN: 9781424416042.

• A. Dal Palù, J. He, E. Pontelli, Y. Lu. A Constraint Logic Programming approach to associate 1D and 3D structural components for large protein complexes. In International Journal of Data Mining and Bioinformatics, 1(4), 352-371, 2007.

• A.Dal Palù, A.Dovier and E. Pontelli. A constraint solver for discrete lattices, its parallelization, and application to protein structure prediction. In Software: Practice and Experience DOI 10.1002/spe.810

Publications 2006

• A. Dal Palù, A. Dovier, and E. Pontelli. Global Constraints for Discrete Lattices. In 2nd International Workshop on Constraint Based Methods for Bioinformatics (CP2006). Nantes, France, Sept 2006.

• A. Dal Palù, J. He, E. Pontelli, Y. Lu. Identification of alpha-Helices from Low Resolution Protein Density Maps. In proceedings of Computational Systems Bioinformatics Conference (CSB) 2006.

• A.Dal Palù, E. Pontelli and D. Ranjan Sequential And Parallel Algorithms For The Nca Pproblem On Pure Pointer Machines. In Theoretical Computer Science, 352(1-3):108-135, 7 March 2006.

• A.Dal Palù, Enrico Pontelli, Jing He, Yonggang Lu. A Constraint Logic Programming Approach to 3D Structure Determination of Large Protein Complexes. In proceedings of Symposium on Applied Computing (SAC) 2006, April 23-27 Dijon, Bourgogne, France.

Publications 2005

• A.Dal Palù, A.Dovier and E. Pontelli. A New Constraint Solver for 3-D Lattices and its Application to the Protein Folding Problem. In proceedings of LPAR 2005, 2-6 Dec 2005, Montego Bay, Jamaica, LNCS 3835, DOI: 10.1007/11591191_5.

• A.Dal Palù, A.Dovier, E. Pontelli. Heuristics, Optimizations, and Parallelism for Protein Structure Prediction in CLP(FD). In proceedings of CILC 2005, Rome 21-22 June 2005.

• A.Dal Palù, A.Dovier and E.Pontelli. Heuristics, Optimizations, and Parallelism for Protein Structure Prediction in CLP(FD). In PPDP 2005, Lisbon, 11-13 July 2005. Acm press, ISBN 1-59593-090-6, pp. 230-241.

• L. Bortolussi, A.Dal Palù, A.Dovier and F.Fogolari. Simulazione del processo di ripiegamento di una proteina utilizzando un sistema ad agenti Agent-based Protein Folding Simulation. In Intelligenza Artificiale. 1:56-61, 2005.

Publications 2004

• A.Dal Palù, A.Dovier and F.Fogolari. Constraint Logic Programming approach to protein structure prediction BMC Bioinformatics, 2004, 5:186.

• L. Bortolussi, A.Dal Palù, A.Dovier and F.Fogolari. Protein Folding Simulation in CCP. Proceeding of AI*IA04, 15—17 Sept 2004, Perugia, Italy.

• L. Bortolussi, A.Dal Palù, A.Dovier and F.Fogolari. Protein Folding Simulation in CCP. In Proceedings of BioConcur04, 30 August 2004 London.

• F. Avanzini, D. Rocchesso, A. Dal Palù, A. Dovier, A. Belussi, Designing an urban-scale auditory alert system for high tides in Venice. In IEEE Computers, 37(9):55--61, September 2004.

• A. Dal Palù, S. Will, R. Backofen, and A. Dovier. Constraint Based Protein Structure Prediction Exploiting Secondary Structure Information. CILC 2004, 16-17 june 2004, Research Report "Quaderno del Dipartimento di Matematica", Universita' di Parma, n. 390, Novembre 2004.

Publications 2003

• A.Dal Palù, A.Dovier, and F.Fogolari. Protein Folding in CLP(FD) with Empirical Contact Energies. In K. R. Apt, F. Fages, F. Rossi, P. Szeredi, and J. Vancza, editors, Selected papers of the Joint ERCIM/CoLogNET International Workshop on Constraint Solving and Constraint Logic Programming, volume 3010 of Lecture Notes in Artificial Intelligence, 2004.

• F.Avanzini, A.Belussi, D.Rocchesso, A.Dal Palù and A.Dovier. Acqua alta a Venezia: design of a urban scale auditory warning system. In Proceedings of the International Conference on Auditory Display 2003, Joint Conference on Declarative Programming, Boston MA, USA, July 6--9 2003.

• A.Dal Palù, A.Dovier, E.Pontelli, and G.Rossi. Integrating Finite Domain Constraints and CLP with Sets. Presented at Wflp 2003, Valencia, Spain, June 12--14 2003.

• A.Dal Palù, A.Dovier, and F.Fogolari. Protein Folding in CLP(FD) with Empirical Contact Energies. In proceedings of Joint Annual Workshop of the ERCIM Working Group on Constraints and the CoLogNET area on Constraint and Logic Programming. Budapest, Hungary 30 June - 2 July, 2003.

• A.Dal Palù, A.Dovier, E.Pontelli, and G.Rossi. Integrating Finite Domain Constraints and CLP with Sets. In D. Miller, ed., Proc. of Fifth ACM-SIGPLAN International Conference on Principles and Practice of Declarative Programming Uppsala, Sweden, pp. 219--229, 27-29 August 2003.
   

Publications 2002

• A.Dal Palù, E.Pontelli, D.Ranjan. An Optimal Algorithm for Finding NCA on Pure Pointer Machines. In Algorithm Theory - SWAT 2002, Proceedings, Springer-Verlag, LNCS 2368, 428-438, 2002.

• A.Dal Palù, E.Pontelli, D.Ranjan. An Efficient Parallel Pointer Machine Algorithm for Nearest-Common Ancestor Problem. In IFIP International Conference on Theoretical Computer Science, (223) 157-168, 2002.

• D.Ranjan, E.Pontelli, A.Dal Palù. An Optimal Data Structure to Handle Dynamic Environment in Non-deterministic Computations. In Computer Languages,  28(2):181--201, 2002.

• F.Avanzini, A.Belussi, A.Dal Palù, A.Dovier, and D.Rocchesso. Optimal Placement of Acoustic Sources in a Built-up Area using CLP(FD). In J. J. Moreno-Navarro and J. M. Carballo eds., APPIA-GULP-PRODE 2002, Joint Conference on Declarative Programming, Madrid, Spain, 16--18 September 2002, pp. 139--154.

Book chapters - Editor

• Book chapter. Constraint Based Methods for Bioinformatics in Trends in Constraint Programming, Frederic Benhamou, Narendra Jussien and Barry O'Sullivan eds. (co-editor). ISBN: 9781905209972, DOI: 10.1002/9780470612309.ch6, 2007

• Constraints Journal, Special Issue on Constraint based methods for Bioinformatics (co-editor), Constraints, 13(1):1-2, 2008, DOI: 10.1007/s10601-007-9030-z.

Posters

• A.Dal Palù, A.Dovier and F.Fogolari. Protein Folding Simulation in CCP. In Proc. of ICLP 2004, LNCS 3132 pp. 452-453, Saint Malo, France.

• A.Dal Palù, A.Dovier and F.Fogolari. Protein Folding in CLP(FD) with Empirical Contact Energies. Abstract poster at European Conference in Computational Biology ECCB'2003, Paris 26--30 Sept.

Techical Reports

• A. Dal Palu', A. Dovier, E. Pontelli, G. Rossi. A Constraint Logic Programming Framework for Effective Programming with Sets and Finite Domains. "Quaderno del Dipartimento di Matematica", n. 437, Universita' di Parma, March 2006.

• E. Pontelli, D. Ranjan, and A. Dal Palu'. Ancestor Problems on Pure Pointer Machines. NMSU-CS-2001-005, Dept. of Computer Science, New Mexico State University, USA, Nov 2001.

• A. Dal Palu', E. Pontelli, and D. Ranjan. An Optimal Algorithm for Finding NCA on Pure Pointer Machines. NMSU-CS-2001-007, Dept. of Computer Science, New Mexico State University, USA, Nov 2001.

• A. Dal Palu', E. Pontelli, and D. Ranjan. An Efficient Parallel Pointer Machine Algorithm for Nearest-Common Ancestor Problem. NMSU-CS-2001-009, Dept. of Computer Science, New Mexico State University, USA, Nov 2001.
  
  
  

Program Committee

• 1st International Workshop on Constraint Based Methods for Bioinformatics (WCB) 2005 (associated to ICLP), Sitges, Spain, October 2005.

• 2nd International Workshop on Constraint Based Methods for Bioinformatics (WCB) 2006 (associated to CP), Nantes, France, September 2006. (co-chair)

• 3rd International Workshop on Constraint Based Methods for Bioinformatics (WCB) 2007 (associated to ICLP), Porto, Portugal, September 2007. (co-chair)

• 4th International Workshop on Constraint Based Methods for Bioinformatics (WCB) 2008 (associated to CPAIOR), Paris, France, May 2008.

• 5th International Workshop on Constraint Based Methods for Bioinformatics (WCB) 2009 (associated to CP), Lisbon, Portugal, Sep 2009 (co-chair).

• 6th International Workshop on Constraint Based Methods for Bioinformatics (WCB) 2010 (associated to ICLP), Edinburgh, Scotland, Jul 2010 (co-chair).

• 7th International Workshop on Constraint Based Methods for Bioinformatics (WCB) 2011 (associated to CP), Perugia, Italy Sep 2011 (co-chair).

• Convegno Italiano logica computazionale (CILC) 2008, Perugia, Italy, Jul 2008.

• ICLP (International conference on logic programming) Dec 2008, Udine: commettee member and publicity co-chair.

• Convegno Italiano logica computazionale (CILC) 2009, Ferrara, Italy, Jun 2009.

• Bio-Logical: Logic-based Approaches in Bioinformatics 2009, Reggio Emilia, Italy, Dec 2009.

• Doctoral Consortium, ICLP10 (co-chair).

• Convegno Italiano logica computazionale (CILC) 2010, Rende, Italy, Jul 2010.

• Doctoral Consortium, ICLP11 (co-chair).

• ICLP (International conference on logic programming) 2011: PC member.

• IJCAI 2011: PC member.

• Convegno Italiano logica computazionale (CILC) 2011, Pescara, Italy, Sept 2011.

Awards

• "Marco Cadoli" Award given by GULP for best Ph.D. thesis on computational logics. Photo.

• Best paper award at ICLP 2010 (CLP-based protein fragment assembly)

• Best paper award: A. Dal Palù, A. Dovier, F. Fogolari, and E. Pontelli CLP-based protein fragment assembly . ICLP 2010.

Seminars

• Protein structure prediction methods (Doctoral school) (4-6/07/11, Sissa, TS).

• A constraint-based framework to model protein structure: applications and examples (Workshop on Structural Bioinformatics and Computational Biophysics) (7/07/11, Sissa, TS).

• Constraint-based Assembling of Protein Fragments (Coprod, El Paso, TX (17/03/11)).

• Bioinformatica: l'Informatica come strumento di nuove scoperte scientiche (19/10/10, Parma).

• Constraint based protein fragment assembly (19/11/09, Freiburg Germany).

• Global constraints for discrete lattices (25/01/07, Freiburg Germany).

• New techniques to analyze and exploit density maps (01/12/04, New Mexico State University).

• Protein Folding with CLP (13/09/04, New Mexico State University).

• An Optimal Data Structure to Handle Dynamic Environments in Non-deterministic Computations (27/11/02, Università di Parma).

• Protein Folding Complexity (05/05/03, Università di Udine).

We probably met here

• IJCAI, Barcelona (18-22/07/11).

• Sissa, Trieste (4-8/07/11).

• Las Cruces, NM (Jan-May 2011).

• Coprod, El Paso, TX (17/03/11).

• CP, St. Andrews (6-10/09/10).

• ICLP + WCB, Edinburgh (16-21/07/10).

• CILC, Rende(CS) (7-9/07/10).

• RCRA, Bologna (10/06/10).

• Bio-Logical, Reggio Emilia (12/12/09).

• Visiting Bioinformatics Group, Freiburg University (16-19/11/09).

• WCB 09, Sep 20th 2009, Lisbon, Portugal.

• International Conference on Logic Programming, Jul 13-17 2009, Pasadena, CA, USA.

• CILC 09 Convegno Italiano di Logica Computazionale, Jun 24-26 2009, Ferrara, Italy.

• International Conference on Logic Programming, December 9-13 2008, Udine, Italy.

• LaSh 2008: LOGIC AND SEARCH. Leuven Belgium, November 6-7th 2008.

• CILC 08 Convegno Italiano di Logica Computazionale. Perugia, Italy. 10-12 July 2008.

• CPAIOR08 Paris, France. May 20-23, 2008.

• BIBM - IEEE Intl Conference on Bioinformatics and Biomedicine. San Jose CA, 2nd-4th Nov 07.

• From Structural Genomics to Drug Discovery Modeling the Flexibility. Parma 20-21 Sept 07

• ICLP 2007, International Conference on Logic Programming, Porto, Portugal, 6-13 Sep 2007.

• Bioinformatics Group Freiburg - Winter-Seminar January 2007, Freiburg Germany.

• 2nd International Workshop on Constraint Based Methods for Bioinformatics (WCB) 2006, Nantes, France, Sept 2006.

• Third International School on Biology, Computation and Information (BCI 2006) Dobbiaco (BZ), Italy, September 11-15, 2006.

• ACM SAC 2006, Dijon, France, 23-27 April 2006. Talk

• LPAR 2005 International Conference on Logic for Programming Artificial Intelligence and Reasoning, Montego Bay, Jamaica, Dec 2005.

• ICLP 2005, International Conference on Logic Programming, Sitges, Spain, 1-5 Oct 2005.

• BCI, Summer School, Dobbiaco, Italy, 12-16 Sept 2005.

• PPDP 2005 Lisboa, Protugal, 11-13 July 2005.

• Cilc 2005 Roma, Italy, 21-22 June 2005.

• ANALISI SPERIMENTALE E BENCHMARK DI ALGORITMI PER L'INTELLIGENZA ARTIFICIALE del gruppo RCRA dell'AI*IA, Ferrara, Italy, 10 June 2005.

• ISPA 2004, International Symposium on Parallel and Distributed Processing and Applications, Hong Kong, China, 13-15th December 2004.

• CILC 2004, Convegno Italiano di Logica Computazionale, Parma, Italy, 15-16th June 2004.

• Advanced BioMedicine and BioInformatics Summer School 2004. Molecular and Computational Analysis of Human Phenotype. Lipari, Italy, May 29 - June 5, 2004.

• Lipari Summer School 2003. Algorithmics for Data Mining and Pattern Discovery. Lipari, Italy July 13 - July 26 2003

• ERCIM 2003, Joint Annual Workshop of the ERCIM Working Group on Constraints and the CoLogNET area on Constraint and Logic Programming. Budapest, Hungary, 30 June--2 July 2003.

• SWAT 2002, Scandinavian Workshop on Algorithm Theory, Turku Finland, 3rd-5th July 2002.

• IFIP World Computer Congress 17th edition, Montreal 2002, 25th-30th August 2002.

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