Antonio Mucherino's publications


For my publication list sorted by number of citations, please visit my Google Scholar citations page.

 Books

  1. A. Mucherino, P. Papajorgji, P.M. Pardalos, Data Mining in Agriculture, 274 pages, Springer, 2009. Detailed description. Available for purchase on Springer.com or Amazon.com

  2. A. Mucherino, C. Lavor, L. Liberti, N. Maculan (Eds.), Distance Geometry: Theory, Methods and Applications, 410 pages, Springer, 2013. See list of contributions. Available for purchase on Springer.com or Amazon.com


Special issues

  1. A. Mucherino, A. Nixon, M. Sitharam, H. Wolkowicz, Open Problems and Solutions: Rigidity and Distance Geometry, special issue of Discrete Applied Mathematics, Virtual special issue 0166-218X, Elsevier, 2023.

  2. A.D. Báez-Sánchez, C. Lavor, A. Mucherino, Optimization in Distance Geometry, special issue of Journal of Global Optimization 83(1), Springer, 1-185, 2022.

  3. A. Mucherino, C. Lavor, Distances in Optimization and Graphs dedicated to the Memory of Michel Deza, special issue of Optimization Letters 14(2), Springer, 269-507, 2020.

  4. A. Mucherino, R. de Freitas, C. Lavor, Distance Geometry and Applications, special issue of Discrete Applied Mathematics 197, Elsevier, 1-144, 2015.


Books of conference proceedings

  1. A. Andrioni, R. de Freitas, C. Lavor, L. Liberti, N. Maculan, A. Mucherino (Eds.), Proceedings of Distance Geometry and Applications, DGA13, Manaus, Amazonas, Brazil, June 24-27, 2013. Download the book of proceedings.

  2. S. Cafieri, A. Mucherino, G. Nannicini, F. Tarissan, L. Liberti (Eds.), Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, CTW09, Paris, France, June 2-4, 2009. See table of contents. Download the book of proceedings.


International journals

  1. G. Abud, J. Alencar, C. Lavor, L. Liberti, A. Mucherino, An Impossible Combinatorial Counting Method in Distance Geometry, Discrete Applied Mathematics 354, 83-93, 2024. Download paper.

  2. D. Förster, J. Idier, L. Liberti, A. Mucherino, JH. Lin, T.E. Malliavin, Low-Resolution Description of the Conformational Space for Intrinsically Disordered Proteins, Scientific Reports 12, 19057, 16 pages, 2022. Download paper.

  3. S. Hengeveld, N. Rubiano da Silva, D.S. Gonçalves, P.H. Souto Ribeiro, A. Mucherino, An Optical Processor for Matrix-by-Vector Multiplication: an Application to the Distance Geometry Problem in 1D, Journal of Optics 24(1), 015701, 2022. Download paper. Preliminary version deposited on arXiv:2105.12118, version 1, May 2021.

  4. J. Omer, A. Mucherino, The Referenced Vertex Ordering Problem: Theory, Applications and Solution Methods, Open Journal of Mathematical Optimization 2, article no. 6, 29 pages, 2021. Download paper. Preliminary version deposited on HAL open archives, hal-02509522, version 1, March 2020.

  5. C. Lavor, M.F. de Souza, L.M. Carvalho, D.S. Gonçalves, A. Mucherino, Improving the Sampling Process in the Interval Branch-and-Prune Algorithm for the Discretizable Molecular Distance Geometry Problem, Applied Mathematics and Computations 389(15), 125586, 2021. Download paper.

  6. G. Abud, J. Alencar, C. Lavor, L. Liberti, A. Mucherino, The K-discretization and K-incident Graphs for Discretizable Distance Geometry, Optimization Letters 14(2), 469-482, 2020. Download paper.

  7. A. Mucherino, J. Omer, L. Hoyet, P. Robuffo Giordano, F. Multon, An Application-based Characterization of dynamical Distance Geometry Problems, Optimization Letters 14(2), 493-507, 2020. Download paper.

  8. T.E. Malliavin, A. Mucherino, C. Lavor, L. Liberti, Systematic Exploration of Protein Conformational Space using a Distance Geometry Approach, Journal of Chemical Information and Modeling 59(10), 4486-4503, 2019. Preliminary version available on biorXiv, biorXiv:650903v1. Download paper.

  9. S.J.L. Billinge, Ph.M. Duxbury, D.S. Gonçalves, C. Lavor, A. Mucherino, Recent Results on Assigned and Unassigned Distance Geometry with Applications to Protein Molecules and Nanostructures, Annals of Operations Research 271(1), 161-203, 2018. Download paper.

  10. F. Fidalgo, D.S. Gonçalves, C. Lavor, L. Liberti, A. Mucherino, A Symmetry-based Splitting Strategy for Discretizable Distance Geometry Problems, Journal of Global Optimization 71(4), 717-733, 2018. Download paper.

  11. D.S. Gonçalves, A. Mucherino, C. Lavor, L. Liberti, Recent Advances on the Interval Distance Geometry Problem, Journal of Global Optimization 69(3), 525-545, 2017. Download paper.

  12. S.J.L. Billinge, Ph.M. Duxbury, D.S. Gonçalves, C. Lavor, A. Mucherino, Assigned and Unassigned Distance Geometry: Applications to Biological Molecules and Nanostructures, Quarterly Journal of Operations Research 14(4), 337-376, 2016. Download paper.

  13. D.S. Gonçalves, A. Mucherino, Optimal Partial Discretization Orders for Discretizable Distance Geometry, International Transactions in Operational Research 23(5), 947-967, 2016. Download paper.

  14. A. Cassioli, B. Bardiaux, G. Bouvier, A. Mucherino, R. Alves, L. Liberti, M. Nilges, C. Lavor, T.E. Malliavin, An Algorithm to Enumerate all Possible Protein Conformations verifying a Set of Distance Restraints, BMC Bioinformatics 16:23, 15 pages, 2015. Download paper.

  15. D.S. Gonçalves, A. Mucherino, Discretization Orders and Efficient Computation of Cartesian Coordinates for Distance Geometry, Optimization Letters 8(7), 2111-2125, 2014. Download paper.

  16. V. Costa, A. Mucherino, C. Lavor, A. Cassioli, L.M. Carvalho, N. Maculan, Discretization Orders for Protein Side Chains, Journal of Global Optimization 60(2), 333-349, 2014. Download paper.

  17. L. Liberti, C. Lavor, N. Maculan, A. Mucherino, Euclidean Distance Geometry and Applications, SIAM Review 56(1), 3-69, 2014. Preliminary version available on arXiv, arXiv:1205.0349v1. Download paper.

  18. L. Liberti, B. Masson, J. Lee, C. Lavor, A. Mucherino, On the Number of Realizations of Certain Henneberg Graphs arising in Protein Conformation, Discrete Applied Mathematics 165, 213-232, 2014. Download paper.

  19. C. Lavor, L. Liberti, A. Mucherino, The interval Branch-and-Prune Algorithm for the Discretizable Molecular Distance Geometry Problem with Inexact Distances, Journal of Global Optimization 56(3), 855-871, 2013. Download paper.

  20. A. Mucherino, C. Lavor, L. Liberti, The Discretizable Distance Geometry Problem, Optimization Letters 6(8), 1671-1686, 2012. Download paper.

  21. A. Mucherino, C. Lavor, L. Liberti, Exploiting Symmetry Properties of the Discretizable Molecular Distance Geometry Problem, Journal of Bioinformatics and Computational Biology 10(3), 1242009(1-15), 2012. Download paper.

  22. C. Lavor, L. Liberti, N. Maculan, A. Mucherino, The Discretizable Molecular Distance Geometry Problem, Computational Optimization and Applications 52, 115-146, 2012. Download paper.

  23. C. Lavor, J. Lee, A. Lee-St.John, L. Liberti, A. Mucherino, M. Sviridenko, Discretization Orders for Distance Geometry Problems, Optimization Letters 6(4), 783-796, 2012. Download paper.

  24. C. Lavor, L. Liberti, N. Maculan, A. Mucherino, Recent Advances on the Discretizable Molecular Distance Geometry Problem, European Journal of Operational Research 219, 698-706, 2012. Download paper.

  25. C. Lavor, A. Mucherino, L. Liberti, N. Maculan, On the Computation of Protein Backbones by using Artificial Backbones of Hydrogens, Journal of Global Optimization 50(2), 329-344, 2011. Download paper.

  26. L. Liberti, C. Lavor, A. Mucherino, N. Maculan, Molecular Distance Geometry Methods: from Continuous to Discrete, International Transactions in Operational Research 18(1), 33-51, 2011. Download paper. ITOR Top Article in 2013.

  27. C. Lavor, A. Mucherino, L. Liberti, N. Maculan, Discrete Approaches for Solving Molecular Distance Geometry Problems using NMR Data, International Journal of Computational Biosciences 1(1), 88-94, 2010. Download paper.

  28. A. Mucherino, A. Masello, Statistical Analysis on the Globular Shape of Protein Conformations, JP Journal of Biostatistics 4(1), 1-12, 2010. Download paper.

  29. A. Mucherino, P.J. Papajorgji, P.M. Pardalos, A Survey of Data Mining Techniques Applied to Agriculture, Operational Research: An International Journal 9(2), 121-140, 2009. Download paper.

  30. A. Mucherino, S. Costantini, D. di Serafino, M. D'Apuzzo, A. Facchiano, G. Colonna, Understanding the Role of the Topology in Protein Folding by Computational Inverse Folding Experiments, Computational Biology and Chemistry 32(4), 233-239, 2008. Download paper.

  31. S. Cafieri, M. D'Apuzzo, M. Marino, A. Mucherino, G. Toraldo, Interior Point Solver for Large-Scale Quadratic Programming Problems with Bound Constraints, Journal of Optimization Theory and Applications 129(1), 55-75, 2006. Download paper.


National journals

  1. A. Mucherino, Introducing the Interaction Distance in the context of Distance Geometry for Human Motions, Chebyshevskii sbornik 20(2), 263-273, 2019. Download paper.

  2. A. Mucherino, C. Lavor, L. Liberti, N. Maculan, On the Definition of Artificial Backbones for the Discretizable Molecular Distance Geometry Problem, Mathematica Balkanica 23(3-4), 289-302, 2009. Download paper.


Conference papers (refereed)

  1. W. Da Rocha, T.E. Malliavin, A. Mucherino, L. Liberti, Impact of Local Geometry on Methods for Constructing Protein Conformations. to appear in IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS24), Workshop on Computational Optimization (WCO24), Belgrade, Serbia, September 2024.

  2. S.B. Hengeveld, A. Mucherino, Variable Neighborhood Search in Hamming Space, Lecture Notes in Computer Science 13952, I. Lirkov, S. Margenov (Eds.), Proceedings of the 14th International Conference on Large-Scale Scientific Computations (LSSC23), Sozopol, Bulgaria, 253-261, 2024. Download paper.

  3. A. Mucherino, J-H. Lin, The Coherent Multi-Representation Problem for Protein Structure Determination, Lecture Notes in Computer Science 14321, H. Moosaei et al. (Eds.), Proceedings of the 6th International Conference on Dynamics of Information Systems (DIS23), Prague, Czech Republic, 194-202, 2023. Download paper.

  4. S.B. Hengeveld, F. Plastria, A. Mucherino, D.A. Pelta, A Linear Program for Points of Interest Relocation in Adaptive Maps, Lecture Notes in Computer Science 14072 (part 2), F. Nielsen, F. Barbaresco (Eds.), Proceedings of Geometric Science of Information (GSI23), Saint Malo, France, 551-559, 2023. Download paper.

  5. A. Mucherino, The Coherent Multi-Representation Problem with Applications in Structural Biology, Lecture Notes in Computer Science 13919, Lecture Notes in Bioinformatics series, Proceedings of the 10th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO23), Gran Canaria, Spain, 338-346, 2023. Download paper.

  6. S.B. Hengeveld, A. Mucherino, On the Feasible Regions Delimiting Natural Human Postures in a Novel Skeletal Representation, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS22), 4th International Workshop on Artificial Intelligence in Machine Vision and Graphics (AIMaViG22), Sofia, Bulgaria, 175-179, 2022. Download paper. Extended version available on HAL Open archives.

  7. D.S. Gonçalves, A. Mucherino, A Distance Geometry Procedure using the Levenberg-Marquardt Algorithm and with Applications in Biology but not only, Lectures Notes in Computer Science 13347, Lecture Notes in Bioinformatics series, Proceedings of the 9th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO22), Gran Canaria, Spain, 142-152, 2022. Download paper.

  8. A. Mucherino, binMeta: a New Java Package for Meta-Heuristic Searches, Lecture Notes in Computer Science 13127, Proceedings of the 13th International Conference on Large-Scale Scientific Computations (LSSC21), Sozopol, Bulgaria, 242-249, 2022. Download paper.

  9. S.B. Hengeveld, T. Malliavin, J.H. Lin, L. Liberti, A. Mucherino, A Study on the Impact of the Distance Types Involved in Protein Structure Determination by NMR, IEEE Conference Proceedings, Computational Structural Bioinformatics Workshop (CSBW21), International Conference on Bioinformatics & Biomedicine (BIBM21), online event, 9 pages, 2021. Download paper.

  10. S.B. Hengeveld, A. Mucherino, On the Representation of Human Motions and Distance-based Retargeting, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS21), Workshop on Computational Optimization (WCO21), online event, 181-189, 2021. Download paper.

  11. A. Mucherino, D.S. Gonçalves, L. Liberti, J-H. Lin, C. Lavor, N. Maculan, MD-jeep: a New Release for Discretizable Distance Geometry Problems with Interval Data, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS20), Workshop on Computational Optimization (WCO20), Sofia, Bulgaria, 289-294, 2020. Download paper.

  12. S. Hu, H.P.H. Shum, A. Mucherino, DSPP: Deep Shape and Pose Priors of Humans, ACM Conference Proceedings, Motion, Interaction and Games 2019 (MIG19), Newcastle, UK, 6 pages, 2019. Download paper.

  13. A. Mucherino, J-H. Lin, An Efficient Exhaustive Search for the Discretizable Distance Geometry Problem with Interval Data, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS19), Workshop on Computational Optimization (WCO19), Leipzig, Germany, 135-141, 2019. Download paper.

  14. A. Mucherino, J-H. Lin, D.S. Gonçalves, A Coarse-Grained Representation for Discretizable Distance Geometry with Interval Data, Lecture Notes in Computer Science 11465, Lecture Notes in Bioinformatics series, I. Rojas et al (Eds.), Proceedings of the 7th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO19), Part I, Granada, Spain, 3-13, 2019. Download paper.

  15. Z. Liu, A. Mucherino, L. Hoyet, F. Multon, Surface based Motion Retargeting by Preserving Spatial Relationship, ACM Conference Proceedings, Motion, Interaction, and Games 2018 (MIG18), Limassol, Cyprus, Greece, 12 pages, 2018. Download paper.

  16. A. Bernardin, L. Hoyet, A. Mucherino, D.S. Gonçalves, F. Multon, Normalized Euclidean Distance Matrices for Human Motion Retargeting, ACM Conference Proceedings, Motion in Games 2017 (MIG17), Barcelona, Spain, November 2017. Download paper (as well as the video clip shown during the conference).

  17. A. Mucherino, D.S. Gonçalves, An Approach to dynamical Distance Geometry, Lecture Notes in Computer Science 10589, F. Nielsen, F. Barbaresco (Eds.), Proceedings of Geometric Science of Information (GSI17), Paris, France, 821--829, 2017. Download paper. The video of the presentation is available on YouTube.

  18. W. Gramacho, A. Mucherino, J-H. Lin, C. Lavor, A New Approach to the Discretization of Multidimensional Scaling, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS16), Workshop on Computational Optimization (WCO16), Gdansk, Poland, 601-609, 2016. Download paper.

  19. S. Fidanova, O. Roeva, A. Mucherino, K. Kapanova, InterCriteria Analysis of Ant Algorithm with Environment Change for GPS Surveying Problem, Lecture Notes in Artificial Interlligence 9883, Proceedings of the 17th International Conference on Artificial Intelligence: Methodology, Systems, Applications (AIMSA16), Varna, Bulgaria, 271-278, 2016. Download paper.

  20. A. Mucherino, Optimal Discretization Orders for Distance Geometry: a Theoretical Standpoint, Lecture Notes in Computer Science 9374, Proceedings of the 10th International Conference on Large-Scale Scientific Computations (LSSC15), Sozopol, Bulgaria, 234-242, 2015. Download paper.

  21. A. Mucherino, S. Fidanova, M. Ganzha, Ant Colony Optimization with Environment Changes: an Application to GPS Surveying, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS15), Workshop on Computational Optimization (WCO15), Lodz, Poland, 495-500, 2015. Download paper.

  22. A. Mucherino, A Pseudo de Bruijn Graph Representation for Discretization Orders for Distance Geometry, Lecture Notes in Computer Science 9043, Lecture Notes in Bioinformatics series, F. Ortuño, I. Rojas (Eds.), Proceedings of the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO15), Part I, Granada, Spain, 514-523, 2015. Download paper.

  23. D.S. Gonçalves, A. Mucherino, C. Lavor, An Adaptive Branching Scheme for the Branch & Prune Algorithm applied to Distance Geometry, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS14), Workshop on Computational Optimization (WCO14), Warsaw, Poland, 463-469, 2014. Download paper.

  24. D.S. Gonçalves, A. Mucherino, C. Lavor, Energy-based Pruning Devices for the BP Algorithm for Distance Geometry, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS13), Workshop on Computational Optimization (WCO13), Krakov, Poland, 335-340, 2013. Download paper.

  25. A. Mucherino, On the Identification of Discretization Orders for Distance Geometry with Intervals, Lecture Notes in Computer Science 8085, F. Nielsen and F. Barbaresco (Eds.), Proceedings of Geometric Science of Information (GSI13), Paris, France, 231-238, 2013. Download paper. The video of the presentation is available on YouTube: part1, part2, part3.

  26. V. Costa, A. Mucherino, C. Lavor, L.M. Carvalho, N. Maculan, On Suitable Orders for Discretizing Molecular Distance Geometry Problems related to Protein Side Chains, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS12), Workshop on Computational Optimization (WCO12), Wroclaw, Poland, 397-402, 2012. Download paper.

  27. A. Mucherino, C. Lavor, L. Liberti, N. Maculan, On the Discretization of Distance Geometry Problems, ITHEA Conference Proceedings, Mathematics of Distances and Applications 2012 (MDA12), Varna, Bulgaria, 160-168, 2012. Download paper.

  28. W. Gramacho, A. Mucherino, C. Lavor, N. Maculan, A Parallel BP Algorithm for the Discretizable Distance Geometry Problem, IEEE Conference Proceedings, Workshop on Parallel Computing and Optimization (PCO12), 26th IEEE International Parallel & Distributed Processing Symposium (IPDPS12), Shanghai, China, 1756-1762, 2012. Download paper.

  29. A. Mucherino, M. Fuchs, X. Vasseur, S. Gratton, Variable Neighborhood Search for Robust Optimization and Applications to Aerodynamics, Lecture Notes in Computer Science 7116, I. Lirkov, S. Margenov, J. Wansiewski (Eds.), Proceedings of the 8th International Conference on Large-Scale Scientific Computations (LSSC11), Sozopol, Bulgaria, 230-237, 2012. Very preliminary version published as Cerfacs Technical Report TR/PA/11/25 in April 2011. Download paper.

  30. A. Mucherino, C. Lavor, L. Liberti, A Symmetry-Driven BP Algorithm for the Discretizable Molecular Distance Geometry Problem, IEEE Conference Proceedings, Computational Structural Bioinformatics Workshop (CSBW11), International Conference on Bioinformatics & Biomedicine (BIBM11), Atlanta, GA, USA, 390-395, 2011. Download paper.

  31. A. Mucherino, Extending the Definition of β-Consistent Biclustering for Feature Selection, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS11), Workshop on Computational Optimization (WCO11), Szczecin, Poland, 269-274, 2011. Download paper.

  32. A. Mucherino, A. Urtubia, Feature Selection for Datasets of Wine Fermentations, Proceedings of the 10th International Conference on Modeling and Applied Simulation (MAS11), Rome, Italy, 309-313, 2011. Download paper.

  33. A. Mucherino, G. Ruß, Recent Developments in Data Mining and Agriculture, IbaI Conference Proceedings, Industrial Conference on Data Mining (ICDM11), Workshop on Data Mining in Agriculture (DMA11), New York City, USA, 90-98, 2011. Download paper.

  34. L. Liberti, B. Masson, J. Lee, C. Lavor, A. Mucherino, On the Number of Solutions of the Discretizable Molecular Distance Geometry Problem, Lecture Notes in Computer Science 6831, W. Wang, X. Zhu, D-Z. Du (Eds.), Proceedings of the 5th Annual International Conference on Combinatorial Optimization and Applications (COCOA11), Zhangjiajie, China, 322-342, 2011. Download paper. Preliminary version available on arXiv.

  35. A. Mucherino, C. Lavor, T. Malliavin, L. Liberti, M. Nilges, N. Maculan, Influence of Pruning Devices on the Solution of Molecular Distance Geometry Problems, Lecture Notes in Computer Science 6630, P.M. Pardalos, S. Rebennack (Eds.), Proceedings of the 10th International Symposium on Experimental Algorithms (SEA11), Crete, Greece, 206-217, 2011. Download paper.

  36. C. Lavor, L. Liberti, A. Mucherino, On the Solution of Molecular Distance Geometry Problems with Interval Data, IEEE Conference Proceedings, International Workshop on Computational Proteomics (IWCP10), International Conference on Bioinformatics & Biomedicine (BIBM10), Hong Kong, 77-82, 2010. Download paper.

  37. A. Mucherino, L. Liberti, C. Lavor, MD-jeep: an Implementation of a Branch & Prune Algorithm for Distance Geometry Problems, Lectures Notes in Computer Science 6327, K. Fukuda et al. (Eds.), Proceedings of the 3rd International Congress on Mathematical Software (ICMS10), Kobe, Japan, 186-197, 2010. Download paper.

  38. A. Mucherino, A. Urtubia, Consistent Biclustering and Applications to Agriculture, IbaI Conference Proceedings, Proceedings of the Industrial Conference on Data Mining (ICDM10), Workshop on Data Mining in Agriculture (DMA10), Berlin, Germany, 105-113, 2010. Download paper.

  39. A. Mucherino, C. Lavor, L. Liberti, E-G. Talbi, A Parallel Version of the Branch & Prune Algorithm for the Molecular Distance Geometry Problem, IEEE Conference Proceedings, ACS/IEEE International Conference on Computer Systems and Applications (AICCSA10), Hammamet, Tunisia, 1-6, 2010. Download paper.

  40. C. Lavor, A. Mucherino, L. Liberti, N. Maculan, An Artificial Backbone of Hydrogens for Finding the Conformation of Protein Molecules, IEEE Conference Proceedings, Computational Structural Bioinformatics Workshop (CSBW09), Washington D.C., USA, 152-155, 2009. Download paper.

  41. A. Mucherino, C. Lavor, The Branch and Prune Algorithm for the Molecular Distance Geometry Problem with Inexact Distances, Proceedings of World Academy of Science, Engineering and Technology 58, International Conference on Bioinformatics and Biomedicine (ICBB09), Venice, Italy, 349-353, 2009. Download paper.

  42. C. Lavor, A. Mucherino, L. Liberti, N. Maculan, Computing Artificial Backbones of Hydrogen Atoms in order to Discover Protein Backbones, IEEE Conference Proceedings, International Multiconference on Computer Science and Information Technology (IMCSIT09), Workshop on Computational Optimization (WCO09), Mragowo, Poland, 751-756, 2009. Download paper.

  43. A. Mucherino, L. Liberti, C. Lavor, N. Maculan, Comparisons between an Exact and a Meta-Heuristic Algorithm for the Molecular Distance Geometry Problem, ACM Conference Proceedings, Genetic and Evolutionary Computation Conference (GECCO09), Montréal, Canada, 333-340, 2009. Download paper.

  44. F. Marinelli, O. de Weck, D. Krob, L. Liberti, A. Mucherino, A General Framework for Combined Module- and Scale-based Product Platform Design, 2nd International Symposium on Engineering Systems Proceedings, MIT, Cambridge, Massachusetts, June 2009. Download paper.

  45. A.R. Kammerdiner, A. Mucherino, P.M. Pardalos, Application of Monkey Search Meta-Heuristic to Solving Instances of the Multidimensional Assignment Problem, Lecture Notes in Control and Information Sciences 381, M.J. Hirsch, C. Commander, P.M. Pardalos, R. Murphey (Eds.), Proceedings of the 8th International Conference on Optimization and Cooperative Control Strategies (CCO08), Gainesville, Florida, 385-397, 2009. Download paper.

  46. A. Mucherino, O. Seref, Monkey Search: A Novel Meta-Heuristic Search for Global Optimization, AIP Conference Proceedings 953, O. Seref, O.E. Kundakcioglu, P.M. Pardalos (Eds.), Proceedings of the Conference "Data Mining, System Analysis and Optimization in Biomedicine", Gainesville, Florida, 162-173, 2007. Download paper.


Book chapters (refereed)

  1. A. Mucherino, Manipulating Two-Dimensional Animations by dynamical Distance Geometry. In: "Recent Advances in Computational Optimization", S. Fidanova (Ed.), Studies in Computational Intelligence 838, 147-153, 2020. Download paper.

  2. A. Mucherino, On the Exact Solution of the Distance Geometry with Interval Distances in Dimension 1. In: "Recent Advances in Computational Optimization", S. Fidanova (Ed.), Studies in Computational Intelligence 717, 123-134, 2018. Download paper.

  3. A. Mucherino, S. Fidanova, M. Ganzha, Introducing the Environment in Ant Colony Optimization. In: "Recent Advances in Computational Optimization", S. Fidanova (Ed.), Studies in Computational Intelligence 655, 147-158, 2016. Download paper.

  4. D.S. Gonçalves, J. Nicolas, A. Mucherino, C. Lavor, Finding Optimal Discretization Orders for Molecular Distance Geometry by Answer Set Programming. In: "Recent Advances in Computational Optimization", S. Fidanova (Ed.), Studies in Computational Intelligence 610, 1-15, 2015. Download paper.

  5. J. Seo, J-K. Kim, J. Ryu, C. Lavor, A. Mucherino, D-S. Kim, BetaMDGP: Protein Structure Determination Algorithm Based on the Beta-complex. In: "Transactions on Computational Science XXII", M.L. Gavrilova, C.J.K. Tan (Eds.), Lecture Notes in Computer Science 8360, 130-155, 2014. Download paper.

  6. T.E. Malliavin, A. Mucherino, M. Nilges, Distance Geometry in Structural Biology: New Perspectives. In: "Distance Geometry: Theory, Methods and Applications", A. Mucherino, C. Lavor, L. Liberti, N. Maculan (Eds.), 329-350, 2013. Download paper.

  7. L. Liberti, C. Lavor, A. Mucherino, The Discretizable Molecular Distance Geometry Problem seems Easier on Proteins. In: "Distance Geometry: Theory, Methods and Applications", A. Mucherino, C. Lavor, L. Liberti, N. Maculan (Eds.), 47-60, 2013. Download paper.

  8. A. Mucherino, L. Liberti, A VNS-based Heuristic for Feature Selection in Data Mining. In: "Hybrid Meta-Heuristics", Studies in Computational Intelligence 434, E-G. Talbi (Ed.), 353-368, 2013. Download paper.

  9. A. Mucherino, O. Seref, Modeling and Solving Real Life Global Optimization Problems with Meta-Heuristic Methods. In: "Advances in Modeling Agricultural Systems", Springer Optimization and Its Applications 25, P.J. Papajorgji, P.M. Pardalos (Eds.), 403-420, 2008. Download paper.

  10. G. Ceci, A. Mucherino, M. D'Apuzzo, D. di Serafino, S. Costantini, A. Facchiano, G. Colonna, Computational Methods for Protein Fold Prediction: an Ab-Initio Topological Approach. In: "Data Mining in Biomedicine", Springer Optimization and Its Applications 7, P.M. Pardalos, V. Boginski and A. Vazacopoulos (Eds.), 391-429, 2007. Download paper.


Short conference papers (up to 4 pages, refereed)

  1. S.B. Hengeveld, A. Mucherino, A GPU Approach to Distance Geometry in 1D: an Implementation in C/CUDA, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS22), Workshop on Computational Optimization (WCO22), Sofia, Bulgaria, 333-336, 2022. Download paper. Extended version (including code snippets) available on HAL Open archives.

  2. S.B. Hengeveld, A. Mucherino, The Discrete Side of Distance Geometry: a Focus on the 1-dimensional Case, Proceedings of Discrete Math Days (DMD22), Santander, 301-305, 2022. Download paper.

  3. F. Elain, A. Mucherino, L. Hoyet, R. Kulpa, Feature Selection in Time-Series Motion Databases, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS18), Workshop on Computational Optimization (WCO18), Poznan, Poland, 245-248, 2018. Download paper.

  4. A. Mucherino, D.S. Gonçalves, A. Bernardin, L. Hoyet, F. Multon, A Distance-Based Approach for Human Posture Simulations, IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS17), Workshop on Computational Optimization (WCO17), Prague, Czech Republic, 441-444, 2017. Download paper.

  5. R. Alves, A. Cassioli, A. Mucherino, C. Lavor, L. Liberti, Adaptive Branching in iBP with Clifford Algebra, Proceedings of Distance Geometry and Applications (DGA13), Manaus, Amazonas, Brazil, 65-69, 2013. Download paper.

  6. V. Costa, A. Mucherino, L.M. Carvalho, N. Maculan, On the Discretization of iDMDGP instances regarding Protein Side Chains with Rings, Proceedings of Distance Geometry and Applications (DGA13), Manaus, Amazonas, Brazil, 99-102, 2013. Download paper.

  7. W. Gramacho, D.S. Gonçalves, A. Mucherino, N. Maculan, A new Algorithm to Finding Discretizable Orderings for Distance Geometry, Proceedings of Distance Geometry and Applications (DGA13), Manaus, Amazonas, Brazil, 149-152, 2013. Download paper.

  8. C. Lavor, A. Mucherino, L. Liberti, N. Maculan, Finding Low-Energy Homopolymer Conformations by a Discrete Approach, Proceedings of Global Optimization Workshop 2012 (GOW12), Natal, Brazil, 3-6, 2012. Download paper.

  9. A. Mucherino, I. Wohlers, G.W. Klau, R. Andonov, Sparsifying Distance Matrices for Protein-Protein Structure Alignments, Proceedings of the 10th Cologne-Twente Workshop on Graphs and Combinatorial Optimization (CTW11), Rome, Italy, 211-214, 2011. Download paper.

  10. L. Liberti, B. Masson, C. Lavor, A. Mucherino, Branch-and-Prune Trees with Bounded Width, Proceedings of the 10th Cologne-Twente Workshop on Graphs and Combinatorial Optimization (CTW11), Rome, Italy, 189-193, 2011. Download paper.

  11. A. Mucherino, C. Lavor, L. Liberti, N. Maculan, Strategies for Solving Distance Geometry Problems with Inexact Distances by Discrete Approaches, Proceedings of Toulouse Global Optimization 2010 (TOGO10), Toulouse, France, 93-96, 2010. Download paper.

  12. A. Mucherino, C. Lavor, N. Maculan, The Molecular Distance Geometry Problem Applied to Protein Conformations, Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization (CTW09), Paris, France, 337-240, 2009. Download paper.

  13. C. Lavor, L. Liberti, A. Mucherino, N. Maculan, On a Discretizable Subclass of Instances of the Molecular Distance Geometry Problem, ACM Conference Proceedings, 24th Annual ACM Symposium on Applied Computing, Hawaii, USA, 804-805, 2009. Download paper.


Extended abstracts (refereed)

  1. A. Mucherino, J. Omer, The Referenced Vertex Order Problem: Recent Advances and Future Works, Proceedings of the conference ROADEF23, Rennes, France, February 2023. Download extended abstract.

  2. S.B. Hengeveld, T. Malliavin, L. Liberti, A. Mucherino, Collecting Data for Generating Distance Geometry Graphs for Protein Structure Determination, Proceedings of the conference ROADEF23, Rennes, France, February 2023. Download extended abstract.

  3. A. Mucherino, An Analysis on the Degrees of Freedom of Binary Representations for Solutions to Discretizable Distance Geometry Problems. In: "Recent Advances in Computational Optimization", S. Fidanova (Ed.), Studies in Computational Intelligence 986, 251-255, 2022. Download extended abstract.

  4. A. Mucherino, On the Manipulation of Simple Animations by dynamical Distance Geometry, Proceedings of the XVI international conference on "Algebra, Number Theory, and Discrete Geometry: Modern Problems, Applications, and Problems of History", Tula, Russia, May 2019. Download extended abstract.

  5. J. Omer, A. Mucherino, Integer Programming for the Search of a Discretization Order in Distance Geometry Problems, Proceedings of the conference ROADEF17, Metz, France, February 2017. Download extended abstract.

  6. A. Mucherino, Discretization Orders and Distance Geometry, Proceedings of the conference ROADEF15, Marseille, France, February 2015. Download extended abstract.

  7. D.S. Gonçalves, A. Mucherino, Challenges for Extending Discretizable Molecular Distance Geometry to Interval Data, Proceedings of Many Faces of Distances (MFD14), Campinas, São Paulo, Brazil, October 2014. Download extended abstract.

  8. D.S. Gonçalves, J. Nicolas, A. Mucherino, Searching for Optimal Orders for Discretized Distance Geometry, Proceedings of Many Faces of Distances (MFD14), Campinas, São Paulo, Brazil, October 2014. Download extended abstract.

  9. R. Alves, A. Cassioli, A. Mucherino, C. Lavor, L. Liberti, The Integration of Clifford Algebra in the iBP algorithm for the DMDGP, Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO13), Granada, Spain, 745-746, 2013. Download extended abstract.

  10. M. Le Boudic-Jamin, A. Mucherino, R. Andonov, Modeling Protein Flexibility by Distance Geometry, Proceedings of the conference ROADEF 2012, Angers, France, April 2012. Download extended abstract.

  11. L. Liberti, C. Lavor, A. Mucherino, An Exponential Algorithm for the Discretizable Molecular Distance Geometry Problem is Polynomial on Proteins, Proceedings of the 7th International Symposium on Bioinformatics Research and Applications (ISBRA11), Book of extended abstracts, pages 40-43, Changsha, China, May 2011. Download extended abstract.

  12. A. Mucherino, C. Lavor, L. Liberti, The Discretizable Molecular Distance Geometry Problem: from Ideal to Real Instances, Proceedings of the conference ROADEF 2011, Saint Etienne, France, March 2011. Download extended abstract.

  13. A. Mucherino, L. Jourdan, E-G. Talbi, A Heuristic for Biclustering based on a Bilevel Reformulation, Proceedings of the International Conference on Metaheuristics and Nature Inspired Computing (META10), Djerba, Tunisia, October 2010. Download extended abstract.

  14. A. Mucherino, S. Cafieri, A New Heuristic Algorithm for Consistent Biclustering, Proceedings of the EU/MEeting 2010, Lorient, France, June 2010. Download extended abstract.

  15. A. Mucherino, C. Lavor, L. Liberti, E-G. Talbi, On Suitable Parallel Implementations of the Branch & Prune Algorithm for Distance Geometry, Proceedings of the Grid5000 Spring School, Lille, France, April 2010. Download extended abstract.

  16. A. Mucherino, C. Lavor, L. Liberti, N. Maculan, A Discrete Approach for Finding the Conformation of Molecules from NMR Data, Proceedings of the conference ROADEF 2010, Toulouse, France, February 2010. Download extended abstract.

  17. C. Lavor, L. Liberti, A. Mucherino, N. Maculan, Recent Results on the Discretizable Molecular Distance Geometry Problem, Proceedings of the conference ROADEF 2009, Nancy, France, 283-284, 2009. Download extended abstract.


Other

  1. M. Song, D.S. Gonçalves, W.L. Jung, C. Lavor, A. Mucherino, H. Wolkowicz, On the Local and Global Minimizers of the Smooth Stress Function in Euclidean Distance Matrix Problems, arXiv e-print, arXiv:2408.07256v1, August 2024.

  2. G. Abud, J. Alencar, C. Lavor, L. Liberti, A. Mucherino, An Impossible Utopia in Distance Geometry, arXiv e-print, arXiv:2110.01231v1, October 2021.

  3. M.C. De Cola, A. Mucherino, G. Felici, L. Liberti, Branch-and-Prune Algorithm for the Sensor Network Localization Problem, IASI Technical Report R.4, 2013.

  4. L. Liberti, C. Lavor, B. Masson, A. Mucherino, Polynomial Cases of the Discretizable Molecular Distance Geometry Problem, arXiv e-print, arXiv:1103.1264v1, March 2010.

  5. A. Mucherino, S. Cafieri, A New Heuristic for Feature Selection by Consistent Biclustering, arXiv e-print, arXiv:1003.3279v1, March 2010.

  6. A. Mucherino, O. Seref, P.M. Pardalos, Simulating Protein Conformations through Global Optimization, arXiv e-print, arXiv:0811.3094v1, November 2008.


Theses

  1. A. Mucherino, On the Discretization of Distance Geometry: Theory, Algorithms and Applications, HDR Monograph, University of Rennes 1. July 17, 2018. Download from INRIA's HAL archive.

  2. A. Mucherino, Geometric Aspects in the Simulation of Protein Folding Processes (in Italian), PhD Thesis, Second University of Naples. December 18, 2005.

  3. A. Mucherino, Quadratic Optimization: Algorithms and Software for Dense Problems (in Italian), Master Thesis, Second University of Naples. October 30, 2001.

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