Welcome to PR PS BB 2013, the 2nd International Workshop on Pattern Recognition in Proteomics, Structural Biology and Bioinformatics that will be held in Naples (Italy) in September 10, 2013.

MOTIVATIONS AND AIMS. Pattern recognition, after many years of studies and researches successfully developed in several applicative areas, has now know-how, computing strategies, technologies, methods and tools to exploit in new fields such as proteomics, structural biology and bioinformatics. PR PS BB 2013 integrates and continues the tradition of the international conferences on image analysis and processing, one of the longest running international conferences, that started in Italy, in 1980. Through its informal nature, the workshop is intended to become the foremost platform for exchanging ideas and giving to top researchers, practitioners and students from around the world, of the computing and biological communities, excellent opportunities to meet, interact and rise synergies.

PROGRAM - 10 September 2013 - Villa Doria D'Angri, Naples (Italy)

08:15 - 10:00 Registration

10:00 Welcome message from the chairs

Session 1: Pattern Analysis in Proteomics
Chair: Virginio Cantoni

10:10 Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking
Elodie Laine, Alessandra Carbone (Université Pierre et Marie Curie and CNRS, Paris, France)

10:30 A Supervised Approach to 3D Structural Classification of Proteins
Virginio Cantoni (University of Pavia, Italy), Alessio Ferone, Alfredo Petrosino (University of Naples Parthenope, Italy), Gabriella Sanniti di Baja (National Research Council, Italy)

10:50 - 11:20 Coffee Break

11:20 SVM-Based Classification of Class C GPCRs from Alignment-Free Physicochemical Transformations of Their Sequences
Caroline König (Univ. Politècnica de Catalunya, Barcelona, Spain), Raúl Cruz-Barbosa (Univ. Tecnológica de la Mixteca, Oaxaca, México and Univ. Autònoma de Barcelona, Barcelona, Spain), René Alquézar, Alfredo Vellido (Univ. Politècnica de Catalunya, Barcelona, Spain)

11:40 Structural Investigation of Supercooled Water Confined in Antifreeze Proteins: Models’ performance evaluation between Coarse Grained and Atomistic simulation models
Nghiep H. Vu (Vietnam National University, HCMC, Vietnam), Hung P. N.(Institute for Computational Science and Technology at Ho Chi Minh City, Vietnam), Ly L. (Vietnam National University, HCMC and Institute for Computational Science and Technology at Ho Chi Minh City, Vietnam)

12:00 Comparison of GHT-based Approaches to Structural Motif Retrieval
Alessio Ferone (University of Naples Parthenope, Italy), Ozlem Ozbudak (Istanbul Technical University, Turkey)

12:20 CCMS: A Greedy Approach to Motif Extraction
Giacomo Drago, Marco Ferretti, Mirto Musci (University of Pavia, Italy)

12:40 Structural Blocks Retrieval in Macromolecules: Saliency and Precision Aspects
Virginio Cantoni (University of Pavia, Italy), Dimo T. Dimov (Bulgarian Academy of Sciences, Sofia, Bulgaria)

13:00 - 14:30 Lunch Break

Invited lecture
14:30 Cellular Pattern Recognition and Comparison through Generative Modeling: Image Derived Models of SubcellularOrganization
Robert Murphy (Carnegie Mellon University, USA)

Session 2: Pattern Analysis in Genomics
Chair: Michele Ceccarelli

15:10 Discovering Typical Transcription-Factors Patterns in Gene Expression Levels of Mouse Embryonic Stem Cells by Instance-Based Classifiers
Francesco Gagliardi, Claudia Angelini (IAC- CNR, Naples, Italy)

15:30 Motif-Based Method for the Genome-Wide Prediction of Eukaryotic Gene Clusters
Thomas Wolf, Vladimir Shelest, and Ekaterina Shelest (Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany)

15:50 - 16:20 Coffee Break

16:20 An Approach to Identify miRNA associated with Cancer Altered Pathways
Giovanna Maria Ventola, Antonio Colaprico, Fulvio D’Angelo (BioGeM, Ariano Irpino, Italy), Vittorio Colantuoni (University of Sannio, Benevento, Italy), Giuseppe Viglietto (University of Magna Graecia, Catanzaro, Italy), Luigi Cerulo, and Michele Ceccarelli (University of Sannio and BioGeM, Italy)

16:40 Performance comparison of five exact graph matching algorithms on biological databases
Vincenzo Carletti, Pasquale Foggia, and Mario Vento (University of Salerno, Italy)

17:00 Pardiff: inference of differential expression at base-pair level from RNA-Seq experiments
Bogdan Mirauta (UPMC and CNRS, Paris, France), Pierre Nicolas (INRA, France), and Hugues Richard (UPMC and CNRS, Paris, France)

17:20 Environmental Risk Assessment of Genetically Modified Organisms by a Fuzzy Decision Support System
Francesco Camastra, Angelo Ciaramella (University of Naples Parthenope, Italy), Valeria Giovannelli, Matteo Lener, Valentina Rastelli (ISPRA, Rome, Italy), Antonino Staiano (University of Naples Parthenope, Italy), Giovanni Staiano (ISPRA, Rome, Italy), and Alfredo Starace (University of Naples Parthenope, Italy)

17:40 Conclusions

Program Chairs
  Virginio Cantoni, University of Pavia, Italy
  Michele Ceccarelli, University of Sannio, Italy
  Robert Murphy, Carnegie Mellon University, USA
Program Committee
  Pierre Baldi, Institute for Genomics and Bioinformatics - University of California, USA
  Paola Bertolazzi, IFAC CNR Roma, Italy
  Mario Cannataro, Università della Calabria, Italy
  Virginio Cantoni, University of Pavia, Italy
  Alessandra Carbone, Université Pierre et Marie Curie, Paris, France
  Jens Michael Cartsensen, Videometer A/S, Copenaghen, Denmark
  Rita Casadio, University of Bologna, Italy
  Michele Ceccarelli, University of Sannio, Italy
  Angelo Facchiano, Istituto di Scienze dell'Alimentazione - CNR - Avellino, Italy
  Concettina Guerra, Georgia Institute of Technology, USA
  Alamgir Hossain, Northumbria University, UK
  Tom Lenaerts, Université Libre de Bruxelles, Belgium
  Le Ly, Ho Chi Min International University, Vietnam
  Giuseppe Maino, ENEA & Bologna University, Italy
  Elena Marchiori, Radboud University, The Netherlands
  Giancarlo Mauri, University of Milano Bicocca, Italy
  Robert Murphy, Carnegie Mellon University, USA
  Giovanni Paolella, University of Naples Federico II, Italy
  Alfredo Petrosino, Parthenope University, Italy
  Michael Schroeder, BiOTEC, TU Dresden, Germany
  Ekaterina Shelest, Hans Knoell Institute - Jena, Germany
  Roberto Tagliaferri, Università di Salerno, Italy
  Alfredo Vellido, Universitat Politècnica de Catalunya, Spain
Keynote Speaker
  Robert Murphy, Carnegie Mellon University, USA
Workshop Organization and Scientific Secretary
  Alessandra Setti, University of Pavia, Italy

PAPER SUBMISSION. Papers must be submitted to https://cmt.research.microsoft.com/ICIAPWS2013/. Manuscripts should be in pdf and formatted according to Springer's Lecture Notes in Computer Science (LNCS) style. Information concerning typesetting can be obtained directly from Springer at: http://www.springer.com/comp/lncs/authors.html.
Papers must not exceed 10 pages and should report original work.
All submitted papers will be subject to a rigorous peer-review process. Accepted papers will appear in the workshop proceedings in a Volume of Lecture Notes in Computer Science (Springer).
Submission implies the willingness of at least one of the authors to register and present the paper, if accepted.

VENUE. The venue is Villa Doria D'Angri, situated on the Posillipo hill, about 2 Km far from the venue of the Main Conference (Castel dell'Ovo).
How to reach Villa Doria D'Angri: please visit http://www.iciap2013-naples.org/index.php?option=com_content&view=article&id=55 for information.

REGISTRATION. The participants registration (to Workshop, Tutorial and Main Conference) will start on Monday morning, 8:30, at Villa Doria D'Angri and a workshop material kit will be distributed.

The Workshop rooms are provided with computer, projector and microphone. If you need further equipment, please let us know.

The time slot for each presentation is 20 minutes (15 minutes for presentation + 5 minutes for discussion). For keynote speaker 40-60 minutes are scheduled.

Download the PRPSBB 2013 CFP as PDF.


in conjunction with the
17th International Conference on Image Analysis and Processing (ICIAP)
Naples, Italy


Paper submission: 21 June 2013
Notifications: 25 June 2013
Camera-ready due: 28 June 2013
Workshop: 10 September 2013
Venue: Villa Doria D'Angri, Naples (Italy)

Download the PRPSBB 2013 program as PDF.