68. Casadio R, Paolella G -Aspetti biochimici di Bioinformatica e Biologia Computazionale- in: Biochimica Umana (Edited by Salvatore F) 709-746. Idelson-Gnocchi, Napoli. ISBN 978-88-7947-556-3 (2013)

67. Profiti G , Piovesan D , Martelli PL , Fariselli P , Casadio R -Community detection within clusters helps large scale protein annotation: Preliminary results of modularity maximization for the bar+ database- BIOINFORMATICS 2013 - the International Conference on Bioinformatics Models, Methods and Algorithms. Pag:328-332. 11-14/02/2013, Barcelona (ES) In:BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (Solé-Casals J, Fred A, Gamboa H, Fernandes P eds) 328-332. SciTePress – Science and Technology Publications (2013)

66. Profiti G, Piovesan D, Martelli PL, Fariselli P, Casadio R -Protein Sequence Annotation by means of Community Detection- IWBBIO 2013- International Work-conference on Bioinformatics and Biomedical Engineering. 18-20/03/2013, Granada (ES) In:Proceedings of IWBBIO 2013 (Ortuno F, Rojas I, eds) 753-755. Copicentro Editorial (2013)

65. Casadio R, Martelli PL, Savojardo C, Fariselli P -Large-scale annotation of proteins with labelling methods- 1st International Workshop on Pattern Recognition in Proteomics, Structural Biology and Bioinformatics. 13/9/2011, Ravenna. In: Il Nuovo Cimento C, 5(1);7-25. (2012)

64. Di Lena P, Fariselli P, Margara L, Vassura M, Casadio R -Divide and Conquer strategies for protein structure prediction- In: Mathematical Approaches to Polymer Sequence Analysis (Bruni R, ed) 23-46. Springer, New York (USA) ISBN:9781441967992 (2011)

63. Savojardo C, Fariselli P, Piovesan D, Martelli PL, Casadio R -ISPRED2: A machine-learning method to predict protein interaction sites- 8th INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS. 30/6-2/7/2011, Gargnano-Lago di Garda. In:Lecture Notes in Computer Science. 7548:127-135 (2011)

62. Alhamdoosh M, Savojardo C, Fariselli P, Casadio R -Disulfide connectivity prediction with extreme learning machines- BIOINFORMATICS 2011:International Conference on Bioinformatics Models, Methods and Algorithms. 26/1/2011, Roma. In Proceedings of BIOINFORMATICS 2011, 5-14 (2011)

61. Fariselli P, Bartoli L, Casadio R -Improving Coiled-Coil Prediction with Evolutionary Information- 6th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2009. 15-17/10/2009, Genova. In: Lecture Notes in COmputer Science: Computational Intelligence Methods for Bioinformatics and Biostatistics (Masulli F, Peterson LE, Tagliaferri R eds). 6160:20-32 (Springer-Verlag, Germany) (2010)

60. Fontanesi L, Fronza R, Scotti E, Colombo M, Speroni C, Tognazzi L, Galimberti G, Calò DG, Bonora E, Vargiolu M, Romeo G, Casadio R, Russo V -The FAGenomicH project: towards a whole candidate gene approach to identify markers associated with fatness and production traits in pigs and investigate the pig as a model for human obesity- Proceedings of the ASPA 18th Congress. 9-12/6/2009, Palermo. In: Italian journal of Animal Science 8(2):87-89 (2009)

59. Di Lena P, Fariselli P, Margara L, Vassura M, Casadio R -On the upper bound of the prediction accuracy of residue contacts in proteins with correlated mutations: the case study of the similarity matrices. 9th International Workshop on Algorithms in Bioinformatics (WABI 2009). 12/13/9/2009, Philadelphia (PA, USA). in: Lecture Notes in Computer Science 5724:62-72 (Springer-Verlag, Germany) (2009)

58. Bartoli L, Fariselli P, Casadio R -PS-Coils: A new method for coiled-coil prediction that expolits both single sequence and evolutionary information- SIXTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS. 15-17/10/2009, Genova. in: Proceedings of CIBB 2009, 3:1-8 (2009)

57. Mirto M, Ferramosca A, Tartarini D, Romano S, Negro A, Tasco G, Fiore S, Zara V, Casadio R, Aloisio G -A protein structure prediction service in the ProGenGrid system- HealthGrid2008.2-4/6/2008, Chicago (USA). In: Studies in Health Technology and Informatics Global Healthgrid: e-Science Meets Biomedical Informatics - Proceedings of HealthGrid 2008 (Solomonides T, Silverstein JC et al eds.) Vol 138:135-146. IOS Press Book (Amsterdam) (2008)

56. Casadio R, Fariselli P, Martelli PL, Tasco G -Thinking the impossible: how to solve the protein folding problem with and without homologous structures and more- Methods in molecular biology vol.350:Protein Folding Protocols (Edited by Bai Y, Nussinov R) 350:305-320. Humana Press Inc., Totowa, NJ. ISSN: 1064-3745 ISBN:1-58829-622-9 (2007)

55. Casadio R -Guest Editor's Introduction to the Special Issue on Computational Biology and Bioinformatics- Part 1 IEEE/ACM Trans Comput Biol Bioinform. 3:321-2 (2006)

54. Casadio, R. Fariselli, P. Martelli, P.L. (Volume Editors) -Bioinformatics ITalian Society BITS 2006 Conference proceedings- (Bologna, 28-29/04/06)

53. Capriotti E, Casadio R -A machine learning approach for predicting kinetic order and rate constant of protein folding- WSEAS International Conference on MATHEMATICAL BIOLOGY and ECOLOGY MABE' 18-20/01/2006 Miami, Florida, USA, pag. 123-127

52. Casadio R, Myers G (Volume Editors ) -Algorithms in Bioinformatics: lecture notes in bioinformatics Proceedings of the 5th International Workshop on algorithms in bioinformatics, WABI 2005- Mallorca ( Isole Baleari, Spagna ), 3-6/10/2005, (LNBI 3692), Springer ed.

51. Casadio R, Calabrese R, Capriotti E, Compiani M, Fariselli P, Marani P, Montanucci L, Martelli PL, Rossi I, Tasco G Machine learning and the prediction of protein structure: the state of the art- 10th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU 2004)- Perugia, 4-9/7/2004, Casa Editrice La Sapienza, Roma:933-940

50. Casadio R, Calabrese R, Tasco G, Capriotti E, Compiani M, Marani P, Montanucci L, Rossi I, Martelli PL, Fariselli P-Metodi di Machine Learning per la predizione di strutture proteiche e della loro interazione- Convegno Bioinformatica: sfide e prospettive. Università del Sannio, 17-18/12/2003. F.Angeli Editore

49. Martelli PL, Casadio R -Modelling of proteins with low sequence identity: two sucess stories with chains from the archaeon Sulfolobus solfataricus. VII Workshop sul Calcolo ad Alte Prestazioni in Italia: Modellistica molecolare-Biochimica e Farmaceutica- Milano, 14/11/2003 (CD edition)

48. Casadio R, Capriotti E, Compiani M, Fariselli P, Jacoboni I, Martelli PL, Rossi I, Tasco G -Neural Networks and the prediction of protein structure. In Artificial Intelligence and Heuristic Methods in Bioinformatics. (Frasconi P and Shamir R, eds) pp. 22-33. NATO Science Series. IOS Press, Amsterdam,Netherlands, (2003)

47. Fariselli P, Zauli A, Rossi I, Finelli M, Martelli PL, Casadio R A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes- IEEE International Workshop on Neural Network on Signal Processing 2003- Toulouse (FRANCE), 17-19/9/2003, IEEE Press, pag 33-41 (2003)

46. Casadio R, Capriotti E, Compiani M, Fariselli P, Martelli PL, Malaguti L, Rossi I, Tasco G La predizione strutturale di proteine nellera gnomica ed i metodi di apprendimento automatico- Atti del XV Congresso Internazionale Ordine Nazionale dei Biologi Progresso scientifico, etica, tutela delle risorse: sfide professionali del terzo millennio. Vol 1, pag 61-70 (2002)

45. Fariselli P, Finelli M, Marchignoli D, Casadio R.-MaxSubSeq:an algorithm for finding all the maximal scoring subsequences with costrained segment lengths- AIIA VIII Convegno, Siena 10-13/9/2002. Notizie AIIA, Vol XV no4 pg53-56

44. Casadio R, Fariselli P -From protein sequence to structure with Neural Networks- In: Protein Folding, Stability and Design 2002, (Gromiha MM and Selvaraj S, eds.) pp 79-92, Research Signpost Editions, Trivandrum, India (2002)

43. Fariselli P, Martelli P, Casadio R -A neural network based method for predicting the disulfide connectivity in proteins- Knowledge based intelligent information engineering systems and allied technologies (KES 2002), (Damiani E et al., eds), Vol 1, pp 464-468, IOS Press, Amsterdam (2002)

42. Casadio R, Rossi I, Fariselli P, Arnofi E, Ricobelli P, Rossi E, Boschi S, Facchiano A. -Computer-aided design of peptidomimetic molecules active on vascular cell growth and migration- In Science and Supercomputing at CINECA, (Garofalo F et al, eds) pp 101-107,Technoprint Bologna (2001)

41. Casadio R, Compiani M, Fariselli P, Jacoboni I, Martelli P.L., Rossi I (2001) ­Tools for protein secondary structure prediction: from sequence to structure. In : Protein Sequence Analysis in the Post Genomic Era (Casadio R and Masotti L, eds) pp 115-133, CLUEB, Bologna

40. Fariselli P, Casadio R (2000) - Prediction of the Number of Residue Contacts in Proteins- ISMB 8:146-151 (2000)

39. Casadio R, Rossi I, Fariselli P, Arnofi E, Ricobelli P, Rossi E, Boschi S, Facchiano A (1999) - DRUG: Supercomputing Drug design for Industrial and Academic Partnership. Peptidomimetic molecules active on vascular cell growth and migration- In HPCN Experiences in Biotechnology (Dechema and GMD, eds) pp 1-25, TTN Management Group, Frankfurt

38. Casadio R, Compiani M, Fariselli P, Martelli PL (1999) - A Data Base of Minimally Frustrated Alpha Helical Segments Extracted from Proteins According to an Entropy Criterion- ISMB 7:68-76

37. Casadio R, Fariselli P, Rigo A (1998)-Computational analysis of oxygenated and deoxygenated states of hemocyanin: theoretical support for a putative allosteric model of oxygen binding - Science and Supercomputing at CINECA, 117-121,Technoprint Bologna

36. Fariselli P, Casadio R (1998) - Quantum molecular biophysics: the case study of hemocyanin- in Biophysics of Electron Transfer and Molecular Bioelectronics (Nicolini C, ed) E.L:B.A. Forum Series, Plenum Pub Co, New York, 139-159

35. Casadio R, Arrigo P, Fariselli P, (1998)- Self-organizing neural networks highlight possible functionally relevant regions in the c-DNA coding sequences of G-protein coupled receptors - Proc. of the First international conference on bioinformatics of genome regulation and structure (BGRS'98, Novosibirisk 1998) Vol 2, pp 262-265

34. Fariselli P, Casadio R -A neural network based method for predicting contact maps of protein - In : Proc. of World Multiconference on Systemics, Cybernetics and Informatics (SCI'98, Orlando USA)(1998) V1 527-533.

33. Fariselli P, Casadio R (1998) - A neural network based method for predicting contact maps of proteins- SIMAI'98 v1 pp.272-275

32. Fariselli P, Casadio R (1997) - Pseudodihedral potential of protein residues and the prediction of folding- In: Proc Bio-Computing and Emergent Computation BCEC 97 (1997) (Lundth D et al, eds), pp112-121, World Scientific, Singapore

31. Arrigo P, Fariselli P, Casadio R (1997) - Self-organizing neural map of the coding sequences of G-Protein- coupled receptors reveal local domains associated with potentially functional determinants in the proteins- In : Proc Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB 5), pp 44-47, AAAI Press, Menlo Park, Ca (selected presentation)

30. Martelli PL, Fariselli P, Casadio R - De novo design of proteins: tha alpha-helix engineer-Italian Biochemical Society Transactions (IBST) Vol.8, pg 38-39. (Relazione su invito a Proteine '97)

29. Rost B, Casadio R and Fariselli P- Refining neural network predictions for helical transmembrane proteins by dynamic programming - In : Proc. Fourth International Conference on Intelligent Systems for Molecular Biology ( ISMB 4)(States DJ et al, Eds) pp 192-200 (1996)

28. Arrigo P, Fariselli P, and Casadio R- The identification of locally ordered features on completely unligned genomic sequences by using an unsupervised neural classifiers- In: Computer Science and Biology, Proc of the German conference on Bioinformatics (GBC '96) (Hofestadt R et al., eds) pp 156-159, Leipzig 1996.

27. Compiani M, Fariselli P, and Casadio R- Noise and random-like behaviour of perceptrons: theory and application to protein structure prediction-In: Application and Science of Artificial Neural Networks II, (Rogers SK and Ruck DW, Eds. Proc. Spie 2760) Vol 2760, 587-607 (1996).

26. Casadio R, Compiani M, Fariselli P, Vivarelli F-Predicting free energy contribution to the conformational stability of folded proteins from residue sequence with radial basis function networks- Proc Conf Intelligent Systems for Molecular Biology (ISBM 3) (Rawlings C et al, Eds), pp 81-88 (1995).

25. Compiani M, Fariselli P and Casadio R - Statistical behaviour of perceptrons: the case study of the prediction of protein secondary structures- Int J Neur Sys 6:195-199 (Supp 1995)

24. Fariselli P, Taroni C, Compiani M and Casadio R - Application of neural networks to the prediction of protein structures-In: Primo Seminario di Bioinformatica (Colosimo A, ed), pp 257-274, CNR and University of Camerino (1994)

23. Venturoli G, Corazza A, Casadio R and Melandri BA -Effects of the surface charge on thermodynamics and kinetics of redox and proteolytic reactions in bacterial chromatophores- In: Biothermokinetics (Westerhoff H, ed), pp 337-344, Intercept Ltd, Andover (1994)

22. Compiani M, Fariselli P and Casadio R- Neural networks and prediction of protein structures -In "Neural Networks in Biology and Medicine", pp313-332, World Scientific, Singapore (1994)

21. Compiani M, Fariselli P and Casadio R- The statistical behaviour of perceptrons-In: Parallel Architectures and Neural Networks (Caianiello ER, ed) pp 111-117, World Scientific, Singapore (1992)

20. Compiani M, Fariselli P and Casadio R- Neural Networks extracting general features of protein secondary structures-In: Parallel Architectures and Neural Networks (Caianiello ER, ed) pp 227-237, World Scientific, Singapore (1991)

19. Corazza A, Melandri BA, Venturoli G and Casadio R - Evaluation of the surface potentials at the membrane-solution interface in photosynthetic bacterial systems- In: Electrified Interfaces in Physics, Chemistry and Biology (Guidelli R, ed) NATO ASI Ser Vol 355, pp 505-532, Kluwer Accad Publ, Dortrecht, The Netherlands (1991)

18. Melandri BA, Venturoli G and Casadio R - Electric phenomena in photosynthetic membranes- In: Electrochemical Research in Italy (Soc Ital Chimica, ed), pp 35-39, Scarabeo, Bologna (1991)

17. Fregni V and Casadio R - Kinetic characterization of a membrane-bound ATP-dependent proton pump- In : Conf Proc Vol 31: Cybernetics and Biophysics Italian Conference (Frediani C, ed) pp 155-160, Ital Phys Soc, Bologna (1990)

16. Corazza A, Casadio R, Melandri BA and Venturoli G - Electrostatic potentials at the membrane solution interface of photosynthetic systems- In : Conf Proc Vol 31: Cybernetics and Biophysics Italian Confrence (Frediani C, ed) pp 145-150, Ital Phys Soc, Bologna (1990)

15. Casadio R - The oligomycin-sensitive Ca-ATPase of chromatophores from photosynthetic bacteria is not coupled to Dæ + generation- In: The Ion Pumps. Structure, Function and Regulation (Stein WD, ed)pp 201-206, Alan R Liss Inc, New York (1988)

14. Casadio R and Melandri BA - Energetics of light activation of the ATPase in chromatophores of Rhodobacter sphaeroides- Eur Bioenerg Conf Reports (Congress, ed) Vol 4, p 238, Prague (1986)

13. Casadio R - Conformational dynamics of membrane bound H -ATPase in photosynthetic bacterial chromatophores: an insight into energy coupling at a molecular level- Atti VII Congresso SIBPA- IX CONGRESSO GNCB, Lipari (1985)

12. Casadio R, Venturoli G and Melandri BA - The determination of the electrochemical potential difference of protons in bacterial chromatophores- In: Recent Advances in Biological Membranes Studies (Packer L, ed) NATO ASI Series, Vol 91, pp 409-424, Plenum Press, New York (1985)

11. Casadio R and Melandri BA - On the regulation of the ATPase activity in chromatophores of Rhodopseudomonas sphaeroides- In: H -ATPase Synthase: Structure, Function and Biogenesis (Papa S et al, eds) pp 411-420, Adriatica Editrice, Bari (1984)

10. Melandri BA, Venturoli G, Casadio R, Azzone G, Kell D and Westerhoff H -Is the transmembrane proton potential difference a competent intermediate in membrane associated ATP synthesis ?-Adv Photosynthesis Res (Sybesma C et al, eds) Vol 2, pp 4233-4240 (1984)

9. Casadio R, Venturoli G and Melandri BA - Phospholipid enriched chromatophores: characterization of electron transfer processes- Atti VI Congresso SIBPA - VII Congresso GNCB (Camogli, 1983) pp 48-50 (1983)

8. Casadio R, Venturoli G and Melandri BA - Studies on phospholpid enriched chromatophores: studies and perspectives- Eur Bioener Con Reports (LBTM-CNRS, eds) Vol 2, pp 185-186, Lyon (1982)

7. Casadio R - Reconstitution of a light-driven proton pump: DpH determination in bacterirhodopsin/phospholipid vesicles- In: Transport in Biomembranes. Model Systems and Reconstitution (Antolini et al, eds) pp 201-204, Raven Press, New York (1982)

6. Baccarini Melandri A, Casadio R and Melandri BA - Electron transport, proton translocation and ATP synthesis in bacterial chromatophores- Curr Top Bioenerg 12: 197-258 (1981)

5. Casadio R, Venturoli G and Melandri BA - Transmembrane potential difference in chromatophores of photosynthetic bacteria: measurements with a ion-selective minielectrode- Eur Bioenerg Conf Reports (Patron ed) Vol 1, pp 231-232, Bologna (1980)

4. Stoeckenius W and Casadio R - Dissociation and reconstitution of purple membranes- In: Membrane Bioenergetics (Lee CP et al, eds) pp 229-251, Addison Wesley Publ Co, London (1979)

3. Melandri BA, Casadio R and Baccarini Melandri A - Energy levels and rates of photophosphorylation in bacterial chromatophores- Proc 4th Int Con Photosynthesis (Hall DO et al, eds) pp 601-609, The Biochemical Soc, London (1978)

2. Casadio R, Baccarini Melandri A and Melandri BA - The degree of coupling of ATP syntethase in bacterial photophosphorylation- In: Electron Transfer Chains and Oxidative Phosphorylation (Quagliariello et al, eds) pp 407-410, North Holland, Amsterdam, (1975)

1. Melandri BA, Zannoni D, Casadio R and Baccarini Melandri A - Energy conservation and transduction in photosynthesis and respiration of facultative photosynthetic bacteria- Proc 3rd Int Con Photosynthesis (Avron M, ed) pp 1147-1162, Elsevier, Amsterdam, (1974)