Peer-reviewed scientific papers

 

1. Bernardi F., Bottoni A., Rossi I., Robb M. A.;
   "Theoretical study of substituent-effect on the stability of enolate ions";
   J. Mol. Structure . 300 (1993) 157.

 

2. Bernardi F., Rossi I., Robb M. A., Venturini A. ;
   "Ab-Initio study of the potential energy surface of the reaction of ethylene with nitronium ion";
   J. Org. Chem. 58 (1993) 7074.

 

3. Corchado J. C., Espinosa-Garcia J., Hu W.-P., Rossi I., Truhlar D. G.;
   "Dual-level reaction-path dynamics (The /// approach to VTST with semiclassical tunneling). Application to OH + NH₃ -> H₂O + NH₂";
   J. Phys. Chem. 99 (1995) 687.

 

4. Rossi I., Truhlar D. G.;
   "Parameterization of NDDO wavefunctions using Genetic Algorithms: an evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations for organic reactions";
   Chem. Phys. Lett. 233 (1995) 231.

 

5. Rossi I., Truhlar D. G.;
   "Improved general scaling factors and systematic tests of the SAC method for estimating correlation energies of molecules";
   Chem. Phys. Lett. 234 (1995) 64.

 

6. Rossi I., Olivucci M., Bernardi F., Robb M. A.;
   "Falling down the singlet manifold. A CAS-SCF study of the photochemical [1,2] and [1,3] allyl-shift in hexa-1,5-dienes";
   J. Phys. Chem. 99 (1995) 6757.

 

7. W.-P. Hu, G. C. Lynch, Y.-P. Liu, I. Rossi, J. J. P. Stewart, R. Steckler, B. C. Garrett, A.D. Isaacson, D.-h. Lu, V. S. Melissas, and Truhlar D. G.;
   "MORATE-version 6.5: a new version of a computer program for direct dynamics calculations of chemical reaction rate constants";
   Computer Physics Communications 88 (1995) 344.

 

8. Nguyen K. A., Rossi I., Truhlar D. G.;
   "A dual-level Shepard interpolation method for generating potential energy surfaces for dynamics calculations";
   J. Chem. Phys. 103 (1995) 5522.

 

9. Cacace F., De Petris G., Pepi F., Rossi I., Venturini A.;
   "The gas-phase reaction of Nitronium ion with Ethylene. An experimental and theoretical study";
   J. Am. Chem. Soc. 118 (1996) 12719.

 

10. Bernardi F., Bottoni A., Calcinari M., Robb M. A., Rossi I. ;
    "A Comparison between CASPT2 and DFT in the study of Ni(C₂H₄)₂ complexes";
    J. Phys. Chem. A 101 (1997) 6310.

 

11. Hu W.-P., Rossi I., Corchado J. C., and Truhlar D. G.;
    "Molecular modeling of combustion kinetics. The abstraction of primary and secondary Hydrogens by Hydroxyl radical" ;
    J. Phys. Chem. A 101 (1997) 6911.

 

12. Bottoni A., Costa A. L., Di Tommaso D., Rossi I., and Tagliavini E. ;
    "New computational and experimental evidences on the mechanism of the Sakurai reaction";
    J. Am. Chem. Soc. 119 (1997) 12131

 

13. Bernardi F., Cacace F., De Petris G., Pepi F., and Rossi I..;
    "Gaseous [N₂O₅H]⁺, [N₂O₄H]⁺ and related species from the addition of NO₂⁺ and NO⁺ ions to Nitric Acid and its derivatives";
    J. Phys. Chem. A 102 (1998) 1987.

 

14. Venturini A., Bernardi F., Olivucci M., Robb M. A., and Rossi I.;
"Dimerization of Silaethylene: Computational evidences for a novel mechanism for the formation of 1,3-Disilacyclobutane via a 1,2 Approach";
J. Am. Chem. Soc. 120 (1998) 1912.

 

15. Bernardi F., Cacace F., De Petris G., Pepi F., and Rossi I..;
    "XeNO₃⁺, a gaseous cation characterized by a remarkably stable Xe-O bond";
    J. Phys. Chem. A 102 (1998) 5831.

 

16. Bernardi F., Bottoni A., and Rossi I..;
    "A DFT investigation of Ethylene dimerization catalyzed by Ni(0) complexes";
    J. Am. Chem. Soc. 120 (1998) 7770.

 

17. Caminati W., Moreschini P., Rossi I., and Favero P. G.;
    "The O^...H-O hydrogen bond in the gas-phase. Microwave structure of Ethylene Oxyde-Water";
    J. Am. Chem. Soc. 120 (1998) 11144.

 

18. Attinà M., Bernardi F., Cacace F., and Rossi I..;
    "Gaseous Ethylenexenonium ions C₂H₄Xe⁺ and Ethylenefluoroxenonium C₂H₄XeF⁺ ions. A joint mass spectrometrical and theoretical study";
    Chem. Eur. J. 5 (1999) 1186

 

19. Rossi I., Venturini A., and Zedda A.;
    "Modeling HALS-promoted polymer stabilization: a computational insight into the Nitroxyl-radical regeneration from Aminoethers ";
    J. Am. Chem. Soc. 121 (1999) 7914.

 

20. Caminati W., Melandri S., Rossi I., and Favero P. G.;
    "The C-F^...H-O hydrogen bond in the gas-phase. Microwave structure and ab initio calculations of Difluoromethane-Water";
    J. Am. Chem. Soc. 121 (1999) 10098.

 

21. van Axel Castelli V., Bernardi F., Dalla Cort A., Mandolini L., Rossi I., Schiaffino L.;
    " Rates and Equilibria of the Michael-Type Addition of Benzenethiol to 2-Cyclopenten-1-ones";
    J. Org. Chem. 64 (1999) 8122.

 

22. Casadio R., Rossi I., Fariselli P., Arnofi E., Riccobelli P., Rossi E., Boschi S., Cozzini S., Facchiano A.
    "Protein modeling combining Homology Building and Molecular Dynamics"
    ECCC5 (http://hackberry.chem.niu.edu/ECC5)

 

23. Bernardi F., Cacace F., De Petris G., Pepi F., Rossi I., and Troiani A.;
    "The gas-phase reaction of Nitronium ion with Acetylene and Ethylene. An experimental and theoretical study";
    Chemistry, Eur. J. 6 (2000) 539-544.

 

24. Bernardi F., Bottoni A., Rossi I., Novoa J., Prat J.;
    "Theoretical Study of the Mechanism of Carbonyl Insertion Reactions Catalyzed by Nickel Complexes";
    Organometallics 19 (2000) 2170-2178.

 

25. Bernardi F., Cacace F., Occhiucci G., Ricci A., and Rossi I.;
    "Protonated Cyanogen Fluoride. Structure, Stability, and Reactivity of (FCN)H⁺ Ions ";
    J. Phys. Chem A 104 (2000) 5545-5550.

 

26. Casadio R., Compiani M., Facchiano A., Fariselli P., Jacoboni I., Martelli P.L., Rossi I.
    "Protein structure predictionand biomolecular recognition: from protein sequence to peptidomimetic design with the human Beta-3 integrin"
    SAR QSAR Environ. Res. 13 (2002) 473-486

 

27. Rossi I., Marchignoli D., Medini D., Beltrami R., Donati C., Fariselli P., Covacci A., Casadio R.
    "A simple yet effective implementation of a parallel BLAST for computer clusters"
    Proc. Virt. Conf. Genom. and Bioinf. 1 (2002) 11-16

 

28. Rossi I., Marchignoli D., Fariselli P., Medini D., Beltrami R., Casadio R.
    "DNCBLAST: a parallel BLAST for computer clusters"
    Minerva Biotecnologica 15 (2003) 191-193.

 

29. Fariselli P., Finelli M., Marchignoli D., Martelli P. L., Rossi I., Casadio R.
    "MaxSubSeq: an algorithm for segment-length optimisation. The case study of transmembrane-spanning segments"
    Bioinformatics 19 (2003) 500-505.

 

30. Fariselli P., Zauli A., Rossi I., Finelli M., Martelli P.L., Casadio R.
    "A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes"
    Proceedings of the IEEE International Workshop on Neural Network on Signal Processing 2003, Toulouse (FR), IEEE Press, 33-41 (2003).

 

31. Capriotti E., Fariselli P., Rossi I., Casadio R.
    "A Shannon Entropy-based filter detects high-quality profile-profile alignments in searches for remote homologues"
    Proteins 54 (2004) 351-360.

 

32. Aguzzi M.S., Facchiano F., Ribatti D., Gaeta R., Casadio R., Rossi I., Capogrossi M.C., Facchiano A.
    "A novel RGDS-analog inhibits angiogenesis in vitro and in vivo"
    Biochem. Biophys. Res. Commun. 321 (2004) 809-814.

 

33. Caminati W., Assimo M., Melandri S., and Rossi I.;
    "Free jet rotational spectrum and tunneling motion in Difluoromethane...Kripton";
    Chem. Phys. Lett. (2005) 192-198.

 

34. B. Trebbi, Fanti M., Rossi I., and Zerbetto F.;
    "The intra-residue distribution of energy in proteins";
    J. Phys. Chem. B 109 (2005) 3586-3593

 

35. Fariselli P., Finelli M., Rossi I., Amico M., Zauli A., Martelli P. L., Casadio R.
    "TRAMPLE: the transmembrane protein labelling environment"
    Nucl. Acids Res. 33 (2005) W198-W201.

 

36. Amico M., Finelli M., Rossi I., Zauli A., Elofsson A., Viklund H., von Heijne G., Jones D., Krogh A., Fariselli P., Martelli P.L., and Casadio R.
    "PONGO: a web server for multiple predictions of all-alpha transmembrane proteins
    Nucl. Acids Res. 34 (2006) W169-W172.

 

37. Fariselli P., Rossi I., Capriotti E. and Casadio R.
    "The WWWH of remote homolog detection: the state of the art"
    Brief. Bioinform. 8 (2007) 78-87.

 

38. M. L. Tress, P. L. Martelli, A. Frankish, G. A. Reeves, J. J. Wesselink, C. Yeats, P. Olason, M. Albrecht, H. Hegyi, A. Giorgetti, D. Raimondo, J. Lagarde, R. A. Laskowski, G. López, M. I. Sadowski, J. D. Watson, P. Fariselli, I. Rossi, A. Nagy, W. Kai, Z. Størling, M. Orsini, Y. Assenov, H. Blankenburg, C. Huthmacher, F. Ramírez, A. Schlicker, F. Denoued, P. Jones, S. Kerrien, S. Orchard, S. E. Antonarakis, A. Reymond, E. Birney, S. Brunak, R. Casadio, R. Guigo, J.Harrow, H. Hermjakob, D. T. Jones, T. Lengauer, C. A. Orengo, L. Patthy, J. M. Thornton, Anna Tramontano, and A. Valencia
    "The implications of alternative splicing in the ENCODE protein complement"
    Proc. Natl. Acad. Sci. USA 104 (2007) 5495-500.
39. E. Capriotti, P. Fariselli , I. Rossi, R. Casadio
    "A three-state prediction of single point mutations on protein stability changes."
    BMC Bioinformatics. 9 (2008) Suppl 2:S6.
    

 

40. L. Montanucci, P. Fariselli, P. L. Martelli, I. Rossi, R. Casadio
    "In Silico Evidence of the Relationship Between miRNAs and siRNAs"
    The Open Applied Informatics Journal 2 (2008) 9-13

     

41. A. R. Troisi, G. Aloisio, I. Rossi, P. Fariselli, R. Casadio
    " The Rainbow Prim Algorithm for Selecting Putative Orthologous Protein Sequences"
    The Open Bioinformatics Journal 2 (2008) 60-63
    
    
42. L. Bartoli, P. L. Martelli, I. Rossi, P. Fariselli, R. Casadio
    "Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks"
    Lecture Notes in Computer Science 5688/2009 (2009) 1-17
43. Martelli PL, D'Antonio M, Bonizzoni P, Castrignanò T, D'Erchia AM, D'Onorio De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A, Zambelli F, Casadio R, Pesole G.
    "ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing"
    Nucleic Acids Research  39(Database issue) (2011) D80-5.

Patent

1. Facchiano A., Facchiano F., Rossi I., Casadio R.
"RGD-analog non-peptidic molecules having anti-adhesive, anti-migration anti-proliferative effects"
Patent n. WO 02/066421 A1
Patent n. US 2002/0119932 A1

Book chapters and Technical reports

1. C.J. Cramer, G. D. Hawkins, G. C. Lynch, D. J. Giesen, I. Rossi, J. W. Storer, Truhlar D. G., and D. A. Liotard,
   "AMSOL-version 5.4: An SCF program for Free Energies of Solvation";
   Quantum Chemistry Program Exchange Program 606, based in part on AMPAC-version 2.1 by D. A. Liotard, E. F. Healy, J. M. Ruiz, and M. J. S. Dewar.

 

2. Steckler R., Chuang Y.-Y., Fast P. L., Coitino E. L., Corchado J. C., Hu W.-P., Liu Y.-P., Lynch G. C., Nguyen K. A., Jackels C. F., Gu M. Z., Rossi I., Clayton S., Melissas V. S., Garrett B. C., Isaacson A. D. and Truhlar D. G.;
   "POLYRATE: A computer program for the calculation of chemical reaction rates for polyatomics (version7.3.1)";
   QCPE Bull. 17 (1997) 34.

 

3. Casadio R., Rossi I., Fariselli P., Arnofi E., Riccobelli P., Rossi E., Boschi S., Facchiano A.;
   "DRUG - Supercomputing Drug Design for Industrial and Academic Partnership. Peptidomimetic molecules active on vascular cell growth and migration.";
   Final Report of the Esprit HPCN PST EP 27217 (TTN DRUG) activity. Available online through the European Union database at http://dbs.cordis.lu
4. Casadio R., Compiani M., Fariselli P., Jacoboni I., Martelli P.L., Rossi I.;
   "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), CLUEB, Bologna (2001) 115-133
5. 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"
   in "Convegno Bioinformatica: sfide e prospettive. Università del Sannio, 17-18/12/2003." F.Angeli Ed.
6. 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"
   in "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
   
7. M. Mirto, I. Rossi, I. Epicoco, S. Fiore, P. Fariselli, R. Casadio, G. Aloisio;
   "High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment"
   in ISPA Workshps 2007, Lecture Notes in Computer Science, volume 4743/2007, Springer Berlin / Heidelberg, 414-423

Miscellanea

• Rossi I.
  "BioDec: una start-up bioinformatica"
  in "Da una nuova idea ad una nuova impresa: gli spin-off accademici", MUP, Parma (2003) 51-57