Publications

 

Publications on Journals

  1. Fariselli P, Compiani M, Casadio R - Predicting secondary structures of membrane proteins with neural networks- Eur Biophys J 22: 41-51 (1993)
  2. Fariselli P, Di Bernardo S, Casadio R - A mathematical model relating diffusion of hydrophobic ions to their adsorption on biological membranes as detected with a microdialyzer- J Biol Phys 19: 211-222 (1994)
  3. Rost B, Casadio R, Fariselli P, Sander C - Transmembrane helices predicted at 95% accuracy- Protein Science 4, 521-533 (1995)
  4. Vivarelli F, Giusti G, Villani M, Campanini R, Fariselli P, Compiani M, Casadio R -LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins- Comp Appli Bioscience 11, 253-260 (1995)
  5. Casadio R, Di Bernardo S, Fariselli P, Melandri BA - Characterization of 9-aminoacridine interaction with chromatophore membranes and modelling of the probe response to artificially induced transmembrane DpH's- Biochim Biophys Acta 1237, 23-30 (1995)
  6. Polverini E, Neyroz P, Fariselli P, Casadio R and Masotti L -The effect of membranes on the conformation of neuromedin C- Biochim Biophys Res Commun 214:663-668 (1995)
  7. Compiani M, Fariselli P, 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)
  8. Bernardi F, Bottoni A, Casadio R, Fariselli P and Rigo A - An ab-initio study of dioxygen binding site of hemocyanin: a comparison between a CASSCF and DFT approach - Int J Quantum Chem 56:109-116 (1996)
  9. Fariselli P and Casadio R -HTP: a neural network based method for predicting the topology of helical trasmembrane domains in proteins - Comp Appli Bioscience 12:41-48 (1996)
  10. Casadio R, Fariselli P, Taroni C and Compiani M - A predictor of a-helix trasmembrane domains of proteins based on neural networks- Eur Biophys J 24:165-178 (1996)
  11. Bernardi F, Bottoni A, Casadio R, Fariselli P and Rigo A - An ab-initio study of the mechanism of the binding process of triplet O2 to hemocyanin - Inorg Chem 35, 5207-5212 (1996)
  12. Rost B, Fariselli P, and Casadio R - Topology prediction for helical transmembrane proteins at 86% accuracy- Protein Science 5, 1704-1718 (1996)
  13. Compiani M, Fariselli P, Casadio R - Noise and randomlike behavior of perceptrons: theory and application to protein structure prediction- Phys Rev E 55, 7334-7343 (1997)
  14. Vivarelli, F, Fariselli P and Casadio R - The prediction of protein secondary structure with a casacade correlation learning architecture of neural networks- Neural Comput Applic 6, 57-62 (1997)
  15. Di Bernardo S, Fato R, Casadio R, Fariselli P, Lenaz G -A high diffusion coefficient for coenzyme Q10 might be related to a folded structure- FEBS Lett (1998) 426, 77-80.
  16. Compiani M, Fariselli P, Martelli P, Casadio R - An entropy criterion to detect minimally frustated intermediates in native proteins - Proc Natl Acad Sci 95, 9290-9294 (1998)
  17. Arrigo P, Fariselli P, Casadio R - Can functional regions of proteins be predicted from their coding sequences? The case study of G-protein coupled receptors - GENE GC-221:65-110 (1998)
  18. Compiani M, Fariselli P, Martelli P, Casadio R - Neural networks to study invariant features of protein folding- Theor Chem Acc 101:21-26 (1999)
  19. Fariselli P, Casadio R - Neural network based predictor of residue contacts in proteins - Prot Engng 12:15-21 (1999)
  20. Fariselli P, Bottoni, A, Bernardi F, Casadio R - Quantum mechanical analysis of oxygenated and deoxygenated states of hemocyanin: theoretical clues for a plausible allosteric model of oxygen binding- Protein Science 8:1546-1550 (1999)
  21. Fariselli P, Riccobelli P, Casadio R - Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins - Proteins 36:340-346 (1999)
  22. Casadio R, Compiani M, Fariselli P, Jacoboni I and Martelli PL - Neural Networks predict protein folding and structure: artificial intelligence  faces biomolecular complexity. SAR and QSAR in environmental research 11:149-182 (2000)
  23. Jacoboni I, Martelli PL, Fariselli P,Compiani M, Casadio R - Predictions of protein segments with the same amino acid sequence and different  secondary structure: a benchmark for predictive methods. Proteins 41:535-544 (2000)
  24. Fariselli P, Casadio R - RCNPRED: a server for the prediction of the residue co-ordination numbers in proteins- Bioinformatics 17:202-204 (2001)
  25. Jacoboni I, Martelli PL, Fariselli P, De Pinto V, Casadio R -prediction of the transmembrane regions of beta barrel membrane proteins with a neural network based predictor- Protein sci 10:779-787 (2001)
  26. Pollastri G, Baldi P, Fariselli P, Casadio R. -Improved prediction of the number of residue contacts in proteins by recurrent neural networks- Bioinformatics Suppl 1:S234-S242 (2001)
  27. Fariselli P, Casadio R - Prediction of disulfide connectivity in proteins - Bioinformatics 17:957-964 (2001)
  28. Fariselli P, Olmea O, Valencia A, Casadio R - Prediction of contact maps with neural networks and correlated mutations - Prot Engng 269:835-843 (2001)
  29.  Fariselli P, Olmea O, Valencia A, Casadio R - Progress in predictiing  contact maps of contact maps of proteins with  neural networks and correlated mutations - Proteins Suppl 5:157-162 (2001)
  30. Pollastri G, Baldi P, Fariselli P, Casadio R. -Prediction of coordination number and relative solvent accessibility  in proteins - Proteins   47:142-153 (2002)
  31. Fariselli P, Pazos F, Valencia A, Casadio R - Prediction of protein--protein interaction sites in heterocomplexes with neural networks- Eur J Biochem 269:1356-1361(2002)
  32. Martelli PL, Fariselli P, Krogh A and Casadio R - A Sequence Profile Based HMM for Predicting and Discriminating Beta Barrel Membrane Proteins - Bioinformatics 18: S46-S53 (2002)
  33. Casadio R, Compiani M, Facchiano A, Fariselli P, Martelli PL, Jacoboni I, Rossi I -Protein structure prediction and biomolecular recognition: from protein sequence to peptidomimetic design with the human beta 3 integrin- SAR QSAR Envir Res 13:473-486 (2002)
  34. Martelli PL, Fariselli P, Malaguti L, Casadio R. -Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks- Protein Eng. 15:951-953 (2002)
  35. Rossi I, Marchignoli D, Fariselli P, Beltrami R, Medini D, Casadio R - DNCBLAST: a parallel BLAST for computer clusters - Minerva Biotecnologica 15:191-193 (2003)
  36. Juan D, Grana O, Pazos F, Fariselli P, Casadio R, Valencia A. -A neural network approach to evaluate fold recognition results- Proteins 50:600-608 (2003)
  37. Fariselli P, Finelli M, Marchignoli D, Martelli PL, Rossi I, and Casadio R -MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments- Bioinformatics 19:500-505 (2003)
  38. Casadio R, Fariselli P, Finocchiaro G, Martelli PL -Fishing new proteins in the twilight zone of genomes: The test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria- Protein Sci. 6:1158-1168 (2003)
  39. Martelli PL, Fariselli P, Casadio R - An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins- Bioinformatics Suppl 1:I205-I211 (2003)
  40. Martelli PL, Fariselli P, Tasco G, Casadio R -The prediction of membrane protein structure and genome structural annotation- Compar Funct Genom 4:406- 409 (2003)
  41. Fariselli P, Finocchiaro G, Casadio R -SPEPlip: the detection of signal peptide and lipoprotein cleavage sites- Bioinformatics 19:2498-2499 (2003)
  42. Casadio R, Fariselli P, Martelli PL -In silico prediction of the structure of membrane proteins: Is it feasible?- Brief Bioinf 4:341-348 (2003)
  43. 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 54:351-360 (2004)
  44. Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N -ConSeq: the identification of functionally and structurally important residues in protein sequences- Bioinformatics 20:1322-1324 (2004)
  45. Martelli PL, Fariselli P, Casadio R -The prediction of disulfide-bonded cysteines in proteomes with a Hidden Neural Network- Proteomics 4:1665-1671 (2004)
  46. Capriotti E, Fariselli P, Casadio R. -A neural-network-based method for predicting protein stability changes upon single point mutations - Bioinformatics 20 Suppl 1:I63-I68 (2004)
  47. Capriotti E, Fariselli P, Casadio R. -I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure- Nucl Acids Res 33: W306-W310(2005).
  48. Capriotti E, Fariselli P, Calabrese R, Casadio R -Predicting protein stability changes from sequence with Support Vector Machines- Bioinformatics 21:ii54-ii58 (2005).
  49. Fariselli P, Finelli M, Rossi I, Amico M, Zauli A, Martelli PL, Casadio R. -TRAMPLE: the transmembrane protein labelling environment- Nucl Acids Res 33: W198-W201 (2005).
  50. Fariselli P, Martelli PL, Casadio R. - A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins - BMC Bioinformatics 6 Suppl 4:S12 (2005).
  51. Amico M, Finelli M, Rossi I, Zauli A, Elofsson A, Viklund H, von Heijne G, Jones D, Krogh A, Fariselli P, Martelli PL, Casadio R -PONGO: a web server for multiple predictions of all-alpha transmembrane proteins- Nucleic Acids Res 34(Web server issue):169-172 (2006)
  52. Pierleoni A, Martelli PL, Fariselli P, Casadio R - BaCelLo: a balanced subcellular localization predictor - Bioinformatics 22:e408-e416 (2006)
  53. Pierleoni A, Martelli PL, Fariselli P, Casadio R - eSLDB: eukaryotic subcellular localization database - Nucleic Acids Res 35:D208-12 (2007)
  54. Fariselli P, Rossi I, Capriotti E, Casadio R - The WWWH of remote homolog detection: The state of the art.- Brief Bioinform. 8:78-87 (2007)
  55. Bartoli L, Calabrese R, Fariselli P, Mita DG, Casadio R - A computational approach for detecting peptidases and their specific inhibitors at the genome level - BMC Bioinformatics 8:S3 (2007)
  56. Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PL, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, Lopez G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Storling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramirez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A -The implications of alternative splicing in the ENCODE protein complement- Proc Natl Acad Sci USA 104:5495-54500 (2007)
  57. Montanucci L, Martelli PL, Fariselli P, Casadio R -Robust determinants of thermostability highlighted by a codon frequency index capable of discriminating thermophilic from mesophilic genomes- J Proteome Res 6:2502-2508 (2007) (2007) 
  58.  Bartoli L., Capriotti E., Fariselli P., Martelli P.L., Casadio R. The pros and cons of predicting protein contact maps- Protein structure prediction. Methods In Molecular Biology 413:199 - 218 (2007)
  59. Casadio R.; Fariselli P.; Martelli P.L.; Tasco G. -Thinking the impossible: How to solve the protein folding problem with and without homologous structures and more- Methods In Molecular Biology  350:305-320 (2007)
  60. Bartoli L, Fariselli P, Casadio R -The effect of backbone on the small-world properties of protein contact maps- Phys Biol 4:L1-L5 (2008)
  61. Montanucci L, Fariselli P, Martelli PL, Rossi I, Casadio R -In Silico Evidence of the Relationship Between miRNAs and siRNAs- Open Appl Inf Journal 2:9-13 (2008)
  62. Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R -FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps- Bioinformatics 24:1313-1315 (2008)
  63. Capriotti E, Fariselli P, Rossi I, Casadio R -A three-state prediction of single point mutations on protein stability changes- BMC Bioinformatics 9 Suppl 2:S6 (2008)
  64. Montanucci L, Fariselli P, Martelli PL, Casadio R -Predicting protein thermostability changes from sequence upon multiple mutations- Bioinformatics 24:i190-i195 (2008)
  65. Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R -Reconstruction of 3D structures from protein contact maps- IEEE/ACM Trans Comput Biol Bioinform 5:357-367 (2008)
  66. Vassura M, Margara L, Fariselli P, Casadio R -A graph theoretic approach to protein structure selection- Artif Intell Med  45:229-237 (2009)
  67. Di Lena P, Vassura M, Margara L, Fariselli P, Casadio R- A On the reconstruction of three-dimensional protein structures from contact maps- Algorithms. 2(1):76-92 (2009).
  68. Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML -Progress and challenges in predicting protein-protein interaction sites- Brief Bioinform 10:233-246 (2009)
  69. Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. - Functional annotations improve the predictive score of human disease-related mutations in proteins.- Hum Mutat. 30:1237-1244 (2009).
  70. Bartoli L, Montanucci L, Fronza R, Martelli PL, Fariselli P, Carota L, Donvito G, Maggi G, Casadio R. - The Bologna Annotation Resource: a non-hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis. J Proteome Res. 8:4362 - 4371 (2009).
  71. Bartoli L., Fariselli P., Krogh A., Casadio R. CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinformatics. 25:2757-2763. (2009).
  72. Fariselli P., Savojardo C., Martelli P.L., Casadio R. Grammatical -Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms For Molecular Biology. 22:4 – 13 (2009).
  73.  Fuselli S, de Filippo C, Mona S, Sistonen J, Fariselli P, Destro-Bisol G, Barbujani G, Bertorelle G, Sajantila A. - Evolution of DetoxifyingSystems: the Role of Environment and Population History in Shaping genetic Diversity at Human CYP2D6 Locus- Pharmacogenetics and Genomics 20:485-99. (2010)
  74. Di Lena P, Fariselli P, Vassura M, Margara L, Casadio R -Fast overlapping of protein contact maps by alignment of eigenvectors- Bioinformatics 26:2250-2258. (2010)
  75. Bartoli L, Martelli PL, Rossi I, Fariselli P, Casadio R -The prediction of protein-protein interacting sites in genome-wide protein interaction networks: The Test Case of the Human Cell Cycle- Curr Protein Pept Sci 1;11(7):601-608 (2010).
  76. 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 Res 39:D80-D85 (2011)
  77. Vassura M, Di Lena P, Margara L, Mirto M, Aloisio G, Fariselli P, Casadio R  - Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure- BioData Min. 2011 Jan 13;4(1):1.
  78. Di Lena P, Fariselli P, Vassura M, Margara L, Casadio R- Is there an optimal substitution matrix for contact prediction with correlated mutations? IEEE/ACM Trans. Comput. Biology and Bioinformatics 8(4):1017-1028. (2011).
  79. Pierleoni A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R -MemPype: a pipeline for the annotation of eukaryotic membrane proteins- Nucleic Acids Res 39:W375-W380 (2011).
  80. Piovesan D, Luigi Martelli P, Fariselli P, Zauli A, Rossi I, Casadio R -BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences- Nucleic Acids Res 39:W197-W202 (2011).
  81. Savojardo C, Fariselli P, Alhamdoosh M, Martelli PL, Pierleoni A, Casadio R-Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization- Bioinformatics 27:2224-2230 (2011).
  82. Casadio R, Vassura M, Tiwari S, Fariselli P, Martelli PL -Correlating disease related mutations to their effect on protein stability: a large scale analysis of the human proteome- Hum Mutat 32:1161-1170 (2011).
  83. Savojardo C, Fariselli P, Casadio R -Improving the detection of transmembrane beta-barrel chains with N-to-1 extreme learning machines- Bioinformatics 27:3123-3128 (2011).
  84. Juritz E, Fornasari M, Martelli PL, Fariselli P, Casadio R, Parisi G- On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions BMC Genomics, 13 (Suppl 4):S5 (2012).
  85. Martelli PL, Fariselli P, Balzani E, Casadio R-Predicting cancer-associated germline variations in proteins- BMC Genomics, 13 (Suppl 4):S8 (2012).
  86. Piovesan D, Martelli PL, Fariselli P, Profiti G, Zauli A, Rossi I, Casadio R -How to inherit statistically validated annotation within BAR+ protein clusters- BMC Bioinformatics , 14, Suppl 3:S4 (2013).
  87. Savojardo C, Fariselli P, Martelli PL, Casadio R -Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations- BMC Bioinformatics , 14, Suppl 1:S10 (2013).
  88. Indio V, Martelli PL, Savojardo C, Fariselli P, Casadio -The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.- Bioinformatics , 29:981-988 (2013).
  89. Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R. WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. - BMC Genomics. , 14:S6 (2013).
  90. Savojardo C, Fariselli P, Casadio R. BETAWARE: a machine-learning tool to detect and predict transmembrane beta barrel proteins in Prokaryotes - Bioinformatics , 29:504-505 (2013).

 

Protocols and Reports
 

  1. Pierleoni A, Martelli PL, Fariselli P, Casadio R -BaCelLo: a Balanced subCellular Localization predictor- Nature Protocols DOI:10.1038/nprot.2007.165 (2007)

 

Referred Proceedings
 

  1. 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 (Rawlings C et al, Eds)Vol 4, pp 81-88, AAAI Press, California (ismb 1995)
  2. Compiani M, Fariselli P, 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)
  3. Arrigo P, Fariselli P, 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
  4. Rost B, Casadio R, Fariselli P - Refining neural network predictions for helical transmembrane proteins by dynamic programming - In : Proc. Fourth International Conference on Intelligent Systems for Molecular Biology (States DJ et al, Eds) Vol 4, pp 192-200, AAAI Press, California (ismb 1996)
  5. 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
  6. 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 (Gaasterland T et al, eds) Vol 5, pp44-47, AAAI Press, California (ismb 1997)
  7. Fariselli P, Casadio R (1998)- A neural network based method for predicting contact maps of proteins -Proc. of World Multiconference on Systemics, Cybernetics and Informatics (SCI'98, Orlando USA) Vol 1, pp 527-533
  8. 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
  9. 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- In : Proc Seventh International Conference on Intelligent Systems for Molecular Biology (Lengauer et al, eds) Vol 7, pp68-76, AAAI Press, California (ismb 1999)
  10. Fariselli P, Casadio R  - Prediction of the Number of Residue Contacts in Proteins- ISMB 7: 146-151 (2000) (ismb 2000)
  11. 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)
  12. 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
  13. 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) IEEE Press 33-41 (2003)
  14. Fariselli P, Finocchiaro G, and Casadio R - Prediction of Signal Peptide in Proteins with Neural Networks - Lecture Notes in Computer Science (2003) 2859 237 – 244
  15. Fariselli P, Molinini D, Casadio R, Krogh A - Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models- Lect Notes Comp Sci 4414:292-302 (2007)
  16. Mirto M, Rossi I, Epicoco I, Fiore S, Fariselli P,Casadio R, Aloisio G -High throughput protein similarity searches in the LIBI Grid problem solving environment- Lect Notes Comp Sci 4743:414-423 (2007)
  17. Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R -Fault tolerance for large scale protein 3D reconstruction from contact maps- Lect Notes Comp Sci 4645:25-37 (2007)
  18. Vassura M, Margara L, Fariselli P, Casadio R -A graph theoretic approach to protein structure selection- Lect Notes Comp Sci 4578:497-504 (2007)
  19. Vassura M, Margara L, Medri F, Di Lena P, Fariselli P, Casadio R -Reconstruction of 3D structures form protein contact maps- Lect Notes Comp Sci 4463:578-589 (2007)
  20. Carota L, Bartoli L, Fariselli P, Martelli PL, Montanucci L, Maggi G, Casadio R - High Throughput Comparison of Prokaryotic Genomes- Lect Notes Comp Sci 4967:1200-1209 (2008)
  21. Di Lena P, Fariselli P, Vassura M, Margara L, Fariselli P, 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-  Proc. of the 9th International Workshop on Algorithms in Bioinformatics (WABI2009), Pennsylvania (2009)

108.                     Bartoli L, Fariselli P, Bartoli L, - PS-COILS: a new method for coiled-coil prediction that exploits both single-sequence and evolutionary information- Procedings of the sixth international meeting on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB09), vol. 3, pp. 1 – 8 (2009).

  1. Bartoli L., Martelli P.L., Rossi I., Fariselli P., Casadio R. Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks. Lect Notes Comp Sci. vol. 5688:1 - 17 (2009).
  2. Fariselli P, Bartoli L, Casadio R- Improving coiled-coil prediction with evolutionary information- Lect Notes Comp Sci.  6160:20-32 (2010).
  3. Savojardo C, Fariselli P, Martelli PL, Shukla P, Casadio R. Prediction of cysteine bonding state with machine-learning methods. Procedings of the sixth international meeting on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB10) Vol. 4. (2010).
     

Others
 

  1. Compiani M, Fariselli P, 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)
  2. Compiani M, Fariselli P, Casadio R- The statistical behaviour of perceptrons-In: Parallel Architectures and Neural Networks (Caianiello ER, ed) pp 111-117, World Scientific, Singapore (1992)
  3. Compiani M, Fariselli P, Casadio R - Neural networks and prediction of protein structures - In"Neural Networks in Biology and Medicine", pp 313-332, World Scientific, Singapore (1994)
  4. Fariselli P, Taroni C, Compiani M, 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)
  5. Fariselli P, Hubbard T, Ortigao FR and Reinhardt A - Crococage: a protein designed to bind cholesterol - In EMBO Protein Design Course '95 (Vriend G and Sander S , ed) (1995)
  6. Casadio R, Fariselli P, Rigo A -The role of ligands on the mechanism of oxygen binding to hemocyanin: an ab-initio study based on the density functional theory- Science and Supercomputing at CINECA (1995)

118.    Papa M, Campanini R, Fariselli P, Casadio R, Erbacci G, Vivarelli F, Giusti G -Prediction of protein secondary structures using a committeee of neural networks- Science and Supercomputing at CINECA (1995)

119.    Martelli PL, Fariselli P, and Casadio R - De novo design of proteins: the alpha-helix enginner- In: Italian Biochemical Society Transactions (IBST) Vol. 8, 38-39 (1997) (Invited Speaker at Proteine '97)

120.    Fariselli P, Casadio R (1998)- A neural Network based method for predicting contact maps of proteins Simai '98, Vol 1, pp 272-275

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

122.    Fariselli P, Casadio R - 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 Vol.3, pp 139-159, Plenum Pub Co, New York (1998)

123.    Rossi E, Boschi S, Cozzini S, Casadio R, Rossi I, Fariselli P, Arnofi E, Riccobelli P, Facchiano A (1999) -Protein modeling combining Homology Building and Molecular Dynamics- ECCC5 (http://hackberry.chem.niu.edu/ECC5)

124.    Casadio R, Rossi I, Fariselli P, Arnofi E, Ricobelli 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- In HPCN Experiences in Biotechnology (Dechema and GMD eds) pp 1-25, Frankufurt (1999)

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

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