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Pier Luigi Martelli
E-mail: gigi@lipid.biocomp.unibo.it

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Main Research Fields

Prediction of most stable alpha-helical structures of proteins from aminoacid sequence.
Molecular dynamics of protein systems.
Hidden Markov Models for sequence analysis.
Prediction of the bonding state of cysteines
Protein Modelling
Prediction of the membrane protein topology (for both all-alpha and beta barrel membrane proteins)
Prediction of the subcellular localization of proteins in eukaryotic cells
Prediction of post-translational modifications in proteins

Educational Background

1997: Degree in Physics at the University of Bologna.

Prediction of foldons in proteins

2001: Ph.D. in Physics at the University of Bologna.

Hybrid systems of HMMs and Neural Networks for the protein structure prediction.

Past positions

INBB Fellowship (Istituto Nazionale Biostrutture Biosistemi) (March 2001-February 2002)

CNR Fellowship: Target Project on Molecular Genetics (May 2002- April 2003)

Contract Researcher: FIRB2001 Project on Postgenomics (August 2003-July 2005)

Young Researcher: FIRB 2003: LIBI: International Laboratory of Bioinformatics (October 2005- September 2006)

Researcher at the Faculty of Mathematical, Physical and Natural Sciences of the University of Bologna (Oct 2006-Jan 2015)

Current position

Associate Professor at the School Sciences of the University of Bologna (since Feb 2015)

Past teaching activities

Contract Professor: "Modellistica Molecolare" (University of Ferrara, Degree in Biology) (2000-2001)

Contract Professor: "Fisica Computazionale Applicata alle Macromolecole" (University of Trento, Degree in Biomedical Physics and Technology) (2002-2003)

Contract Professor: "Fisica Computazionale Applicata alle Macromolecole" (University of Trento, Degree in Biomedical Physics and Technology) (2003-2004)

Contract Professor: "Fisica Computazionale Applicata alle Macromolecole" (University of Trento, Degree in Biomedical Physics and Technology) (2004-2005)

Contract Professor: "Fisica Computazionale Applicata alle Macromolecole" (University of Trento, Degree in Biomedical Physics and Technology) (2005-2006)

Master Degree in Bioinformatics: Banche Dati Medico-Biologiche (2006-2007)

Master Degree in Molecular and Industrial Biotechnologies: Banche Dati Medico-Biologiche (2006-2007)

Master Degree in Bioinformatics: Biologia Computazionale (2007-2008)

Current teaching activities at the Bologna University (Since 2008)

International Bologna Master Degree in Bioinformatics: Computational Biology

International Bologna Master Degree in Bioinformatics: Models of Biological Systems

Publications (Peer Reviewed Papers)

1. Compiani M, Fariselli P, Martelli P and Casadio R - An entropy criterion to detect minimally frustrated intermediates in native proteins - Proc Natl Acad Sci USA 95(16): 9290-9294 (1998)

2. Compiani M, Fariselli P, Martelli PL and Casadio R -Neural Networks to Study Invariant Features of Protein Folding- Theor Chem Acc 101: 21-26 (1999)

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

4. 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 env res 11: 149-182 (2000)

5. Sirangelo I, Tavassi S, Martelli PL, Casadio R, Irace G - The effect of tryptophanyl substitution on folding and structure of myoglobin. Eur J Biochem 267: 3937-3945 (2000)

6. Bismuto E, Martelli PL, Casadio R, Irace G - Tryptophanyl fluorescence lifetime distribution of hypertermophilic beta-glycosidase from molecular dynamics simulation: a comparison with the experimental data. Protein Sci 9: 1730-1742 (2000)

7. 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)

8. El-Sherif H, Martelli PL, Casadio R, Portaccio M, Bencivenga U, Mita DG -Urease immobilization on chemically grafted nylon membranes. Part 1: Isothermal characterization- J Mol Catal B: Enzym 14: 15-19 (2001)

9. 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)

10. El Masry MM, De Maio A, Martelli PL, Casadio R, Moustafa AB, Rossi S, Mita DG -Influence of the immobilization process on the activity of beta galactosidase bound to nylon membranes grafted with glycidyl methacrylate. Part 1. Isothermal behavior- J Mol Catal B:Enzym 16: 175-189 (2001)

11. Casadio R, Martelli PL, Giordano A, Rossi M, Raia CA -A low-resolution 3D model of the tetrameric alcohol dehydrogenase from Sulfolobus solfataricus-Protein eng 15:215-223 (2002)

12. Bismuto E, Martelli PL, De Maio A, Mita DG, Irace G, Casadio R - Effect of molecular confinement on internal enzyme dynamics: Frequency domain fluorometry and molecular dynamics simulation studies- Biopolymers (Biospectroscopy) 67:85-95 (2002)

13. 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)

14. Martelli PL, Fariselli P, Krogh A, Casadio R -A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins- Bioinformatics 18: S46-S53 (2002)SGI BEST PAPER AWARD at ISMB02 (Edmonton, Canada, August 2002)

15. 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)

16. 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)

17. 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)

18. 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 12: 1158-1168 (2003)

19. Martelli PL, Fariselli P, Casadio R -An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins- Bioinformatics 19: I205-I211 (2003)

20. Occhipinti E, Martelli PL, Spinozzi F, Corsi F, Formantici C, Molteni L, Amenitsch H, Mariani P, Tortora P, Casadio R -3D structure of Sulfolobus solfataricus carboxypeptidase developed by molecular modeling is confirmed by site-directed mutagenesis and small angle X-ray scattering- Biophys J 85:1165-1175 (2003)

21. 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)

22. Casadio R, Fariselli P, Martelli PL -In silico prediction of the structure of membrane proteins: Is it feasible?- Brief Bioinf 4:341-348 (2003)

23. 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- Proc 13th IEEE Workshop on Neural Networks for Signal Processing (NNSP'03): 33-41 (2003)

24. Martelli PL, Fariselli P, Casadio R -Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network- Proteomics 4:1665-1671 (2004)

25. Durante D, Casadio R, Martelli PL, Tasco G, Portaccio M, De Luca P,Bencivenga U, Rossi S, Di Martino S, Grano V, Diano N, Mita DG -Isothermal and non-isothermal bioreactors in the detoxification of waste waters polluted by aromatic compounds by means of immobilised laccase from Rhus vernicifera- J Mol Catal B: Enzym 27:191-206 (2004)

26. Gianni T, Martelli PL, Casadio R, Campadelli-Fiume G -An internal fusion peptide in herpes simplex virus glycoprotein H enables fusion required for infection of cells- J Virol 79:2931-2940 (2005)

27. 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)

28. 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)

29. Occhipinti E, Bec N, Gambirasio B, Baietta G, Martelli PL, Casadio R, Balny C, Lange R, Tortora P -Pressure and temperature as tools for investigating the role of individual non-covalent interactions in enzymatic reactions Sulfolobus solfataricus carboxypeptidase as a model enzyme- Biochim Biophys Acta 1764:563-572 (2006)

30. 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)

31. Pierleoni A, Martelli PL, Fariselli P, Casadio R -BaCelLo: a balanced subcellular localization predictor- Bioinformatics 22:e408-e416 (2006)

32. 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 Mol Biol 350:305-320 (2007)

33. Pierleoni A, Martelli PL, Fariselli P, Casadio R -eSLDB: eukaryotic Subcellular Localization DataBase- Nucleic Acids Res 35:D208-212 (2007)

34. 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)

35. 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)

36. Fermani S, Sparla F, Falini G, Martelli PL, Casadio R, Pupillo P, Ripamonti A, Trost P -The molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase- Proc Natl Acad Sci USA 104:5495-5500 (2007)

37. Bartoli L, Capriotti E, Fariselli P, Martelli PL, Casadio R -The pros and cons of predicting protein contact maps- Methods Mol Biol 413:199-218 (2007)

38. Sommaruga S, De Palma A, Mauri PL, Trisciani M, Basilico F, Martelli PL, Casadio R, Tortora P, Occhipinti E -A combined approach of mass spectrometry, molecular modeling, and site-directed mutagenesis highlights key structural features responsible for the thermostability of Sulfolobus solfataricus carboxypeptidase- Proteins 71:1843-1852 (2008)

39. Casadio R, Martelli PL, Pierleoni A -The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation- Brief Funct Genomic Proteomic 7:63-73 (2008)

40. Montanucci L, Fariselli P, Martelli PL, Casadio R -Predicting protein thermostability changes from sequence upon multiple mutations- Bioinformatics 24:i190-195 (2008)

41. Bartoli L, Capriotti E, Fariselli P, Martelli PL, Casadio R -The pros and cons of predicting protein contact maps- Methods Mol Biol413:199-217 (2008)

42. 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)

43. Pierleoni A, Martelli PL, Casadio R -PredGPI: a GPI anchor predictor- BMC Bioinformatics 9:392 (2008)

44. 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)

45. Bartoli L, Montanucci L, Fronza R, Martelli PL, Fariselli P, Carota L, Donvito G, Maggi GP, 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)

46. Fariselli P, Savojardo C, Martelli PL, Casadio R -Grammatical-restrained hidden conditional random fields for bioinformatics applications- Algorithms Mol Biol 22:4-13 (2009)

47. 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 11:601-608 (2010)

48. Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall'Olio S, Colombo M, Casadio R, Russo V, Portolano B -An initial comparative map of copy number variations in the goat (Capra hircus) genome- BMC Genomics 11:639 (2010)

49. Fontanesi L, Beretti F, Martelli PL, Colombo M, Dall'Olio S, Occidente M, Portolano B, Casadio R, Matassino D, Russo V -A first comparative map of copy number variations in the sheep genome- Genomics 97:158-165 (2011)

50. Martelli PL, D'Antonio M, Bonizzoni P, Castrignano`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:D80-85 (2011)

51. Pierleoni A, Martelli PL, Casadio R -MemLoci: predicting subcellular localization of membrane proteins in Eukaryotes- Bioinformatics 27:1224-1230 (2011)

52. Pantaleo MA, Astolfi A, Indio V, Moore R, Thiessen N, Heinrich MC, Gnocchi C, Santini D, Catena F, Formica S, Martelli PL, Casadio R, Pession A, Biasco G -SDHA Loss-of-Function Mutations in KIT-PDGFRA Wild-Type Gastrointestinal Stromal Tumors Identified by Massively Parallel Sequencing- J Natl Cancer Inst 103:983-987 (2011)

53. 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)

54. 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)

55. 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)

56. Pippucci T, Benelli M, Magi A, Martelli PL, Magini P, Torricelli F, Casadio R, Seri M, Romeo G -EX-HOM (EXome-HOMozygosity): a proof of principle- Hum Hered 72:45-53 (2011)

57. 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)

58. Pantaleo MA, Nannini M, Astolfi A, Biasco G; GIST Study Group Bologna -A distinct pediatric-type gastrointestinal stromal tumor in adults: potential role of succinate dehydrogenase subunit A mutations- Am J Surg Pathol 35:1750-1752 (2011)

59. Fontanesi L, Galimberti G, Calò DG, Fronza R, Martelli PL, Scotti E, Colombo M, Schiavo G, Casadio R, Buttazzoni L, Russo V -Identification and association analysis of several hundred single nucleotide polymorphisms within candidate genes for backfat thickness in Italian Large White pigs using a selective genotyping approach- J Anim Sci 90:2450-2464 (2012)

60. Martelli PL, Fariselli P, Balzani E, Casadio R -Predicting cancer-associated germline variations in proteins- BMC Genomics 13,Suppl 4:S8 (2012)

61. Fontanesi L, Martelli PL, Scotti E, Russo V, Rogel-Gaillard C, Casadio R -Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization- Genomics 100:245-251(2012)

62. Piovesan D, Profiti G, Martelli PL, Casadio R -The human "magnesome": detecting magnesium binding sites on human proteins- BMC Bioinformatics 13, Suppl 14:S10 (2012)

63. Fontanesi L, Schiavo G, Galimberti G, Calò DG, Scotti E, Martelli PL, Buttazzoni L, Casadio R, Russo V -A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes- BMC Genomics 13:583 (2012)

64. Porcellini E, Carbone I, Martelli PL, Ianni M, Casadio R, Pession A, Licastro F -Haplotype of Single Nucleotide Polymorphisms in Exon 6 of the MZF-1 Gene and Alzheimer's Disease- J Alzheimers Dis 34:439-447 (2013)

65. 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)

66. Indio V, Martelli PL, Savojardo C, Fariselli P, Casadio R -The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields- Bioinformatics (2013, in press)

67. 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)

68. Savojardo C, Fariselli P, Martelli PL, Casadio R -BCov: A method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming- Bioinformatics 29:3151-3157 (2013)

69. Piovesan D, Profiti G, Martelli PL, Fariselli P, Fontanesi L, Casadio R -SUS-BAR: A database of pig proteins with statistically validated structural and functional annotation- Database 2013:bat065 (2013)

70. 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 14s3:S6 (2013)

71. Di Lena P, Wu G, Martelli PL, Casadio R, Nardini C -MIMO: An efficient tool for molecular interaction maps overlap- BMC Bioinformatics 14:159 (2013)

72. Savojardo C, Martelli PL, Fariselli P, Casadio R -TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs- Bioinformatics 30:2973-2974 (2014)

73. Bertolini F, Schiavo G, Scotti E, Ribani A, Martelli PL, Casadio R, Fontanesi L -Highthroughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by next-generation semiconductor-based sequencing- Animal Genetics 45:304-307 (2014)

74. Martelli PL, Fontanesi L, Piovesan D, Fariselli P, Casadio R -Mapping and annotating obesity related genes in pig and human genomes- Protein and Peptide Letters 21:840-846 (2014)

75. Sazzini M, Schiavo G, De Fanti S, Martelli PL, Casadio R, Luiselli D -Searching for signatures of cold adaptations in modern and archaic humans: Hints from the brown adipose tissue genes(- Heredity 113:259-267 (2014)

76. Di Lena P, Martelli PL, Fariselli P, Casadio R -NET-GE: A novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases- BMC Genomics 16:S6 (2015)

77. Martelli PL, Savojardo C, Fariselli P, Tasco G, Casadio R -Computer-based prediction of mitochondria-targeting peptides- Mitochondrial Medicine 1:305-320 (2015)

78. Fariselli P, Martelli PL, Savojardo C, Casadio R -INPS: Predicting the impact of nonsynonymous variations on protein stability from sequence- Bioinformatics 31:2816-2821 (2015)

79. Savojardo C, Martelli PL, Fariselli P, Casadio R -TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins- Bioinformatics 31:3269-3275 (2015)

80.Profiti G, Piovesan D, Martelli PL, Fariselli P, Casadio R -Protein sequence annotation by means of community detection Current Bioinformatics10:139-143 (2015)

81.Akcapinar GB, Venturini A, Martelli PL, Casadio R, Sezerman UO -Modulating the thermostability of Endoglucanase I from trichoderma reesei using computational approaches- Protein Engineering, Design and Selection 28:127-135 (2015)

82. Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R -A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding Plant Biotechnology Journal 13:648-663 (2015)

83. Sazzini M, De Fanti S, Cherubini A, Quagliariello A, Profiti G, Martelli PL, Casadio R, Ricci C, Campieri M, Lanzini A, Volta U, Caio G, Franceschi C, Spisni E, Luiselli D -Ancient pathogen drivenad aptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations- Genes and Nutrition 23:5 (2016)

84. Jiang Y, Oron TR, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy- Genome Biology 17:184 (2016)

85. Savojardo C, Fariselli P, Martelli PL, Casadio R -INPS-MD: A web server to predict stability of protein variants from sequence and structure- Bioinformatics 32:2542-2544 (2016)

86. Martelli PL, Fariselli P, Savojardo C, Babbi G, Aggazio F, Casadio R -Large scale analysis of protein stability in OMIM disease related human protein variants- BMC Genomics 17:397 (2016)

87. Savojardo C, Martelli PL, Fariselli P, Casadio R -SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartmets- Bioinformatics (2016,in press)

Publications (Book Chapters)

1. 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)

2. Casadio R, Fariselli P, Martelli PL, Pierleoni A, Rossi I, von Heijne G -The state of the art of membrane protein structure prediction: from sequence to 3D structure- In: "Modern Genome Annotation: the Biosapiens Network" (Frishman D, Valencia A eds) Springer-Verlag( Austria), (2008, in press) ISBN: 978-3-211-75122-0

3. Tramontano A, Jones D, Rychlewski L, Casadio R, Martelli PL, Raimondo D, Giorgetti A -Protein structure prediction- In: Modern Genome Annotation: the Biosapiens Network" (Frishman D, Valencia A eds) Springer-Verlag( Austria), (2008, in press) ISBN: 978-3-211-75122-0

4. Tress M, Casadio R, Giorgetti A, Hallin PF, Juncker AS, Kulberkyte E, Martelli PL, Raimondo D, Reeves GA, Thornton JM, Tramontano A, Wang K, Wesselink JJ, Valencia A -Alternative Splicing in the ENCODE Protein- Complement- In: Modern Genome Annotation: the Biosapiens Network" (Frishman D, Valencia A eds) Springer-Verlag( Austria), (2008, in press) ISBN: 978-3-211-75122-0

5. Borsetti F, Martelli P, Casadio R, and Zannoni D (2008) Metals and metalloids in photosynthetic bacteria: interactions, resistance and putative homeostasis revealed by genome analysis. In: The Purple Phototrophic Bacteria Hunter (N, Daldal F, Thurnauer M, and Beatty T eds) , volume 28. Springer, Dordrecht, ISBN: 978-1-4020-8814-8 pp 655-689

6. Mirto M, Epicoco I, Fiore S, Cafaro M, Ferramosca A, Zara V, Aloisio G, Scioscia G, Leo P, Donvito G, Cuscela G, Maggi G, Pierro A, Falciano F, Rossi E, Castrignano` T, Fariselli P, Fronza R, Margara L, Montanucci L, Martelli PL, Rossi R, Vassura M, Di Lena P, Casadio R, Anselmo A, Grillo G, Horner D, Licciulli F, Liuni S, Gisel A, Mignone F, Pavesi G, Pesole G, Picardi E, Piccolo V, Re M, Saccone C, Santamaria M, Vicario S, Zambelli F- The LIBI Grid Platform an International Laboratory for Bioinformatics- In: Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare, PISCATAWAY, IGI global, 2009, pp. 557 - 613