Publications

For updated lists see PUBMED


• Savojardo C, Manfredi M, Martelli PL, Casadio R. Solvent Accessibility of Residues Undergoing Pathogenic Variations in Humans: From Protein Structures to Protein Sequences. Front Mol Biosci. 7:626363 (2021)
• Savojardo C, Martelli PL, Casadio R, Fariselli P. On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. Brief Bioinform. 22(1):601-603 (2021)
• Savojardo C, Martelli PL, Tartari G, Casadio R. Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito. BMC Bioinformatics. 21:266 (2020)
• Babbi G, Baldazzi D, Savojardo C, Martelli PL, Casadio R. Highlighting Human Enzymes Active in Different Metabolic Pathways and Diseases: The Case Study of EC 1.2.3.1 and EC 2.3.1.9. Biomedicines. 8:250 (2020)
• Turri V, Latinovic OS, Bonafè M, Toyang N, Parigi M, Calassanzio M, Martelli PL, Vagheggini A, Abbati G, Sarnelli A, Casadio R, Ratti C, Massi P, Schoelz JE, Salvato MS, Piccinini F, Martinelli G. Cauliflower Mosaic Virus TAV, a Plant Virus Protein That Functions like Ribonuclease H1 and is Cytotoxic to Glioma Cells. Biomed Res Int. 2020:7465242 (2020)
• Bovo S, Martelli PL, Di Lena P, Casadio R. NETGE-PLUS: Standard and Network-Based Gene Enrichment Analysis in Human and Model Organisms. J Proteome Res ;19:2873-2878 (2020)
• Zhou N, Jiang Y, ..., Profiti G, Savojardo C, Martelli PL, Casadio R, ..., Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 20:244 (2019)
• Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Nodzak C, Pal LR, Radivojac P, Savojardo C, Shi X, Zhou Y, Uppal A, Xu Q, Yin Y, Pejaver V, Wang M, Wei L, Moult J, Yu GK, Brenner SE, LeBowitz JH. Assessment of predicted enzymatic activity of a-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Hum Mutat. 40:1519-1529 (2019)
• Kasak L, Hunter JM, Udani R, Bakolitsa C, Hu Z, Adhikari AN, Babbi G, Casadio R, Gough J, Guerrero RF, Jiang Y, Joseph T, Katsonis P, Kotte S, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Moult J, Pal LR, Poitras J, Radivojac P, Rao A, Sivadasan N, Sunderam U, Saipradeep VG, Yin Y, Zaucha J, Brenner SE, Meyn MS. CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases. Hum Mutat. 40:1373-1391 (2019)
• Babbi G, Martelli PL, Casadio R. PhenPath: a tool for characterizing biological functions underlying different phenotypes. BMC Genomics. 20:548 (2019)
• Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Radivojac P, Rousseau F, Pal LR, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Valiaho J, Repo S, Moult J, Brenner SE, Friedberg I. Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Hum Mutat.:1530-1545(2019)
• Mount SM, Avsec Z, Carmel L, Casadio R, Celik MH, Chen K, Cheng J, Cohen NE, Fairbrother WG, Fenesh T, Gagneur J, Gotea V, Holzer T, Lin CF, Martelli PL, Naito T, Nguyen TYD, Savojardo C, Unger R, Wang R, Yang Y, Zhao H. Assessing predictions of the impact of variants on splicing in CAGI5. Hum Mutat.:1215-1224 (2019)
• Cline MS, Babbi G, Bonache S, Cao Y, Casadio R, de la Cruz X, Díez O, Gutiérrez-Enríquez S, Katsonis P, Lai C, Lichtarge O, Martelli PL, Mishne G, Moles-Fernández A, Montalban G, Mooney SD, O'Conner R, Ootes L, Ozkan S, Padilla N, Pagel KA, Pejaver V, Radivojac P, Riera C, Savojardo C, Shen Y, Sun Y, Topper S, Parsons MT, Spurdle AB, Goldgar DE; ENIGMA Consortium. Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants. Hum Mutat. 40:1546-1556
• Zhang J, Kinch LN, Cong Q, Katsonis P, Lichtarge O, Savojardo C, Babbi G, Martelli PL, Capriotti E, Casadio R, Garg A, Pal D, Weile J, Sun S, Verby M, Roth FP, Grishin NV. Assessing predictions on fitness effects of missense variants in calmodulin. Hum Mutat. 40:1463-1473 (2019)
• Monzon AM, Carraro M, Chiricosta L, Reggiani F, Han J, Ozturk K, Wang Y, Miller M, Bromberg Y, Capriotti E, Savojardo C, Babbi G, Martelli PL, Casadio R, Katsonis P, Lichtarge O, Carter H, Kousi M, Katsanis N, Andreoletti G, Moult J, Brenner SE, Ferrari C, Leonardi E, Tosatto SCE. Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5. Hum Mutat. 40(9):1474-1485 (2019)
• Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner SE, Kann MG. Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Hum Mutat. 40:1612-1622 (2019).
• Savojardo C, Bruciaferri N, Tartari G, Martelli PL, Casadio R. DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks. Bioinformatics. 36(1):56-64 (2019)
• Savojardo C, Petrosino M, Babbi G, Bovo S, Corbi-Verge C, Casadio R, Fariselli P, Folkman L, Garg A, Karimi M, Katsonis P, Kim PM, Lichtarge O, Martelli PL, Pasquo A, Pal D, Shen Y, Strokach AV, Turina P, Zhou Y, Andreoletti G, Brenner SE, Chiaraluce R, Consalvi V, Capriotti E. Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge. Hum Mutat. 40:1392-1399 (2019)
• Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, Pal LR, Savojardo C, Yin Y, Zhou Y, Radivojac P, Bromberg Y. Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Hum Mutat. 40:1495-1506 (2019)
• McInnes G, Daneshjou R, Katsonis P, Lichtarge O, Srinivasan R, Rana S, Radivojac P, Mooney SD, Pagel KA, Stamboulian M, Jiang Y, Capriotti E, Wang Y, Bromberg Y, Bovo S, Savojardo C, Martelli PL, Casadio R, Pal LR, Moult J, Brenner SE, Altman R. Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat. 40:1314-1320 (2019)
• Savojardo C, Babbi G, Bovo S, Capriotti E, Martelli PL, Casadio R. Are machine learning based methods suited to address complex biological problems? Lessons from CAGI-5 challenges. Hum Mutat. 40:1455-1462 (2019)
• Vendramin V, Ormanbekova D, Scalabrin S, Scaglione D, Maccaferri M, Martelli PL, Salvi S, Jurman I, Casadio R, Cattonaro F, Tuberosa R, Massi A, Morgante M. Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm. BMC Genomics 20:278 (2019)
• Savojardo C, Babbi G, Martelli PL, Casadio R. Functional and Structural Features of Disease-Related Protein Variants. Int J Mol Sci. 20:1530 (2019)
• Nannini M, Tarantino G, Indio V, Ravegnini G, Astolfi A, Urbini M, De Leo A, Santini D, Ceccarelli C, Gruppioni E, Altimari A, Castellucci P, Fanti S, Di Scioscio V, Saponara M, Gatto L, Pession A, Martelli PL, Casadio R, Pantaleo MA. Molecular modelling evaluation of exon 18 His845_Asn848delinsPro PDGFRa mutation in a metastatic GIST patient responding to imatinib. Sci Rep. 9:2172 (2019)
• Montanucci L, Savojardo C, Martelli PL, Casadio R, Fariselli P. On the biases in predictions of protein stability changes upon variations: the INPS test case. Bioinformatics 35:2525-2527 (2019)
• Savojardo C, Luchetti A, Martelli PL, Casadio R, Mantovani B. Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca). Mol Ecol Resour. 19:235-244 (2019)
• Savojardo C, Martelli PL, Fariselli P, Profiti G, Casadio R. BUSCA: an integrative web server to predict subcellular localization of proteins. Nucleic Acids Res. 46:W459-W466 (2018)
• Diquigiovanni C, Bergamini C, Evangelisti C, Isidori F, Vettori A, Tiso N, Argenton F, Costanzini A, Iommarini L, Anbunathan H, Pagotto U, Repaci A, Babbi G, Casadio R, Lenaz G, Rhoden KJ, Porcelli AM, Fato R, Bowcock A, Seri M, Romeo G, Bonora E. Mutant MYO1F alters the mitochondrial network and induces tumor proliferation in thyroid cancer. Int J Cancer. 143:1706-1719 (2018)
• Savojardo C, Martelli PL, Fariselli P, Casadio R. DeepSig: deep learning improves signal peptide detection in proteins. Bioinformatics 34:1690-1696 (2018)
PMC5946842.
• Babbi G, Martelli PL, Profiti G, Bovo S, Savojardo C, Casadio R. eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes. BMC Genomics 18:554 (2017).
• Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA. Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat 38:1182-1192 (2017).
• Profiti G, Martelli PL, Casadio R. The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. Nucleic Acids Research 45:W285-W290 (2017).
• Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Hum Mutat 38:1042-1050 (2017)
• Xu Q, Tang Q, Katsonis P, Lichtarge O, Jones D, Bovo S, Babbi G, Martelli PL, Casadio R, Lee GR, Seok C, Fenton AW, Dunbrack RL Jr. Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Hum Mutat 38:1123-1131 (2017)
• Zuntini R, Cortesi L, Calistri D, Pippucci T, Luigi Martelli P, Casadio R, Capizzi E, Santini D, Miccoli S, Medici V, Danesi R, Marchi I, Zampiga V, Fiorentino M, Ferrari S, Turchetti D. BRCA1 p.His1673del is a pathogenic mutation associated with a predominant ovarian cancer phenotype. Oncotarget. 8(14):22640-22648 (2017)
• Savojardo C, Fariselli P, Martelli PL, Casadio R. ISPRED4: Interaction Sites PREDiction in protein structures with a refining grammar model. Bioinformatics. 33:1656-1663(2017)
• Capriotti E, Martelli PL, Fariselli P, Casadio R. Blind Prediction of Deleterious Amino Acid Variations with SNPs&GO. Hum Mutat. 38:1064-1071 (2017)
• Savojardo C, Martelli PL, Fariselli P, Casadio R. SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. Bioinformatics. 33:347-353 (2017)
• Jiang, Y, Oron, RT, Clark, TW, Bankapur, RA, D’Andrea, D, Lepore, R, Funk, SC, Kahanda, I, Verspoor, MK, Ben-Hur, A, Koo, EDC, Penfold-Brown, D, Shasha, D, Youngs, N, Bonneau, R, Lin, A, Sahraeian, ESM, Martelli, LP, Profiti, G, Casadio, R, Cao, R, Zhong, Z, Cheng, J, Altenhoff, A, Skunca, N, Dessimoz, C, Dogan, T, Hakala, K, Kaewphan, S, Mehryary, F, Salakoski, T, Ginter, F, Fang, H, Smithers, B, Oates, M, Gough, J, Törönen, P, Koskinen, P, Holm, L, Chen, C-T, Hsu, W-L, Bryson, K, Cozzetto, D, Minneci, F, Jones, TD, Chapman, S, BKC, D, Khan, KI, Kihara, D, Ofer, D, Rappoport, N, Stern, A, Cibrian-Uhalte, E, Denny, P, Foulger, ER, Hieta, R, Legge, D, Lovering, CR, Magrane, M, Melidoni, NA, Mutowo-Meullenet, P, Pichler, K, Shypitsyna, A, Li, B, Zakeri, P, ElShal, S, Tranchevent, L-C, Das, S, Dawson, LN, Lee, D, Lees, GJ, Sillitoe, I, Bhat, P, Nepusz, T, Romero, EA, Sasidharan, R, Yang, H, Paccanaro, A, Gillis, J, Sedeño-Cortés, EA, Pavlidis, P, Feng, S, Cejuela, MJ, Goldberg, T, Hamp, T, Richter, L, Salamov, A, Gabaldon, T, Marcet-Houben, M, Supek, F, Gong, Q, Ning, W, Zhou, Y, Tian, W, Falda, M, Fontana, P, Lavezzo, E, Toppo, S, Ferrari, C, Giollo, M, Piovesan, D, Tosatto, CES, del Pozo, A, Fernández, MJ, Maietta, P, Valencia, A, Tress, LM, Benso, A, Di Carlo, S, Politano, G, Savino, A, Rehman, UH, Re, M, Mesiti, M, Valentini, G, Bargsten, WJ, van Dijk, JAD, Gemovic, B, Glisic, S, Perovic, V, Veljkovic, V, Veljkovic, N, Almeida-e-Silva, CD, Vencio, NRZ, Sharan, M, Vogel, J, Kansakar, L, Zhang, S, Vucetic, S, Wang, Z, Sternberg, EMJ, Wass, NM, Huntley, PR, Martin, JM, O’Donovan, C, Robinson, NP, Moreau, Y, Tramontano, A, Babbitt, CP, Brenner, ES, Linial, M, Orengo, AC, Rost, B, Greene, SC, Mooney, DS, Friedberg, I, Radivojac, P -An expanded evaluation of protein function prediction methods shows an improvement in accuracy Genome Biology 17(184) (2016)
• 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-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations Genes and Nutrition 11(15) (2016)
• 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(Suppl 2)(397):239-247 (2016)
• 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(16):2542-2544 (2016)
• Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S -Tools and data services registry: a community effort to document bioinformatics resources- Nucleic Acids Res. 44:D38-47 (2016)
• Profiti G, Fariselli P, Casadio R -AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints- Bioinformatics 31:3841-3843 (2015)
• 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 Suppl 8:S6 (2015)
• 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)
• Fariselli P, Martelli PL, Savojardo C, Casadio R -INPS: predicting the impact of non-synonymous variations on protein stability from sequence- Bioinformatics 31:2816-2821 (2015)
• Bayram Akcapinar G, Venturini A, Martelli PL, Casadio R, Sezerman UO. Modulating the thermostability of Endoglucanase I from Trichoderma reesei using computational approaches Protein Eng Des Sel 28:127-135 (2015)
• Martelli PL, Savojardo C, Fariselli P, Tasco G, Casadio R -Computer-based prediction of mitochondria-targeting peptides- Methods Mol Biol 1264:305-320 (2015)
• 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 Biotechnol J 13:648-63 (2015)
• 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)
• 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 (Edinb) 113:259-267 (2014)
• Ciccarese S, Vaccarelli G, Lefranc MP, Tasco G, Consiglio A, Casadio R, Linguiti G, Antonacci R -Characteristics of the somatic hypermutation in the Camelus dromedarius T cell receptor gamma (TRG) and delta (TRD) variable domains. Dev Comp Immunol 46:300-313 (2014)
• Martelli PL, Fontanesi L, Piovesan D, Fariselli P, Casadio R -Mapping and annotating obesity-related genes in pig and human genomes. Protein Pept Lett 21:840-846 (2014)
• Bertolini F, Schiavo G, Scotti E, Ribani A, Martelli PL, Casadio R, Fontanesi L -High-throughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by next-generation semiconductor-based sequencing- Anim Genet 45:304-307 (2014).
• Pantaleo MA, Astolfi A, Urbini M, Nannini M, Paterini P, Indio V, Saponara M, Formica S, Ceccarelli C, Casadio R, Rossi G, Bertolini F, Santini D, Pirini MG, Fiorentino M, Basso U, Biasco G -Analysis of all subunits, SDHA, SDHB, SDHC, SDHD, of the succinate dehydrogenase complex in KIT/PDGFRA wild-type GIST Eur J Hum Genet 22:33-39 (2014).
• Abruzzo PM,Marini M,Bolotta A, Malisardi G, Manfredini S,Ghezzo A, Pini A, Tasco G, Casadio R -Frataxin mRNA Isoforms in FRDA Patients and Normal Subjects: Effect of Tocotrienol Supplementation- BioMed Res Int 2013:276808 (2013).
• 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)
• 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,Suppl 3:S6 (2013)
• 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)
• Piovesan D, Profiti G, Martelli PL, Fariselli P, Casadio R -Extended and robust protein sequence annotation over conservative nonhierarchical clusters: The case study of the ABC transporters- ACM Journal on Emerging Technologies in Computing Systems 9:27 (2013)
• 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 (Oxford) 2013:bat065 (2013)
• 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)
• 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 29:981-988 (2013)
• Masetti R, Pigazzi M, Togni M, Astolfi A, Indio V, Manara E, Casadio R, Pession A, Basso G, Locatelli F -CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype- Blood 121:3469-3472 (2013)
• 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)
• Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I -A large-scale evaluation of computational protein function prediction- Nat Methods 10:221-227 (2013)
• Squerzanti M, Cervellati C, Ura B, Mischiati C, Pucci P, Annunziata S, Iannone C, Casadio R, Bergamini CM, Esposito C -The side chain of glutamine 13 is the acyl-donor amino acid modified by type 2 transglutaminase in subunit T of the native rabbit skeletal muscle troponin complex- Amino Acids 44:227-34. (2013)
• 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)
• Nannini M, Astolfi A, Paterini P, Urbini M, Santini D, Catena F, Indio V, Casadio R, Pinna AD, Biasco G, Pantaleo MA- Expression of IGF-1 receptor in KIT/PDGF receptor-alpha wild-type gastrointestinal stromal tumors with succinate dehydrogenase complex dysfunction- Future Oncol. 9:121-126 (2013)
• 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)
• 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)
• 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)
• 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)
• Beninati S, Iorio RA, Tasco G, Serafini-Fracassini D, Casadio R and Del Duca S. Expression of different forms of transglutaminases by immature cells of Helianthus tuberosus sprout apices- Amino Acids 44:271-283 (2013)
• Bleve G, Lezzi C, Spagnolo S, Tasco G, Tufariello M, Casadio R, Mita G, Rampino P, Grieco F -Role of the C-terminus of Pleurotus eryngii Ery4 laccase in determining enzyme structure, catalytic properties and stability- Protein Eng Des Sel 26:1-13 (2013) (Cover picture)
• Martelli PL, Fariselli P, Balzani E, Casadio R -Predicting cancer-associated germline variations in proteins- BMC Genomics 13,Suppl 4:S8 (2012)
• Vaccarelli G, Antonacci R, Tasco G, Yang F, El Ashmaoui HM, Hassanane MS, Massari S, Casadio R, Ciccarese S -Generation of diversity by somatic mutation in the Camelus dromedarius T-cell receptor gamma (TCRG) variable domains -Eur J Immunol 42:3416-28 (2012)
• 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 90:2450-64 (2012)
• 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)
• 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)
• 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)
• 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 72:46-53 (2011)
• 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)
• 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)
• 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)
• 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)
• Pierleoni A, Martelli PL, Casadio R -MemLoci: predicting subcellular localization of membrane proteins in Eukaryotes- Bioinformatics 27:1224-1230 (2011)
• Di Lena P, Fariselli P, Margara L, Vassura M, Casadio R -Is there an optimal substitution matrix for contact prediction with correlated mutations?- IEEE/ACM Trans Comput Biol Bioinform , Jul-Aug;8(4):1017-28 (2011)
• Vassura M, Di Lena P, Margara L, Mirto M, Aloisio G, Fariselli P, Casadio R -Blurring contact maps of thousands proteins: what we can learn by reconstructing 3D structure- BioData Min 4:1 (2011)
• 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)
• Iacopetta D, Madeo M, Tasco G, Carrisi C, Curcio R, Martello E, Casadio R, Capobianco L, Dolce V -A novel subfamily of mitochondrial dicarboxylate carrier from Drosophila melanogaster: Biochemical and computational studies- Biochim Biophys Acta 1807:251-261 (2011)
• 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)
• 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)
• Casadio R -Bioinformatics and Computational Biology- Public Service Rev EU19:196-197
• 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).
• Di Lena P, Fariselli P, Margara L, Vassura M, Casadio R -Fast overlapping of protein contact maps by alignment of eigenvectors- Bioinformatics 26:2250-2258 (2010)
• Bergamini CM, Dondi A, Lanzara V, Squerzanti M, Cervellati C, Montin K, Mischiati C, Tasco G, Collighan R, Griffin M, Casadio R -Thermodynamics of binding of regulatory ligands to tissue transglutaminase- Amino Acids 39:297-304 (2010)
• Ricci G, Dondi A, Belotti T, Baldi E, Tartarini S, Paris R, Pagliarani G, Serafini-Fracassini D, Casadio R, Giannetti A, Masi M -Allergenicity of different apple cultivars assessed by means of skin prick test and sensitisation to recombinant allergens Mal d 1 and Mal d 3 in a group of Italian apple-allergic patients. Int J Food Sci Tech 45:1517-1523 (2010)
• Bartoli L, Martelli PL, 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 5688:1-17 (2009)
• Fariselli P, Savojardo C, Martelli PL, Casadio R -Grammatical-restrained hidden conditional random fields for bioinformatics applications- Algorithms Mol Biol 22:4-13 (2009)
• Bartoli L, Fariselli P, Krogh A, Casadio R (2009) -CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information- Bioinformatics 25:2757-2763 (2009)
• 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)
• 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) (Selected for the Human Mutation Virtual Issue "Evaluating Mutation Patogenicity"; Tavtigian SV and Greenblatt MS, eds; May 2010)
• Serafini-Fracassini D, Della Mea M, Tasco G, Casadio R, Del Duca S -Plant and animal transglutaminases: do similar functions imply similar structures?- Amino Acids 36:643-657(2009)
• Di Lena P, Vassura M, Margara L, Fariselli P, Casadio R -On the reconstruction of three-dimensional protein structures from contact maps- Algorithms 2:76-92 (2009)
• 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)
• Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S -Sequence-based feature prediction and annotation of proteins- Genome Biol 10:206 (2009)
• Vassura M, Margara L, Fariselli P, Casadio R -A graph theoretic approach to protein structure selection- Artif Intell Med 45:229-237 (2009)
• 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, Castrignanò 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- Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare , PISCATAWAY, IGI global, 2009, pp. 557 - 613
• Pierleoni A, Martelli PL, Casadio R -PredGPI: a GPI anchor predictor- BMC Bioinformatics 9:392 (2008)
• 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)
• 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)
• Montanucci L, Fariselli P, Martelli PL, Casadio R -Predicting protein thermostability changes from sequence upon multiple mutations- Bioinformatics 24:i190-i195 (2008)
• 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- Stud Health Technol Inform 138:135-146 (2008)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• Capriotti E, Arbiza L, Casadio R, Dopazo J, Dopazo H, Marti-Renom MA -Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans- Hum Mutat29:198-204 (2008)
• 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)
• Vassura M, Margara L, Fariselli P, Casadio R -A graph theoretic approach to protein structure selection- Lect Notes Comp Sci 4578:497-504 (2007)
• 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)
• 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)
• 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)
• 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 104:11109-11114 (2007)
• 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)
• 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)
• 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)
• Pierleoni A, Martelli PL, Fariselli P, Casadio R -BaCelLo: a Balanced subCellular Localization predictor- Nature Protocols DOI:10.1038/nprot.2007.165 (2007)
• 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)
• Tassoni A, Franceschetti M, Tasco G, Casadio R, Bagni N -Cloning, functional identification and structural modelling of Vitis vinifera S-adenosylmethionine decarboxylase- J Plant Physiol 164:1208-1219 (2007)
• Bartoli L, Calabrese R, Fariselli P, Mita D, Casadio R -A computational approach for detecting peptidases and their specific inhibitors at the genome level- BMC Bioinformatics 8:S3 (2007)
• Capriotti E, Casadio R -K-Fold: a tool for the prediction of the protein folding kinetic order and rate- Bioinformatics 23:385-386 (2007)
• Pierleoni A, Martelli PL, Fariselli P, Casadio R -eSLDB: eukaryotic subcellular localization database- Nucleic Acids Res 35:D208-12 (2007)
• 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)
• Grandi F, Sandal M, Guarguaglini G, Capriotti E, Casadio R, Samori' B -Hierarchical mechanochemical switches in angiostatin- Chembiochem 7:1774-82 (2006)
• Capriotti E, Calabrese R, Casadio R -Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information- Bioinformatics 22:2729-34 (2006)
• Pierleoni A, Martelli PL, Fariselli P, Casadio R -BaCelLo: a balanced subcellular localization predictor- Bioinformatics 22:e408-e416 (2006)
• 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)
• 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)
• Marani P, Wagner S, Baars L, Genevaux P, de Gier JW, Nilsson I, Casadio R, von Heijne G -New Escherichia coli outer membrane proteins identified through prediction and experimental verification- Protein Sci 15:884-889 (2006)
• Milanesi L, Petrillo M, Sepe L, Boccia A, D'Agostino N, Passamano M, Di Nardo S, Tasco G, Casadio R, Paolella G -Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity- BMC Bioinformatics i 6,Suppl 4:S20 (2005)
• 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)
• Scotto d'Abusco A, Casadio R, Tasco G, Giangiacomo L, Giartosio A, Calamia V, Di Marco S, Chiaraluce R, Consalvi V, Scandurra R, Politi L -Oligomerization of Sulfolobus solfataricus signatured amidase is promoted by acidic pH and temperature- Archaea 1:411-423 (2005)
• Becker L, Bannwarth M, Meisinger C, Hill K, Model K, Krimmer T, Casadio R, Truscott KN, Schulz GE, Pfanner N, Wagner R -Preprotein Translocase of the Outer Mitochondrial Membrane: Reconstituted Tom40 Forms a Characteristic TOM Pore- J Mol Biol 353:1011-1020 (2005)
• Morozzo della Rocca B, Miniero DV, Tasco G, Dolce V, Falconi M, Ludovico A, Cappello AR, Sanchez P, Stipani I, Casadio R, Desideri A, Palmieri F -Substrate-induced conformational changes of the mitochondrial oxoglutarate carrier: a spectroscopic and molecular modelling study- Mol Membr Biol 22:443-452 (2005)(Cover picture)
• Capriotti E, Fariselli P, Calabrese R, Casadio R -Predicting protein stability changes from sequence with Support Vector Machines- Bioinformatics 21:ii54-ii58 (2005)
• Calonghi N, Cappadone C, Pagnotta E, Boga C, Bertucci C, Fiori J, Tasco G, Casadio R, Masotti L -Histone deacetylase 1: a target of 9-hydroxystearic acid in the inhibition of cell growth in human colon cancer- J Lipid Res 46:1569-1603 (2005) (Cover Picture)
• 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)
• Capriotti E, Fariselli P, Casadio R -I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure- Nucl Acids Res 33:W303-W305 (2005)
• 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)
• Aguzzi MS, Facchiano F, Ribatti D, Gaeta R, Casadio R, Rossi I, Capogrossi MC, Facchiano A -A novel RGD-analog inhibits angiogenesis in vitro and in vivo- Biochem Biophys Res Commun 321:809-814 (2004)
• Compiani M, Capriotti E, Casadio R -Dynamics of the minimally frustrated helices determine the hierarchical folding of small helical proteins- Phys Rev E 69:051905.1-051905.8 (2004)
• Grano V, Diano N, Bencivenga U, De Santo NG, Salamino F, Cotrufo M, Nappi GA, De Santo LS, Casadio R, Compiani M, Citton C, Oliva A, Mita DG -A new biotechnological approach to reduce the increase of the protease concentration during extracorporeal blood circulation in hemodyalisis or cardiopulmonary bypass operations- Recent Res Devel Biotech Bioeng 6:1-17 (2004)
• Capriotti E, Fariselli P, Casadio R -A neural-network-based method for predicting protein stability changes upon single point mutations- Bioinformatics 20:I63-I68 (2004)
• Grano V, Tasco G, Casadio R, Diano N, Portaccio M, Rossi S, Bencivenga U, Compiani M, De Maio A, Mita DG -Reduction of active elastase concentration by means of immobilized inhibitors: a novel therapeutic approach- Biotechnol Prog 20:968-974 (2004)
• 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)
• Martelli PL, Fariselli P, Casadio R -Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network- Proteomics 4:1665-1671 (2004)
• Aiello R, Messina A, Schiffler B, Benz R, Tasco G, Casadio R, De Pinto V -Functional characterization of a second porin isoform in drosophila melanogster: DmPorin2 forms voltage-independent cation selective pores- J Biol Chem 279:25364-25373 (2004)
• 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)
• 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)
• Rossi I, Marchignoli D, Fariselli P, Beltrami D, Medini R, Casadio R -DCNBLAST: a parallel BLAST for computer clusters-Minerva Biotec15: 191-193 (2003)
• 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)
• Casadio R, Fariselli P, Martelli PL -In silico prediction of the structure of membrane proteins: Is it feasible?- Brief Bioinf 4:341-348 (2003)
• Fariselli P, Finocchiaro G, Casadio R -SPEPlip: the detection of signal peptide and lipoprotein cleavage sites- Bioinformatics 19:2498-2499 (2003)
• Fariselli P, Finocchiaro G, Casadio R -Prediction of Signal Peptide in Proteins with Neural Networks- Lecture Notes in Computer Science 2859:237-244 (2003)
• 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)
• Casadio R -The 4th Bologna Winter School: hot topics in structural genomics (Conference Report)- Compar Funct Genom 4:394-396 (2003)
• 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)
• Martelli PL, Fariselli P, Casadio R -An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins- Bioinformatics 19:I205-I211 (2003)
• 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 11:1158-1168 (2003)
• De Pinto V, Messina A, Accardi R, Aiello R, Guarino F, Tomasello MF, Tommasino M, Tasco G, Casadio R, Benz R, De Giorni F, Ichas F, Baker M, Lawen A -New functions of an old protein: the eukaryotic porin or voltage dependent anion selective channel (VDAC). Minireview- Ital J Biochem 52:17-24 (2003)
• Fariselli P, Finelli M, Marchignoli D, Martelli PL, Rossi I, Casadio R -MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments- Bioinformatics 19:500-505 (2003) (evaluated as Recommended by Faculty of 1000, Biology reports)
• 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)
• 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)
• 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)
• Scagliarini A, Ciulli S, Battilani M, Jacoboni I, Montesi F, Casadio R, Prosperi S -Characterisation of immunodominant protein encoded by the F1L gene of orf virus strains isolated in Italy Brief Report- Arch Virol 147: 1989-1995 (2002)
• Griffin M, Casadio R, Bergamini C -Transglutaminases, nature's biological glues- Biochemical Journal 368:377-396 (2002)
• 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 ISMB2002) (Evaluated as Recommended by Faculty of 1000, Biology reports)
• Casadio R, Jacoboni I, Messina A, De Pinto V -A 3D model of the voltage-dependent anion channel (VDAC)- FEBS Lett 520:1-7 (2002)
• 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)
• Menotti L, Casadio R, Bertucci C, Lopez M, Campadelli-Fiume G -Substitution in the murine nectin1 receptor of a single conserved amino acid at a position distal from the Herpes Simplex virus gD binding site confers high-affinity binding to gD- J Virol 76:5463-5471 (2002)
• 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)
• Pollastri G, Baldi P, Fariselli P, Casadio R -Prediction of coordination number and relative solvent accessibility in proteins- Proteins 47:142-53 (2002)
• 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)
• 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)
• 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)
  
• Fariselli P, Olmea O, Valencia A, Casadio R -Progress in predicting inter- residue contacts of proteins with neural networks and correlated mutations- Proteins: 45 Suppl 5: 157-162 (2001)
• Fariselli P, Olmea O, Valencia A, Casadio R -Prediction of contact maps with neural networks and correlated mutations- Protein eng 14: 835-843 (2001)
• Fariselli P, Casadio R -Prediction of disulfide connectivity in proteins- Bioinformatics 17: 957-964 (2001)
• Pollastri G, Baldi P, Fariselli P, Casadio R -Improved prediction of the number of residue contacts in proteins by recurrent neural network- Bioinformatics 17, Suppl 1: 234-242 (2001)
• Casadio R, Frigimelica E, Bossu P, Neumann D, Martin MU, Tagliabue A, Boraschi D - Model of interaction of the IL-1 receptor accessory protein IL-1RAcP with the IL-1beta/IL-1R(I) complex- FEBS Lett 499: 65-68 (2001)
• Battilani M, Scagliarini A, Tisato E, Turilli C, Jacoboni I, Casadio R, Prosperi S -Analysis of canine parvovirus sequences from wolves and dogs isolated in Italy- J Gen Virol 82: 1555-1560 (2001)
• Musiani F, Arnofi E, Casadio R, Ciurli S -Structure based computational study of the catalytic and inhibition mechanisms of urease- J Biol Inorg Chem 6: 300-314 (2001)
• 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)
• Fariselli P, Casadio R - RCNPRED: a server for the prediction of the residue co-ordination numbers in proteins- Bioinformatics 17: 202-204 (2001)
• 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)
• 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)
• 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)
• 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)
• Fariselli P, Casadio R  - Prediction of the Number of Residue Contacts in Proteins- ISMB 8: 146-151 (2000)
• 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)
• 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)
• Mariani P, Carsughi F, Spinozzi F, Romanzetti S, Meier G, Casadio R, Bergamini CM - Ligand-induced conformational changes in tissue transglutaminase: Monte Carlo analysis of small-angle scattering data.  Biophys J 78: 3240-3251 (2000)
• Casadio R, Polverini E, Mariani P, Spinozzi F, Flavio C, Fontana A, Polverino de Laureto P, Matteucci G, Bergamini CM - The structural basis for the regulation of tissue transglutaminase by calcium ions- Eur J Biochem 262: 672-679 (1999)
• 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)
• Fariselli P, Riccobelli P, Casadio R - The role of evolutionary information in predicting the disulfide bonding state of cysteines in proteins- Proteins 36: 340-346 (1999)
• 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 bindig- Protein Sci 8: 1546-1550 (1999)
• Fariselli P, Casadio R - Neural network based predictor of residue contacts in proteins - Prot Engng12: 15-21 (1999)
• 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)
• 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 221: 65-110 (1998)
• 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)  527-533 (1998)
• 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)
• 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(1): 77-80
• Fariselli P, Casadio R (1998) - Quantum molecular biophysics: the case study of hemocyanin- in Biophysics of Electron Transfer Molecular Bioelectronics (Nicolini C, ed) E.L:B.A. Forum Series, Plenum Pub Co, New York, 139-159 (1998)
• Polverini E, Casadio R, Neyroz P, Masotti L - Conformational changes of Neuromedin B and Delta sleep inducing peptide induced by their interaction with lipid membranes as revealed by spectroscopic techniques and molecular dynamics simulation- Arch Biochem Biophys 349: 225-235 (1998)
• Fariselli P and Casadio R. -Pseudodihedral poteintial of protein residues and the prediction of folding- In : Proc.Bio-Computing and Emergent Computation (Skovde, Sweden) 112-121 World Scientific, Singapore (1997).
• Vivarelli F, Fariselli P, Casadio R - The prediction of protein secondary structure with a cascade correlation learning architecture of neural networks- Neural Comp and Appl 6: 57-62 (1997)
• Mariani P, Casadio R, Carsughi F, Ceretti M, Rustichelli F - Structural analysis of membranes from photosynthetic bacteria by SANS- Europhys Lett 37: 433-438 (1997)
• Compiani M, Fariselli P, and Casadio R - Noise and randomlike behaviour of perceptrons: theory and applications to protein structure prediction- Phys Rev E, 55: 7334-7343 (1997)
• Arrigo P, Fariselli P, Casadio R -Self-organizing neural maps of the coding sequences of G-coupled protein receptors reveal local domains associated with potentially functional determinants in the protein- In : Proc. Fifth International Conference on Intelligent Systems for Molecular Biology ( ISMB 5)(Thesseloniki, Greece ) 44-47 (1997)
• Arrigo P, Fariselli P, Casadio R -The identification of locally ordered features on completely unaligned genomic sequence using an unsupervised neural classifier - In: Proc. Computer Science and Biology (Leipzig, Germany) 156-158 (1996)
• Rost B, Fariselli P, and Casadio R - Topology prediction for helical transmembrane proteins at 86% accuracy- Protein Sci 5: 1704-1718(1996)
• Zanotti F, Casadio R, Perrucci C and Guerrieri F -DCCD sensitive proton permeability of bacterial photosynthetic membranes. Cross-reconstitution studies with purified bovine heart Fo subunits- Biochim Biophys Acta 1276: 80-86 (1996)
• Casadio R and Melandri BA -CaATP inhibits the MgATP-dependent proton pump (H-ATPase) in bacterial photosynthetic membranes with a mechanism of alternative substrate inhibition- J Bioinorg Chem 1: 284-291(1996)
• 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)
• 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)
• 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).
• Fariselli P and Casadio R -HTP: a neural network based method for predicting the topology of helical trasmembrane domains in proteins- Comput Applic Biosci 12: 41-48 (1996).
• 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).
• Compiani M, Fariselli P and Casadio R -Noise and random-lke bejaviour of perceptrons: theory and application to protein structure prediction- Proc. SPIE (Orlando USA) 2760: 597-607 (1996)
• 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).
• 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 1995) (Rawlings C et al, Eds), pp 81-88 (1995).
• 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)
• 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 Biosci 11: 253-260 (1995)
• Rost B, Casadio R, Fariselli P, Sander C - Transmembrane helices predicted at 95% accuracy- Protein Sci 4: 521-533 (1995)
• Compiani M, Fariselli P, Casadio R -x Statistical behaviour of perceptrons: the case study of the prediction of protein secondary structures-Int J Neur Sys 6: 195-199 (Supp 1995)