Biomolecules Folding and Disease


Selected papers

Since 2004 we have published 73 peer-reviewed manuscripts (13 reviews) in international journal with impact factor and 7 book chapters. A selected list of papers grouped by topics are reported below. The full list of research articles, reviews and book chapters is available at this webpage.

Genomic variations and disease

  • Capriotti E†*, Montanucci L†, Profiti G, Rossi I, Giannuzzi D, Aresu L, Fariselli P*. (2019). Fido-SNP: The first webserver for scoring the impact of single nucleotide variants in the dog genome. Nucleic Acids Research. 47(W1): W136-W141.
     

  • Capriotti E*, Fariselli P*. (2017). PhD-SNPg: A webserver and lightweight tool for scoring single nucleotide variants. Nucleic Acids Research. 45: W247-W252.
     

  • Tian R, Basu MK, Capriotti E*. (2014). ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. Bioinformatics. 30: i572-i578.
     

  • Capriotti E*, Altman RB, Bromberg Y* (2013). Collective judgment predicts disease-associated single nucleotide variants. BMC Genomics. 14 Suppl 3:S2.
     

  • Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. (2009). Functional annotations improve the predictive score of human disease-related mutations in proteins. Human Mutation. 30: 1237-1244.
     

  • Capriotti E, Calabrese R, Casadio R. (2006). Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics. 22: 2729-2734.
     

Protein folding stability and kinetics

  • Montanucci L†, Capriotti E†, Birolo G, Benevenuta S, Pancotti C, Lal D, Fariselli P (2022). DDGun: an untrained predictor of protein stability changes upon amino acid variants. Nucleic Acids Research. DOI:10.1093/nar/gkac325.
     

  • Turina P, Fariselli P*, Capriotti E*. (2021). ThermoScan: Semi-automatic identification of protein stability data from PubMed. Frontiers in Molecular Biosciences.8:620475. DOI:10.3389/fmolb.2021.620475
     

  • Capriotti E, Fariselli P, Rossi I, Casadio R. (2008). A three-state prediction of single point mutations on protein stability changes. BMC Bioinfomatics. 9 (Suppl 2): S6.
     

  • Capriotti E*, Casadio R. (2007). K-Fold: a tool for the prediction of the protein folding kinetic order and rate. Bioinformatics. 23: 385-386.
     

  • Capriotti E, Fariselli P, Casadio R. (2005). I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Research. 33(Web Server issue): W306-W310.
     

  • Capriotti E, Fariselli P, Calabrese R, Casadio R. (2005) Predicting protein stability changes from sequences using support vector machines. Bioinformatics. 21: ii54-ii58.
     

  • Capriotti E, Fariselli, Casadio R (2004). A neural network-based method for predicting protein stability changes upon single point mutations. Bioinformatics. 20 (Suppl 1): I63-I68
     

RNA and protein structure comparison and prediction

  • Capriotti E†, Norambuena T†, Marti-Renom MA, Melo F. (2011). All atom knowledge-based potential for RNA structure prediction and assessment. Bioinformatics. 27; 1086-1093.
     

  • Capriotti E, Marti-Renom MA. (2010). Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. BMC Bioinformatics. 11: 322.
     

  • Capriotti E, Marti-Renom MA. (2009). SARA: a server for function annotation of RNA structures. Nucleic Acids Research. 37 (Web Server issue): W260-W265.
     

  • Capriotti E, Marti-Renom MA. (2008). RNA structure alignment by a unit-vector approach. Bioinformatics. 24: i112-i116.
     

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

Other topics

  • Khass M, Blackburn T, Burrows PD, Walter MR, Capriotti E, Schroeder HW Jr. (2016). VpreB serves as an invariant surrogate antigen for selecting immunoglobulin antigen-binding sites. Science Immunology. 1: aaf6628.
     

  • Bau D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. (2011). The three-dimensional folding of the alpha-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol. 18: 107-114.
     

Reviews

  • Capriotti E*, Ozturk K, Carter H*. (2019). Integrating molecular network with genetic variant interpretation for precision medicine. WIREs Systems Biology and Medicine. 11: e1443.
     

  • Tian R, Basu MK, Capriotti E*. (2015). Computational methods and resources for the interpretation of genomic variants in cancer. BMC Genomics. 16 (Suppl. 8): S7.
     

  • Compiani M†*, Capriotti E†*. (2013). Computational and theoretical methods for protein folding. Biochemistry. 52: 8601-8624.
     

  • Capriotti E†*, Nehrt NL†, Kann MG†**, Bromberg Y†*. (2012). Bioinformatics for personal genome interpretation. Briefings in Bioinformatics. 13; 495-512.
     

  • Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB. (2011). Bioinformatics challenges for personalized medicine. Bioinformatics. 27; 1741-1748
     

  • Capriotti E, Marti-Renom MA. (2008). Computational RNA structure prediction. Current Bioinformatics. 3: 32-45.
     


Citations