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Faculty Detail    
Name EMIDIO CAPRIOTTI
 
Campus Address WP P220 Zip 7331
Phone 205-975-2928
E-mail emidio@uab.edu
Other websites http://biofold.org/emidio/
     

Education
Undergraduate  University of Bologna    1999  Degree in Physics 
Graduate  University of Bologna    2004  Degree in Physics 


Faculty Appointment(s)
Appointment Type Department Division Rank
Primary  Pathology   Pathology Informatics Assistant Professor
Center  Comprehensive Cancer Center  Comprehensive Cancer Center Assistant Professor

Graduate Biomedical Sciences Affiliations
Biochemistry and Structural Biology 
Genetics and Genomic Sciences 
Pathobiology and Molecular Medicine 

Biographical Sketch 
I am assistant professor at the Department of Pathology at the University of Alabama at Birmingham (UAB). I was a Marie Curie IOF researcher in the Department of Mathematics and Computer Science at the University of Balearic Islands (Spain), and in the Helix Group at the Bioengineering Department at Stanford University. I was postdoc for 2 years at the University of Bologna (Italy) in the Biocomputing Group and 3 years in the Structural Bioinformatics Unit at CIPF of Valencia (Spain).
I am PhD in physical sciences from the University of Bologna. My scientific background is in Structural Bioinformatics and in the last years my research activity moved toward the study of the effect of SNPs resulting in single amino acid polymorphisms. I applied tools for the analysis of protein three-dimensional structure to predict the effect of single point protein mutations on the protein stability, developing machine learning methods to evaluate the free energy change upon single amino acid polymorphisms (SAPs). More recently, I have been interested to study the relationship between SAPs and the insurgence of human disease. Using information derived from protein sequence and sequence profile, I implemented web server tools to predict disease-related protein variants. The final goal of my research activity is the understanding of the relationship between genomic variations and disease using large amount of data derived from high-throughput techniques. I am interested to design new disease-specific algorithms and new tools for personal genomics and personalized medicine.

Society Memberships
Organization Name Position Held Org Link
American Medical Informatics Association (AMIA)  Member  http://www.amia.org 
F1000 Biology  Faculty  http://f1000.com/ 
International Society of Computational Biology (ISCB)   Member  http://www.iscb.org/  

Research/Clinical Interest
Title
Computational Biology/Bioinformatics
Description
Dr. Capriotti’s research interests include protein structure prediction by threading methods and building by homology; molecular dynamics of protein systems; protein folding kinetics; prediction of protein stability changes upon mutations; prediction of disease-related protein mutations; machine learning approaches in molecular biology; protein-protein interactions; and RNA structure comparison and prediction.

Selected Publications 
Publication PUBMEDID
Compiani M, Capriotti E. Computational and theoretical methods for protein folding. Biochemistry. 2013 Nov 4. (Epub)  24187909 
Norambuena T, Cares JF, Capriotti E, Melo F. (2013). WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures. Bioinformatics. 29:2649-2650  23929030 
Capriotti E, Altman RB, Bromberg Y. (2013) Collective judgment predicts disease-associated single nucleotide variants. BMC Genomics. 14 Suppl 3, S2.  23819846 
Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R. (2013). WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variations using functional annotation. BMC Genomics. 14 Suppl 3, S6.  23819482 
Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Cedric Notredame C. (2013). Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Bioinformatics. 29:1112-1119.  23449094 
Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB. (2012). Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface. 9; 1409-1437.
 
22552919 
Capriotti E, Nehrt NL, Kann MG, Bromberg Y. (2012). Bioinformatics for personal genome interpretation. Briefings in Bioinformatics. 13; 495-512.
 
22247263  
Capriotti E, Altman RB. (2011). Improving the prediction of disease-related variants using protein three-dimensional structure. BMC Bioinformatics. 12 (Suppl 4); S3
 
21992054 
Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA. (2011). Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLOS Genetics. 7; e1002280.
 
21935354 
Capriotti E, Altman RB. (2011). A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics. 98; 310-317.
 
21763417 
Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB. (2011). Bioinformatics challenges for personalized medicine. Bioinformatics. 27; 1741-1748
 
21596790 
Liu T, Tang GW, Capriotti E. (2011). Comparative modeling: the state of the art and protein drug target structure prediction. Combinatorial Chemistry & High Throughput Screening. 14: 532-547
 
21521153 
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.
 
21349865 
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.
 
21131981 
Capriotti E, Marti-Renom MA. (2010). Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. BMC Bioinformatics. 11: 322.
 
20550657 
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.
 
19514061 
Capriotti E, Marti-Renom MA. (2009). SARA: a server for function annotation of RNA structures. Nucleic Acids Research. 37 (Web Server issue): W260-W265.
 
19483098 
Capriotti E, Marti-Renom MA. (2008). RNA structure alignment by a unit-vector approach. Bioinformatics. 24: i112-i116.
 
18689811 
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.
 
18387208  
Capriotti E, Arbiza L, Casadio R, Dopazo J, Dopazo H, Marti-Renom MA. (2008). The use of estimated evolutionary strength at the codon level improves the prediction of disease related protein mutations in human. Human Mutation. 29: 198-204.
 
17935148 
Capriotti E, Casadio R. (2007). K-Fold: a tool for the prediction of the protein folding kinetic order and rate. Bioinformatics. 23: 385-386.
 
17138584 
Fariselli P, Rossi I, Capriotti E, Casadio R. (2007) The WWWH of remote homolog detection: The state of the art. Brief. Bioinformatics. 8: 78-87.
 
17003074 
Grandi F, Sandal M, Guarguaglini G, Capriotti E, Casadio R, Samori B. Hierarchical Mechanochemical Switches in Angiostatin. Chembiochem. 7: 1774-1782.
 
16991168 
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.
 
16895930 
Stizza A, Capriotti E, Compiani M. (2005). A Minimal Model of Three-State Folding Dynamics of Helical Proteins. J. Phys. Chem. B. 109: 4215-4226.
 
16851484 
Capriotti E, Compiani M. (2006). Diffusion-collision of foldons elucidates the kinetic effects of point mutations and suggests control strategies of the folding process of helical proteins. Proteins. 64: 198-209.
 
16609971 
Capriotti E, Fariselli P, Calabrese R, Casadio R. (2005) Predicting protein stability changes from sequences using support vector machines. Bioinformatics. 21: ii54-ii58.
 
16204125 
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.
 
15980478 
Capriotti E, Fariselli, Casadio R (2004). A neural network-based method for predicting protein stability changes upon single point mutations. Bioinformatics. Suppl 1: I63-I68
 
15262782 
Compiani M, Capriotti E, Casadio R. (2004). The Dynamics of the Minimally Frustrated Helices Determine the Hierarchical Folding of Small Helical Proteins. Physical Review E. 69: 051905
 
15244845 
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.
 
14696197 
Capriotti E, Marti-Renom MA. (2008). Computational RNA structure prediction. Current Bioinformatics. 3: 32-45.S6.
 
 

Keywords
protein and RNA three-dimensional structure, folding and stability, genomic variations, disease-related variants, machine-learning