Emidio Capriotti

Emidio Capriotti

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Emidio Capriotti

Emidio Capriotti

Publications by authors named "Emidio Capriotti"

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Are machine learning based methods suited to address complex biological problems? Lessons from CAGI-5 challenges.

Hum Mutat 2019 09 18;40(9):1455-1462. Epub 2019 Jun 18.

Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1002/humu.23784DOI Listing
September 2019

Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome.

Nucleic Acids Res 2019 Jul;47(W1):W136-W141

Department of Comparative Biomedicine and Food Science. University of Padova, Viale dell'Università, 16, 35020 Legnaro (Padova), Italy.

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http://dx.doi.org/10.1093/nar/gkz420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602425PMC
July 2019

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations.

BMC Bioinformatics 2019 Jul 3;20(Suppl 14):335. Epub 2019 Jul 3.

Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy.

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http://dx.doi.org/10.1186/s12859-019-2923-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6606456PMC
July 2019

VarI-COSI 2018: a forum for research advances in variant interpretation and diagnostics.

BMC Genomics 2019 Jul 16;20(Suppl 8):550. Epub 2019 Jul 16.

Division of Medical Genetics, Department of Medicine, University of California, San Diego, CA, 92093, USA.

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http://dx.doi.org/10.1186/s12864-019-5862-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6631439PMC
July 2019

Integrating molecular networks with genetic variant interpretation for precision medicine.

Wiley Interdiscip Rev Syst Biol Med 2019 May 12;11(3):e1443. Epub 2018 Dec 12.

Department of Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.

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http://dx.doi.org/10.1002/wsbm.1443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450710PMC
May 2019

Blind prediction of deleterious amino acid variations with SNPs&GO.

Hum Mutat 2017 09 2;38(9):1064-1071. Epub 2017 May 2.

Biocomputing Group, BiGeA / Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna University of Bologna, Bologna, Italy.

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http://doi.wiley.com/10.1002/humu.23179
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http://dx.doi.org/10.1002/humu.23179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522651PMC
September 2017

PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants.

Nucleic Acids Res 2017 07;45(W1):W247-W252

Department of Comparative Biomedicine and Food Science. University of Padova, Viale dell'Università, 16, 35020 Legnaro, PD, Italy.

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http://dx.doi.org/10.1093/nar/gkx369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570245PMC
July 2017

VpreB serves as an invariant surrogate antigen for selecting immunoglobulin antigen-binding sites.

Sci Immunol 2016 Jul;1(1)

Department of Medicine, University of Alabama at Birmingham, Birmingham, AL; Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL.

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http://dx.doi.org/10.1126/sciimmunol.aaf6628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315267PMC
July 2016

VarI-SIG 2015: methods for personalized medicine - the role of variant interpretation in research and diagnostics.

BMC Genomics 2016 06 23;17 Suppl 2:425. Epub 2016 Jun 23.

Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Dr., 92093, La Jolla, CA, USA.

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http://dx.doi.org/10.1186/s12864-016-2721-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928159PMC
June 2016

WALTZ-DB: a benchmark database of amyloidogenic hexapeptides.

Bioinformatics 2015 May 18;31(10):1698-700. Epub 2015 Jan 18.

VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv027DOI Listing
May 2015

ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples.

Bioinformatics 2014 Sep;30(17):i572-8

Division of Informatics, Department of Pathology, Department of Clinical and Diagnostic Sciences and Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35249, USA Division of Informatics, Department of Pathology, Department of Clinical and Diagnostic Sciences and Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35249, USA Division of Informatics, Department of Pathology, Department of Clinical and Diagnostic Sciences and Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35249, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147919PMC
September 2014

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.

Nucleic Acids Res 2014 Jul 27;42(Web Server issue):W356-60. Epub 2014 Jun 27.

Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gku459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086076PMC
July 2014

Computational and theoretical methods for protein folding.

Biochemistry 2013 Dec 21;52(48):8601-24. Epub 2013 Nov 21.

School of Sciences and Technology, University of Camerino , Camerino, Macerata 62032, Italy.

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http://dx.doi.org/10.1021/bi4001529DOI Listing
December 2013

WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation.

BMC Genomics 2013 28;14 Suppl 3:S6. Epub 2013 May 28.

Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham AL, USA.

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http://dx.doi.org/10.1186/1471-2164-14-S3-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665478PMC
October 2013

Thoughts from SNP-SIG 2012: future challenges in the annotation of genetic variations.

BMC Genomics 2013 28;14 Suppl 3:S1. Epub 2013 May 28.

Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.

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http://dx.doi.org/10.1186/1471-2164-14-S3-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665538PMC
October 2013

Collective judgment predicts disease-associated single nucleotide variants.

BMC Genomics 2013 28;14 Suppl 3:S2. Epub 2013 May 28.

Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.

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http://dx.doi.org/10.1186/1471-2164-14-S3-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839641PMC
October 2013

WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures.

Bioinformatics 2013 Oct 7;29(20):2649-50. Epub 2013 Aug 7.

Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19 st. south, Birmingham, AL 35249, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789544PMC
October 2013

Bioinformatics for personal genome interpretation.

Brief Bioinform 2012 Jul 13;13(4):495-512. Epub 2012 Jan 13.

Department of Mathematics and Computer Science, University of Balearic Islands, ctra. de Valldemossa Km 7.5, Palma de Mallorca, 07122 Spain.

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http://dx.doi.org/10.1093/bib/bbr070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404395PMC
July 2012

Bioinformatics and variability in drug response: a protein structural perspective.

J R Soc Interface 2012 Jul 2;9(72):1409-37. Epub 2012 May 2.

Department of Bioengineering, Stanford University, Stanford, CA, USA.

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http://rsif.royalsocietypublishing.org/cgi/doi/10.1098/rsif.
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http://dx.doi.org/10.1098/rsif.2011.0843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367825PMC
July 2012

SNP-SIG Meeting 2011: identification and annotation of SNPs in the context of structure, function, and disease.

BMC Genomics 2012 Jun 18;13 Suppl 4:S1. Epub 2012 Jun 18.

Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, USA.

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http://dx.doi.org/10.1186/1471-2164-13-S4-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395891PMC
June 2012

Improving the prediction of disease-related variants using protein three-dimensional structure.

BMC Bioinformatics 2011 5;12 Suppl 4:S3. Epub 2011 Jul 5.

Department of Bioengineering, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1186/1471-2105-12-S4-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194195PMC
December 2011

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants.

Genomics 2011 Oct 7;98(4):310-7. Epub 2011 Jul 7.

Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.ygeno.2011.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371640PMC
October 2011

Comparative modeling: the state of the art and protein drug target structure prediction.

Comb Chem High Throughput Screen 2011 Jul;14(6):532-47

Department of Bioengineering, Stanford University, 318 Campus Dr, Room S240 Mail code: 5448, Stanford, CA 94305, USA.

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http://dx.doi.org/10.2174/138620711795767811DOI Listing
July 2011

Bioinformatics challenges for personalized medicine.

Bioinformatics 2011 Jul 19;27(13):1741-8. Epub 2011 May 19.

Biomedical Informatics Training Program, Stanford University School of Medicine, Department of Bioengineering, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117361PMC
July 2011

All-atom knowledge-based potential for RNA structure prediction and assessment.

Bioinformatics 2011 Apr 23;27(8):1086-93. Epub 2011 Feb 23.

Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Principe Felipe, 46012 Valencia, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btr093DOI Listing
April 2011

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.

Nat Struct Mol Biol 2011 Jan 5;18(1):107-14. Epub 2010 Dec 5.

Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.

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http://dx.doi.org/10.1038/nsmb.1936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056208PMC
January 2011

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.

BMC Bioinformatics 2010 Jun 15;11:322. Epub 2010 Jun 15.

Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.

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http://dx.doi.org/10.1186/1471-2105-11-322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904352PMC
June 2010

Functional annotations improve the predictive score of human disease-related mutations in proteins.

Hum Mutat 2009 Aug;30(8):1237-44

Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna, Bologna 40126, Italy.

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http://dx.doi.org/10.1002/humu.21047DOI Listing
August 2009

SARA: a server for function annotation of RNA structures.

Nucleic Acids Res 2009 Jul 29;37(Web Server issue):W260-5. Epub 2009 May 29.

Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkp433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703911PMC
July 2009

RNA structure alignment by a unit-vector approach.

Bioinformatics 2008 Aug;24(16):i112-8

Bioinformatics and Genomics Department, Structural Genomics Unit, Centro de Investigación Príncipe Felipe, Valencia, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btn288DOI Listing
August 2008

The pros and cons of predicting protein contact maps.

Methods Mol Biol 2008 ;413:199-217

CIRB/Department of Biology, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1007/978-1-59745-574-9_8DOI Listing
June 2008

A three-state prediction of single point mutations on protein stability changes.

BMC Bioinformatics 2008 Mar 26;9 Suppl 2:S6. Epub 2008 Mar 26.

Structural Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.

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http://dx.doi.org/10.1186/1471-2105-9-S2-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323669PMC
March 2008

Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans.

Hum Mutat 2008 Jan;29(1):198-204

Structural Genomics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.

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http://dx.doi.org/10.1002/humu.20628DOI Listing
January 2008

The WWWH of remote homolog detection: the state of the art.

Brief Bioinform 2007 Mar 26;8(2):78-87. Epub 2006 Sep 26.

Biocomputing Group, Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy.

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http://dx.doi.org/10.1093/bib/bbl032DOI Listing
March 2007

Hierarchical mechanochemical switches in angiostatin.

Chembiochem 2006 Nov;7(11):1774-82

Department of Biochemistry, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.

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http://doi.wiley.com/10.1002/cbic.200600227
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http://dx.doi.org/10.1002/cbic.200600227DOI Listing
November 2006

Diffusion-collision of foldons elucidates the kinetic effects of point mutations and suggests control strategies of the folding process of helical proteins.

Proteins 2006 Jul;64(1):198-209

Laboratory of Biocomputing, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1002/prot.20980DOI Listing
July 2006

Predicting protein stability changes from sequences using support vector machines.

Bioinformatics 2005 Sep;21 Suppl 2:ii54-8

Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bti1109DOI Listing
September 2005

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W306-10

Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna via Irnerio 42, 40126 Bologna, Italy.

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http://dx.doi.org/10.1093/nar/gki375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160136PMC
July 2005

A minimal model of three-state folding dynamics of helical proteins.

J Phys Chem B 2005 Mar;109(9):4215-26

Department of Mathematics and Physics, Catholic University, Brescia, Italy.

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http://dx.doi.org/10.1021/jp045228dDOI Listing
March 2005

A neural-network-based method for predicting protein stability changes upon single point mutations.

Bioinformatics 2004 Aug;20 Suppl 1:i63-8

Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bth928DOI Listing
August 2004

A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues.

Proteins 2004 Feb;54(2):351-60

Department of Physics, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1002/prot.10564DOI Listing
February 2004