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

Bromberg Y, Capriotti E, Carter H.

BMC Genomics. 2019 Jul 16;20(Suppl 8):550. doi: 10.1186/s12864-019-5862-3. No abstract available.


Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants.

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, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I.

Hum Mutat. 2019 Sep;40(9):1530-1545. doi: 10.1002/humu.23868. Epub 2019 Sep 3.


Assessing predictions on fitness effects of missense variants in calmodulin.

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.

Hum Mutat. 2019 Sep;40(9):1463-1473. doi: 10.1002/humu.23857. Epub 2019 Sep 3.


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

Montanucci L, Capriotti E, Frank Y, Ben-Tal N, Fariselli P.

BMC Bioinformatics. 2019 Jul 3;20(Suppl 14):335. doi: 10.1186/s12859-019-2923-1.


Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5.

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.

Hum Mutat. 2019 Sep;40(9):1474-1485. doi: 10.1002/humu.23856. Epub 2019 Aug 17.


Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer.

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.

Hum Mutat. 2019 Sep;40(9):1612-1622. doi: 10.1002/humu.23849. Epub 2019 Aug 17.


Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge.

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.

Hum Mutat. 2019 Sep;40(9):1392-1399. doi: 10.1002/humu.23843. Epub 2019 Jul 12.


Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

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.

Hum Mutat. 2019 Sep;40(9):1314-1320. doi: 10.1002/humu.23825. Epub 2019 Jun 24.


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

Capriotti E, Montanucci L, Profiti G, Rossi I, Giannuzzi D, Aresu L, Fariselli P.

Nucleic Acids Res. 2019 Jul 2;47(W1):W136-W141. doi: 10.1093/nar/gkz420.


Characterization of human frataxin missense variants in cancer tissues.

Petrosino M, Pasquo A, Novak L, Toto A, Gianni S, Mantuano E, Veneziano L, Minicozzi V, Pastore A, Puglisi R, Capriotti E, Chiaraluce R, Consalvi V.

Hum Mutat. 2019 Sep;40(9):1400-1413. doi: 10.1002/humu.23789. Epub 2019 Jun 18.


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

Savojardo C, Babbi G, Bovo S, Capriotti E, Martelli PL, Casadio R.

Hum Mutat. 2019 Sep;40(9):1455-1462. doi: 10.1002/humu.23784. Epub 2019 Jun 18.


Integrating molecular networks with genetic variant interpretation for precision medicine.

Capriotti E, Ozturk K, Carter H.

Wiley Interdiscip Rev Syst Biol Med. 2019 May;11(3):e1443. doi: 10.1002/wsbm.1443. Epub 2018 Dec 12. Review.


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

Capriotti E, Fariselli P.

Nucleic Acids Res. 2017 Jul 3;45(W1):W247-W252. doi: 10.1093/nar/gkx369.


Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.

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.

Hum Mutat. 2017 Sep;38(9):1042-1050. doi: 10.1002/humu.23235. Epub 2017 May 16.


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

Khass M, Blackburn T, Burrows PD, Walter MR, Capriotti E, Schroeder HW Jr.

Sci Immunol. 2016 Jul 14;1(1). pii: aaf6628. doi: 10.1126/sciimmunol.aaf6628.


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

Capriotti E, Martelli PL, Fariselli P, Casadio R.

Hum Mutat. 2017 Sep;38(9):1064-1071. doi: 10.1002/humu.23179. Epub 2017 May 2.


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

Bromberg Y, Capriotti E, Carter H.

BMC Genomics. 2016 Jun 23;17 Suppl 2:425. doi: 10.1186/s12864-016-2721-3. No abstract available.


Computational methods and resources for the interpretation of genomic variants in cancer.

Tian R, Basu MK, Capriotti E.

BMC Genomics. 2015;16 Suppl 8:S7. doi: 10.1186/1471-2164-16-S8-S7. Epub 2015 Jun 18. Review.


VarI-SIG 2014--From SNPs to variants: interpreting different types of genetic variants.

Bromberg Y, Capriotti E.

BMC Genomics. 2015;16 Suppl 8:I1. doi: 10.1186/1471-2164-16-S8-I1. Epub 2015 Jun 18. No abstract available.


WALTZ-DB: a benchmark database of amyloidogenic hexapeptides.

Beerten J, Van Durme J, Gallardo R, Capriotti E, Serpell L, Rousseau F, Schymkowitz J.

Bioinformatics. 2015 May 15;31(10):1698-700. doi: 10.1093/bioinformatics/btv027. Epub 2015 Jan 18.


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

Tian R, Basu MK, Capriotti E.

Bioinformatics. 2014 Sep 1;30(17):i572-8. doi: 10.1093/bioinformatics/btu466.


In silico comparative characterization of pharmacogenomic missense variants.

Li B, Seligman C, Thusberg J, Miller JL, Auer J, Whirl-Carrillo M, Capriotti E, Klein TE, Mooney SD.

BMC Genomics. 2014;15 Suppl 4:S4. doi: 10.1186/1471-2164-15-S4-S4. Epub 2014 May 20.


SNP-SIG 2013: from coding to non-coding--new approaches for genomic variant interpretation.

Bromberg Y, Capriotti E.

BMC Genomics. 2014;15 Suppl 4:S1. doi: 10.1186/1471-2164-15-S4-S1. Epub 2014 May 20. No abstract available.


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

Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, Notredame C.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60. doi: 10.1093/nar/gku459. Epub 2014 Jun 27.


Computational and theoretical methods for protein folding.

Compiani M, Capriotti E.

Biochemistry. 2013 Dec 3;52(48):8601-24. doi: 10.1021/bi4001529. Epub 2013 Nov 21. Review.


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

Norambuena T, Cares JF, Capriotti E, Melo F.

Bioinformatics. 2013 Oct 15;29(20):2649-50. doi: 10.1093/bioinformatics/btt441. Epub 2013 Aug 7.


Collective judgment predicts disease-associated single nucleotide variants.

Capriotti E, Altman RB, Bromberg Y.

BMC Genomics. 2013;14 Suppl 3:S2. doi: 10.1186/1471-2164-14-S3-S2. Epub 2013 May 28.


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

Bromberg Y, Capriotti E.

BMC Genomics. 2013;14 Suppl 3:S1. doi: 10.1186/1471-2164-14-S3-S1. Epub 2013 May 28. No abstract available.


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

Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R.

BMC Genomics. 2013;14 Suppl 3:S6. doi: 10.1186/1471-2164-14-S3-S6. Epub 2013 May 28.


Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package.

Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C.

Bioinformatics. 2013 May 1;29(9):1112-9. doi: 10.1093/bioinformatics/btt096. Epub 2013 Feb 28.


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

Bromberg Y, Capriotti E.

BMC Genomics. 2012 Jun 18;13 Suppl 4:S1. doi: 10.1186/1471-2164-13-S4-S1. No abstract available.


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

Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB.

J R Soc Interface. 2012 Jul 7;9(72):1409-37. doi: 10.1098/rsif.2011.0843. Epub 2012 May 2. Review.


Bioinformatics for personal genome interpretation.

Capriotti E, Nehrt NL, Kann MG, Bromberg Y.

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


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

Capriotti E, Altman RB.

BMC Bioinformatics. 2011;12 Suppl 4:S3. doi: 10.1186/1471-2105-12-S4-S3. Epub 2011 Jul 5.


Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.

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.

PLoS Genet. 2011 Sep;7(9):e1002280. doi: 10.1371/journal.pgen.1002280. Epub 2011 Sep 15.


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

Capriotti E, Altman RB.

Genomics. 2011 Oct;98(4):310-7. doi: 10.1016/j.ygeno.2011.06.010. Epub 2011 Jul 7.


Bioinformatics challenges for personalized medicine.

Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB.

Bioinformatics. 2011 Jul 1;27(13):1741-8. doi: 10.1093/bioinformatics/btr295. Epub 2011 May 19. Erratum in: Bioinformatics. 2011 Aug 15;27(16):2323.


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

Liu T, Tang GW, Capriotti E.

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


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

Capriotti E, Norambuena T, Marti-Renom MA, Melo F.

Bioinformatics. 2011 Apr 15;27(8):1086-93. doi: 10.1093/bioinformatics/btr093. Epub 2011 Feb 23.


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

Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA.

Nat Struct Mol Biol. 2011 Jan;18(1):107-14. doi: 10.1038/nsmb.1936. Epub 2010 Dec 5.


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

Capriotti E, Marti-Renom MA.

BMC Bioinformatics. 2010 Jun 15;11:322. doi: 10.1186/1471-2105-11-322.


Monochromatic excimer light 308 nm in monotherapy and combined with topical khellin 4% in the treatment of vitiligo: a controlled study.

Saraceno R, Nisticò SP, Capriotti E, Chimenti S.

Dermatol Ther. 2009 Jul-Aug;22(4):391-4. doi: 10.1111/j.1529-8019.2009.01252.x.


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

Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R.

Hum Mutat. 2009 Aug;30(8):1237-44. doi: 10.1002/humu.21047.


SARA: a server for function annotation of RNA structures.

Capriotti E, Marti-Renom MA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W260-5. doi: 10.1093/nar/gkp433. Epub 2009 May 29.


RNA structure alignment by a unit-vector approach.

Capriotti E, Marti-Renom MA.

Bioinformatics. 2008 Aug 15;24(16):i112-8. doi: 10.1093/bioinformatics/btn288.


Expression of T-plastin, FoxP3 and other tumor-associated markers by leukemic T-cells of cutaneous T-cell lymphoma.

Capriotti E, Vonderheid EC, Thoburn CJ, Wasik MA, Bahler DW, Hess AD.

Leuk Lymphoma. 2008 Jun;49(6):1190-201. doi: 10.1080/10428190802064917.


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

Capriotti E, Fariselli P, Rossi I, Casadio R.

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S6. doi: 10.1186/1471-2105-9-S2-S6.


Efficacy of monochromatic excimer light (308 nm) in the treatment of atopic dermatitis in adults and children.

Nisticò SP, Saraceno R, Capriotti E, Felice CD, Chimenti S.

Photomed Laser Surg. 2008 Feb;26(1):14-8. doi: 10.1089/pho.2007.2116.


Monochromatic excimer light (308 nm) in the treatment of prurigo nodularis.

Saraceno R, Nisticò SP, Capriotti E, de Felice C, Rhodes LE, Chimenti S.

Photodermatol Photoimmunol Photomed. 2008 Feb;24(1):43-5. doi: 10.1111/j.1600-0781.2008.00318.x.


The pros and cons of predicting protein contact maps.

Bartoli L, Capriotti E, Fariselli P, Martelli PL, Casadio R.

Methods Mol Biol. 2008;413:199-217. Review.


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