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Items: 1 to 20 of 211

1.

BUSCA: an integrative web server to predict subcellular localization of proteins.

Savojardo C, Martelli PL, Fariselli P, Profiti G, Casadio R.

Nucleic Acids Res. 2018 Jul 2;46(W1):W459-W466. doi: 10.1093/nar/gky320.

2.

Mutant MYO1F alters the mitochondrial network and induces tumor proliferation in thyroid cancer.

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.

Int J Cancer. 2018 Apr 19. doi: 10.1002/ijc.31548. [Epub ahead of print]

PMID:
29672841
3.

DeepSig: deep learning improves signal peptide detection in proteins.

Savojardo C, Martelli PL, Fariselli P, Casadio R.

Bioinformatics. 2018 May 15;34(10):1690-1696. doi: 10.1093/bioinformatics/btx818.

4.

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes.

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

BMC Genomics. 2017 Aug 11;18(Suppl 5):554. doi: 10.1186/s12864-017-3911-3.

5.

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

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.

Hum Mutat. 2017 Sep;38(9):1182-1192. doi: 10.1002/humu.23280. Epub 2017 Jul 7.

6.

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

Profiti G, Martelli PL, Casadio R.

Nucleic Acids Res. 2017 Jul 3;45(W1):W285-W290. doi: 10.1093/nar/gkx330.

7.

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.

8.

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4.

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.

Hum Mutat. 2017 Sep;38(9):1123-1131. doi: 10.1002/humu.23222. Epub 2017 May 2.

9.

BRCA1 p.His1673del is a pathogenic mutation associated with a predominant ovarian cancer phenotype.

Zuntini R, Cortesi L, Calistri D, Pippucci T, Martelli PL, Casadio R, Capizzi E, Santini D, Miccoli S, Medici V, Danesi R, Marchi I, Zampiga V, Fiorentino M, Ferrari S, Turchetti D.

Oncotarget. 2017 Apr 4;8(14):22640-22648. doi: 10.18632/oncotarget.15151.

10.

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments.

Savojardo C, Martelli PL, Fariselli P, Casadio R.

Bioinformatics. 2017 Feb 1;33(3):347-353. doi: 10.1093/bioinformatics/btw656.

11.

ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.

Savojardo C, Fariselli P, Martelli PL, Casadio R.

Bioinformatics. 2017 Jun 1;33(11):1656-1663. doi: 10.1093/bioinformatics/btx044.

PMID:
28130235
12.

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.

13.

Erratum to: Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human.

Linguiti G, Antonacci R, Tasco G, Grande F, Casadio R, Massari S, Castelli V, Consiglio A, Lefranc MP, Ciccarese S.

BMC Genomics. 2016 Oct 5;17(1):778. No abstract available.

14.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, 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 CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, 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 SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

15.

Ancient pathogen-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations.

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.

Genes Nutr. 2016 May 23;11:15. doi: 10.1186/s12263-016-0532-4. eCollection 2016.

16.

Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human.

Linguiti G, Antonacci R, Tasco G, Grande F, Casadio R, Massari S, Castelli V, Consiglio A, Lefranc MP, Ciccarese S.

BMC Genomics. 2016 Aug 15;17(1):634. doi: 10.1186/s12864-016-2841-9. Erratum in: BMC Genomics. 2016 Oct 5;17 (1):778.

17.

NET-GE: a web-server for NETwork-based human gene enrichment.

Bovo S, Di Lena P, Martelli PL, Fariselli P, Casadio R.

Bioinformatics. 2016 Nov 15;32(22):3489-3491. Epub 2016 Aug 2.

PMID:
27485441
18.

Large scale analysis of protein stability in OMIM disease related human protein variants.

Martelli PL, Fariselli P, Savojardo C, Babbi G, Aggazio F, Casadio R.

BMC Genomics. 2016 Jun 23;17 Suppl 2:397. doi: 10.1186/s12864-016-2726-y.

19.

INPS-MD: a web server to predict stability of protein variants from sequence and structure.

Savojardo C, Fariselli P, Martelli PL, Casadio R.

Bioinformatics. 2016 Aug 15;32(16):2542-4. doi: 10.1093/bioinformatics/btw192. Epub 2016 Apr 10.

PMID:
27153629
20.

Tools and data services registry: a community effort to document bioinformatics resources.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3.

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