Publications
2014
Data integration in the era of omics: current and future challenges
David Gomez-Cabrero, Imad Abugessaisa, Dieter Maier, Andrew Teschendorff, Matthias Merkenschlager, Andreas Gisel, Esteban Ballestar, Erik Bongcam-Rudloff, Ana Conesa, Jesper Tegnér
BMC Systems Biology 2014, 8(Suppl 2):I1
2013
2012
Viroids: how to infect a host and cause disease without encoding proteins.
Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, Di Serio F.
Biochimie. 2012 Jul;94(7):1474-80.
PMID: 22738729
Navarro, B Gisel, A Rodio, ME Degado, S Flores, R Di Serio, F
Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide degradation of a host mRNA as predicted by RNA silencing.
Plant J Feb 14 2012
PMID: 22332758
2011
Attwood, T.K Gisel, A Eriksson, N-E and Bongcam-Rudloff, E
Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective.
Bioinformatics, edited by: Dr. Mahmood Akhavan Mahdavi, INTECH
ISBN 978-953-307-282-1
Tulipano A, Marangi C, Angelini L, Donvito G, Cuscela G, Maggi GP, Gisel A
GRID distribution supports clustering validation of large mixed microarray data sets.
EMBnet.journal 17 (1): 18-25
Ruiz-Ruiz S, Navarro B, Gisel A, Peña L, Navarro L, Moreno P, Di Serio F, Flores R
Citrus tristeza virus infection induces the accumulation of viral small RNAs (21- 24-nt) mapping preferentially at the 3’-terminal region of the genomic RNA and affects the host small RNA profile.
Plant Mol Biol. 2011 Feb 15
PMID: 21327514
2010
Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine.
Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A, Moxon S, Dalmay T, Bisztray G, Burgyan J.
Virology. 2010 Dec 5;408(1):49-56. Epub 2010 Sep 26.
RNA-dependent RNA polymerase 6 delays accumulation and precludes meristem invasion of a viroid that replicates in the nucleus.
Di Serio F, Martínez de Alba AE, Navarro B, Gisel A, Flores R.
J Virol. 2010 Mar;84(5):2477-89. Epub 2009 Dec 16.
PMID: 20015979
2009
PDB_REDO: automated re-refinement of X-ray structure models in the PDB.
Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G.
J Appl Crystallogr. 2009 Jun 1;42(Pt 3):376-384. Epub 2009 Apr 3.
PMID: 22477769
Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction.
Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyán J.
PLoS One. 2009 Nov 5;4(11):e7686.
PMID: 19890399
Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis.
Di Serio F, Gisel A, Navarro B, Delgado S, Martínez de Alba AE, Donvito G, Flores R.
PLoS One. 2009 Oct 21;4(10):e7539.
PMID: 19847296
Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining.
Turi A, Loglisci C, Salvemini E, Grillo G, Malerba D, D'Elia D.
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S25.
PMID: 19534751
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community.
D'Elia D, Gisel A, Eriksson NE, Kossida S, Mattila K, Klucar L, Bongcam-Rudloff E.
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S1.
PMC: 2697632
2007
Gene analogue finder: a GRID solution for finding functionally analogous gene products.
Tulipano A, Donvito G, Licciulli F, Maggi G, Gisel A.
BMC Bioinformatics. 2007 Sep 3;8:329.
PMID: 17767718
p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data.
Sbisà E, Catalano D, Grillo G, Licciulli F, Turi A, Liuni S, Pesole G, De Grassi A, Caratozzolo MF, D'Erchia AM, Navarro B, Tullo A, Saccone C, Gisel A.
BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S20.
PMID: 17430565
2006
The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae.
D'Elia D, Catalano D, Licciulli F, Turi A, Tripoli G, Porcelli D, Saccone C, Caggese C.
Mitochondrion. 2006 Oct;6(5):252-7. Epub 2006 Jul 21.
PMID: 16982216
The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae.
D'Elia D, Catalano D, Licciulli F, Turi A, Tripoli G, Porcelli D, Saccone C, Caggese C.
Mitochondrion. 2006 Oct;6(5):252-7. Epub 2006 Jul 21.
PMID: 16982216
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.
Catalano D, Licciulli F, Turi A, Grillo G, Saccone C, D'Elia D.
BMC Bioinformatics. 2006 Jan 24;7:36.
PMID: 16433928
2005
Evolution of nuclearly encoded mitochondrial genes in Metazoa.
De Grassi A, Caggese C, D'Elia D, Lanave C, Pesole G, Saccone C.
Gene. 2005 Jul 18;354:181-8.
PMID: 15975737
Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae.
Tripoli G, D'Elia D, Barsanti P, Caggese C.
Genome Biol. 2005;6(2):R11. Epub 2005 Jan 31.
PMID: 15693940
2004
DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions.
Gisel A, Panetta M, Grillo G, Licciulli VF, Liuni S, Saccone C, Pesole G.
Bioinformatics. 2004 Dec 12;20(18):3676-9. Epub 2004 Jul 15.
PMID: 15256403
2002
Leaf-to-shoot apex movement of symplastic tracer is restricted coincident with flowering in Arabidopsis.
Gisel A, Hempel FD, Barella S, Zambryski P.
Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1713-7. Epub 2002 Jan 29.
PMID: 11818578
2000
Nuclear localization of turnip crinkle virus movement protein p8.
Cohen Y, Qu F, Gisel A, Morris TJ, Zambryski PC.
Virology. 2000 Aug 1;273(2):276-85.
PMID: 10915598
Cell-to-cell and systemic movement of recombinant green fluorescent protein-tagged turnip crinkle viruses.
Cohen Y, Gisel A, Zambryski PC.
Virology. 2000 Aug 1;273(2):258-66.
PMID: 10915596
Update of KEYnet: a gene and protein names database for biosequences functional organisation.
Catalano D, Licciulli F, D'Elia D, Attimonelli M.
Nucleic Acids Res. 2000 Jan 1;28(1):372-3.
PMID: 10592277
MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status.
Attimonelli M, Altamura N, Benne R, Brennicke A, Cooper JM, D'Elia D, Montalvo A, Pinto B, De Robertis M, Golik P, Knoop V, Lanave C, Lazowska J, Licciulli F, Malladi BS, Memeo F, Monnerot M, Pasimeni R, Pilbout S, Schapira AH, Sloof P, Saccone C.
Nucleic Acids Res. 2000 Jan 1;28(1):148-52.
PMID: 10592207
1999
Temporal and spatial regulation of symplastic trafficking during development in Arabidopsis thaliana apices.
Gisel A, Barella S, Hempel FD, Zambryski PC.
Development. 1999 May;126(9):1879-89.
PMID: 10101122
KEYnet: a keywords database for biosequences functional organization.
Licciulli F, Catalano D, D'Elia D, Lorusso V, Attimonelli M.
Nucleic Acids Res. 1999 Jan 1;27(1):365-7.
PMID: 9847230
Update of the Human MitBASE database.
Attimonelli M, Cooper JM, D'Elia D, de Montalvo A, De Robertis M, Lehväslaiho H, Malladi SB, Memeo F, Stevens K, Schapira AH, Saccone C.
Nucleic Acids Res. 1999 Jan 1;27(1):143-6.
PMID: 9847160
MitBASE: a comprehensive and integrated mitochondrial DNA database.
Attimonelli M, Altamura N, Benne R, Boyen C, Brennicke A, Carone A, Cooper JM, D'Elia D, de Montalvo A, de Pinto B, De Robertis M, Golik P, Grienenberger JM, Knoop V, Lanave C, Lazowska J, Lemagnen A, Malladi BS, Memeo F, Monnerot M, Pilbout S, Schapira AH, Sloof P, Slonimski P, Saccone C, et al.
Nucleic Acids Res. 1999 Jan 1;27(1):128-33.
PMID: 9847157
1997
Chitin oligosaccharides can induce cortical cell division in roots of Vicia sativa when delivered by ballistic microtargeting.
Schlaman HR, Gisel AA, Quaedvlieg NE, Bloemberg GV, Lugtenberg BJ, Kijne JW, Potrykus I, Spaink HP, Sautter C.
Development. 1997 Dec;124(23):4887-95.
PMID: 9428425
In organello footprinting analysis of rat mitochondrial DNA: protein interaction upstream of the Ori-L.
Cingolani G, Capaccio L, D'Elia D, Gadaleta G.
Biochem Biophys Res Commun. 1997 Feb 24;231(3):856-60.
PMID: 9070910
1996
Isolation of a 25-kDa protein binding to a curved DNA upstream the origin of the L strand replication in the rat mitochondrial genome.
Gadaleta G, D'Elia D, Capaccio L, Saccone C, Pepe G.
J Biol Chem. 1996 Jun 7;271(23):13537-41.
PMID: 8662779
In vivo observation of large foreign DNA molecules in host plant cells.
Gisel A, Rothen B, Iglesias VA, Potrykus I, Sautter C.
Eur J Cell Biol. 1996 Apr;69(4):368-72.
PMID: 8741219
1995
A 67-kDa protein binding to the curved DNA in the main regulatory region of the rat mitochondrial genome.
Gadaleta G, D'Elia D, Saccone C, Pepe G.
Gene. 1995 Jul 28;160(2):229-34.
PMID: 7642100