Publications from the Unit

2016

• Chung HR, Xu C, Fuchs A, Mund A, Lange M, Staege H, Schubert T, Bian C, Dunkel I, Eberharter A, Regnard C, Klinker H, Meierhofer D, Cozzuto L, Winterpacht A, Di Croce L, Min J, Will H, Kinkley S. PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3. Elife. 2016 May 25;5
• Antonio Figueras, Diego Robledo, André Corvelo, Miguel Hermida, Patricia Pereiro, Juan A. Rubiolo, Jèssica Gómez-Garrido, Laia Carreté, Xabier Bello, Marta Gut, Ivo Glynne Gut, Marina Marcet-Houben, Gabriel Forn-Cuní, Beatriz Galán, José Luis García, José Luis Abal-Fabeiro, Belen G. Pardo, Xoana Taboada, Carlos Fernández, Anna Vlasova, Antonio Hermoso-Pulido, Roderic Guigó, José Antonio Álvarez-Dios, Antonio Gómez-Tato, Ana Viñas, Xulio Maside, Toni Gabaldón, Beatriz Novoa, Carmen Bouza, Tyler Alioto, and Paulino Martínez. Whole Genome Sequencing of Turbot (Scophthalmus maximus; Pleuronectiformes): A Fish Adapted to Demersal Life. DNA Res first published online March 6, 2016
• Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ Jr, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol. 2016 Feb 25;17(1):32.
• Eckert D, Andrée N, Razanau A, Zock-Emmenthal S, Lützelberger M, Plath S, Schmidt H, Guerra-Moreno A, Cozzuto L, Ayté J, Käufer NF. Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation. PLoS Genet. 2016 Jan 5;12(1):e1005768.

2015

• Lluch-Senar M, Cozzuto L, Cano J, Delgado J, Llórens-Rico V, Pereyre S, Bebear C, Serrano L. Comparative "-omics" in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors. PLoS One. 2015 Sep 3;10(9):e0137354.

2014

• Cicin-Sain D*, Hermoso Pulido A*, Crombach A*, Wotton KR, Jiménez-Guri E, Taly JF, Roma G, Jaeger J. SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos. Nucleic Acids Res. 2014 Nov 17
• Wodke J, Alibés A, Cozzuto L, Hermoso A, Yus E, Lluch-Senar M, Serrano L and Roma G. MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. Nucl. Acids Res. 2014 First published online: November 6, 2014
• Aloia L, Di Stefano B, Sessa A, Morey L, Santanach A, Gutierrez A, Cozzuto L, Benitah SA, Graf T, Broccoli V, Di Croce L. Zrf1 is required to establish and maintain neural progenitor identity. Genes Dev. 2014 Jan 15;28(2):182-97

2013

• Simboeck E, Gutierrez A, Cozzuto L, Beringer M, Caizzi L, M Keyes W, Di Croce L. DPY30 regulates pathways in cellular senescence through ID protein expression. EMBO J. 2013 Jul 19.
• Jiménez-Guri E*, Huerta-Cepas J*, Cozzuto L *, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J. Comparative transcriptomics of early dipteran development. BMC Genomics. 2013 Feb 24;14(1):123. (* joint first authors)

2012

• Morey L, Aloia L, Cozzuto L, Benitah SA, Di Croce L. RYBP and Cbx7 Define Specific Biological Functions of Polycomb Complexes in Mouse Embryonic Stem Cells. Cell Rep. 2012 Dec 26
• Sanseverino W, Hermoso A, D'Alessandro R, Vlasova A, Andolfo G, Frusciante L, Lowy E, Roma G, Ercolano MR. PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. Nucleic Acids Res. 2012 Nov 17.
• Doles J, Storer M, Cozzuto L, Roma G, Keyes WM. Age-associated inflammation inhibits epidermal stem cell function. Genes Dev. 2012 Sep 12
• Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutiérrez S, Blanca J, Cañizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodríguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Melé M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Picó B, Gabaldón T, Roma G, Guigó R, Casacuberta JM, Arús P, Puigdomènech P. The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A. 2012 Jul 2.
• Morey L, Pascual G, Cozzuto L, Roma G, Wutz A, Benitah SA, Di Croce L. Nonoverlapping Functions of the Polycomb Group Cbx Family of Proteins in Embryonic Stem Cells. Cell Stem Cell. 2012 Jan 6;10(1):47-62.

2011

• Mancuso FM, Montfort M, Carreras A, Alibes A, Roma G. HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data. BMC Research Notes 2011 Dec 19; 4:546.
• Mihailovich M, Wurth L, Zambelli F, Abaza I, Militti C, Mancuso FM, Roma G, Pavesi G, Gebauer F. Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. RNA. 2011 Nov 18;.
• Uribesalgo I, Buschbeck M, Gutiérrez A, Teichmann S, Demajo S, Kuebler B, Nomdedéu JF, Martín-Caballero J, Roma G, Benitah SA, Di Croce L. E-box-independent regulation of transcription and differentiation by MYC. Nat Cell Biol. 2011 Oct 23;13(12):1443-9. doi: 10.1038/ncb2355.
• Luis NM, Morey L, Mejetta S, Pascual G, Janich P, Kuebler B, Cozzuto L, Roma G, Nascimento E, Frye M, Di Croce L, Benitah SA. Regulation of Human Epidermal Stem Cell Proliferation and Senescence Requires Polycomb- Dependent and -Independent Functions of Cbx4. Cell Stem Cell. 2011 Sep 2;9(3):233-46. (Erratum in Cell Stem Cell, Volume 9, Issue 5, 486, 4 November 2011)
• Hummel M, Bonnin S, Lowy E, Roma G. TEQC: an R-package for quality control in target capture experiments. Bioinformatics. 2011 May 1;27(9):1316-7.

2010

• Hermoso A, Bertero M, Speroni S, Alloza M, Roma G. Lab Service Wiki: a wiki-based data management solution for laboratories production services. SemWiki2010 - Conference Proceedings. 2010 May.
• Sanseverino W*, Roma G*, De Simone M, Faino L, Melito S, Stupka E, Frusciante L, Ercolano MR. “PRGdb: a bioinformatics platform for plant resistance gene analysis.” Nucleic Acids Res. 2010 Jan;38(Database issue):D814-21. (* joint first authors)
• Romito A, Lonardo E, Roma G, Minchiotti G, Ballabio A and Cobellis G, “Lack of Sik1 in Mouse Embryonic Stem Cells Impairs Cardiomyogenesis by Down-Regulating the Cyclin-Dependent Kinase Inhibitor p57kip2.” PLoS One. 2010 Feb 3;5(2):e9029.