Publications

Dmitrijeva M; Ossowski S; Serrano L; Schaefer MH, 2018. Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates.  Nucleic Acids Res.

Blanco JD; Radusky L; Climente-González H; Serrano L, 2018. FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1).  Nucleic Acids Res 46(8):3852-3863

Carleton LA; Chakravarthy R; van der Sloot AM; Mnich K; Serrano L; Samali A; Gorman AM, 2018. Generation of rationally-designed nerve growth factor (NGF) variants with receptor specificity.  Biochem Biophys Res Commun 495(1):700-705

Zapata L; Pich O; Serrano L; Kondrashov FA; Ossowski S; Schaefer MH, 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.  Genome Biol 19(1):67

Miravet-Verde S; Lloréns-Rico V; Serrano L, 2017. Alternative transcriptional regulation in genome-reduced bacteria.  Curr Opin Microbiol 39:89-95

Yus E; Yang JS; Sogues A; Serrano L, 2017. A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants.  Nat Commun 8(1):368

Stojanovski K; Ferrar T; Benisty H; Uschner F; Delgado J; Jimenez J; Solé C; de Nadal E; Klipp E; Posas F; Serrano L; Kiel C, 2017. Interaction Dynamics Determine Signaling and Output Pathway Responses.  Cell Rep 19(1):136-149

Crépieux P; Poupon A; Langonné-Gallay N; Reiter E; Delgado J; Schaefer MH; Bourquard T; Serrano L; Kiel C, 2017. A Comprehensive View of the β-Arrestinome.  Front Endocrinol (Lausanne) 8:32

Trussart M; Yus E; Martinez S; Baù D; Tahara YO; Pengo T; Widjaja M; Kretschmer S; Swoger J; Djordjevic S; Turnbull L; Whitchurch C; Miyata M; Marti-Renom MA; Lluch-Senar M; Serrano L, 2017. Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae.  Nat Commun 8:14665

Kiel C; Lastrucci C; Luthert PJ; Serrano L, 2017. Simple and complex retinal dystrophies are associated with profoundly different disease networks.  Sci Rep 7:41835

Kiel C; Benisty H; Lloréns-Rico V; Serrano L, 2016. The yin-yang of kinase activation and unfolding explains the peculiarity of Val600 in the activation segment of BRAF.  Elife 5:e12814

O'Leary L; van der Sloot AM; Reis CR; Deegan S; Ryan AE; Dhami SP; Murillo LS; Cool RH; Correa de Sampaio P; Thompson K; Murphy G; Quax WJ; Serrano L; Samali A; Szegezdi E, 2016. Decoy receptors block TRAIL sensitivity at a supracellular level: the role of stromal cells in controlling tumour TRAIL sensitivity.  Oncogene 35(10):1261-70

Lluch-Senar M; Mancuso FM; Climente-González H; Peña-Paz MI; Sabido E; Serrano L, 2016. Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome.  Proteomics 16(4):554-63

Chen WH; van Noort V; Lluch-Senar M; Hennrich ML; Wodke JA; Yus E; Alibés A; Roma G; Mende DR; Pesavento C; Typas A; Gavin AC; Serrano L; Bork P, 2016. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.  Nucleic Acids Res 44(3):1192-202

Schaefer MH; Serrano L, 2016. Cell type-specific properties and environment shape tissue specificity of cancer genes.  Sci Rep 6:20707

Lloréns-Rico V; Cano J; Kamminga T; Gil R; Latorre A; Chen WH; Bork P; Glass JI; Serrano L; Lluch-Senar M, 2016. Bacterial antisense RNAs are mainly the product of transcriptional noise.  Sci Adv 2(3):e1501363

Junier I; Unal EB; Yus E; Lloréns-Rico V; Serrano L, 2016. Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium.  Cell Syst 2(6):391-401

Cramer D; Serrano L; Schaefer MH, 2016. A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference.  Elife 5.

Beltran-Sastre V; Benisty H; Burnier J; Berger I; Serrano L; Kiel C, 2015. Tuneable endogenous mammalian target complementation via multiplexed plasmid-based recombineering.  Sci Rep 5:17432

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

Schaefer MH; Serrano L; Andrade-Navarro MA, 2015. Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types.  Front Genet 6:260

Verschueren E; Spiess M; Gkourtsa A; Avula T; Landgraf C; Mancilla VT; Huber A; Volkmer R; Winsor B; Serrano L; Hochstenbach F; Distel B, 2015. Evolution of the SH3 Domain Specificity Landscape in Yeasts.  PLoS One 10(6):e0129229

Toufighi K; Yang JS; Luis NM; Aznar Benitah S; Lehner B; Serrano L; Kiel C, 2015. Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses.  PLoS Comput Biol 11(5):e1004256

Trussart M; Serra F; Baù D; Junier I; Serrano L; Marti-Renom MA, 2015. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains.  Nucleic Acids Res 43(7):3465-77

Lloréns-Rico V; Lluch-Senar M; Serrano L, 2015. Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae.  Nucleic Acids Res 43(7):3442-53

Lluch-Senar M; Delgado J; Chen WH; Lloréns-Rico V; O'Reilly FJ; Wodke JA; Unal EB; Yus E; Martínez S; Nichols RJ; Ferrar T; Vivancos A; Schmeisky A; Stülke J; van Noort V; Gavin AC; Bork P; Serrano L, 2015. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.  Mol Syst Biol 11(1):780

Wodke JA; Alibés A; Cozzuto L; Hermoso A; Yus E; Lluch-Senar M; Serrano L; Roma G, 2015. MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae.  Nucleic Acids Res 43(Database issue):D618-23

Hasenhindl C; Lai B; Delgado J; Traxlmayr MW; Stadlmayr G; Rüker F; Serrano L; Oostenbrink C; Obinger C, 2014. Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.  Biochim Biophys Acta 1844(9):1530-40

Kiel C; Ebhardt HA; Burnier J; Portugal C; Sabidó E; Zimmermann T; Aebersold R; Serrano L, 2014. Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins.  J Proteome Res 13(1):300-13

Lloréns-Rico V; Serrano L; Lluch-Senar M, 2014. Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?  BMC Genomics 15:633

Kiel C; Serrano L, 2014. Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations.  Mol Syst Biol 10:727

Yang JS; Sabidó E; Serrano L; Kiel C, 2014. TAPAS: tools to assist the targeted protein quantification of human alternative splice variants.  Bioinformatics 30(20):2989-90

Schaefer MH; Yang JS; Serrano L; Kiel C, 2014. Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways.  PLoS Comput Biol 10(6):e1003659

Paetzold B; Carolis C; Ferrar T; Serrano L; Lluch-Senar M, 2013. In situ overlap and sequence synthesis during DNA assembly.  ACS Synth Biol 2(12):750-5

Maier T; Marcos J; Wodke JA; Paetzold B; Liebeke M; Gutiérrez-Gallego R; Serrano L, 2013. Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae.  Mol Biosyst 9(7):1743-55

Verschueren E; Vanhee P; Rousseau F; Schymkowitz J; Serrano L, 2013. Protein-peptide complex prediction through fragment interaction patterns.  Structure 21(5):789-97

Wodke JA; Puchałka J; Lluch-Senar M; Marcos J; Yus E; Godinho M; Gutiérrez-Gallego R; dos Santos VA; Serrano L; Klipp E; Maier T, 2013. Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling.  Mol Syst Biol 9:653

Lluch-Senar M; Luong K; Lloréns-Rico V; Delgado J; Fang G; Spittle K; Clark TA; Schadt E; Turner SW; Korlach J; Serrano L, 2013. Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution.  PLoS Genet 9(1):e1003191

Magis C; van der Sloot AM; Serrano L; Notredame C, 2012. An improved understanding of TNFL/TNFR interactions using structure-based classifications.  Trends Biochem Sci 37(9):353-63

Kiel C; Serrano L, 2012. Challenges ahead in signal transduction: MAPK as an example.  Curr Opin Biotechnol 23(3):305-14

Yang JS; Campagna A; Delgado J; Vanhee P; Serrano L; Kiel C, 2012. SAPIN: a framework for the structural analysis of protein interaction networks.  Bioinformatics 28(22):2998-9

Kiel C; Serrano L, 2012. Structural data in synthetic biology approaches for studying general design principles of cellular signaling networks.  Structure 20(11):1806-13

Kiel C; Vogt A; Campagna A; Chatr-aryamontri A; Swiatek-de Lange M; Beer M; Bolz S; Mack AF; Kinkl N; Cesareni G; Serrano L; Ueffing M, 2011. Structural and functional protein network analyses predict novel signaling functions for rhodopsin.  Mol Syst Biol 7:551

Güell M; Yus E; Lluch-Senar M; Serrano L, 2011. Bacterial transcriptomics: what is beyond the RNA horiz-ome?  Nat Rev Microbiol 9(9):658-69

Maier T; Schmidt A; Güell M; Kühner S; Gavin AC; Aebersold R; Serrano L, 2011. Quantification of mRNA and protein and integration with protein turnover in a bacterium.  Mol Syst Biol 7:511

Verschueren E; Vanhee P; van der Sloot AM; Serrano L; Rousseau F; Schymkowitz J, 2011. Protein design with fragment databases.  Curr Opin Struct Biol 21(4):452-9

Vivancos AP; Güell M; Dohm JC; Serrano L; Himmelbauer H, 2010. Strand-specific deep sequencing of the transcriptome.  Genome Res 20(7):989-99

Grünberg R; Serrano L, 2010. Strategies for protein synthetic biology.  Nucleic Acids Res 38(8):2663-75

Grünberg R; Ferrar TS; van der Sloot AM; Constante M; Serrano L, 2010. Building blocks for protein interaction devices.  Nucleic Acids Res 38(8):2645-62

Güell M; van Noort V; Yus E; Chen WH; Leigh-Bell J; Michalodimitrakis K; Yamada T; Arumugam M; Doerks T; Kühner S; Rode M; Suyama M; Schmidt S; Gavin AC; Bork P; Serrano L, 2009. Transcriptome complexity in a genome-reduced bacterium.  Science 326(5957):1268-71

Yus E; Maier T; Michalodimitrakis K; van Noort V; Yamada T; Chen WH; Wodke JA; Güell M; Martínez S; Bourgeois R; Kühner S; Raineri E; Letunic I; Kalinina OV; Rode M; Herrmann R; Gutiérrez-Gallego R; Russell RB; Gavin AC; Bork P; Serrano L, 2009. Impact of genome reduction on bacterial metabolism and its regulation.  Science 326(5957):1263-8

Tur V; van der Sloot AM; Reis CR; Szegezdi E; Cool RH; Samali A; Serrano L; Quax WJ, 2008. DR4-selective tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) variants obtained by structure-based design.  J Biol Chem 283(29):20560-8

Isalan M; Lemerle C; Michalodimitrakis K; Horn C; Beltrao P; Raineri E; Garriga-Canut M; Serrano L, 2008. Evolvability and hierarchy in rewired bacterial gene networks.  Nature 452(7189):840-5

Santori MI; Gonzalez C; Serrano L; Isalan M, 2006. Localized transfection with magnetic beads coated with PCR products and other nucleic acids.  Nat Protoc 1(2):526-31

Publication list retrieved from NCBI using ImpactPubs

.