• Fernández-Torras A, Duran-Frigola M, Aloy P. Encircling the regions of the pharmacogenomic landscape that determine drug response. Genome Med. 2019 Mar 26;11(1):17.
  • doi: 10.1186/s13073-019-0626-x.
  • PMID: 30914058
  •  
  • Merkel A, Fernández-Callejo M, Casals E, Marco-Sola S, Schuyler R, Gut IG, Heath SC. gemBS: high throughput processing for DNA methylation data from bisulfite sequencing. Bioinformatics. 2019 Mar 1;35(5):737-742.
  • doi:10.1093/bioinformatics/bty690.
  • PubMed PMID: 30137223.
  •  
  • Navío D, Rosell M, Aguirre J, de la Cruz X, Fernández-Recio J. Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. Int J Mol Sci. 2019 Mar 29;20(7). pii: E1583.
  • doi: 10.3390/ijms20071583.
  • PubMed PMID: 30934865
  •  
  • Sieracki ME, Poulton NJ, Jaillon O, Wincker P, de Vargas C, Rubinat-Ripoll L, Stepanauskas R, Logares R, Massana R. Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems. Sci Rep. 2019 Apr 15;9(1):6025.
  • doi: 10.1038/s41598-019-42487-1.
  • PubMed PMID: 30988337
  •  
  • Salvadores M, Mas-Ponte D, Supek F. Passenger mutations accurately classify human tumors. PLoS Comput Biol. 2019 Apr 15;15(4):e1006953.
  • doi: 10.1371/journal.pcbi.1006953. eCollection 2019 Apr.
  • PubMed PMID: 30986244
  •  
  • Gómez S, Garrido-Garcia A, Garcia-Gerique L, Lemos I, Suñol M, de Torres C, Kulis M, Pérez-Jaume S, Carcaboso ÁM, Luu B, Kieran MW, Jabado N, Kozlenkov A, Dracheva S, Ramaswamy V, Hovestadt V, Johann P, Jones DTW, Pfister SM, Morales La Madrid A, Cruz O, Taylor MD, Martin-Subero JI, Mora J, Lavarino C. A Novel Method for Rapid Molecular Subgrouping of Medulloblastoma. Clin Cancer Res. 2018 Mar 15;24(6):1355-1363.
  • doi: 10.1158/1078-0432.CCR-17-2243.
  • PubMed PMID: 29351917.
  •  
  • Palomo L, Fuster-Tormo F, Alvira D, Ademà V, Armengol MP, Gómez-Marzo P, de Haro N, Mallo M, Xicoy B, Zamora L, Solé F. Inspecting Targeted Deep Sequencing of Whole Genome Amplified DNA Versus Fresh DNA for Somatic Mutation Detection: A Genetic Study in Myelodysplastic Syndrome Patients. Biopreserv Biobank. 2017 Aug;15(4):360-365.
  • doi: 10.1089/bio.2016.0094.
  • PubMed PMID: 28586236.
  •  
  • Mangot JF, Logares R, Sánchez P, Latorre F, Seeleuthner Y, Mondy S, Sieracki ME, Jaillon O, Wincker P, Vargas C, Massana R. Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells. Sci
  • Rep. 2017 Jan 27;7:41498.
  • doi: 10.1038/srep41498.
  • PubMed PMID: 28128359
  •  
  • Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, Martinez X, Varela E, Sarrabayrouse G, Machiels K, Vermeire S, Sokol H, Guarner F, Manichanh C. A microbial signature for Crohn's disease. Gut. 2017 May;66(5):813-822.
  • doi: 10.1136/gutjnl-2016-313235. Epub 2017 Feb 7.
  • PubMed PMID: 28179361
  •  
  • Ruiz-Arenas C, González JR. Redundancy analysis allows improved detection of methylation changes in large genomic regions. BMC Bioinformatics. 2017 Dec 14;18(1):553.
  • doi: 10.1186/s12859-017-1986-0.
  • PubMed PMID: 29237399
  •  
  • Costa D, Castelo R. Umbilical cord gene expression reveals the molecular architecture of the fetal inflammatory response in extremely preterm newborns. Pediatr Res. 2016 Mar;79(3):473-81.
  • doi: 10.1038/pr.2015.233. 
  •  

  • Pérez-Granado J, Piñero J, Furlong LI. ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer. Database (Oxford). 2019 Jan 1;2019. pii: baz060. doi: 10.1093/database/baz060.

  • PMID: 31169290


  • Castillo-Lara S, Abril JF. PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. Bioinformatics. 2018 Mar 15;34(6):1016-1023.

    doi: 10.1093/bioinformatics/btx738.

    PMID: 29186384

     

    Climente-González H, Porta-Pardo E, Godzik A, Eyras E. The Functional Impact of Alternative Splicing in Cancer. Cell Rep. 2017;20(9):2215-2226. doi:10.1016/j.celrep.2017.08.012.

    PMID: 28854369.

     

    Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ, Eyras E. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol. 2018;19(1):40. doi:10.1186/s13059-018-1417-1.

    PMID: 29571299;

     

    Lecina D, Gilabert JF, Guallar V. Adaptive simulations, towards interactive protein-ligand modeling. Sci Rep. 2017;7(1):8466. doi:10.1038/s41598-017-08445-5.

    PMID: 28814780

     

    Lanzós A, Carlevaro-Fita J, Mularoni L, Reverter F, Palumbo E, Guigó R, Johnson R. Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features. Sci Rep. 2017; 7:41544. doi: 10.1038/srep41544.

    PMID: 28128360;

     

    Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. RNA. 2017;23(7):1080-1087. doi: 10.1261/rna.060814.117

    PMID: 28386015

     

    Martínez-Rosell G, Giorgino T, De Fabritiis G. PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations. J Chem Inf Model. 2017;57(7):1511-1516. doi: 10.1021/acs.jcim.7b00190.

    PMID: 28594549.

     

    Mateo L, Rech GE, González J. Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations. Sci Rep. 2018;8(1):16143. doi: 10.1038/s41598-018-34267-0.

    PMID: 30385770

     

    Radchenko T, Brink A, Siegrist Y, Kochansky C, Bateman A, Fontaine F, Morettoni L, Zamora I. Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry. PLoS One. 2017;12(11):e0186461. doi:10.1371/journal.pone.0186461. eCollection 2017.

    PMID: 29091918

     

    Martinez-Corral R, Raimundez E, Lin Y, Elowitz MB, Garcia-Ojalvo J. Self-Amplifying Pulsatile Protein Dynamics without Positive Feedback. Cell Syst. 2018;7(4):453-462.e1. doi: 10.1016/j.cels.2018.08.012.

    PMID: 30316816.

     

    Rodríguez-Martín B, Palumbo E, Marco-Sola S, Griebel T, Ribeca P, Alonso G, Rastrojo A, Aguado B, Guigó R, Djebali S. ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. BMC Genomics. 2017;18(1):7. doi: 10.1186/s12864-016-3404-9.

    PMID: 28049418

     

    Jiménez-García B, Roel-Touris J, Romero-Durana M, Vidal M, Jiménez-González D, Fernández-Recio J. LightDock: a new multi-scale approach to protein-protein docking. Bioinformatics. 2018 Jan 1;34(1):49-55. doi:10.1093/bioinformatics/btx555.

    2PMID: 28968719

     

  • Carlevaro-Fita J, Rahim A, Guigó R, Vardy LA, Johnson R. Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. RNA. 2016; 22(6):867-82. doi: 10.1261/rna.053561.115. Epub 2016 Apr 18.

    PMID: 27090285

     

    Schikora-Tamarit MÀ, Toscano-Ochoa C, Domingo Espinós J, Espinar L, Carey LB. A synthetic gene circuit for measuring autoregulatory feedback control. Integr Biol (Camb). 2016; 8(4):546-55

    PMID: 26728081.

     

  • Frigola J, Iturbide A, Lopez-Bigas N, Peiro S, Gonzalez-Perez A. Altered oncomodules underlie chromatin regulatory factors driver mutations. Oncotarget 2016;7(21):30748-59. doi: 10.18632/oncotarget.8752.

    PMID: 27095575

     

    Nadeu F, Delgado J, Royo C, Baumann T, Stankovic T, Pinyol M, Jares P, Navarro A, Martín-García D, Beà S, Salaverria I, Oldreive C, Aymerich M, Suárez-Cisneros H, Rozman M, Villamor N, Colomer D, López-Guillermo A, González M, Alcoceba M, Terol MJ, Colado E, Puente XS, López-Otín C, Enjuanes A, Campo E. Clinical impact of clonal and subclonal TP53, SF3B1, BIRC3, NOTCH1 and ATM mutations in chronic lymphocytic leukemia. Blood. 2016; 127(17):2122-30 doi: 10.1182/blood-2015-07-659144

    PMID: 26837699

     

    Pernice MC, Giner CR, Logares R, Perera-Bel J, Acinas SG, Duarte CM, Gasol JM, Massana R. Large variability of bathypelagic microbial eukaryotic communities across the world's oceans. ISME J. 2016;10(4):945-58. doi:10.1038/ismej.2015.170.

    PMID: 26451501.

     

    Frías-López C, Sánchez-Herrero JF, Guirao-Rico S, Mora E, Arnedo MA, Sánchez-Gracia A, Rozas J. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model

    organisms. Bioinformatics. 2016;32(24):3753-3759.

    PMID: 27531104

     

    Alamancos GP, Pagès A, Trincado JL, Bellora N, Eyras E. Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA. 2015;21(9):1521-31. doi: 10.1261/rna.051557.115.

    PMID: 26179515

     

    Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science. 2015;348(6231):242-5.

    PMID: 25859046

     

    Dobon B, Hassan HY, Laayouni H, Luisi P, Ricaño-Ponce I, Zhernakova A, Wijmenga C, Tahir H, Comas D, Netea MG, Bertranpetit J. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape. Sci Rep. 2015;5:9996.

    PMID: 26017457;

     

    Ferruz N, Harvey MJ, Mestres J, De Fabritiis G. Insights from Fragment Hit Binding Assays by Molecular Simulations. J Chem Inf Model. 2015; 55(10):2200-5.

    PMID: 26376295.

     

    Liu J, Prindle A, Humphries J, Gabalda-Sagarra M, Asally M, Lee DY, Ly S, Garcia-Ojalvo J, Süel GM. Metabolic co-dependence gives rise to collective oscillations within biofilms. Nature 2015; 523(7562):550-4.

    PMID: 26200335.

     

    Juan-Blanco T, Duran-Frigola M, Aloy P. IntSide: a web server for the chemical and biological examination of drug side effects. Bioinformatics. 2015;31(4):612-3.

    PMID: 25380960.

     

    Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K, Kliver S, Schmidt-Küntzel A, Koepfli KP, Johnson W, Kuderna LF, García-Pérez R, Manuel Md, Godinez R, Komissarov A, Makunin A, Brukhin V, Qiu W, Zhou L, Li F, Yi J, Driscoll C, Antunes A, Oleksyk TK, Eizirik E, Perelman P, Roelke M, Wildt D, Diekhans M, Marques-Bonet T, Marker L, Bhak J, Wang J, Zhang G, O'Brien SJ. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol. 2015;16:277.

    PMID: 26653294

     

    Pozuelo M, Panda S, Santiago A, Mendez S, Accarino A, Santos J, Guarner F, Azpiroz F, Manichanh C. Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome. Sci Rep. 2015; 5:12693.

    PMID: 26239401

     

    Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O’Donoghue SI, Jensen LJ. Comprehensive comparison of large-scale tissue expression datasets. Vision T, ed. PeerJ. 2015;3:e1054. doi:10.7717/peerj.1054.

  • PMC: 4493645

     

    Aterido A, Palacio C, Marsal S, Avila G, Julià A. Novel insights into the regulatory architecture of CD4+ T cells in rheumatoid arthritis. PLoS One. 2014; 9(6):e100690.

    PMID: 24959711

     

    Hartasánchez DA, Vallès-Codina O, Brasó-Vives M, Navarro A. Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario. G3 (Bethesda). 2014;4(8):1479-89.

    PMID: 24906640

     

    Grande-García A, Lallous N, Díaz-Tejada C, Ramón-Maiques S. Structure, functional characterization, and evolution of the dihydroorotase domain of human CAD. Structure. 2014;22(2):185-98.

    PMID: 24332717

     

    Cuenca S, Sanchez E, Santiago A, El Khader I, Panda S, Vidal S, Camilo Nieto J, Juárez C, Sancho F, Guarner F, Soriano G, Guarner C, Manichanh C. Microbiome composition by pyrosequencing in mesenteric lymph nodes of rats with CCl4-induced cirrhosis. J Innate Immun. 2014;6(3):263-71.

    PMID: 24296725

     

  • Madrigal I, Alvarez-Mora MI, Karlberg O, Rodríguez-Revenga L, Elurbe DM, Rabionet R, Mur A, Pie J, Ballesta F, Sauer S, Syvänen AC, Milà M. Efficient application of next-generation sequencing for the diagnosis of rare genetic syndromes. J Clin Pathol. 2014; 67(12):1099-103.

    PMID: 25271213.

     

    Santiago A, Panda S, Mengels G, Martinez X, Azpiroz F, Dore J, Guarner F, Manichanh C. Processing faecal samples: a step forward for standards in microbial community analysis. BMC Microbiol. 2014;14:112.

    PMID: 24884524

     

    Guixà-González R, Rodriguez-Espigares I, Ramírez-Anguita JM, Carrió-Gaspar P, Martinez-Seara H, Giorgino T, Selent J. MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics. 2014;30(10):1478-80.

    PMID: 24451625.

     

    Schroeder MP, Rubio-Perez C, Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action. Bioinformatics. 2014; 30(17):i549-55.

    PMID: 25161246

     

    Fuster F, Altes A, Beneitez D, Bruguera M, Felez J, Lopez, R, Matute MF, Perez-Lucena MJ, Remacha A, Ruiz MA, Sanz C, Torres M, Sanchez, M. Highferritin: a medical web tool for diagnosis and recommendations in patients with hyperferritinemia. Am J Hematol 2013; 88(5):E206

  • http://highferritin.imppc.org/


    Gayà-Vidal M, Albà MM. Uncovering adaptive evolution in the human lineage. BMC Genomics. 2014;15(1):599. doi:10.1186/1471-2164-15-5999.

  • PMID: 25030307

  • Duran-Frigola M, Aloy P. Analysis of chemical and biological features yields mechanistic insights into drug side effects. Chem Biol, 2013; 20(4): 594-603. doi: 10.1016/j.chembiol.2013.03.017. 

  • PMID: 23601648

  • González-Mendióroz M, Alvarez-Vázquez AB, Rubio-Martinez J. Suluctural analysis of the inhibition of APRIL by TACI and BCMA through molecular Dynamics simulations. J Mol Graph Model, 2013 ;39: 13-22. doi: 10.1016/j.jmgm.2012.11.002. 

  • PMID: 23202984

  • Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, Knights D, Knight R, Esulella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada JR, Guarner F, Azpiroz F. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut. 2013.

  • PMID: 23766444

  • Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E,Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Berulanpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T. The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics, 2013; 14:363. doi: 10.1186/1471-2164-14-363. 

  • PMID: 23721540

  • Sammito M, Millán C, Rodríguez DD, de Ilarduya IM, Meindl K, De Marino I, Peulillo G, Buey RM, de Pereda JM, Zeth K, Sheldrick GM, Usón I. Exploiting tertiary sulucture through local folds for crystallographic phasing. Nat Methods, 2013 Sep 15. doi: 10.1038/nmeth.2644

  • PMID: 24037245

  • Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics, 2013; 29(18): 2238-44. doi: 10.1093/bioinformatics/btt395.

  • PMID: 23884480

  • Tamborero D, Lopez-Bigas N, Gonzalez-Perez A. Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression. PLoS One, 2013; 8(2): e55489. doi: 10.1371/journal.pone.0055489. 

  • PMID: 23408991

  • Villanueva-Cañas JL, Laurie S, Albà MM. Improving genome-wide scans of positive selection by using protein isoforms of similar length. Genome Biol Evol, 2013; 5(2): 457-67. doi: 10.1093/gbe/evt017. 

  • PMID: 23377868

  • Althammer S, Pagès A, Eyras E. Predictive models of gene regulation from high-throughput epigenomics data. Comp Funct Genomics, 2012; 284786. doi:10.1155/2012/284786. PMID: 22924024

  • PMID: 22924024

  • Bleda M, Medina I, Alonso R, De Maria A, Salavert F, Dopazo J. Inferring the regulatory network behind a gene expression experiment. Nucleic Acids Res, 2012 Jul; 40(Web Server issue):W168-72. doi: 10.1093/nar/gks573

  • PMID: 22693210

  • Carrascosa MC, Massaguer OL, Mesules J. PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget Drug Discovery. Mol Inform, 2012 Aug; 31(8):537-541.

  • PMID: 23548981

  • Mora O, Engelbrecht G, Bisbal J. A service-oriented disulibuted semàntic mediator: integrating multiscale biomedical information. IEEE J Biomed Health Inform, 2012. doi: 10.1109/TITB.2012.2215045. 

  • PMID: 22929464

  • Sfriso P, Emperador A, Orellana L, Hospital A,  Gelpi JL, Orozco M. Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations.  J Chem Theory Comput, 2012; 8 (11): 4707-4718.

  • http://pubs.acs.org/doi/abs/10.1021/ct300494q

  • Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics. 2011 Dec 15;27(24):3333-40.

  • PMID: 21994224

  • Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, Gabaldón T. PhylomeDB v3.0: an expanding repository of genome-wide collections of ulees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res, 2011 Jan; 39(Database issue):D556-60. doi: 10.1093/nar/gkq1109

  • PMID: 21075798

  • Perez-Llamas C, Lopez-Bigas N. Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One, 2011; 6(5):e19541. doi:10.1371/journal.pone.0019541.

  • PMID: 21602921