Sacristán-Horcajada E, González-de la Fuente S, Peiró-Pastor R, Carrasco-Ramiro F, Amils R, Requena JM, Berenguer J, Aguado B, 2021. ARAMIS: From systematic errors of NGS long reads to accurate assemblies. Brief Bioinform. 2020. , Identification and Isolation of Two Different Subpopulations Within African Swine Fever Virus Arm/07 Stock. Vaccines (Basel) 8. 2020. , Draft Genome Sequence of the Trypanosoma cruzi B. M. López Strain (TcIa), Isolated from a Colombian Patient. Microbiol Resour Announc 9. 2020. , Trypanosoma cruzi Ikiakarora (TcIII) Draft Genome Sequence. Microbiol Resour Announc 9. 2020. , The Experimental Proteome of Leishmania infantum Promastigote and Its Usefulness for Improving Gene Annotations. Genes (Basel) 11 D, 2020. Liquid biopsy by NGS: Differential presence of exons (DPE) is related to metastatic potential in a colon-cancer model in the rat. Transl Oncol 13(11):100837 2019. , Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation. Sci Rep 9(1):6127 2019. , Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins. Genome Res 29(5):784-797 2019. , Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp. Microorganisms 7. 2019. , Complete Genome Sequence of Mycolicibacterium hassiacum DSM 44199. Microbiol Resour Announc 8. 2018. , Complete and de novo assembly of the Leishmania braziliensis (M2904) genome. Mem Inst Oswaldo Cruz 114:e180438 2018. , Liquid biopsy by NGS: differential presence of exons (DPE) in cell-free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer. Cancer Med 7(5):1706-1716 2017. , Genomic cartography and proposal of nomenclature for the repeated, interspersed elements of the Leishmania major SIDER2 family and identification of SIDER2-containing transcripts. Mol Biochem Parasitol 212:9-15 2017. , ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. BMC Genomics 18(1):7 2017. , Dataset for distribution of SIDER2 elements in the Leishmania major genome and transcriptome. Data Brief 11:39-43 2017. , RNA-Seq Based Transcriptome Analysis of the Type I Interferon Host Response upon Vaccinia Virus Infection of Mouse Cells. J Immunol Res 2017:5157626 2017. , Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs. Sci Rep 7(1):18050 2017. , Identification of Fungal Species in Brain Tissue from Alzheimer’s Disease by Next-Generation Sequencing. J Alzheimers Dis 58(1):55-67 2017. , Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin. Nucleic Acids Res 45(14):8358-8368 2017. , Human genomics projects and precision medicine. Gene Ther 24(9):551-561 2016. , Resequencing and assembly of seven complex loci to improve the Leishmania major (Friedlin strain) reference genome. Parasit Vectors 9:74 2016. , Basolateral sorting and transcytosis define the Cu+-regulated translocation of ATP7B to the bile canaliculus. J Cell Sci 129(11):2190-201 2016. , Histone H3 Dynamics Reveal Domains with Distinct Proliferation Potential in the Arabidopsis Root. Plant Cell 28(6):1361-71 2016. , Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana. Plant Mol Biol 92(4-5):457-471 2015. , Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Mol Ecol 24(19):4812-25 2015. , Global variability in gene expression and alternative splicing is modulated by mitochondrial content. Genome Res 25(5):633-44 2014. , The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States. Plant Cell 26(6):2351-2366 2013. , Mobility of the native Bacillus subtilis conjugative plasmid pLS20 is regulated by intercellular signaling. PLoS Genet 9(10):e1003892 2013. , R-RAS2 overexpression in tumors of the human central nervous system. Mol Cancer 12(1):127 2013. , The need for transparency and good practices in the qPCR literature. Nat Methods 10(11):1063-7 2013. , Intron retention and transcript chimerism conserved across mammals: Ly6g5b and Csnk2b-Ly6g5b as examples. BMC Genomics 14:199 Publications
Rubio-Ramos A, Bernabé-Rubio M, Labat-de-Hoz L, Casares-Arias J, Kremer L, Correas I, Alonso MA, 2022. MALL, a membrane-tetra-spanning proteolipid overexpressed in cancer, is present in membraneless nuclear biomolecular condensates. Cell Mol Life Sci. Pérez-Liébana I, Juaristi I, González-Sánchez P, González-Moreno L, Rial E, Podunavac M, Zakarian A, Molgó J, Vallejo-Illarramendi A, Mosqueira-Martín L, Lopez de Munain A, Pardo B, Satrústegui J, Del Arco A, 2022. A Ca2+-Dependent Mechanism Boosting Glycolysis and OXPHOS by Activating Aralar-Malate-Aspartate Shuttle, upon Neuronal Stimulation. J Neurosci. Del Álamo AC, Pariente MI, Molina R, Martínez F, 2022. Advanced bio-oxidation of fungal mixed cultures immobilized on rotating biological contactors for the removal of pharmaceutical micropollutants in a real hospital wastewater. J Hazard Mate. Mavian C, López-Bueno A, Martín R, Nitsche A, Alcamí A, 2021. Comparative Pathogenesis, Genomics and Phylogeography of Mousepox. Viruses. López-Muñoz AD, Rastrojo A, Kropp KA, Viejo-Borbolla A, Alcamí A, 2021. Combination of long- and short-read sequencing fully resolves complex repeats of herpes simplex virus 2 strain MS complete genome. Microbial Genomics. Rothenbücher TSP, Gürbüz H, Pereira MP, Heiskanen A, Emneus J, Martinez-Serrano A, 2021. Next generation human brain models: engineered flat brain organoids featuring gyrification. Biofabrication. Oller J, Gabandé-Rodríguez E, Ruiz-Rodriguez MJ, Desdín-Micó G, Aranda JF, Rodrigues-Diez R, Ballesteros-Martínez C, Blanco EM, Roldan-Montero R, Acuña P, Forteza Gil A, Martín-López CE, Nistal JF, Lino Cardenas CL, Lindsay ME, Martín-Ventura JL, Briones AM, Redondo JM, Mittelbrunn M, 2021. Extracellular Tuning of Mitochondrial Respiration Leads to Aortic Aneurysm. Circulation. Garcia-Lopez E, Moreno A, Bartolomé M, Leunda M, Sancho C, Cid C, 2021. Glacial Ice Age Shapes Microbiome Composition in a Receding Southern European Glacier. Front Microbiol. Elorza A, Márquez Y, Cabrera JR, Sánchez-Trincado JL, Santos-Galindo M, Hernández IH, Picó S, Díaz-Hernández JI, García-Escudero R, Irimia M, Lucas JJ, 2021. Huntington’s disease-specific mis-splicing unveils key effector genes and altered splicing factors. Brain. Martínez JM, Escudero C, Leandro T, Mateos G, Amils R, 2021. Draft Genome Sequence of Pseudomonas sp. Strain T2.31D-1, Isolated from a Drilling Core Sample Obtained 414 Meters below Surface in the Iberian Pyrite Belt. Microbiol Resour Announc. Esparza-Moltó PB, Romero-Carramiñana I, Núñez de Arenas C, Pereira MP, Blanco N, Pardo B, Bates GR, Sánchez-Castillo C, Artuch R, Murphy MP, Esteban JA, Cuezva JM, 2021. Generation of mitochondrial reactive oxygen species is controlled by ATPase inhibitory factor 1 and regulates cognition. PLoS Biol. Simsa, R., Rothenbücher, T., Gürbüz, H., Ghosheh, N., Emneus, J., Jenndahl, L., Kaplan, D. L., Bergh, N., Serrano, A. M., & Fogelstrand, P, 2021. Brain organoid formation on decellularized porcine brain ECM hydrogels. PloS one. Asif A, García-López S, Heiskanen A, Martínez-Serrano A, Keller SS, Pereira MP, Emnéus J, 2020. Pyrolytic Carbon Nanograss Enhances Neurogenesis and Dopaminergic Differentiation of Human Midbrain Neural Stem Cells. Adv Healthc Mater Ollà I, Santos-Galindo M, Elorza A, Lucas JJ, 2020. P2X7 Receptor Upregulation in Huntington’s Disease Brains. Front Mol Neurosci. Sánchez-Costa, M.; Blesa, A.; Berenguer, J, 2020. Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution. Genes. Mestre, L., Carrillo-Salinas, F. J., Feliú, A., Mecha, M., Alonso, G., Espejo, C., Calvo-Barreiro, L., Luque-García, J. L., Estevez, H., Villar, L. M., & Guaza, C, 2020. How oral probiotics affect the severity of an experimental model of progressive multiple sclerosis? Bringing commensal bacteria into the neurodegenerative process. Gut microbes. 2020. Draft Genome Sequence of Shewanella sp. Strain T2.3D-1.1, Isolated from 121.8 Meters Deep in the Subsurface of the Iberian Pyrite Belt. Microbiol Resour Announc 9. , 2020. A thermostable DNA primase-polymerase from a mobile genetic element involved in defence against environmental DNA. Environ Microbiol. , 2020. Herpes Simplex Virus Type 2 Counteracts Neurite Outgrowth Repulsion During Infection In A Nerve Growth Factor-Dependent Manner. J Virol. , 2020. Hsv-1 Endocytic Entry into a Human Oligodendrocytic Cell Line is Mediated by Clathrin and Dynamin but Not Caveolin. Viruses 12. , 2020. Pathogenic SREK1 decrease in Huntington’s disease lowers TAF1 mimicking X-linked dystonia parkinsonism. Brain 143(7):2207-2219 , 2020. Dysfunctional oxidative phosphorylation shunts branched-chain amino acid catabolism onto lipogenesis in skeletal muscle. EMBO J 39(14):e103812 , 2020. Compensatory increase of VE-cadherin expression through ETS1 regulates endothelial barrier function in response to TNFα. Cell Mol Life Sci 77(11):2125-2140 , García-Ortiz A; Serrador JM, 2020. ERM Proteins at the Crossroad of Leukocyte Polarization, Migration and Intercellular Adhesion. Int J Mol Sci 21. 2020. Parkinson’s Disease: A Comprehensive Analysis of Fungi and Bacteria in Brain Tissue. Int J Biol Sci 16(7):1135-1152 , 2020. GRK2 levels in myeloid cells modulate adipose-liver crosstalk in high fat diet-induced obesity. Cell Mol Life Sci. , 2020. ICETh1 and ICETh2, two interdependent mobile genetic elements in Thermus thermophilus transjugation. Environ Microbiol 22(1):158-169 , 2020. MiR-9-5p protects from kidney fibrosis by metabolic reprogramming. FASEB J 34(1):410-431 , 2020. Autophagy mediates hepatic GRK2 degradation to facilitate glucagon-induced metabolic adaptation to fasting. FASEB J 34(1):399-409 , 2019. Analysis of mRNA processing at whole transcriptome level, transcriptomic profile and genome sequence refinement of Trypanosoma cruzi. Sci Rep 9(1):17376 , 2019. Brain Microbiota in Huntington’s Disease Patients. Front Microbiol 10:2622 , 2019. Draft Genome Sequence of Brevundimonas sp. Strain T2.26MG-97, Isolated from a Rock Core Sample from 492.6 Meters Deep on the Subsurface of the Iberian Pyrite Belt. Microbiol Resour Announc 8. , 2019. Differential regulation of Kidins220 isoforms in Huntington’s disease. Brain Pathol. , 2019. Manipulation of Gut Microbiota Influences Immune Responses, Axon Preservation, and Motor Disability in a Model of Progressive Multiple Sclerosis. Front Immunol 10:1374 , 2019. Sfrp3 modulates stromal-epithelial crosstalk during mammary gland development by regulating Wnt levels. Nat Commun 10(1):2481 , 2019. Draft Genome Sequence of Rhodoplanes sp. Strain T2.26MG-98, Isolated from 492.6 Meters Deep on the Subsurface of the Iberian Pyrite Belt. Microbiol Resour Announc 8. , 2019. Draft Genome Sequences of Sporulation-Impaired Bacillus pumilus Strain NRS576 and Its Native Plasmid p576. Microbiol Resour Announc 8. , 2019. Bacterial Ligase D preternary-precatalytic complex performs efficient abasic sites processing at double strand breaks during nonhomologous end joining. Nucleic Acids Res 47(10):5276-5292 , 2019. Searching for Bacteria in Neural Tissue From Amyotrophic Lateral Sclerosis. Front Neurosci 13:171 , 2018. Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing. Nature 560(7719):441-446 , 2018. Draft Genome Sequence of Rhizobium sp. Strain T2.30D-1.1, Isolated from 538.5 Meters Deep on the Subsurface of the Iberian Pyrite Belt. Microbiol Resour Announc 7. , 2018. Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity. Sci Rep 8(1):14631 , 2018. Multiple sclerosis and mixed microbial infections. Direct identification of fungi and bacteria in nervous tissue. Neurobiol Dis 117:42-61 , 2018. Infection of Fungi and Bacteria in Brain Tissue From Elderly Persons and Patients With Alzheimer’s Disease. Front Aging Neurosci 10:159 , 2018. Involvement of G protein-coupled receptor kinase 2 (GRK2) in the development of non-alcoholic steatosis and steatohepatitis in mice and humans. Biochim Biophys Acta Mol Basis Dis 1864(12):3655-3667 , 2018. R-Ras1 and R-Ras2 Are Essential for Oligodendrocyte Differentiation and Survival for Correct Myelination in the Central Nervous System. J Neurosci 38(22):5096-5110 , 2017. Alternative polyadenylation in a family of paralogous EPB41 genes generates protein 4.1 diversity. RNA Biol 14(2):236-244 , 2017. Fungal infection in neural tissue of patients with amyotrophic lateral sclerosis. Neurobiol Dis 108:249-260 , 2017. Complete Genome Sequence of Tessaracoccus sp. Strain T2.5-30 Isolated from 139.5 Meters Deep on the Subsurface of the Iberian Pyritic Belt. Genome Announc 5. , 2016. The evolutionarily conserved transcription factor Sp1 controls appendage growth through Notch signaling. Development 143(19):3623-3631 , 2016. RhoB controls endothelial barrier recovery by inhibiting Rac1 trafficking to the cell border. J Cell Biol 213(3):385-402 , 2016. Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis. J Virol 90(20):9293-304 , 2015. Decreased glycogen synthase kinase-3 levels and activity contribute to Huntington’s disease. Hum Mol Genet 24(17):5040-52 , 2015. Reversal of diet-induced obesity and insulin resistance by inducible genetic ablation of GRK2. Sci Signal 8(386):ra73 , 2014. Huntington’s disease is a four-repeat tauopathy with tau nuclear rods. Nat Med 20(8):881-5 , 2020. How oral probiotics affect the severity of an experimental model of progressive multiple sclerosis? Bringing commensal bacteria into the neurodegenerative process. Gut Microbes 12(1):1813532 , Acknowledgments