المؤلفون: Schikora Tamarit, Miquel Àngel

المساهمون: University/Department: Universitat de Barcelona. Facultat de Biologia

Thesis Advisors: Gabaldón Estevan, Juan Antonio, Gelpi Buchaca, Josep Lluís

المصدر: TDX (Tesis Doctorals en Xarxa)

مصطلحات موضوعية: Medicaments antifúngics, Agentes antifúngicos, Antifungal agents, Resistència als medicaments, Resistencia a los medicamentos, Drug resistance, Genòmica, Genómica, Genomics, Adaptation (Biology), Candidiasis, Adaptació (Biologia), Candidiasi, Adaptación (Biología), Ciències de la Salut

وصف الملف: application/pdf

URL الوصول: http://hdl.handle.net/10803/689610

المؤلفون: Ksiezopolska, Ewa, Schikora Tamarit, Miquel Àngel, Nunez Rodriguez, Juan Carlos, Gabaldon, Toni

المساهمون: Barcelona Supercomputing Center

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Drug resistance, Nakaseomyces glabratus (Candida glabrata), Drug resistance stability, Aneuploidy, Mutations, Microevolution, Simulació per ordinador, Genòmica

وصف الملف: application/pdf

Relation: https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2024.1416509; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126067NB-I00/ES/ORIGEN, EVOLUCION Y ADAPTACION EN PATOGENOS DEL GENERO CANDIDA: UNA APROXIMACION GENOMICA Y TRANSCRIPTOMICA/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/CPP2021-008552/ES/LactAs: desarrollo de un bioterapéutico vivo recombinante para el tratamiento del asma grave/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PCI2022-135066-2/ES/DISRUPTING DRUG RESISTANCE BY EXPLOITING COLLATERAL SENSITIVITY TO DESIGN NOVEL THERAPEUTIC STRATEGIES FOR C. AURIS AND C. GLABRATA/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PDC2022-133266-I00/ES/NUEVOS COMPUESTOS ANTIFUNGICOS CONTRA CANDIDA MULTIRESISTENTE/; info:eu-repo/grantAgreement/EC/H2020/724173/EU/Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes./RETVOLUTION; http://hdl.handle.net/2117/415410

الاتاحة: http://hdl.handle.net/2117/415410
https://doi.org/10.3389/fcimb.2024.1416509

المؤلفون: Schikora Tamarit, Miquel Àngel, Gabaldon, Toni

المساهمون: Barcelona Supercomputing Center

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Drug resistance, Fungal infections, Evolutionary genetics, Fungi, Pathogens, Genòmica, Càndida

وصف الملف: application/pdf

Relation: https://www.nature.com/articles/s41564-023-01547-z; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126067NB-I00/ES/ORIGEN, EVOLUCION Y ADAPTACION EN PATOGENOS DEL GENERO CANDIDA: UNA APROXIMACION GENOMICA Y TRANSCRIPTOMICA/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PCI2022-135066-2/ES/DISRUPTING DRUG RESISTANCE BY EXPLOITING COLLATERAL SENSITIVITY TO DESIGN NOVEL THERAPEUTIC STRATEGIES FOR C. AURIS AND C. GLABRATA/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PDC2022-133266-I00/ES/NUEVOS COMPUESTOS ANTIFUNGICOS CONTRA CANDIDA MULTIRESISTENTE/; Schikora Tamarit, M.À.; Gabaldon, T. Recent gene selection and drug resistance underscore clinical adaptation across Candida species. "Nature Microbiology", 2024, vol. 9, p. 284-307.; http://hdl.handle.net/2117/405153

الاتاحة: http://hdl.handle.net/2117/405153
https://doi.org/10.1038/s41564-023-01547-z

المؤلفون: Schikora-Tamarit, Miquel Àngel, Gabaldón#, Toni

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors, High performance computing, Candida, population genomics, drug resistance, Càlcul intensiu (Informàtica)

وصف الملف: 1 p.; application/pdf

Relation: Schikora-Tamarit, M.À.; Gabaldón#, T. Exploring the recent evolution of yeast pathogens using the CandidaMine database. A: . Barcelona Supercomputing Center, 2022, p. 92.; http://hdl.handle.net/2117/384133

الاتاحة: http://hdl.handle.net/2117/384133

المؤلفون: Barcelona Supercomputing Center, Schikora Tamarit, Miquel Àngel, Gabaldon, Toni

مصطلحات الفهرس: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Drug resistance, Fungal infections, Evolutionary genetics, Fungi, Pathogens, Genòmica, Càndida, Article

URL: http://hdl.handle.net/2117/405153
https://www.nature.com/articles/s41564-023-01547-z
https://www.nature.com/articles/s41564-023-01547-z
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126067NB-I00/ES/ORIGEN, EVOLUCION Y ADAPTACION EN PATOGENOS DEL GENERO CANDIDA: UNA APROXIMACION GENOMICA Y TRANSCRIPTOMICA
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PCI2022-135066-2/ES/DISRUPTING DRUG RESISTANCE BY EXPLOITING COLLATERAL SENSITIVITY TO DESIGN NOVEL THERAPEUTIC STRATEGIES FOR C. AURIS AND C. GLABRATA
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PDC2022-133266-I00/ES/NUEVOS COMPUESTOS ANTIFUNGICOS CONTRA CANDIDA MULTIRESISTENTE

المؤلفون: Schikora Tamarit, Miquel Àngel, Gabaldón, Toni

المساهمون: Barcelona Supercomputing Center

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Eukaryotic cell genetics, Structural variants, Variant calling, Short reads, Parameter optimization, Simulació per ordinador

وصف الملف: application/pdf

Relation: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02737-4; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-099921-B-I00/ES/EVOLUCION GENOMICA Y FENOTIPICA EN PATOGENOS DEL GENERO CANDIDA/; info:eu-repo/grantAgreement/EC/H2020/724173/EU/Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes./RETVOLUTION; PerSVade is available at https://github.com/Gabaldonlab/perSVade [39] and can be installed using either conda environments or through a docker image containing the pipeline, available at https://hub.docker.com/r/mikischikora/persvade. The github repository is released under an open source GNU General Public License (GPL). In addition, the code can be accessed in Zenodo through the DOI 10.5281/zenodo.6866529 [86]. The github repository contains detailed examples on how to install and run perSVade using conda, docker, or singularity. We have tested perSVade on several Linux and Mac architectures, and the docker image may be run in any machine in a reproducible way. All the results shown in this paper were generated using the script https://github.com/Gabaldonlab/perSVade/blob/master/scripts/perSVade.py from version 1.0, which is a wrapper to execute several modules with a single command. Since perSVade is an actively used (and maintained) pipeline, we have created a few new releases since version 1.0, which include an improved documentation, more unit tests, and the implementation of an efficient debugging of inputs. Note that these changes do not affect the functionality of the modules as implemented in version 1.0. Hence, we recommend the usage of the latest version (version 1.02.7 at the time of publication), which is the one with the best documentation and usability. In addition, note that this one-liner wrapper is not recommended for broad usage. All the data used for testing perSVade was obtained from the SRA database or public ftp servers, and is listed in Additional file 1: Table S1 and “Methods.” All the code necessary to reproduce the results and plots shown in this paper is in https://github.com/Gabaldonlab/perSVade/tree/master/testing.; Schikora Tamarit, M.À.; Gabaldón, T. PerSVade: personalized structural variant detection in any species of interest. "Genome Biology", 2022, vol. 23, 175.; http://hdl.handle.net/2117/372015

الاتاحة: http://hdl.handle.net/2117/372015
https://doi.org/10.1186/s13059-022-02737-4

المؤلفون: Schikora-Tamarit, Miquel Àngel, Gabaldón, Toni

المصدر: Biochemical Society Transactions ; volume 50, issue 3, page 1259-1268 ; ISSN 0300-5127 1470-8752

الاتاحة: http://dx.doi.org/10.1042/bst20211123
https://portlandpress.com/biochemsoctrans/article-pdf/50/3/1259/934389/bst-2021-1123c.pdf

المؤلفون: Schikora-Tamarit, Miquel Àngel, Gabaldón, Toni

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors, High performance computing, genomics, structural variation, variant calling, Càlcul intensiu (Informàtica)

وصف الملف: 1 p.; application/pdf

Relation: Schikora-Tamarit, M.À.; Gabaldón, T. PerSVade: personalized structural variation detection in your species of interest. A: . Barcelona Supercomputing Center, 2021, p. 67.; http://hdl.handle.net/2117/346354

الاتاحة: http://hdl.handle.net/2117/346354

المؤلفون: Ksiezopolska, Ewa, Schikora Tamarit, Miquel Àngel, Beyer, Reinhard, Nuñez Rodriguez, Juan Carlos, Schüller, Christoph, Gabaldon, Toni

المساهمون: Barcelona Supercomputing Center

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Fungal infections, Drug resistance, Candida glabrata, Experimental evolution, Antifungal, Cross-resistance, Multidrug resistance, Càndida, Genòmica

وصف الملف: 24 p.; application/pdf

Relation: https://doi.org/10.1016/j. cub.2021.09.084; https://www.sciencedirect.com/science/article/pii/S096098222101352X#!; info:eu-repo/grantAgreement/EC/H2020/724173/EU/Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes./RETVOLUTION; info:eu-repo/grantAgreement/EC/H2020/793699/EU/Not one but many: adopting structural flexibility in the analysis of the evolution of lncRNAs./MULTI_FOLDS; Ksiezopolska, E. [et al.]. Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata. "Current Biology", 2021, vol. 31, núm. 23, p. 5314-5326.; http://hdl.handle.net/2117/358214

الاتاحة: http://hdl.handle.net/2117/358214
https://doi.org/10.1016/j.cub.2021.09.084

المؤلفون: Schikora Tamarit, Miquel Àngel, Marcet Houben, Marina, Nosek, Jozef, Gabaldón, Toni

المساهمون: Barcelona Supercomputing Center

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Comparative genomics, Eukaryotic cells, Yeast, Complex I, Oxidative stress, Mitochondria, Phylogenomics, Oxidative phosphorylation, Genòmica -- Models matemàtics

وصف الملف: 15 p.; application/pdf

Relation: info:eu-repo/grantAgreement/EC/H2020/724173/EU/Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes./RETVOLUTION; Schikora Tamarit, M.À. [et al.]. Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi. "Open Biology", 2021, vol. 11, núm. 4, 200362.; http://hdl.handle.net/2117/345586

الاتاحة: http://hdl.handle.net/2117/345586
https://doi.org/10.1098/rsob.200362

المؤلفون: Schikora-Tamarit, Miquel Àngel, Gabaldon, Toni

المساهمون: Barcelona Supercomputing Center

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Evolutionary biology, Fungal diseases, Fungal genetics, Pathogenesis, Drug resistance, Genomics, Infection, Mycology, Genòmica, Bioinformàtica

وصف الملف: 10 p.; application/pdf

Relation: https://portlandpress.com/biochemsoctrans/article/50/3/1259/231437/Using-genomics-to-understand-the-mechanisms-of; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-099921-B-I00/ES/EVOLUCION GENOMICA Y FENOTIPICA EN PATOGENOS DEL GENERO CANDIDA/; info:eu-repo/grantAgreement/EC/H2020/724173/EU/Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes./RETVOLUTION; Schikora-Tamarit, M.À.; Gabaldon, T. Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens. "Biochemical Society Transactions", Juny 2020, vol. 50, núm. 3, p. 1259-1268.; http://hdl.handle.net/2117/369487

الاتاحة: http://hdl.handle.net/2117/369487

المؤلفون: Espinar, Lorena, Schikora Tamarit, Miquel Àngel, Domingo Espinós, Júlia, 1991-, Carey, Lucas, 1980-

وصف الملف: application/pdf

Relation: Genome Research. 2018;28(4):509-18; info:eu-repo/grantAgreement/ES/1PE/BFU2015-68351-P; http://hdl.handle.net/10230/36039; http://dx.doi.org/10.1101/gr.230458.117

الاتاحة: http://hdl.handle.net/10230/36039
https://doi.org/10.1101/gr.230458.117

المؤلفون: Schikora Tamarit, Miquel Àngel, López-Grado i Salinas, Guillem, González Navasa, Carolina, Calderón, Irene, Marcos Fa, Xavi, Sas, Miquel, Carey, Lucas, 1980-

مصطلحات موضوعية: Feedback, Fitness, Gene expression, Mathematical modeling, Systems biology, Transcription, Yeast

وصف الملف: application/pdf

Relation: Cell Reports. 2018;24(3):755-65; info:eu-repo/grantAgreement/ES/1PE/BFU2015-68351-P; http://hdl.handle.net/10230/35202; http://dx.doi.org/10.1016/j.celrep.2018.06.059

الاتاحة: http://hdl.handle.net/10230/35202
https://doi.org/10.1016/j.celrep.2018.06.059

المؤلفون: Schikora-Tamarit, Miquel Àngel, Carey, Lucas B.

المساهمون: Agència de Gestió d’Ajuts Universitaris i de Recerca, MINECO

المصدر: Transcription ; volume 9, issue 5, page 327-333 ; ISSN 2154-1264 2154-1272

الاتاحة: http://dx.doi.org/10.1080/21541264.2018.1511676
https://www.tandfonline.com/doi/pdf/10.1080/21541264.2018.1511676

المؤلفون: Barcelona Supercomputing Center, Schikora Tamarit, Miquel Àngel, Gabaldón, Toni

مصطلحات الفهرس: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Eukaryotic cell genetics, Structural variants, Variant calling, Short reads, Parameter optimization, Simulació per ordinador, Article

URL: http://hdl.handle.net/2117/372015
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02737-4
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02737-4
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-099921-B-I00/ES/EVOLUCION GENOMICA Y FENOTIPICA EN PATOGENOS DEL GENERO CANDIDA
info:eu-repo/grantAgreement/EC/H2020/724173/EU/Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes./RETVOLUTION
PerSVade is available at https://github.com/Gabaldonlab/perSVade [39] and can be installed using either conda environments or through a docker image containing the pipeline, available at https://hub.docker.com/r/mikischikora/persvade. The github repository is released under an open source GNU General Public License (GPL). In addition, the code can be accessed in Zenodo through the DOI 10.5281/zenodo.6866529 [86]. The github repository contains detailed examples on how to install and run perSVade using conda, docker, or singularity. We have tested perSVade on several Linux and Mac architectures, and the docker image may be run in any machine in a reproducible way. All the results shown in this paper were generated using the script https://github.com/Gabaldonlab/perSVade/blob/master/scripts/perSVade.py from version 1.0, which is a wrapper to execute several modules with a single command. Since perSVade is an actively used (and maintained) pipeline, we have created a few new releases since version 1.0, which include an improved documentation, more unit tests, and the implementation of an efficient debugging of inputs. Note that these changes do not affect the functionality of the modules as implemented in version 1.0. Hence, we recommend the usage of the latest version (version 1.02.7 at the time of publication), which is the one with the best documentation and usability. In addition, note that this one-liner wrapper is not recommended for broad usage. All the data used for testing perSVade was obtained from the SRA database or public ftp servers, and is listed in Additional file 1: Table S1 and “Methods.” All the code necessary to reproduce the results and plots shown in this paper is in https://github.com/Gabaldonlab/perSVade/tree/master/testing.

المؤلفون: Schikora-Tamarit, Miquel Àngel, Gabaldón, Toni

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::07473b0f8c6914d9f3fe800cdf2f3288

المؤلفون: Schikora-Tamarit, Miquel Àngel, Gabaldón, Toni

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::75c9fa8fce5ebd8185571f0b9eb13f22

المؤلفون: Schikora-Tamarit, Miquel Àngel, Marcet-Houben, Marina, Nosek, Jozef, Gabaldón, Toni

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::79e3d38315c322d23ca483b536982741

المؤلفون: Schikora-Tamarit, Miquel Àngel, Marcet-Houben, Marina, Nosek, Jozef, Gabaldón, Toni

مصطلحات موضوعية: fungi

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::27aff9658cf8231ee8e647870e4c85c9

المؤلفون: Schikora-Tamarit, Miquel Àngel, Marcet-Houben, Marina, Nosek, Jozef, Gabaldón, Toni

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::21f80381cb730ddc08408aad07dbe5f5