Enhanced RNA-targeting CRISPR-Cas technology in zebrafish

Authors: Ismael Moreno-Sánchez, Luis Hernández-Huertas, Daniel Nahón-Cano, Pedro Manuel Martínez-García, Anthony J. Treichel, Carlos Gómez-Marin, Laura Tomás-Gallardo, Gabriel da Silva Pescador, Gopal Kushawah, Rhonda Egidy, Anoja Perera, Alejandro Díaz-Moscoso, Alejandra Cano-Ruiz, John A. Walker, Manuel J. Muñoz, Kevin Holden, Joan Galcerán, M. Ángela Nieto, Ariel A. Bazzini, Miguel A. Moreno-Mateos

Source: Nature Communications, Vol 16, Iss 1, Pp 1-20 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/df5191f9a47f4d78880010be756ebfa4

Application of XAI to the prediction of CTCF binding sites

Authors: Thomas Vanhaeren, Angela del Robledo Troncoso-García, José Francisco Torres Maldonado, Federico Divina, Pedro Manuel Martínez-García

Source: Results in Engineering, Vol 25, Iss , Pp 103776- (2025)

Subject Terms: Xai, Genomics, Deep learning, Machine learning, Random forest, Xgboost, Technology

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S259012302402019X; https://doaj.org/toc/2590-1230

Access URL: https://doaj.org/article/5aa7868e7dbe456a8860a89b14f8796b

Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci

Authors: Eva D’haene, Víctor López-Soriano, Pedro Manuel Martínez-García, Soraya Kalayanamontri, Alfredo Dueñas Rey, Ana Sousa-Ortega, Silvia Naranjo, Stijn Van de Sompele, Lies Vantomme, Quinten Mahieu, Sarah Vergult, Ana Neto, José Luis Gómez-Skarmeta, Juan Ramón Martínez-Morales, Miriam Bauwens, Juan Jesús Tena, Elfride De Baere

Source: Genome Biology, Vol 25, Iss 1, Pp 1-24 (2024)

Subject Terms: 3D genome structure, Hi-C, HiChIP, UMI-4C, Neural retina, Retinal pigment epithelium (RPE), Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/a3d8d2ce3b6a449b865a48720cdd33d6

Data of transcriptional effects of the merbarone-mediated inhibition of TOP2

Authors: Fernando M. Delgado-Chaves, Pedro Manuel Martínez-García, Andrés Herrero-Ruiz, Francisco Gómez-Vela, Federico Divina, Silvia Jimeno-González, Felipe Cortés-Ledesma

Source: Data in Brief, Vol 44, Iss , Pp 108499- (2022)

Subject Terms: Topoisomerase inhibition, Differential gene expression, DNA supercoiling, Merbarone, RNA-Seq, Computer applications to medicine. Medical informatics, R858-859.7, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S235234092200693X; https://doaj.org/toc/2352-3409

Access URL: https://doaj.org/article/d89eac8543cc469fb29754a4a04edb84

Endogenous topoisomerase II-mediated DNA breaks drive thymic cancer predisposition linked to ATM deficiency

Authors: Alejandro Álvarez-Quilón, José Terrón-Bautista, Irene Delgado-Sainz, Almudena Serrano-Benítez, Rocío Romero-Granados, Pedro Manuel Martínez-García, Silvia Jimeno-González, Cristina Bernal-Lozano, Cristina Quintero, Lourdes García-Quintanilla, Felipe Cortés-Ledesma

Source: Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/9f1676662817487ea864a82ec0a5a86d

Topoisomerase IIα represses transcription by enforcing promoter-proximal pausing

Authors: Andrés Herrero-Ruiz, Pedro Manuel Martínez-García, José Terrón-Bautista, Gonzalo Millán-Zambrano, Jenna Ariel Lieberman, Silvia Jimeno-González, Felipe Cortés-Ledesma

Source: Cell Reports, Vol 35, Iss 2, Pp 108977- (2021)

Subject Terms: DNA supercoiling, DNA topology, DNA topoisomerases, transcription elongation, promoter-proximal pausing, gene expression, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124721002916; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/8dfac8784fd141728490e80ccebfe46c

Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility.

Authors: Pedro Manuel Martínez-García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado-Sainz, Francisco Gómez-Vela, Felipe Cortés-Ledesma

Source: PLoS Computational Biology, Vol 17, Iss 1, p e1007814 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/f3813029516c458b84441737d5695e46

The Pseudomonas syringae pv. tomato DC3000 PSPTO_0820 multidrug transporter is involved in resistance to plant antimicrobials and bacterial survival during tomato plant infection.

Authors: Saray Santamaría-Hernando, Marta Senovilla, Almudena González-Mula, Pedro Manuel Martínez-García, Sandra Nebreda, Pablo Rodríguez-Palenzuela, Emilia López-Solanilla, José Juan Rodríguez-Herva

Source: PLoS ONE, Vol 14, Iss 6, p e0218815 (2019)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/920462b17bd74187a2540ba454d7feea

T346Hunter: a novel web-based tool for the prediction of type III, type IV and type VI secretion systems in bacterial genomes.

Authors: Pedro Manuel Martínez-García, Cayo Ramos, Pablo Rodríguez-Palenzuela

Source: PLoS ONE, Vol 10, Iss 4, p e0119317 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4395097?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/4045c00f82cf4101bcbe92c7c4601d42

Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle.

Authors: Pedro Manuel Martínez-García, Pablo Rodríguez-Palenzuela, Eva Arrebola, Víctor J Carrión, José Antonio Gutiérrez-Barranquero, Alejandro Pérez-García, Cayo Ramos, Francisco M Cazorla, Antonio de Vicente

Source: PLoS ONE, Vol 10, Iss 8, p e0136101 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4551802?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/48641383197c4d18b19684b61067a2c3