Profiles
Non OA copies
Publications
- Robinson, M., Cai, P., Emons, M., Gerber, R., Germain, P.L., Gunz, S., Luo, S., Moro, G., Sonder, E., Sonrel, A., Wang, J., Wissel, D., & Mallona, I.. (2024). Ten simple rules for collaborating with wet lab researchers for computational researchers. arXiv
- Hruska-Plochan, M., Wiersma, V., Betz, K., Mallona, I., Ronchi, S., Maniecka, Z., Hock, E.M., Tantardini, E., Laferriere, F., Sahadevan, S., Hoop, V., Delvendahl, I., Pérez-Berlanga, M., Gatta, B., Panatta, M., Bourg, A., Bohaciakova, D., Sharma, P., De Vos, L., Frontzek, K., Aguzzi, A., Lashley, T., Robinson, M., Karayannis, T., Mueller, M., Hierlemann, A., & Polymenidou, M. (2024). A model of human neural networks reveals NPTX2 pathology in ALS and FTLD. Nature, 626(8001), 1073–1083.
- Teske, M., Wertheimer, T., Butz, S., Zwicky, P., Mallona, I., Elling, U., Lancrin, C., Becher, B., Grosso, A., Baubec, T., & Schmolka, N. (2024). Targeted CRISPR-Cas9 screening identifies transcription factor network controlling murine haemato-endothelial fate commitment. bioRxiv.
- Pérez‐Berlanga, M., Wiersma, V., Zbinden, A., De Vos, L., Wagner, U., Foglieni, C., Mallona, I., Betz, K., Cléry, A., Weber, J., Guo, Z., Rigort, R., Rossi, P., Manglunia, R., Tantardini, E., Sahadevan, S., Stach, O., Hruska‐Plochan, M., Allain, F., Paganetti, P., & Polymenidou, M. (2023). Loss of TDP‐43 oligomerization or RNA binding elicits distinct aggregation patterns. The EMBO Journal, 42(17).
- Anthony Sonrel, Almut Luetge, Charlotte Soneson, Izaskun Mallona, Pierre-Luc Germain, Sergey Knyazev, Jeroen Gilis, Reto Gerber, Ruth Seurinck, Dominique Paul, Emanuel Sonder, Helena L. Crowell, Imran Fanaswala, Ahmad Al-Ajami, Elyas Heidari, Stephan Schmeing, Stefan Milosavljevic, Yvan Saeys, Serghei Mangul, & Mark D. Robinson (2023). Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability. Genome Biology, 24(1).
- Bottes, S., Jaeger, B., Pilz, G.A., Jörg, D., Cole, J., Kruse, M., Harris, L., Korobeynyk, V., Mallona, I., Helmchen, F., Guillemot, F., Simons, B., & Jessberger, S. (2020). Long-term self-renewing stem cells in the adult mouse hippocampus identified by intravital imaging. Nature Neuroscience, 24(2), 225–233.
- Izaskun Mallona, Ioana Mariuca Ilie, Ino Dominiek Karemaker, Stefan Butz, Massimiliano Manzo, Amedeo Caflisch, & Tuncay Baubec (2020). Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Research.
- Berta Martín, Stella Pappa, Anna D\iez-Villanueva, Izaskun Mallona, Joaqu\'\in Custodio, Mar\'\ia José Barrero, Miguel A. Peinado, & Mireia Jordà (2020). Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics, 15(6-7), 765–779.
- Manca, P., Mallona, I., Santini, D., Tonini, G., Rolfo, C., Robinson, M., & Pantano, F. (2019). A new bioinformatic pipeline allows the design of small, targeted gene panels for efficient TMB estimation. Annals of Oncology, 30, ii8.
- Tao Y, Kang B, Petkovich DA, Bhandari YR, In J, Stein-O'Brien G, Kong X, Xie W, Zachos N, Maegawa S, Vaidya H, Brown S, Chiu Yen RW, Shao X, & Easwaran H (2019). Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and BrafV600E-Induced Tumorigenesis.. Cancer cell.
- Izaskun Mallona, Susanna Ausso, Anna Diez-Villanueva, Victor Moreno, & Miguel A. Peinado (2018). DNA co-methylation networks outline the structure and remodeling dynamics of colorectal cancer epigenome. bioRxiv.
- Buj R, Mallona I, Díez-Villanueva A, Zafón C, Mate JL, Roca M, Puig-Domingo M, Reverter JL, Mauricio D, Peinado MA, & Jordà M (2018). Kallikreins stepwise scoring reveals three subtypes of papillary thyroid cancer with prognostic applications.. Thyroid : official journal of the American Thyroid Association.
- Mallona I, Sierco A, & Peinado MA (2018). The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data.. Methods in molecular biology (Clifton, N.J.).
- Mallona, I., & Peinado, M. (2017). Truke, a web tool to check for and handle excel misidentified gene symbols. BMC Genomics, 18(1).
- Mallona, I., Díez-Villanueva, A., Martín, B., & Peinado, M. (2017). Chainy: an universal tool for standardized relative quantification in real-time PCR. Bioinformatics, 33(9), 1411–1413.
- Jordà, M., Díez-Villanueva, A., Mallona, I., Martín, B., Lois, S., Barrera, V., Esteller, M., Vavouri, T., & Peinado, M. (2016). The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells. Genome Research, 27(1), 118–132.
- Buj, R., Mallona, I., Díez-Villanueva, A., Barrera, V., Mauricio, D., Puig-Domingo, M., Reverter, J., Matias-Guiu, X., Azuara, D., Ramírez, J., Alonso, S., Rosell, R., Capellà, G., Perucho, M., Robledo, M., Peinado, M., & Jordà, M. (2016). Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples. Oncotarget, 7(9), 10536–10546.
- Mallona, I., Jordà, M., & Peinado, M. (2016). A knowledgebase of the human Alu repetitive elements. Journal of Biomedical Informatics, 60, 77–83.
- Carrió, E., Díez-Villanueva, A., Lois, S., Mallona, I., Cases, I., Forn, M., Peinado, M., & Suelves, M. (2015). Deconstruction of DNA methylation patterns during myogenesis reveals specific epigenetic events in the establishment of the skeletal muscle lineage. STEM CELLS, n/a–n/a.
- Terry, M., & Mallona, I. (2015). First record of albinism in salema, Sarpa salpa (Perciformes: Sparidae), in the Mediterranean Sea. Marine Biodiversity Records, 8.
- Díez-Villanueva, A., Mallona, I., & Peinado, M. (2015). Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer. Epigenetics & Chromatin, 8(1).
- Mallona, I., Díez-Villanueva, A., & Peinado, M. (2014). Methylation plotter: a web tool for dynamic visualization of DNA methylation data. Source Code for Biology and Medicine, 9(1).
- Weiss, J., Mallona, I., Gomez-di-Marco, P., Fernández-Valera, J., & Egea-Cortines, M. (2012). Genotyping< i> Antirrhinum commercial varieties using miniature inverted-repeat transposable elements (MITEs). Scientia Horticulturae, 144, 161-167.
- Mallona, I., Egea-Cortines, M., & Weiss, J. (2011). Conserved and Divergent Rhythms of Crassulacean Acid Metabolism-Related and Core Clock Gene Expression in the Cactus Opuntia ficus-indica . Plant Physiology, 156(4), 1978–1989.
- Mallona, I., Weiss, J., & Egea-Cortines, M. (2011). pcrEfficiency: a Web tool for PCR amplification efficiency prediction. BMC Bioinformatics, 12(1).
- Mallona, I., Lischewski, S., Weiss, J., Hause, B., & Egea-Cortines, M. (2010). Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida. BMC Plant Biology, 10(1).