All Stories

  1. fastder: fast, annotation-agnostic detection of expressed regions from RNA-seq coverage and splicing data

    Article • June 2026, openRxiv

    Izaskun Mallona

  2. Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation

    Article • May 2026, openRxiv

    Izaskun Mallona

  3. rhapsodist: a reproducible Snakemake workflow for BD Rhapsody single-cell RNA-seq data

    Article • April 2026, openRxiv

    Izaskun Mallona

  4. A scalable human-zebrafish xenotransplantation model reveals gastrosome-mediated processing of dying neurons by human microglia

    Article • Communications Biology, April 2026, Springer Science + Business Media

    Izaskun Mallona

  5. BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration

    Article • PLoS Computational Biology, February 2026, PLOS

    Izaskun Mallona

  6. Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment

    Article • Nature Communications, December 2025, Springer Science + Business Media

    Izaskun Mallona

  7. RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing

    Article • Nature Communications, December 2025, Springer Science + Business Media

    Izaskun Mallona

  8. Building a continuous benchmarking ecosystem in bioinformatics

    Article • PLoS Computational Biology, November 2025, PLOS

    Izaskun Mallona

  9. Harnessing the potential of spatial statistics for spatial omics data with pasta

    Article • Nucleic Acids Research, September 2025, Oxford University Press (OUP)

    Izaskun Mallona

  10. A scalable human-zebrafish xenotransplantation model reveals gastrosome-mediated processing of dying neurons by human microglia

    Article • August 2025, openRxiv

    Izaskun Mallona

  11. BiCLUM: Bilateral Contrastive Learning for Unpaired Single-Cell Multi-Omics Integration

    Article • March 2025, Cold Spring Harbor Laboratory Press

    Izaskun Mallona

  12. Ten simple rules for computational biologists collaborating with wet lab researchers

    Article • PLoS Computational Biology, June 2024, PLOS

    Izaskun Mallona

  13. RoCK and ROI: Single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing

    Article • May 2024, Cold Spring Harbor Laboratory Press

    Izaskun Mallona

  14. A model of human neural networks reveals NPTX2 pathology in ALS and FTLD

    Article • Nature, February 2024, Springer Science + Business Media

    Izaskun Mallona

  15. Targeted CRISPR-Cas9 screening identifies transcription factor network controlling murine haemato-endothelial fate commitment

    Article • January 2024, Cold Spring Harbor Laboratory Press

    Izaskun Mallona

  16. Loss of TDP‐43 oligomerization or RNA binding elicits distinct aggregation patterns

    Article • The EMBO Journal, July 2023, Springer Science + Business Media

    Izaskun Mallona

  17. Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability

    Article • Genome Biology, May 2023, Springer Science + Business Media

    Izaskun Mallona

  18. Long-term self-renewing stem cells in the adult mouse hippocampus identified by intravital imaging

    Article • Nature Neuroscience, December 2020, Springer Science + Business Media

    Izaskun Mallona

  19. Flanking sequence preference modulates de novo DNA methylation in the mouse genome

    Article • Nucleic Acids Research, December 2020, Oxford University Press (OUP)

    Izaskun Mallona

  20. Flanking sequence preference modulatesde novoDNA methylation in the mouse genome

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Izaskun Mallona

  21. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat

    Article • Epigenetics, February 2020, Taylor & Francis

    Izaskun Mallona

  22. A new bioinformatic pipeline allows the design of small, targeted gene panels for efficient TMB estimation

    Article • Annals of Oncology, April 2019, Elsevier

    Izaskun Mallona

  23. Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and BrafV600E-Induced Tumorigenesis

    Article • Cancer Cell, February 2019, Elsevier

    Izaskun Mallona

  24. Modular dynamics of DNA co-methylation networks exposes the functional organization of colon cancer cells' genome

    Article • September 2018, Cold Spring Harbor Laboratory Press

    Izaskun Mallona

  25. Kallikreins Stepwise Scoring Reveals Three Subtypes of Papillary Thyroid Cancer with Prognostic Implications

    Article • Thyroid, May 2018, Mary Ann Liebert Inc

    Izaskun Mallona

  26. A UCSC Genome Browser layer to the pancancer TCGA DNA methylation data

    Article • January 2018, Springer Science + Business Media

    Izaskun Mallona

  27. Truke, a Web tool for checking for and fixing genomic data corrupted by spreadsheet software

    Article • BMC Genomics, March 2017, Springer Science + Business Media

    Izaskun Mallona

  28. Chainy, a Web tool to analyze real-time PCR data

    Article • Bioinformatics, January 2017, Oxford University Press (OUP)

    Izaskun Mallona

  29. The epigenetic landscape ofAlurepeats delineates the structural and functional genomic architecture of colon cancer cells

    Article • Genome Research, December 2016, Cold Spring Harbor Laboratory Press

    Izaskun Mallona

  30. An organized collection of data related to human Alu repeats

    Article • Journal of Biomedical Informatics, April 2016, Elsevier

    Izaskun Mallona

  31. Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples

    Article • Oncotarget, February 2016, Impact Journals, LLC

    Izaskun Mallona

  32. Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer

    Article • Epigenetics & Chromatin, June 2015, Springer Science + Business Media

    Izaskun Mallona

  33. Deconstruction of DNA Methylation Patterns During Myogenesis Reveals Specific Epigenetic Events in the Establishment of the Skeletal Muscle Lineage

    Article • Stem Cells, April 2015, Wiley

    Izaskun Mallona

  34. First record of albinism in salema, Sarpa salpa (Perciformes: Sparidae), in the Mediterranean Sea

    Article • Marine Biodiversity Records, January 2015, Cambridge University Press

    Izaskun Mallona

  35. Methylation plotter: a web tool for dynamic visualization of DNA methylation data

    Article • Source Code for Biology and Medicine, January 2014, Springer Science + Business Media

    Izaskun Mallona

  36. Genotyping Antirrhinum commercial varieties using miniature inverted-repeat transposable elements (MITEs)

    Article • Scientia Horticulturae, September 2012, Elsevier

    Izaskun Mallona

  37. Conserved and Divergent Rhythms of Crassulacean Acid Metabolism-Related and Core Clock Gene Expression in the Cactus Opuntia ficus-indica

    Article • PLANT PHYSIOLOGY, June 2011, American Society of Plant Biologists (ASPB)

    Izaskun Mallona

  38. Is PCR efficiency predictable?

    Article • BMC Bioinformatics, January 2011, Springer Science + Business Media

    Izaskun Mallona

  39. Reference gene selection for real time QPCR in Petunia

    Article • BMC Plant Biology, January 2010, Springer Science + Business Media

    Izaskun Mallona