Jose Espejo Valle-Inclan

Employment

• Champalimaud Foundation Principal Investigator
  2024 - Present
• European Bioinformatics Institute Postdoctoral Fellow
  2021 - Present
• Universitair Medisch Centrum Utrecht PhD student
  2016 - 2020

Education

• UMC Utrecht PhD
  2016 - 2020
• Wageningen University & Research MSc Bioinformatics
  2014 - 2016
• Universidad Autonoma de Madrid Facultad de Ciencias BSc Biochemistry
  2010 - 2014

Projects & Funding

Projects & funding information is unavailable.

Publications (27)

• SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing
  Nature Methods 2025 DOI: 10.1038/s41592-025-02708-0
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• Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution
  Cell 2025 DOI: 10.1016/j.cell.2024.12.005
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• The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance
  Cell 2024 DOI: 10.1016/j.cell.2024.08.001
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• SAVANA: reliable analysis of somatic structural variants and copy number aberrations in clinical samples using long-read sequencing
  2024 DOI: 10.1101/2024.07.25.604944
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• De novo detection of somatic mutations in high-throughput single-cell profiling data sets
  Nature Biotechnology 2024 DOI: 10.1038/s41587-023-01863-z
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• Noncoding mutations drive persistence of a founder preleukemic clone which initiates late relapse in T-ALL
  David O’Connor, Jose Espejo Valle-Inclán, Lucía Conde +15 more
  Blood 2024 DOI: 10.1182/blood.2023021906
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• Mechanisms underpinning osteosarcoma genome complexity and evolution
  2023 DOI: 10.1101/2023.12.29.573403
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• ReConPlot-an R package for the visualization and interpretation of genomic rearrangements.
  Bioinformatics (Oxford, England) 2023 DOI: 10.1093/bioinformatics/btad719
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• Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors
  2023 DOI: 10.1101/2023.08.10.552800
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• ERα-associated translocations underlie oncogene amplifications in breast cancer
  Nature 2023 DOI: 10.1038/s41586-023-06057-w
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• ReConPlot – an R package for the visualization and interpretation of genomic rearrangements
  2023 DOI: 10.1101/2023.02.24.529890
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• Mitotic clustering of pulverized chromosomes from micronuclei
  2022 DOI: 10.1101/2022.07.19.500697
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• GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.
  Genome biology 2021 DOI: 10.1186/s13059-021-02423-x
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• Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients.
  Genome medicine 2021 DOI: 10.1186/s13073-021-00899-7
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• Patient-derived organoids model cervical tissue dynamics and viral oncogenesis in cervical cancer.
  Cell stem cell 2021 DOI: 10.1016/j.stem.2021.03.012
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• A multi-platform reference for somatic structural variation detection
  2020 DOI: 10.1101/2020.10.15.340497
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• GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
  2020 DOI: 10.1101/2020.07.09.196527
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• Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing.
  Nature communications 2020 DOI: 10.1038/s41467-020-16641-7
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• Patient-Derived Ovarian Cancer Organoids Mimic Clinical Response and Exhibit Heterogeneous Inter- and Intrapatient Drug Responses.
  Cell reports 2020 DOI: 10.1016/j.celrep.2020.107762
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• Rapid identification of genomic structural variations with nanopore sequencing enables blood-based cancer monitoring
  2019 DOI: 10.1101/19011932
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