| An organoid platform for ovarian cancer captures intra-and interpatient heterogeneity O Kopper, CJ De Witte, K Lõhmussaar, JE Valle-Inclan, N Hami, L Kester, ... Nature medicine 25 (5), 838-849, 2019 | 738 | 2019 |
| Mapping and phasing of structural variation in patient genomes using nanopore sequencing M Cretu Stancu, MJ Van Roosmalen, I Renkens, MM Nieboer, ... Nature communications 8 (1), 1326, 2017 | 411 | 2017 |
| Patient-derived ovarian cancer organoids mimic clinical response and exhibit heterogeneous inter-and intrapatient drug responses CJ de Witte, JE Valle-Inclan, N Hami, K Lõhmussaar, O Kopper, ... Cell reports 31 (11), 2020 | 218 | 2020 |
| Patient-derived organoids model cervical tissue dynamics and viral oncogenesis in cervical cancer K Lõhmussaar, R Oka, JE Valle-Inclan, MHH Smits, H Wardak, J Korving, ... Cell Stem Cell 28 (8), 1380-1396. e6, 2021 | 146 | 2021 |
| GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing DL Cameron, J Baber, C Shale, JE Valle-Inclan, N Besselink, ... Genome biology 22 (1), 1-25, 2021 | 133 | 2021 |
| Long-read annotation: automated eukaryotic genome annotation based on long-read cDNA sequencing DE Cook, JE Valle-Inclan, A Pajoro, H Rovenich, BPHJ Thomma, L Faino Plant physiology 179 (1), 38-54, 2019 | 66 | 2019 |
| ERα-associated translocations underlie oncogene amplifications in breast cancer JJK Lee, YL Jung, TC Cheong, J Espejo Valle-Inclan, C Chu, DC Gulhan, ... Nature 618 (7967), 1024-1032, 2023 | 64 | 2023 |
| Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing C Stangl, S de Blank, I Renkens, L Westera, T Verbeek, JE Valle-Inclan, ... Nature Communications 11 (1), 2861, 2020 | 63 | 2020 |
| GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number DL Cameron, J Baber, C Shale, AT Papenfuss, JE Valle-Inclan, ... BioRxiv, 781013, 2019 | 60 | 2019 |
| De novo detection of somatic mutations in high-throughput single-cell profiling data sets F Muyas, CM Sauer, JE Valle-Inclán, R Li, R Rahbari, TJ Mitchell, ... Nature biotechnology 42 (5), 758-767, 2024 | 46 | 2024 |
| Mitotic clustering of pulverized chromosomes from micronuclei YF Lin, Q Hu, A Mazzagatti, JE Valle-Inclán, EG Maurais, R Dahiya, ... Nature 618 (7967), 1041-1048, 2023 | 45 | 2023 |
| Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients JE Valle-Inclan, C Stangl, AC de Jong, LF van Dessel, MJ van Roosmalen, ... Genome medicine 13 (1), 86, 2021 | 33* | 2021 |
| A multi-platform reference for somatic structural variation detection JE Valle-Inclan, NJM Besselink, E de Bruijn, DL Cameron, J Ebler, ... Cell Genomics 2 (6), 2022 | 29 | 2022 |
| The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only E Datema, RJM Hulzink, L Blommers, J Espejo Valle-Inclan, ... BioRxiv, 084772, 2016 | 25 | 2016 |
| Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors Q Hu, J Espejo Valle-Inclán, R Dahiya, A Guyer, A Mazzagatti, ... Nature communications 15 (1), 5611, 2024 | 7 | 2024 |
| ReConPlot: an R package for the visualization and interpretation of genomic rearrangements J Espejo Valle-Inclán, I Cortés-Ciriano Bioinformatics 39 (12), btad719, 2023 | 7 | 2023 |
| The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance JL Engel, X Zhang, M Wu, Y Wang, JE Valle-Inclán, Q Hu, ... Cell 187 (21), 6055-6070. e22, 2024 | 5 | 2024 |
| SAVANA: reliable analysis of somatic structural variants and copy number aberrations in clinical samples using long-read sequencing H Elrick, CM Sauer, J Espejo Valle-Inclan, K Trevers, M Tanguy, ... bioRxiv, 2024.07. 25.604944, 2024 | 4 | 2024 |
| Noncoding mutations drive persistence of a founder preleukemic clone which initiates late relapse in T-ALL D O’Connor, JE Valle-Inclán, L Conde, G Bloye, S Rahman, JR Costa, ... Blood 143 (10), 933-937, 2024 | 4 | 2024 |
| Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution JE Valle-Inclan, S De Noon, K Trevers, H Elrick, IAEM van Belzen, ... Cell 188 (2), 352-370. e22, 2025 | 1* | 2025 |
