Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Cretu Stancu, Mircea, van Roosmalen, Markus J., Renkens, Ivo, Nieboer, Marleen M., Middelkamp, Sjors, de Ligt, Joep, Pregno, Giulia, Giachino, Daniela, Mandrile, Giorgia, Espejo Valle-Inclan, Jose, Korzelius, Jerome, de Bruijn, Ewart, Cuppen, Edwin, Talkowski, Michael E., Marschall, Tobias, de Ridder, Jeroen, Kloosterman, Wigard P.
Published in Nature communications (06.11.2017)
Published in Nature communications (06.11.2017)
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Journal Article
Patient-Derived Ovarian Cancer Organoids Mimic Clinical Response and Exhibit Heterogeneous Inter- and Intrapatient Drug Responses
de Witte, Chris Jenske, Espejo Valle-Inclan, Jose, Hami, Nizar, Lõhmussaar, Kadi, Kopper, Oded, Vreuls, Celien Philomena Henrieke, Jonges, Geertruida Nellie, van Diest, Paul, Nguyen, Luan, Clevers, Hans, Kloosterman, Wigard Pieter, Cuppen, Edwin, Snippert, Hugo Johannes Gerhardus, Zweemer, Ronald Peter, Witteveen, Petronella Oda, Stelloo, Ellen
Published in Cell reports (Cambridge) (16.06.2020)
Published in Cell reports (Cambridge) (16.06.2020)
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Journal Article
Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing
Stangl, Christina, de Blank, Sam, Renkens, Ivo, Westera, Liset, Verbeek, Tamara, Valle-Inclan, Jose Espejo, González, Rocio Chamorro, Henssen, Anton G., van Roosmalen, Markus J., Stam, Ronald W., Voest, Emile E., Kloosterman, Wigard P., van Haaften, Gijs, Monroe, Glen R.
Published in Nature communications (05.06.2020)
Published in Nature communications (05.06.2020)
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Journal Article
A multi-platform reference for somatic structural variation detection
Espejo Valle-Inclan, Jose, Besselink, Nicolle J.M., de Bruijn, Ewart, Cameron, Daniel L., Ebler, Jana, Kutzera, Joachim, van Lieshout, Stef, Marschall, Tobias, Nelen, Marcel, Priestley, Peter, Renkens, Ivo, Roemer, Margaretha G.M., van Roosmalen, Markus J., Wenger, Aaron M., Ylstra, Bauke, Fijneman, Remond J.A., Kloosterman, Wigard P., Cuppen, Edwin
Published in Cell genomics (08.06.2022)
Published in Cell genomics (08.06.2022)
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Journal Article
Patient-derived organoids model cervical tissue dynamics and viral oncogenesis in cervical cancer
Lõhmussaar, Kadi, Oka, Rurika, Espejo Valle-Inclan, Jose, Smits, Milou H.H., Wardak, Hila, Korving, Jeroen, Begthel, Harry, Proost, Natalie, van de Ven, Marieke, Kranenburg, Onno W., Jonges, Trudy G.N., Zweemer, Ronald P., Veersema, Sebastiaan, van Boxtel, Ruben, Clevers, Hans
Published in Cell stem cell (05.08.2021)
Published in Cell stem cell (05.08.2021)
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Journal Article
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
Cameron, Daniel L, Baber, Jonathan, Shale, Charles, Valle-Inclan, Jose Espejo, Besselink, Nicolle, van Hoeck, Arne, Janssen, Roel, Cuppen, Edwin, Priestley, Peter, Papenfuss, Anthony T
Published in Genome Biology (12.07.2021)
Published in Genome Biology (12.07.2021)
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Journal Article
ERα-associated translocations underlie oncogene amplifications in breast cancer
Lee, Jake June-Koo, Jung, Youngsook Lucy, Cheong, Taek-Chin, Espejo Valle-Inclan, Jose, Chu, Chong, Gulhan, Doga C., Ljungström, Viktor, Jin, Hu, Viswanadham, Vinayak V., Watson, Emma V., Cortés-Ciriano, Isidro, Elledge, Stephen J., Chiarle, Roberto, Pellman, David, Park, Peter J.
Published in Nature (London) (29.06.2023)
Published in Nature (London) (29.06.2023)
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Journal Article
Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors
Hu, Qing, Espejo Valle-Inclán, Jose, Dahiya, Rashmi, Guyer, Alison, Mazzagatti, Alice, Maurais, Elizabeth G., Engel, Justin L., Lu, Huiming, Davis, Anthony J., Cortés-Ciriano, Isidro, Ly, Peter
Published in Nature communications (04.07.2024)
Published in Nature communications (04.07.2024)
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Journal Article
Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients
Valle-Inclan, Jose Espejo, Stangl, Christina, de Jong, Anouk C, van Dessel, Lisanne F, van Roosmalen, Markus J, Helmijr, Jean C A, Renkens, Ivo, Janssen, Roel, de Blank, Sam, de Witte, Chris J, Martens, John W M, Jansen, Maurice P H M, Lolkema, Martijn P, Kloosterman, Wigard P
Published in Genome medicine (18.05.2021)
Published in Genome medicine (18.05.2021)
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Journal Article
ReConPlot: an R package for the visualization and interpretation of genomic rearrangements
Espejo Valle-Inclán, Jose, Cortés-Ciriano, Isidro
Published in Bioinformatics (Oxford, England) (01.12.2023)
Published in Bioinformatics (Oxford, England) (01.12.2023)
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Journal Article
De novo detection of somatic mutations in high-throughput single-cell profiling data sets
Muyas, Francesc, Sauer, Carolin M., Valle-Inclán, Jose Espejo, Li, Ruoyan, Rahbari, Raheleh, Mitchell, Thomas J., Hormoz, Sahand, Cortés-Ciriano, Isidro
Published in Nature biotechnology (06.07.2023)
Published in Nature biotechnology (06.07.2023)
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Journal Article
Mitotic clustering of pulverized chromosomes from micronuclei
Lin, Yu-Fen, Hu, Qing, Mazzagatti, Alice, Valle-Inclán, Jose Espejo, Maurais, Elizabeth G., Dahiya, Rashmi, Guyer, Alison, Sanders, Jacob T., Engel, Justin L., Nguyen, Giaochau, Bronder, Daniel, Bakhoum, Samuel F., Cortés-Ciriano, Isidro, Ly, Peter
Published in Nature (London) (29.06.2023)
Published in Nature (London) (29.06.2023)
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Journal Article
The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance
Engel, Justin L., Zhang, Xiao, Wu, Mingming, Wang, Yan, Espejo Valle-Inclán, Jose, Hu, Qing, Woldehawariat, Kidist S., Sanders, Mathijs A., Smogorzewska, Agata, Chen, Jin, Cortés-Ciriano, Isidro, Lo, Roger S., Ly, Peter
Published in Cell (17.10.2024)
Published in Cell (17.10.2024)
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Journal Article
Noncoding mutations drive persistence of a founder preleukemic clone which initiates late relapse in T-ALL
O’Connor, David, Valle-Inclán, Jose Espejo, Conde, Lucia, Bloye, Gianna, Rahman, Sunniyat, Costa, Joana R., Bartram, Jack, Adams, Stuart, Wright, Gary, Elrick, Hillary, Wall, Kerry, Dyer, Sara, Howell, Christopher, Jigoulina, Galina, Herrero, Javier, Cortes-Ciriano, Isidro, Moorman, Anthony V., Mansour, Marc R.
Published in Blood (07.03.2024)
Published in Blood (07.03.2024)
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Journal Article
Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors
Hu, Qing, Valle-Inclan, Jose Espejo, Dahiya, Rashmi, Guyer, Alison, Mazzagatti, Alice, Maurais, Elizabeth G, Engel, Justin L, Cortés-Ciriano, Isidro, Ly, Peter
Published in bioRxiv (11.08.2023)
Published in bioRxiv (11.08.2023)
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Journal Article
An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity
Kopper, Oded, de Witte, Chris J., Lõhmussaar, Kadi, Valle-Inclan, Jose Espejo, Hami, Nizar, Kester, Lennart, Balgobind, Anjali Vanita, Korving, Jeroen, Proost, Natalie, Begthel, Harry, van Wijk, Lise M., Revilla, Sonia Aristín, Theeuwsen, Rebecca, van de Ven, Marieke, van Roosmalen, Markus J., Ponsioen, Bas, Ho, Victor W. H., Neel, Benjamin G., Bosse, Tjalling, Gaarenstroom, Katja N., Vrieling, Harry, Vreeswijk, Maaike P. G., van Diest, Paul J., Witteveen, Petronella O., Jonges, Trudy, Bos, Johannes L., van Oudenaarden, Alexander, Zweemer, Ronald P., Snippert, Hugo J. G., Kloosterman, Wigard P., Clevers, Hans
Published in Nature medicine (01.05.2019)
Published in Nature medicine (01.05.2019)
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Journal Article
Abstract LB080: SAVANA: a computational method to characterize structural variation in human cancer genomes using nanopore sequencing
Elrick, Hillary, Valle-Inclan, Jose Espejo, Trevers, Katherine E., Muyas, Francesc, Cascão, Rita, Afonso, Angela, Faria, Cláudia C., Flanagan, Adrienne M., Cortés-Ciriano, Isidro
Published in Cancer research (Chicago, Ill.) (14.04.2023)
Published in Cancer research (Chicago, Ill.) (14.04.2023)
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