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ArticlesPeer ReviewedFull Text
Accurate detection of mosaic variants in sequencing data without matched controls
Author / Creator:Dou, Yanmei ; Kwon, Minseok ; Rodin, Rachel E. ; Cortés-Ciriano, Isidro ; Doan, Ryan ; Luquette, Lovelace J. ; Galor, Alon ; Bohrson, Craig ; Walsh, Christopher A. ; Park, Peter J.
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2020-03, Vol.38 (3), p.314-319
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A user guide for the online exploration and visualization of PCAWG data
Author / Creator:Goldman, Mary J. ; Zhang, Junjun ; Fonseca, Nuno A. ; Cortés-Ciriano, Isidro ; Xiang, Qian ; Craft, Brian ; Piñeiro-Yáñez, Elena ; O’Connor, Brian D. ; Bazant, Wojciech ; Barrera, Elisabet ; Muñoz-Pomer, Alfonso ; Petryszak, Robert ; Füllgrabe, Anja ; Al-Shahrour, Fatima ; Keays, Maria ; Haussler, David ; Weinstein, John N. ; Huber, Wolfgang ; Valencia, Alfonso ; Park, Peter J. ; Papatheodorou, Irene ; Zhu, Jingchun ; Ferretti, Vincent ; Vazquez, Miguel
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-07, Vol.11 (1), p.3400-3400, Article 3400
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Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors
Author / Creator: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
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-07, Vol.15 (1), p.5611-13, Article 5611
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Transcriptional signals of transformation in human cancer
Author / Creator:Kildisiute, Gerda ; Kalyva, Maria ; Elmentaite, Rasa ; van Dongen, Stijn ; Thevanesan, Christine ; Piapi, Alice ; Ambridge, Kirsty ; Prigmore, Elena ; Haniffa, Muzlifah ; Teichmann, Sarah A ; Straathof, Karin ; Cortés-Ciriano, Isidro ; Behjati, Sam ; Young, Matthew D
Publisher:England: BioMed Central Ltd
Journal title:Genome medicine, 2024-01, Vol.16 (1), p.8-10, Article 8
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Profilin 1 deficiency drives mitotic defects and reduces genome stability
Author / Creator:Scotto di Carlo, Federica ; Russo, Sharon ; Muyas, Francesc ; Mangini, Maria ; Garribba, Lorenza ; Pazzaglia, Laura ; Genesio, Rita ; Biamonte, Flavia ; De Luca, Anna Chiara ; Santaguida, Stefano ; Scotlandi, Katia ; Cortés-Ciriano, Isidro ; Gianfrancesco, Fernando
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2023-01, Vol.6 (1), p.9-9, Article 9
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Detecting the mutational signature of homologous recombination deficiency in clinical samples
Author / Creator:Gulhan, Doga C. ; Lee, Jake June-Koo ; Melloni, Giorgio E. M. ; Cortés-Ciriano, Isidro ; Park, Peter J.
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2019-05, Vol.51 (5), p.912-919
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Computational analysis of cancer genome sequencing data
Author / Creator:Cortés-Ciriano, Isidro ; Gulhan, Doga C. ; Lee, Jake June-Koo ; Melloni, Giorgio E. M. ; Park, Peter J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Genetics, 2022-05, Vol.23 (5), p.298-314
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KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images
Author / Creator:Cortés-Ciriano, Isidro ; Bender, Andreas
Publisher:Cham: Springer International Publishing
Journal title:Journal of cheminformatics, 2019-06, Vol.11 (1), p.41-16, Article 41
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QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction
Author / Creator:Cortés-Ciriano, Isidro ; Škuta, Ctibor ; Bender, Andreas ; Svozil, Daniel
Publisher:Cham: Springer International Publishing
Journal title:Journal of cheminformatics, 2020-06, Vol.12 (1), p.41-17, Article 41
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The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients
Author / Creator:Muyas, Francesc ; Rodriguez, Manuel José Gómez ; Cascão, Rita ; Afonso, Angela ; Sauer, Carolin M. ; Faria, Claudia C. ; Cortés-Ciriano, Isidro ; Flores, Ignacio
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-01, Vol.15 (1), p.82-82, Article 82
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A molecular portrait of microsatellite instability across multiple cancers
Author / Creator:Cortes-Ciriano, Isidro ; Lee, Sejoon ; Park, Woong-Yang ; Kim, Tae-Min ; Park, Peter J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2017-06, Vol.8 (1), p.15180-15180, Article 15180
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Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
Author / Creator:Cortés-Ciriano, Isidro ; Lee, Jake June-Koo ; Xi, Ruibin ; Jain, Dhawal ; Jung, Youngsook L. ; Yang, Lixing ; Gordenin, Dmitry ; Klimczak, Leszek J. ; Zhang, Cheng-Zhong ; Pellman, David S. ; Park, Peter J.
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2020-03, Vol.52 (3), p.331-341
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Patterns of somatic structural variation in human cancer genomes
Author / Creator:Li, Yilong ; Roberts, Nicola D. ; Wala, Jeremiah A. ; Shapira, Ofer ; Schumacher, Steven E. ; Kumar, Kiran ; Khurana, Ekta ; Waszak, Sebastian ; Korbel, Jan O. ; Haber, James E. ; Imielinski, Marcin ; Weischenfeldt, Joachim ; Beroukhim, Rameen ; Campbell, Peter J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2020-02, Vol.578 (7793), p.112-121
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ERα-associated translocations underlie oncogene amplifications in breast cancer
Author / Creator: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.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2023-06, Vol.618 (7967), p.1024-1032
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Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
Author / Creator:Akdemir, Kadir C. ; Le, Victoria T. ; Chandran, Sahaana ; Li, Yilong ; Verhaak, Roel G. ; Beroukhim, Rameen ; Campbell, Peter J. ; Chin, Lynda ; Dixon, Jesse R. ; Futreal, P. Andrew
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2020-03, Vol.52 (3), p.294-305
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ArticlesPeer ReviewedFull Text
Mitotic clustering of pulverized chromosomes from micronuclei
Author / Creator: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
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2023-06, Vol.618 (7967), p.1041-1048
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Linked-read analysis identifies mutations in single-cell DNA-sequencing data
Author / Creator:Bohrson, Craig L. ; Barton, Alison R. ; Lodato, Michael A. ; Rodin, Rachel E. ; Luquette, Lovelace J. ; Viswanadham, Vinay V. ; Gulhan, Doga C. ; Cortés-Ciriano, Isidro ; Sherman, Maxwell A. ; Kwon, Minseok ; Coulter, Michael E. ; Galor, Alon ; Walsh, Christopher A. ; Park, Peter J.
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2019-04, Vol.51 (4), p.749-754
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The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts
Author / Creator:Saini, Natalie ; Roberts, Steven A ; Klimczak, Leszek J ; Chan, Kin ; Grimm, Sara A ; Dai, Shuangshuang ; Fargo, David C ; Boyer, Jayne C ; Kaufmann, William K ; Taylor, Jack A ; Lee, Eunjung ; Cortes-Ciriano, Isidro ; Park, Peter J ; Schurman, Shepherd H ; Malc, Ewa P ; Mieczkowski, Piotr A ; Gordenin, Dmitry A
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2016-10, Vol.12 (10), p.e1006385
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Genomic basis for RNA alterations in cancer
Author / Creator:Calabrese, Claudia ; Davidson, Natalie R. ; Demircioğlu, Deniz ; Fonseca, Nuno A. ; He, Yao ; Kahles, André ; Lehmann, Kjong-Van ; Liu, Fenglin ; Shiraishi, Yuichi ; Soulette, Cameron M. ; Urban, Lara ; Greger, Liliana ; Li, Siliang ; Liu, Dongbing ; Perry, Marc D. ; Xiang, Qian ; Zhang, Fan ; Zhang, Junjun ; Bailey, Peter ; Erkek, Serap ; Hoadley, Katherine A. ; Hou, Yong ; Huska, Matthew R. ; Kilpinen, Helena ; Korbel, Jan O. ; Marin, Maximillian G. ; Markowski, Julia ; Nandi, Tannistha ; Pan-Hammarström, Qiang ; Pedamallu, Chandra Sekhar ; Siebert, Reiner ; Stark, Stefan G. ; Su, Hong ; Tan, Patrick ; Waszak, Sebastian M. ; Yung, Christina ; Zhu, Shida ; Awadalla, Philip ; Creighton, Chad J. ; Meyerson, Matthew ; Ouellette, B. F. Francis ; Wu, Kui ; Yang, Huanming ; Brazma, Alvis ; Brooks, Angela N. ; Göke, Jonathan ; Rätsch, Gunnar ; Schwarz, Roland F. ; Stegle, Oliver ; Zhang, Zemin
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2020-02, Vol.578 (7793), p.129-136
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ArticlesPeer ReviewedFull Text
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules
Author / Creator:Paricharak, Shardul ; Cortés-Ciriano, Isidro ; IJzerman, Adriaan P ; Malliavin, Thérèse E ; Bender, Andreas
Publisher:Cham: Springer International Publishing
Journal title:Journal of cheminformatics, 2015-04, Vol.7 (1), p.15-15, Article 15
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Showing 1 to 20 of 78 results

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Accurate detection of mosaic variants in sequencing data without matched controls

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A user guide for the online exploration and visualization of PCAWG data

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Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors

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Transcriptional signals of transformation in human cancer

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Profilin 1 deficiency drives mitotic defects and reduces genome stability

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Detecting the mutational signature of homologous recombination deficiency in clinical samples

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Computational analysis of cancer genome sequencing data

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KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images

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QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction

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The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

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A molecular portrait of microsatellite instability across multiple cancers

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Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

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Patterns of somatic structural variation in human cancer genomes

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ERα-associated translocations underlie oncogene amplifications in breast cancer

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Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

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Mitotic clustering of pulverized chromosomes from micronuclei

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Linked-read analysis identifies mutations in single-cell DNA-sequencing data

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The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts

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Genomic basis for RNA alterations in cancer

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Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules

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