Zobrazeno 1 - 10
of 23
pro vyhledávání: '"Erik N Bergstrom"'
Autor:
Azhar Khandekar, Raviteja Vangara, Mark Barnes, Marcos Díaz-Gay, Ammal Abbasi, Erik N. Bergstrom, Christopher D. Steele, Nischalan Pillay, Ludmil B. Alexandrov
Publikováno v:
BMC Genomics, Vol 24, Iss 1, Pp 1-9 (2023)
Abstract Background All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fi
Externí odkaz:
https://doaj.org/article/e277fb79cb7e4bdb8efd3acb49845605
Autor:
Burçak Otlu, Marcos Díaz-Gay, Ian Vermes, Erik N. Bergstrom, Maria Zhivagui, Mark Barnes, Ludmil B. Alexandrov
Publikováno v:
Cell Reports, Vol 42, Iss 8, Pp 112930- (2023)
Summary: The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay between mut
Externí odkaz:
https://doaj.org/article/2bad3d2278f34f4d858be7fc84bbc8cd
Publikováno v:
BMC Bioinformatics, Vol 21, Iss 1, Pp 1-10 (2020)
Abstract Background Performing a statistical test requires a null hypothesis. In cancer genomics, a key challenge is the fast generation of accurate somatic mutational landscapes that can be used as a realistic null hypothesis for making biological d
Externí odkaz:
https://doaj.org/article/607653a1f6194867833f277b9264359a
SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events
Autor:
Erik N. Bergstrom, Mi Ni Huang, Uma Mahto, Mark Barnes, Michael R. Stratton, Steven G. Rozen, Ludmil B. Alexandrov
Publikováno v:
BMC Genomics, Vol 20, Iss 1, Pp 1-12 (2019)
Abstract Background Cancer genomes are peppered with somatic mutations imprinted by different mutational processes. The mutational pattern of a cancer genome can be used to identify and understand the etiology of the underlying mutational processes.
Externí odkaz:
https://doaj.org/article/15d692f5dc384868a0328f08ea0f4215
Autor:
Lise Mangiante, Nicolas Alcala, Alexandra Sexton-Oates, Alex Di Genova, Abel Gonzalez-Perez, Azhar Khandekar, Erik N. Bergstrom, Jaehee Kim, Xiran Liu, Ricardo Blazquez-Encinas, Colin Giacobi, Nolwenn Le Stang, Sandrine Boyault, Cyrille Cuenin, Severine Tabone-Eglinger, Francesca Damiola, Catherine Voegele, Maude Ardin, Marie-Cecile Michallet, Lorraine Soudade, Tiffany M. Delhomme, Arnaud Poret, Marie Brevet, Marie-Christine Copin, Sophie Giusiano-Courcambeck, Diane Damotte, Cecile Girard, Veronique Hofman, Paul Hofman, Jérôme Mouroux, Charlotte Cohen, Stephanie Lacomme, Julien Mazieres, Vincent Thomas de Montpreville, Corinne Perrin, Gaetane Planchard, Nathalie Rousseau, Isabelle Rouquette, Christine Sagan, Arnaud Scherpereel, Francoise Thivolet, Jean-Michel Vignaud, Didier Jean, Anabelle Gilg Soit Ilg, Robert Olaso, Vincent Meyer, Anne Boland-Auge, Jean-Francois Deleuze, Janine Altmuller, Peter Nuernberg, Alejandro Ibáñez-Costa, Justo P. Castaño, Sylvie Lantuejoul, Akram Ghantous, Charles Maussion, Pierre Courtiol, Hector Hernandez-Vargas, Christophe Caux, Nicolas Girard, Nuria Lopez-Bigas, Ludmil B. Alexandrov, Françoise Galateau-Salle, Matthieu Foll, Lynnette Fernandez-Cuesta
Publikováno v:
Nature Genetics
Nature Genetics, 2023, 55 (4), pp.607-618. ⟨10.1038/s41588-023-01321-1⟩
Nature Genetics, 2023, 55 (4), pp.607-618. ⟨10.1038/s41588-023-01321-1⟩
Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::34bf4a959d167d30c59abf20d776d9d7
https://www.hal.inserm.fr/inserm-04062865
https://www.hal.inserm.fr/inserm-04062865
Publikováno v:
Bioinformatics. 38:3470-3473
Motivation Clustered mutations are found in the human germline as well as in the genomes of cancer and normal somatic cells. Clustered events can be imprinted by a multitude of mutational processes, and they have been implicated in both cancer evolut
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fed42e4ba540d81442e4e29ddd4180f2
https://doi.org/10.1093/bioinformatics/btac335
https://doi.org/10.1093/bioinformatics/btac335
Autor:
Erik N. Bergstrom, Jens Luebeck, Mia Petljak, Azhar Khandekar, Mark Barnes, Tongwu Zhang, Christopher D. Steele, Nischalan Pillay, Maria Teresa Landi, Vineet Bafna, Paul S. Mischel, Reuben S. Harris, Ludmil B. Alexandrov
Publikováno v:
Nature. 602:510-517
Clustered somatic mutations are common in cancer genomes and previous analyses reveal several types of clustered single-base substitutions, which include doublet- and multi-base substitutions1–5, diffuse hypermutation termed omikli6, and longer str
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2c67f65fea310de64ce9bb584e5ddde2
https://doi.org/10.1038/s41586-022-04398-6
https://doi.org/10.1038/s41586-022-04398-6
Autor:
Erik N. Bergstrom, Ammal Abbasi, Marcos Díaz-Gay, Loïck Galland, Scott M. Lippman, Sylvain Ladoire, Ludmil B. Alexandrov
Breast and ovarian cancers harboring homologous recombination deficiencies (HRD) can benefit from platinum-based chemotherapies and PARP inhibitors. Standard diagnostic tests for detecting HRD utilize molecular profiling, which is not universally ava
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::00c5c756fadca0c9ed9830696c6695c7
https://doi.org/10.1101/2023.02.23.23285869
https://doi.org/10.1101/2023.02.23.23285869
Autor:
S M Ashiqul Islam, Irina I. Abnizova, James McKay, Yudou He, Estelle Chanudet, Behnoush Abedi-Ardekani, Dariush Nasrollahzadeh, Michael Eden, Alisa M. Goldstein, Jon W. Teague, Blandina T. Mmbaga, Nan Hu, Karl Smith-Byrne, Sandra Perdomo, Jingwei Wang, Christine Carreira, Jean-Yves Scoazec, Rebecca C. Fitzgerald, Luis Felipe Ribeiro, Michael R. Stratton, Samad Gharavi, Sergey Senkin, Erik N Bergstrom, Hiva Saffar, Sarah Moody, Sheila Coelho Soares-Lima, Pauline E Bucciarelli, Stefano Serra, Ghislaine Scelo, Charles Dzamalala, Valerie McCormack, Reza Malekzadeh, Hossein Poustchi, Valerie Gaborieau, Lia S Campos, Joshua R. Atkins, Paul Brennan, Emily Thomas, David T. Jones, Paul Richman, Farid Azmoudeh-Ardalan, Masoud Sotoudeh, Ahmadreza Niavarani, Tatsuhiro Shibata, Calli Latimer, Stephen Fitzgerald, Ludmil B Alexandrov, Ricardo Cortez Cardoso Penha, Abdolreza Fazel, Laura Humphreys, Azhar Khandekar, Arash Nikmanesh, Diana Menya
Publikováno v:
Nature Genetics. 53:1553-1563
Esophageal squamous cell carcinoma (ESCC) shows remarkable variation in incidence that is not fully explained by known lifestyle and environmental risk factors. It has been speculated that an unknown exogenous exposure(s) could be responsible. Here w
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::66b1022f330ee49ffe06d2fa49c29076
https://doi.org/10.1038/s41588-021-00928-6
https://doi.org/10.1038/s41588-021-00928-6
Autor:
S.M. Ashiqul Islam, Marcos Díaz-Gay, Yang Wu, Mark Barnes, Raviteja Vangara, Erik N. Bergstrom, Yudou He, Mike Vella, Jingwei Wang, Jon W. Teague, Peter Clapham, Sarah Moody, Sergey Senkin, Yun Rose Li, Laura Riva, Tongwu Zhang, Andreas J. Gruber, Christopher D. Steele, Burçak Otlu, Azhar Khandekar, Ammal Abbasi, Laura Humphreys, Natalia Syulyukina, Samuel W. Brady, Boian S. Alexandrov, Nischalan Pillay, Jinghui Zhang, David J. Adams, Iñigo Martincorena, David C. Wedge, Maria Teresa Landi, Paul Brennan, Michael R. Stratton, Steven G. Rozen, Ludmil B. Alexandrov
Publikováno v:
Cell genomics, vol 2, iss 11
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d66650f68920d43fde2ce688d861fe80
https://escholarship.org/uc/item/9b82739r
https://escholarship.org/uc/item/9b82739r