Signatures of copy number alterations in human cancer
Steele, Christopher D., Abbasi, Ammal, Islam, S. M. Ashiqul, Bowes, Amy L., Khandekar, Azhar, Haase, Kerstin, Hames-Fathi, Shadi, Ajayi, Dolapo, Verfaillie, Annelien, Dhami, Pawan, McLatchie, Alex, Lechner, Matt, Light, Nicholas, Shlien, Adam, Malkin, David, Feber, Andrew, Proszek, Paula, Lesluyes, Tom, Mertens, Fredrik, Flanagan, Adrienne M., Tarabichi, Maxime, Van Loo, Peter, Alexandrov, Ludmil B., Pillay, Nischalan
Published in Nature (London) (30.06.2022)
Published in Nature (London) (30.06.2022)
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Genomic and evolutionary classification of lung cancer in never smokers
Zhang, Tongwu, Joubert, Philippe, Ansari-Pour, Naser, Zhao, Wei, Hoang, Phuc H., Lokanga, Rachel, Moye, Aaron L., Rosenbaum, Jennifer, Gonzalez-Perez, Abel, Martínez-Jiménez, Francisco, Castro, Andrea, Muscarella, Lucia Anna, Hofman, Paul, Consonni, Dario, Pesatori, Angela C., Kebede, Michael, Li, Mengying, Gould Rothberg, Bonnie E., Peneva, Iliana, Schabath, Matthew B., Poeta, Maria Luana, Costantini, Manuela, Hirsch, Daniela, Heselmeyer-Haddad, Kerstin, Hutchinson, Amy, Olanich, Mary, Lawrence, Scott M., Lenz, Petra, Duggan, Maire, Bhawsar, Praphulla M. S., Sang, Jian, Kim, Jung, Mendoza, Laura, Saini, Natalie, Klimczak, Leszek J., Islam, S. M. Ashiqul, Otlu, Burcak, Khandekar, Azhar, Cole, Nathan, Stewart, Douglas R., Choi, Jiyeon, Brown, Kevin M., Caporaso, Neil E., Wilson, Samuel H., Pommier, Yves, Lan, Qing, Rothman, Nathaniel, Almeida, Jonas S., Carter, Hannah, Ried, Thomas, Kim, Carla F., Lopez-Bigas, Nuria, Garcia-Closas, Montserrat, Shi, Jianxin, Bossé, Yohan, Zhu, Bin, Gordenin, Dmitry A., Alexandrov, Ludmil B., Chanock, Stephen J., Wedge, David C., Landi, Maria Teresa
Published in Nature genetics (01.09.2021)
Published in Nature genetics (01.09.2021)
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Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator
Khandekar, Azhar, Vangara, Raviteja, Barnes, Mark, Díaz-Gay, Marcos, Abbasi, Ammal, Bergstrom, Erik N, Steele, Christopher D, Pillay, Nischalan, Alexandrov, Ludmil B
Published in BMC genomics (21.08.2023)
Published in BMC genomics (21.08.2023)
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Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA
Bergstrom, Erik N., Luebeck, Jens, Petljak, Mia, Khandekar, Azhar, Barnes, Mark, Zhang, Tongwu, Steele, Christopher D., Pillay, Nischalan, Landi, Maria Teresa, Bafna, Vineet, Mischel, Paul S., Harris, Reuben S., Alexandrov, Ludmil B.
Published in Nature (London) (17.02.2022)
Published in Nature (London) (17.02.2022)
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Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence
Moody, Sarah, Senkin, Sergey, Islam, S. M. Ashiqul, Wang, Jingwei, Nasrollahzadeh, Dariush, Cortez Cardoso Penha, Ricardo, Fitzgerald, Stephen, Bergstrom, Erik N., Atkins, Joshua, He, Yudou, Khandekar, Azhar, Smith-Byrne, Karl, Carreira, Christine, Gaborieau, Valerie, Latimer, Calli, Thomas, Emily, Abnizova, Irina, Bucciarelli, Pauline E., Jones, David, Teague, Jon W., Abedi-Ardekani, Behnoush, Serra, Stefano, Scoazec, Jean-Yves, Saffar, Hiva, Azmoudeh-Ardalan, Farid, Sotoudeh, Masoud, Nikmanesh, Arash, Poustchi, Hossein, Niavarani, Ahmadreza, Gharavi, Samad, Eden, Michael, Richman, Paul, Campos, Lia S., Fitzgerald, Rebecca C., Ribeiro, Luis Felipe, Soares-Lima, Sheila Coelho, Dzamalala, Charles, Mmbaga, Blandina Theophil, Shibata, Tatsuhiro, Menya, Diana, Goldstein, Alisa M., Hu, Nan, Malekzadeh, Reza, Fazel, Abdolreza, McCormack, Valerie, McKay, James, Perdomo, Sandra, Scelo, Ghislaine, Chanudet, Estelle, Humphreys, Laura, Alexandrov, Ludmil B., Brennan, Paul, Stratton, Michael R.
Published in Nature genetics (01.11.2021)
Published in Nature genetics (01.11.2021)
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Individual, interpersonal, and organisational factors of healthcare conflict: A scoping review
Kim, Sara, Bochatay, Naike, Relyea-Chew, Annemarie, Buttrick, Elizabeth, Amdahl, Chris, Kim, Laura, Frans, Elise, Mossanen, Matthew, Khandekar, Azhar, Fehr, Ryan, Lee, Young-Mee
Published in Journal of interprofessional care (01.05.2017)
Published in Journal of interprofessional care (01.05.2017)
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Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor
Islam, S.M. Ashiqul, Díaz-Gay, Marcos, Wu, Yang, Barnes, Mark, Vangara, Raviteja, Bergstrom, Erik N., He, Yudou, Vella, Mike, Wang, Jingwei, Teague, Jon W., Clapham, Peter, Moody, Sarah, Senkin, Sergey, Li, Yun Rose, Riva, Laura, Zhang, Tongwu, Gruber, Andreas J., Steele, Christopher D., Otlu, Burçak, Khandekar, Azhar, Abbasi, Ammal, Humphreys, Laura, Syulyukina, Natalia, Brady, Samuel W., Alexandrov, Boian S., Pillay, Nischalan, Zhang, Jinghui, Adams, David J., Martincorena, Iñigo, Wedge, David C., Landi, Maria Teresa, Brennan, Paul, Stratton, Michael R., Rozen, Steven G., Alexandrov, Ludmil B.
Published in Cell genomics (09.11.2022)
Published in Cell genomics (09.11.2022)
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Abstract LB286: Extrachromosomal DNA in lung cancer from never smokers
Khandekar, Azhar, Zhang, Tongwu, Diaz-Gay, Marcos, Luebeck, Jens, Alexandrov, Ludmil, Landi, Maria
Published in Cancer research (Chicago, Ill.) (05.04.2024)
Published in Cancer research (Chicago, Ill.) (05.04.2024)
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Geographic variation of mutagenic exposures in kidney cancer genomes
Senkin, Sergey, Moody, Sarah, Díaz-Gay, Marcos, Abedi-Ardekani, Behnoush, Cattiaux, Thomas, Ferreiro-Iglesias, Aida, Wang, Jingwei, Fitzgerald, Stephen, Kazachkova, Mariya, Vangara, Raviteja, Le, Anh Phuong, Bergstrom, Erik N., Khandekar, Azhar, Otlu, Burçak, Cheema, Saamin, Latimer, Calli, Thomas, Emily, Atkins, Joshua Ronald, Smith-Byrne, Karl, Cortez Cardoso Penha, Ricardo, Carreira, Christine, Chopard, Priscilia, Gaborieau, Valérie, Keski-Rahkonen, Pekka, Jones, David, Teague, Jon W., Ferlicot, Sophie, Asgari, Mojgan, Sangkhathat, Surasak, Attawettayanon, Worapat, Świątkowska, Beata, Jarmalaite, Sonata, Sabaliauskaite, Rasa, Shibata, Tatsuhiro, Fukagawa, Akihiko, Mates, Dana, Jinga, Viorel, Rascu, Stefan, Mijuskovic, Mirjana, Savic, Slavisa, Milosavljevic, Sasa, Bartlett, John M. S., Albert, Monique, Phouthavongsy, Larry, Ashton-Prolla, Patricia, Botton, Mariana R., Silva Neto, Brasil, Bezerra, Stephania Martins, Curado, Maria Paula, Zequi, Stênio de Cássio, Reis, Rui Manuel, Faria, Eliney Ferreira, de Menezes, Nei Soares, Ferrari, Renata Spagnoli, Banks, Rosamonde E., Vasudev, Naveen S., Zaridze, David, Mukeriya, Anush, Shangina, Oxana, Matveev, Vsevolod, Foretova, Lenka, Navratilova, Marie, Holcatova, Ivana, Hornakova, Anna, Janout, Vladimir, Purdue, Mark P., Rothman, Nathaniel, Chanock, Stephen J., Ueland, Per Magne, Johansson, Mattias, McKay, James, Scelo, Ghislaine, Chanudet, Estelle, Humphreys, Laura, de Carvalho, Ana Carolina, Perdomo, Sandra, Alexandrov, Ludmil B., Stratton, Michael R., Brennan, Paul
Published in Nature (London) (23.05.2024)
Published in Nature (London) (23.05.2024)
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Abstract LB231: The mutagenic forces shaping the genomic landscape of lung cancer in never smokers
Diaz-Gay, Marcos, Zhang, Tongwu, Khandekar, Azhar, Otlu, Burçak, Nandi, Shuvro, Steele, Christopher D., Rothman, Nathaniel, Chanock, Stephen J., Lan, Qing, Alexandrov, Ludmil B., Landi, Maria Teresa
Published in Cancer research (Chicago, Ill.) (05.04.2024)
Published in Cancer research (Chicago, Ill.) (05.04.2024)
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Abstract LB226: Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition
Zhang, Tongwu, Zhao, Wei, Wirth, Christopher, Díaz-Gay, Marcos, Yin, Jinhu, Hoang, Phuc H., Sang, Jian, McElderry, John, Klein, Alyssa, Khandekar, Azhar, Hartman, Caleb, Rosenbaum, Jennifer, Colon-Matos, Frank, Jones, Kristine M., Caporaso, Neil E., Homer, Robert, Pesatori, Angela C., Consonni, Dario, Yang, Lixing, Zhu, Bin, Shi, Jianxin, Brown, Kevin, Rothman, Nathaniel, Chanock, Stephen J., Alexandrov, Ludmil B., Choi, Jiyeon, Cardelli, Maurizio, Lan, Qing, Nowak, Martin A., Wedge, David C., Landi, Maria Teresa
Published in Cancer research (Chicago, Ill.) (05.04.2024)
Published in Cancer research (Chicago, Ill.) (05.04.2024)
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Detecting HRD in whole-genome and whole-exome sequenced breast and ovarian cancers
Abbasi, Ammal, Steele, Christopher D, Bergstrom, Erik N, Khandekar, Azhar, Farswan, Akanksha, Mckay, Rana R, Pillay, Nischalan, Alexandrov, Ludmil B
Published in medRxiv : the preprint server for health sciences (14.07.2024)
Published in medRxiv : the preprint server for health sciences (14.07.2024)
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Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator
Khandekar, Azhar, Vangara, Raviteja, Barnes, Mark, Díaz-Gay, Marcos, Abbasi, Ammal, Bergstrom, Erik N, Steele, Christopher D, Pillay, Nischalan, Alexandrov, Ludmil B
Published in bioRxiv : the preprint server for biology (04.02.2023)
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Published in bioRxiv : the preprint server for biology (04.02.2023)
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The mutagenic forces shaping the genomic landscape of lung cancer in never smokers
Díaz-Gay, Marcos, Zhang, Tongwu, Hoang, Phuc H, Khandekar, Azhar, Zhao, Wei, Steele, Christopher D, Otlu, Burçak, Nandi, Shuvro P, Vangara, Raviteja, Bergstrom, Erik N, Kazachkova, Mariya, Pich, Oriol, Swanton, Charles, Hsiung, Chao Agnes, Chang, I-Shou, Wong, Maria Pik, Leung, Kin Chung, Sang, Jian, McElderry, John, Yang, Lixing, Nowak, Martin A, Shi, Jianxin, Rothman, Nathaniel, Wedge, David C, Homer, Robert, Yang, Soo-Ryum, Lan, Qing, Zhu, Bin, Chanock, Stephen J, Alexandrov, Ludmil B, Landi, Maria Teresa
Published in medRxiv : the preprint server for health sciences (17.05.2024)
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Published in medRxiv : the preprint server for health sciences (17.05.2024)
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Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator
Khandekar, Azhar, Vangara, Raviteja, Barnes, Mark, Diaz-Gay, Marcos, Abbasi, Ammal, Bergstrom, Erik N, Steele, Christopher D, Pillay, Nischalan, Alexandrov, Ludmil B
Published in bioRxiv (04.02.2023)
Published in bioRxiv (04.02.2023)
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Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor
Ashiqul Islam, S M, Wu, Yang, Diaz-Gay, Marcos, Bergstrom, Erik N, He, Yudou, Barnes, Mark, Vella, Mike, Wang, Jingwei, Teague, Jon W, Clapham, Peter, Moody, Sarah, Senkin, Sergey, Yun Rose Li, Riva, Laura, Zhang, Tongwu, Gruber, Andreas J, Vangara, Raviteja, Steele, Christopher D, Otlu, Burcak, Khandekar, Azhar, Abbasi, Ammal, Humphreys, Laura, Syulyukina, Natalia, Brady, Samuel W, Boian Stoianov Alexandrov, Pillay, Nischalan, Zhang, Jinghui, Adams, David J, Marticorena, Inigo, Wedge, David C, Landi, Maria Teresa, Brennan, Paul, Stratton, Michael R, Rozen, Steven G, Alexandrov, Ludmil B
Published in bioRxiv (16.05.2021)
Published in bioRxiv (16.05.2021)
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Disentangling heterogeneity of Malignant Pleural Mesothelioma through deep integrative omics analyses
Mangiante, Lise, Alcala, Nicolas, Alex Di Genova, Sexton-Oates, Alexandra, Gonzalez-Perez, Abel, Khandekar, Azhar, Bergstrom, Erik, Kim, Jaehee, Giacobi, Colin, Le-Stang, Nolwenn, Boyault, Sandrine, Cuenin, Cyrille, Tabone-Eglinger, Severine, Damiola, Francesca, Voegele, Catherine, Ardin, Maude, Marie-Cecile Michallet, Soudade, Lorraine, Delhomme, Tiffany, Poret, Arnaud, Brevet, Marie, Marie-Christine Copin, Giusiano-Courcambeck, Sophie, Damotte, Diane, Girard, Cecile, Hofman, Veronique, Hofman, Paul, Mouroux, Jerome, Lacomme, Stephanie, Mazieres, Julien, De Montpreville, Vincent Thomas, Perrin, Corinne, Planchard, Gaetane, Rouquette, Isabelle, Sagan, Christine, Scherpereel, Arnaud, Thivolet, Francoise, Jean-Michel Vignaud, Dider Jean, Anabelle Gilg Soit Ilg, Olaso, Robert, Meyer, Vincent, Boland, Anne, Deleuze, Jean-Francois, Altmuller, Janine, Nuernberg, Peter, Lantuejoul, Sylvie, Ghantous, Akram, Maussion, Charles, Courtiol, Pierre, Hernandez-Vargas, Hector, Caux, Christophe, Girard, Nicolas, Lopez-Bigas, Nuria, Alexandrov, Ludmil, Francoise Galateau Salle, Foll, Matthieu, Fernandez-Cuesta, Lynnette
Published in bioRxiv (29.09.2021)
Published in bioRxiv (29.09.2021)
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