Publications

2026

198. Mutational signatures of environmental carcinogens in human tissue organoids revealed by duplex sequencing

 Jill E Kucab, Shuvro P Nandi, Halh Al-Serori, Ellie Dunstone, Rebekah SS Beck, Angela L Caipa Garcia, Eleanor C Wilde, Safa Saeed, Hayley Francies, Mathew J Garnett, Beiyuan Fu, Fengtang Yang, Kourosh Saeb-Parsy, Meritxell Huch, Jarno Drost, Matthias Zilbauer, Laura Humphreys, Glen Kisby, Volker M Arlt, Michael R Stratton, Ludmil B Alexandrov and David H Phillips(2026) Cell Reports Volume: 45, Issue:6.

197. DREAM repressive activity links somatic mutation, lifespan and disease

Zane Koch, Shuvro P Nandi, Kate Licon, Arturo Bujarrabal-Dueso, David H Meyer, Safa Saeed, Pirunthan Perampalam, Frederick A Dick, Björn Schumacher, Ludmil B Alexandrov and Trey Ideker (2026) Nature Aging Pages: 1-14.

196. Genetically defined immune-checkpoint inhibitor resistance in aggressive precursors of hpv--head and neck squamous cancer

Scott M LIPPMAN, Ludmil B Alexandrov, Shuvro P Nandi, Webster K Cavenee and Glenn J Hanna (2026) Patent office: US, Application number: 19116947.

195. Systemic mutagen exposures reported by normal kidney cell genomes

Yichen Wang, William Knight, Aida Ferreiro-Iglesias, Behnoush Abedi-Ardekani, My H Pham, Sarah Moody, Yvette Hooks, Federico Abascal, Charles Nunn, Stephen Fitzgerald, Thomas Cattiaux, Valérie Gaborieau, Akihiko Fukagawa, Viorel Jinga, Stefan Rascu, Cristian Sima, David Georgievich Zaridze, Anush Felixovna Mukeria, Ivana Holcatova, Anna Hornakova, Naveen S Vasudev, Rosamonde E Banks, Simona Ognjanovic, Slavisa Savic, Maria Paula Curado, Stênio de Cássio Zequi, Rui Manuel Reis, Wesley Justino Magnabosco, Fernanda Vianna, Brasil Silva Neto, Sonata Jarmalaite, Algirdas Zalimas, Lenka Foretova, Marie Navratilova, Larry Phouthavongsy, Carolyn Shire, Worapat Attawettayanon, Surasak Sangkhathat, Chuling Ding, Andrew RJ Lawson, Calli Latimer, Laura Humphreys, Peter J Campbell, Sandra Perdomo, Iñigo Martincorena, Ludmil B Alexandrov, Sam Behjati, Kourosh Saeb-Parsy, Tatsuhiro Shibata, Paul Brennan and  Michael R Stratton (2026) bioRxiv Pages: 2026.04. 07.716715.

194. Early-Life Mutagenesis and the Rise of Early-Onset Colorectal Cancer

Ludmil B Alexandrov, Paul Brennan and Michael R Stratton(2026) Cancer Discovery Volume: 16, Issue: 4, Pages: 644-646.

193. Biallelic Germline Inactivation of HROB Causes Primary Gonadal Insufficiency and is Potentially Associated with Colonic Polyposis Predisposition

 Noah C Helderman, Carli M Tops, Jelmer Legebeke, Ting Yang, Marcos Díaz Gay, Diantha Terlouw, Lisa EELO Lashley, Stefan Aretz, Anna K Sommer, Mariona Terradas, Laura Valle, Richarda M De Voer, Ludmil B Alexandrov, Hans Morreau, Tom Van Wezel and Maartje Nielsen (2026) American Journal of Medical Genetics Part A, Pages: e70128.

192. Ancestry and somatic profile indicate acral melanoma origin and prognosis

Patricia Basurto-Lozada, Martha Estefania Vázquez-Cruz, Christian Molina-Aguilar, Amanda Jiang, Dekker C Deacon, Dennis Cerrato-Izaguirre, Irving Simonin-Wilmer, Fernanda G Arriaga-González, Kenya L Contreras-Ramírez, Emiliano Ferro-Rodríguez, Jamie Billington, Eric T Dawson, J Rene C Wong-Ramirez, Johana Itzel Ramos-Galguera, Alethia Álvarez-Cano, Dorian Y García-Ortega, O Isaac García-Salinas, Alfredo Hidalgo-Miranda, Mireya Cisneros-Villanueva, Peter A Johansson, Héctor Martínez-Said, Pilar Gallego-García, Mark J Arends, Ingrid Ferreira, Mark Tullett, Rebeca Olvera-León, Louise Van Der Weyden, Martín del Castillo Velasco-Herrera, Rodrigo Roldán-Marín, Helena Vidaurri De La Cruz, Luis Alberto Tavares-de-la-Paz, Diego Hinojosa-Ugarte, Rachel L Belote, D Timothy Bishop, Marcos Díaz-Gay, Ludmil B Alexandrov, Yesennia Sánchez-Pérez, Gino K In, Richard M White, Patrícia A Possik, Robert L Judson-Torres, David J Adams and Carla Daniela Robles-Espinoza (2026) Nature Volume: 651, Issue: 8104, Pages: 221-230.

191. Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression

Shams Al-Azzam, Isabella Stuewe, Sunandini Sharma, Miki Yamada-Hara, Arisachi Tanaka, Kegan Stringer, Merna Behnam, Norah Al-Azzam, Shuvro Nandi, Maria Zhivagui, Janelle Duong, Ting Yang, Scott Herdman, Maripat Corr, Nicholas JG Webster, Eyal Raz, Ludmil B Alexandrov and Samuel Bertin (2026), Neoplasia Volume: 73, Pages: 101275.

190. Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types

Andrew Everall, Avraam Tapinos, Aliah Hawari, Alex J Cornish, Amit Sud, Daniel Chubb, Ben Kinnersley, Anna Frangou, Miguel Barquin, Josephine Jung, David N Church, Ludmil B Alexandrov, Richard S Houlston, Andreas J Gruber and David C Wedge (2026) Nature Genetics Pages: 1-12.

189. Community assembly modeling of the microbiome within Barrett’s esophagus and esophageal adenocarcinoma

Caitlin Guccione, Igor Sfiligoi, Antonio Gonzalez, Justin P Shaffer, Mariya Kazachkova, Yuhan Weng, Daniel McDonald, Shailja C Shah, Samuel S Minot, Thomas G Paulson, William M Grady, Ludmil B Alexandrov, Rob Knight and Kit Curtius (2026) BMC genomics Volume: 27, Issue: 1, Pages: 236.

188. Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma

Tongwu Zhang, Wei Zhao, Christopher Wirth, Marcos Díaz-Gay, Jinhu Yin, Monia Cecati, Francesca Marchegiani, Phuc H Hoang, Charles Leduc, Marina K Baine, William D Travis, Lynette M Sholl, Philippe Joubert, Jian Sang, John P McElderry, Michelle Antony, Alyssa Klein, Azhar Khandekar, Caleb Hartman, Jennifer Rosenbaum, Frank J Colón-Matos, Mona Miraftab, Monjoy Saha, Olivia W Lee, Kristine M Jones, Neil E Caporaso, Maria Pik Wong, Kin Chung Leung, Chao Agnes Hsiung, Chih-Yi Chen, Eric S Edell, Jacobo Martínez Santamaría, Matthew B Schabath, Sai S Yendamuri, Marta Manczuk, Jolanta Lissowska, Beata Świątkowska, Anush Mukeria, Oxana Shangina, David Zaridze, Ivana Holcatova, Dana Mates, Sasa Milosavljevic, Milan Savic, Yohan Bossé, Bonnie E Gould Rothberg, David C Christiani, Valerie Gaborieau, Paul Brennan, Geoffrey Liu, Paul Hofman, Robert Homer, Soo-Ryum Yang, Angela C Pesatori, Dario Consonni, Lixing Yang, Bin Zhu, Jianxin Shi, Kevin Brown, Nathaniel Rothman, Stephen J Chanock, Ludmil B Alexandrov, Jiyeon Choi, Maurizio Cardelli, Qing Lan, Martin A Nowak, David C Wedge and Maria Teresa Landi (2026) Nature Volume: 650, Issue: 8100, Pages: 230-241.

187: A prognostic signature for lung adenocarcinoma in patients who have never smoked

Wei Zhao, Tongwu Zhang, Xing Hua, Phuc H Hoang, Mona Miraftab, Monjoy Saha, John P McElderry, Jian Sang, Olivia W Lee, Caleb Hartman, Azhar Khandekar, Sunandini Sharma, Frank J Colón-Matos, Samuel Anyaso-Samuel, Difei Wang, Kristine Jones, Amy Hutchinson, Belynda Hicks, Jennifer Rosenbaum, Xiaoming Zhong, Yang Yang, Angela C Pesatori, Dario Consonni, David C Christiani, Kin Chung Leung, Maria Pik Wong, Marta Manczuk, Jolanta Lissowska, Beata Świątkowska, Anush Mukeria, Oxana Shangina, David Zaridze, Ivana Holcatova, Dana Mates, Sasa Milosavljevic, Simona Ognjanovic, Milan Savic, Milica Kontic, Valerie Gaborieau, Paul Brennan, Oscar Arrieta, Yohan Bossé, Eric S Edell, Matthew B Schabath, Paul Hofman, Luis Mas, Sai S Yendamuri, Chih-Yi Chen, I-Shou Chang, Chao Agnes Hsiung, Geoffrey Liu, Jacobo Martinez Santamaría, Bonnie E Gould Rothberg, Karun Mutreja, Scott Lawrence, Nathaniel Rothman, Ludmil B Alexandrov, Charles Leduc, Marina K Baine, Philippe Joubert, Lynette M Sholl, William D Travis, Robert Homer, Qing Lan, Stephen J Chanock, Lixing Yang, Soo-Ryum Yang, Jianxin Shi and Maria Teresa Landi (2026) Cancer discovery Pages: OF1-OF18.

186. CarD-T: an automated pipeline for the nomination and analysis of potential human carcinogens

Jamey O’Neill, Gudur Ashrith Reddy, Nermeeta Dhillon, Osika Tripathi, Ludmil B Alexandrov and Parag Katira (2026) Carcinogenesis Volume: 47, Issue: 1, Pages: bgaf074.

2025

185. Revealing the Drivers Underlying Distinct Evolutionary Trajectories in Lung Adenocarcinoma

Christopher Wirth, Tongwu Zhang, Marcos Díaz-Gay, Christopher D Steele, Phuc H Hoang, Yang Yang, Azhar Khandekar, Wei Zhao, Jian Sang, Charles Leduc, Marina K Baine, William D Travis, Lynette M Sholl, Philippe Joubert, Robert Homer, Soo-Ryum Yang, Thi-Van-Trinh Tran, John P McElderry, Caleb Hartman, Mona Miraftab, Olivia W Lee, Kristine M Jones, Bin Zhu, Jacobo Martínez Santamaría, Matthew B Schabath, Sai S Yendamuri, Marta Manczuk, Jolanta Lissowska, Beata Świątkowska, Anush Mukeria, Oxana Shangina, David Zaridze, Ivana Holcatova, Vladimir Janout, Dana Mates, Simona Ognjanovic, Milan Savic, Milica Kontic, Yohan Bossé, Bonnie E Gould Rothberg, David C Christiani, Valerie Gaborieau, Paul Brennan, Geoffrey Liu, Paul Hofman, Maria Pik Wong, Kin Chung Leung, Chih-Yi Chen, I-Shou Chang, Chao Agnes Hsiung, Angela C Pesatori, Dario Consonni, Nathaniel Rothman, Qing Lan, Martin A Nowak, Stephen J Chanock, Jianxin Shi, Lixing Yang, Ludmil B Alexandrov, David C Wedge and Maria Teresa Landi (2025) bioRxiv Pages: 2025.12. 19.695410.

184. Microbiome analysis of 940 lung cancers in never-smokers reveals lack of clinically relevant associations

John P McElderry, Tongwu Zhang, Wei Zhao, Phuc H Hoang, Samuel Anyaso-Samuel, Jian Sang, Azhar Khandekar, Caleb Hartman, Frank J Colón-Matos, Mona Miraftab, Monjoy Saha, Olivia Lee, Sunandini Sharma, Kristine M Jones, Bin Zhu, Marcos Díaz-Gay, Luis Mas, Oscar Arrieta, Eric S Edell, Jacobo Martínez Santamaría, Matthew B Schabath, Sai Yendamuri, Marta Manczuk, Jolanta Lissowska, Beata Świątkowska, Anush Mukeria, Oxana Shangina, David Zaridze, Ivana Holcatova, Vladimir Janout, Dana Mates, Simona Ognjanovic, Milan Savic, Milica Kontic, Yohan Bossé, Bonnie E Gould Rothberg, David C Christiani, Valerie Gaborieau, Paul Brennan, Geoffrey Liu, Paul Hofman, Maria Pik Wong, Kin Chung Leung, Chih-Yi Chen, Chao Agnes Hsiung, Nathaniel Rothman, Charles Leduc, Marina K Baine, William D Travis, Lynette M Sholl, Philippe Joubert, Robert Homer, Soo-Ryum Yang, Qing Lan, Martin A Nowak, David C Wedge, Ludmil B Alexandrov, Stephen J Chanock, Emily Vogtmann, Christian C Abnet, Jianxin Shi and Maria Teresa Landi (2025), Nature communications Volume: 17, Issue: 1, Pages: 192.

183. The Impact of Variant Calling on Substitution Mutational Signature Inference

Zichen Jiang, Jessica N Au, Mariya Kazachkova, Marcos Díaz-Gay and Raviteja Vangara, Ludmil B Alexandrov (2025) bioRxiv Pages: 2025.12. 09.693327

182. Chromothripsis and ecDNA initiated by N4BP2 nuclease fragmentation of cytoplasm-exposed chromosomes

Ksenia Krupina, Alexander Goginashvili, Michael W Baughn, Stephen Moore, Christopher D Steele, Amy T Nguyen, Daniel L Zhang, Jonas Koeppel, Prasad Trivedi, Aarti Malhotra, David Jenkins, Andrew K Shiau, Yohei Miyake, Tomoyuki Koga, Shunichiro Miki, Frank B Furnari, Peter J Campbell, Ludmil B Alexandrov and Don W Cleveland (2025) Science Volume: 390, Issue: 6778, Pages: 1156-1163.

181. Space-associated stem cell hallmarks of aging and resilience in astronauts

Jessica Pham, Shuvro P Nandi, Larisa Balaian, Claire Engstrom, Patrick Chang, Karla Mack, Inge van der Werf, Emma Klacking, Jenna Sneifer, Neha Katragadda, Kendale Wirtjes, Antonio Ruiz, Daisy Chilin-Fuentes, Elsa Molina, Pinar Mesci, Jana Stoudemire, Sheldon R Morris, Thomas Whisenant, Ludmil B Alexandrov and Catriona HM Jamieson (2025) Cell stem cell Volume: 32, Issue: 12, Pages: 1886-1903. e7.

180. Clinical syndromes linked to biallelic germline variants in MCM8 and MCM9

Noah C Helderman, Ting Yang, Claire Palles, Diantha Terlouw, Hailiang Mei, Ruben HP Vorderman, Davy Cats, Marcos Díaz-Gay, Marjolijn CJ Jongmans, Ashwin Ramdien, Irma Van De Beek, Thomas F Eleveld, Andrew Green, Frederik J Hes, Marry M van den Heuvel-Eibrink, Annelore Van Der Kelen, Sabine Kliesch, Roland P Kuiper, Inge MM Lakeman, Lisa EELO Lashley, Leendert HJ Looijenga, Manon S Oud, Johanna Steingröver, Yardena Tenenbaum-Rakover, Carli M Tops, Frank Tüttelmann, Richarda M de Voer, Dineke Westra, Margot J Wyrwoll, Mariano Golubicki, Marina Antelo, Laia Bonjoch, Mariona Terradas, Laura Valle, Ludmil B Alexandrov, Hans Morreau, Tom Van Wezel, Sergi Castellví-Bel and Yael Goldberg, Maartje Nielsen (2025) Human Genetics and Genomics Advances Volume: 6, Issue: 4.

179. The DREAM complex links somatic mutation, lifespan, and disease

Zane Koch, Shuvro P Nandi, Kate Licon, Arturo Bujarrabal-Dueso, David H Meyer, Safa Saeed, Pirunthan Perampalam, Frederick A Dick, Björn Schumacher, Ludmil B Alexandrov and Trey Ideker(2025) c.

178. A Universal Duplex Sequencing Approach for Accurate Detection of Somatic Mutations

Shuvro P Nandi, Yuhe Cheng, Shams Al-Azzam, Safa Saeed, Audrey Kristin, Nadia Sunico, Isabella R Stuewe, Zichen Jiang, Luka Culibrk, Maria Zhivagui, Xiaoxu Yang, Rachel M Wise, Foster C Jacobs, Bérénice Chavanel, Michael Korenjak, Mia Petljak, Silvia Balbo, Laurie G Hudson, Ke Jian Liu, Jiri Zavadil, Joseph G Gleeson and Ludmil B Alexandrov (2025) bioRxiv.

177. Panorama of Chromosomal Instability in Lung Cancer

Yang Yang, Xiaoming Zhong, William Phillips, Wei Zhao, Phuc H Hoang, Christopher Wirth, Soo-Ryum Yang, Charles Leduc, Marina K Baine, William D Travis, Lynette M Sholl, Philippe Joubert, Robert Homer, Jian Sang, Azhar Khandekar, John P McElderry, Thi-Van-Trinh Tran, Caleb Hartman, Mona Miraftab, Monjoy Saha, Olivia W Lee, Sunandini Sharma, Kristine M Jones, Bin Zhu, Marcos Díaz-Gay, Eric S Edell, Jacobo Martínez Santamaría, Matthew B Schabath, Sai S Yendamuri, Marta Manczuk, Jolanta Lissowska, Beata Świątkowska, Anush Mukeria, Oxana Shangina, David Zaridze, Ivana Holcatova, Vladimir Janout, Dana Mates, Simona Ognjanovic, Milan Savic, Milica Kontic, Yohan Bossé, Bonnie E Gould Rothberg, David C Christiani, Valerie Gaborieau, Paul Brennan, Geoffrey Liu, Paul Hofman, Maria Pik Wong, Kin Chung Leung, Chih-Yi Chen, Chao Agnes Hsiung, Angela C Pesatori, Dario Consonni, Nathaniel Rothman, Qing Lan, Martin A Nowak, David C Wedge, Ludmil B Alexandrov, Stephen J Chanock, Jianxin Shi, Tongwu Zhang, Lixing Yang and Maria Teresa Landi (2025) medRxiv.

176. Nanobioreactor detection of space-associated hematopoietic stem and progenitor cell aging

Jessica Pham, Jane Isquith, Larisa Balaian, Shuvro P Nandi, Claire Engstrom, Karla Mack, Inge van der Werf, Patrick Chang, Jana Stoudemire, Luisa Ladel, Emma Klacking, Antonio Ruiz, Daisy Chilin-Fuentes, Jenna Sneifer, David Mays, Paul Gamble, Shelby Giza, Jiya Janowitz, Trevor Nienaber, Tejaswini Mishra, Anna A Khachatrian, Elsa Molina, Michael P Snyder, Sheldon R Morris, Twyman Clements, Alysson R Muotri, Thomas Whisenant, Ludmil B Alexandrov and Catriona HM Jamieson (2025) Cell stem cell Volume: 32, Issue: 9, Pages: 1403-1420. e8.

175. Examining the role of extrachromosomal DNA in 1,216 lung cancers

Azhar Khandekar, Phuc H Hoang, Jens Luebeck, Marcos Díaz-Gay, Wei Zhao, John P McElderry, Caleb Hartman, Mona Miraftab, Olivia W Lee, Kara M Barnao, Erik N Bergstrom, Yang Yang, Martin A Nowak, Nathaniel Rothman, Robert Homer, Soo-Ryum Yang, Qing Lan, David C Wedge, Lixing Yang, Stephen J Chanock, Tongwu Zhang, Ludmil B Alexandrov and Maria Teresa Landi (2025) BioRxiv.

174. Improved mutation detection in duplex sequencing data with sample-specific error profiles

Yuhe Cheng, Shuvro P Nandi, Luka Culibrk, Audrey Kristin, Isabella Stuewe, Shams Al-Azzam, Mia Petljak and Ludmil B Alexandrov (2025) bioRxiv.

173. The mutagenic forces shaping the genomes of lung cancer in never smokers

Marcos Díaz-Gay, Tongwu Zhang, Phuc H Hoang, Charles Leduc, Marina K Baine, William D Travis, Lynette M Sholl, Philippe Joubert, Azhar Khandekar, Wei Zhao, Christopher D Steele, Burçak Otlu, Shuvro P Nandi, Raviteja Vangara, Erik N Bergstrom, Mariya Kazachkova, Oriol Pich, Charles Swanton, Chao Agnes Hsiung, I-Shou Chang, Maria Pik Wong, Kin Chung Leung, Jian Sang, John P McElderry, Caleb Hartman, Frank J Colón-Matos, Mona Miraftab, Monjoy Saha, Olivia W Lee, Kristine M Jones, Pilar Gallego-García, Yang Yang, Xiaoming Zhong, Eric S Edell, Jacobo Martínez Santamaría, Matthew B Schabath, Sai S Yendamuri, Marta Manczuk, Jolanta Lissowska, Beata Świątkowska, Anush Mukeria, Oxana Shangina, David Zaridze, Ivana Holcatova, Dana Mates, Sasa Milosavljevic, Millica Kontic, Yohan Bossé, Bonnie E Gould Rothberg, David C Christiani, Valerie Gaborieau, Paul Brennan, Geoffrey Liu, Paul Hofman, Lixing Yang, Martin A Nowak, Jianxin Shi, Nathaniel Rothman, David C. Wedge, Robert Homer, Soo-Ryum Yang, Angela C. Pesatori, Dario Consonni, Qing Lan, Bin Zhu, Stephen J. Chanock, Jiyeon Choi, Ludmil B. Alexandrov and Maria Teresa Landi  (2025) Nature Pages: 1-12.

172. Self-amplifying NRF2–EZH2 epigenetic loop converts KRAS-initiated progenitors to invasive pancreatic cancer

Laura Antonucci, Na Li, Angeles Duran, Isidoro Cobo, Chiara Nicoletti, Kosuke Watari, Shuvro Prokash Nandi, Feng Zhu, Yongmei Zhao, Irene Riahi, Motoyuki Tsuda, Vidhi M Shah, Terry Morgan, Trent Waugh, Luca Caputo, Yuan Liu, Alexandra Rundberg Nilsson, Hongxu Xian, Jelena Todoric, Li Gu, Elsa Sanchez-Lopez, Guido Eibl, Emily A Vucic, Michal Krawczyk, Qianlan Xu, Andrew M Lowy, Georgia Hatzivassiliou, Merone Roose-Girma, Dorota Skowronska-Krawczyk, David A Scott, Dafna Bar-Sagi, Pablo Tamayo, Ying Wu, Rosalie C Sears, Christopher K Glass, Ludmil B Alexandrov, Pier Lorenzo Puri, David W Dawson, Yinling Hu, Maria T Diaz-Meco, Jorge Moscat and Michael Karin (2025) Nature cancer Volume: 6, Issue: 7, Pages: 1263-1282.

171. Artificial intelligence architecture for predicting cancer biomarkers

Scott Michael Lippman, Erik Niels Bergstrom and Ludmil Boyanov Alexandrov (2025) Patent office: US.

170. Spatial and multiomics analysis of human and mouse lung adenocarcinoma precursors reveals TIM-3 as a putative target for precancer interception

Bo Zhu, Pingjun Chen, Muhammad Aminu, Jian-Rong Li, Junya Fujimoto, Yanhua Tian, Lingzhi Hong, Hong Chen, Xin Hu, Chenyang Li, Natalie Vokes, Andre L Moreira, Don L Gibbons, Luisa M Solis Soto, Edwin Roger Parra Cuentas, Ou Shi, Songhui Diao, Jie Ye, Frank R Rojas, Eduardo Vilar, Anirban Maitra, Ken Chen, Nicolas Navin, Monique Nilsson, Beibei Huang, Simon Heeke, Jianhua Zhang, Cara L Haymaker, Vamsidhar Velcheti, Daniel H Sterman, Veena Kochat, William I Padron, Ludmil B Alexandrov, Zhubo Wei, Xiuning Le, Linghua Wang, Junya Fukuoka, J Jack Lee, Ignacio I Wistuba, Harvey I Pass, Mark Davis, Samir Hanash, Chao Cheng, Steven Dubinett, Avrum Spira, Kunal Rai, Scott M Lippman, P Andrew Futreal, John V Heymach, Alexandre Reuben, Jia Wu and Jianjun Zhang (2025) Cancer Cell Volume: 43, Issue: 6, Pages: 1125-1140. e10.

169. Identification and Validation of a Previously Missed Mutational Signature in Colorectal Cancer

Mariya Kazachkova, Burçak Otlu, Marcos Díaz-Gay, Ammal Abbasi, Sarah Moody, Sandra Perdomo, David C Wedge, Paul Brennan, Michael R Stratton and Ludmil B Alexandrov (2025), bioRxiv.

168. Long-term latency of highly mutated cells in normal mouse skin is reversed by exposure to tumor promoters and chronic tissue damage

Yun Rose Li, Eve Kandyba, Kyle Halliwill, Reyno Delrosario, Quan Tran, Nora Bayani, Di Wu, Olga K Mirzoeva, Melissa Quino Reeves, SM Ashiqul Islam, Laura Riva, Erik N Bergstrom, Kavya Achanta, John DiGiovanni, Ludmil B Alexandrov and Allan Balmain (2025) Cancer Discovery Volume: 15, Issue: 6, Pages: 1115-1128.

167. Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis

Cameron Durfee, Erik N Bergstrom, Marcos Díaz-Gay, Yufan Zhou, Nuri Alpay Temiz, Mahmoud A Ibrahim, Shuvro P Nandi, Yaxi Wang, Xingyu Liu, Christopher D Steele, Joshua Proehl, Rachel I Vogel, Prokopios P Argyris, Ludmil B Alexandrov and Reuben S Harris (2025) Research Square Pages: rs. 3. rs-5843684.

166. APOBEC affects tumor evolution and age at onset of lung cancer in smokers

Tongwu Zhang, Jian Sang, Phuc H Hoang, Wei Zhao, Jennifer Rosenbaum, Kofi Ennu Johnson, Leszek J Klimczak, John McElderry, Alyssa Klein, Christopher Wirth, Erik N Bergstrom, Marcos Díaz-Gay, Raviteja Vangara, Frank Colon-Matos, Amy Hutchinson, Scott M Lawrence, Nathan Cole, Bin Zhu, Teresa M Przytycka, Jianxin Shi, Neil E Caporaso, Robert Homer, Angela C Pesatori, Dario Consonni, Marcin Imielinski, Stephen J Chanock, David C Wedge, Dmitry A Gordenin, Ludmil B Alexandrov, Reuben S Harris and Maria Teresa Landi (2025) Nature communications Volume: 16, Issue: 1, Pages: 4711.

165. Evaluating topography of mutational signatures with SigProfilerTopography

Burçak Otlu and Ludmil B Alexandrov (2025) Genome Biology Volume: 26, Issue: 1, Pages: 134.

164. Spatial and single-cell profiling of human and murine lung adenocarcinoma precursors reveals TIM-3 as a putative target for precancer interception

Bo Zhu, Pingjun Chen, Muhammad Aminu, Jian-Rong Li, Junya Fujimoto, Yanhua Tian, Lingzhi Hong, Hong Chen, Xin Hu, Chenyang Li, Natalie Vokes, Andre L Moreira, Don L Gibbons, Luisa M Solis Soto, Edwin Roger Parra Cuentas, Ou Shi, Songhui Diao, Jie Ye, Frank R Rojas, Eduardo Vilar, Anirban Maitra, Ken Chen, Nicolas Navin, Monique Nilsson, Beibei Huang, Simon Heeke, Jianhua Zhang, Cara L Haymaker, Vamsidhar Velcheti, Daniel H Sterman, Veena Kochat, William I Padron, Ludmil Alexandrov, Zhubo Wei, Xiuning Le, Linghua Wang, Junya Fukuoka, J Jack Lee, Ignacio I Wistuba, Harvey I Pass, Mark Davis, Samir Hannash, Chao Cheng, Steven Dubinett, Avrum Spira, Kunal Rai, Scott M Lippman, P Andrew Futreal, John V Heymach, Alexandre Reuben, Jia Wu and Jianjun Zhang (2025) Cancer cell Volume: 43, Issue: 6, Pages: 1125.

163. HRProfiler Detects Homologous Recombination Deficiency in Breast and Ovarian Cancers Using Whole-Genome and Whole-Exome Sequencing Data

Ammal Abbasi, Christopher D Steele, Erik N Bergstrom, Azhar Khandekar, Akanksha Farswan, Rana R McKay, Nischalan Pillay and Ludmil B Alexandrov (2025) Cancer Research

162. Geographic and age variations in mutational processes in colorectal cancer

Marcos Díaz-Gay, Wellington Dos Santos, Sarah Moody, Mariya Kazachkova, Ammal Abbasi, Christopher D Steele, Raviteja Vangara, Sergey Senkin, Jingwei Wang, Stephen Fitzgerald, Erik N Bergstrom, Azhar Khandekar, Burçak Otlu, Behnoush Abedi-Ardekani, Ana Carolina de Carvalho, Thomas Cattiaux, Ricardo Cortez Cardoso Penha, Valérie Gaborieau, Priscilia Chopard, Christine Carreira, Saamin Cheema, Calli Latimer, Jon W Teague, Anush Mukeriya, David Zaridze, Riley Cox, Monique Albert, Larry Phouthavongsy, Steven Gallinger, Reza Malekzadeh, Ahmadreza Niavarani, Marko Miladinov, Katarina Erić, Sasa Milosavljevic, Suleeporn Sangrajrang, Maria Paula Curado, Samuel Aguiar, Rui Manuel Reis, Monise Tadin Reis, Luis Gustavo Romagnolo, Denise Peixoto Guimarães, Ivana Holcatova, Jaroslav Kalvach, Carlos Alberto Vaccaro, Tamara Alejandra Piñero, Beata Świątkowska, Jolanta Lissowska, Katarzyna Roszkowska-Purska, Antonio Huertas-Salgado, Tatsuhiro Shibata, Satoshi Shiba, Surasak Sangkhathat, Taned Chitapanarux, Gholamreza Roshandel, Patricia Ashton-Prolla, Daniel C Damin, Francine Hehn de Oliveira, Laura Humphreys, Trevor D Lawley, Sandra Perdomo, Michael R Stratton, Paul Brennan and Ludmil B Alexandrov (2025), Nature Pages: 1-2.

161. The complexity of tobacco smoke-induced mutagenesis in head and neck cancer

Laura Torrens, Sarah Moody, Ana Carolina de Carvalho, Mariya Kazachkova, Behnoush Abedi-Ardekani, Saamin Cheema, Sergey Senkin, Thomas Cattiaux, Ricardo Cortez Cardoso Penha, Joshua R Atkins, Valérie Gaborieau, Priscilia Chopard, Christine Carreira, Ammal Abbasi, Erik N Bergstrom, Raviteja Vangara, Jingwei Wang, Stephen Fitzgerald, Calli Latimer, Marcos Diaz-Gay, David Jones, Jon Teague, Felipe Ribeiro Pinto, Luiz Paulo Kowalski, Jerry Polesel, Fabiola Giudici, José Carlos de Oliveira, Pagona Lagiou, Areti Lagiou, Marta Vilensky, Dana Mates, Ioan N Mates, Lidia M Arantes, Rui Reis, Jose Roberto V Podesta, Sandra V von Zeidler, Ivana Holcatova, Maria Paula Curado, Cristina Canova, Elenora Fabianova, Paula A Rodríguez-Urrego, Laura Humphreys, Ludmil B Alexandrov, Paul Brennan, Michael R Stratton and Sandra Perdomo (2025) Nature Genetics Volume: 57, Issue: 4, Pages: 884-896.

160. Products of manufacture for cul turing or maintaining normal, pre-cancer and cancer stem and progenitor

Catriona Jamieson, Luisa LADEL, Isabelle OLIVER, Larisa Balaian, Christina Wu, Wenxue MA, Ludmil ALEXANDROV, Shuvro NANDI and Thomas WHISENANT (2025) Patent office: US, Application number: 18729810

159. Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity

Siavash Raeisi Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, Jens Luebeck, Kaiyuan Zhu, Gino Prasad, Lena Krockenberger, Guanghui Xu, Biswanath Chowdhury, Utkrisht Rajkumar, Ann Caplin, Daniel Muliaditan, Aditi Gnanasekar, Ceyda Coruh, Qiushi Jin, Kristen Turner, Shu Xian Teo, Andy Wing Chun Pang, Ludmil B Alexandrov, Christelle En Lin Chua, Frank B Furnari, John Maciejowski, Thomas G Paulson, Julie A Law, Howard Y Chang, Feng Yue, Ramanuj DasGupta, Jean Zhao, Paul S Mischel and Vineet Bafna (2025) Nature Communications Volume: 16, Issue: 1, Pages: 1497.

158. Implementing mutational epidemiology on a global scale: lessons from mutographs

Michael R Stratton, Laura Humphreys, Ludmil B Alexandrov, Allan Balmain, Paul Brennan, Peter J Campbell and David H Phillips (2025) Cancer Discovery Volume: 15, Issue: 1, Pages: 22-27.

157. Investigating the origins of the mutational signatures in cancer

Gunnar Boysen, Ludmil B Alexandrov, Raheleh Rahbari, Intawat Nookaew, Dave Ussery, Mu-Rong Chao, Chiung-Wen Hu and Marcus S Cooke (2025) Nucleic acids research Volume: 53, Issue: 1, Pages: gkae1303.

156. FBP1 controls liver cancer evolution from senescent MASH hepatocytes

Li Gu, Yahui Zhu, Shuvro P Nandi, Maiya Lee, Kosuke Watari, Breanna Bareng, Masafumi Ohira, Yuxiao Liu, Sadatsugu Sakane, Rodrigo Carlessi, Consuelo Sauceda, Debanjan Dhar, Souradipta Ganguly, Mojgan Hosseini, Marcos G Teneche, Peter D Adams, David J Gonzalez, Tatiana Kisseleva, Liver Cancer Collaborative Tirnitz-Parker Janina EE 19 Leedman Peter J. 20 Wallace Michael C. 21 Winteringham Louise N. 20 Dwyer Benjamin J. 19 Tibballs Jonathan 22 Carter Kim W. 23 Forrest Alistair RR 20, Janina EE Tirnitz-Parker, M Celeste Simon, Ludmil B Alexandrov and Michael Karin (2025) Nature Volume: 637, Issue: 8045, Pages: 461-469.

2024

155. Clustered mutations for the treatment of cancer

Ludmil B Alexandrov and Erik N Bergstrom(2024) Patent office: US, Application number: 18719020.

154. Preclinical evaluation of avutometinib and defactinib in high‐grade endometrioid endometrial cancer

Tobias Max Philipp Hartwich, Miranda Mansolf, Cem Demirkiran, Michelle Greenman, Stefania Bellone, Blair McNamara, Shuvro P Nandi, Ludmil B Alexandrov, Yang Yang‐Hartwich, Silvia Coma, Jonathan Pachter and Alessandro D Santin (2024) Cancer medicine Volume: 13, Issue: 17, Pages: e70210.

153. The genomic landscape of 2,023 colorectal cancers

Alex J Cornish, Andreas J Gruber, Ben Kinnersley, Daniel Chubb, Anna Frangou, Giulio Caravagna, Boris Noyvert, Eszter Lakatos, Henry M Wood, Steve Thorn, Richard Culliford, Claudia Arnedo-Pac, Jacob Househam, William Cross, Amit Sud, Philip Law, Maire Ni Leathlobhair, Aliah Hawari, Connor Woolley, Kitty Sherwood, Nathalie Feeley, Güler Gül, Juan Fernandez-Tajes, Luis Zapata, Ludmil B Alexandrov, Nirupa Murugaesu, Alona Sosinsky, Jonathan Mitchell, Nuria Lopez-Bigas, Philip Quirke, David N Church, Ian PM Tomlinson, Andrea Sottoriva, Trevor A Graham, David C Wedge and Richard S Houlston (2024) Nature Pages: 1-10.

152. Enhanced precision in immunotherapy

Erik N Bergstrom and Ludmil B Alexandrov (2024) Nature Cancer Volume: 5, Issue: 8, Pages: 1136-1138.

151. Deep Learning Artificial Intelligence Predicts Homologous Recombination Deficiency and Platinum Response From Histologic Slides

Erik N Bergstrom, Ammal Abbasi, Marcos Díaz-Gay, Loïck Galland, Sylvain Ladoire, Scott M Lippman and Ludmil B Alexandrov (2024) Journal of Clinical Oncology Pages: JCO. 23.02641.

150. Human cancer genomes harbor the mutational signature of tobacco-specific nitrosamines NNN and NNK

Michael Korenjak, N Alpay Temiz, Stéphane Keita, Bérénice Chavanel, Claire Renard, Cécilia Sirand, Vincent Cahais, Tanguy Mayel, Karin R Vevang, Foster C Jacobs, Jiehong Guo, William E Smith, Marissa K Oram, Flaviu A Tăbăran, Ozan Ahlat, Ingrid Cornax, M Gerard O’sullivan, Samrat Das, Shuvro P Nandi, Yuhe Cheng, Ludmil B Alexandrov, Silvia Balbo, Stephen S Hecht, Sergey Senkin, Francois Virard, Lisa A Peterson and Jiri Zavadil (2024) bioRxiv, Pages: 2024.06. 28.600253.

149.Geographic variation of mutagenic exposures in kidney cancer genomes

Sergey Senkin, Sarah Moody, Marcos Díaz-Gay, Behnoush Abedi-Ardekani, Thomas Cattiaux, Aida Ferreiro-Iglesias, Jingwei Wang, Stephen Fitzgerald, Mariya Kazachkova, Raviteja Vangara, Anh Phuong Le, Erik N Bergstrom, Azhar Khandekar, Burcak Otlu, Saamin Cheema, Calli Latimer, Emily Thomas, Joshua Ronald Atkins, Karl Smith-Byrne, Ricardo Cortez Cardoso Penha, Christine Carreira, Priscilia Chopard, Valérie Gaborieau, Pekka Keski-Rahkonen, David Jones, Jon W Teague, Sophie Ferlicot, Mojgan Asgari, Surasak Sangkhathat, Worapat Attawettayanon, Beata Świątkowska, Sonata Jarmalaite, Rasa Sabaliauskaite, Tatsuhiro Shibata, Akihiko Fukagawa, Dana Mates, Viorel Jinga, Stefan Rascu, Mirjana Mijuskovic, Slavisa Savic, Sasa Milosavljevic, John MS Bartlett, Monique Albert, Larry Phouthavongsy, Patricia Ashton-Prolla, Mariana R Botton, Brasil Silva Neto, Stephania Martins Bezerra, Maria Paula Curado, Stenio de Cassio Zequi, Rui Manuel Reis, Eliney Ferreira Faria, Nei Soares de Menezes, Renata Spagnoli Ferrari, Rosamonde E Banks, Naveen S Vasudev, David Zaridze, Anush Mukeriya, Oxana Shangina, Vsevolod Matveev, Lenka Foretova, Marie Navratilova, Ivana Holcatova, Anna Hornakova, Vladimir Janout, Mark P Purdue, Nathaniel Rothman, Stephen J Chanock, Per Magne Ueland, Mattias Johansson, James McKay, Ghislaine Scelo, Estelle Chanudet, Laura Humphreys, Ana Carolina de Carvalho, Sandra Perdomo, Ludmil B Alexandrov, Michael R Stratton and Paul Brennan (2024) Nature Volume: 629, Issue: 8013, Pages: 910-918.

148. Integrated mutational landscape analysis of poorly differentiated high-grade neuroendocrine carcinoma of the uterine cervix

Stefania Bellone, Kyungjo Jeong, Mari Kyllesø Halle, Camilla Krakstad, Blair McNamara, Michelle Greenman, Levent Mutlu, Cem Demirkiran, Tobias Max Philipp Hartwich, Yang Yang-Hartwich, Margherita Zipponi, Natalia Buza, Pei Hui, Francesco Raspagliesi, Salvatore Lopez, Biagio Paolini, Massimo Milione, Emanuele Perrone, Giovanni Scambia, Gary Altwerger, Antonella Ravaggi, Eliana Bignotti, Gloria S Huang, Vaagn Andikyan, Mitchell Clark, Elena Ratner, Masoud Azodi, Peter E Schwartz, Charles M Quick, Roberto Angioli, Corrado Terranova, Samir Zaidi, Shuvro Nandi, Ludmil B Alexandrov, Eric R Siegel, Jungmin Choi, Joseph Schlessinger and  Alessandro D Santin (2024) Proceedings of the National Academy of Sciences Volume: 121, Issue: 17, Pages: e2321898121.

147. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers

Tongwu Zhang, Jian Sang, Phuc H Hoang, Wei Zhao, Jennifer Rosenbaum, Kofi Ennu Johnson, Leszek J Klimczak, John McElderry, Alyssa Klein, Christopher Wirth, Erik N Bergstrom, Marcos Díaz-Gay, Raviteja Vangara, Frank Colon-Matos, Amy Hutchinson, Scott M Lawrence, Nathan Cole, Bin Zhu, Teresa M Przytycka, Jianxin Shi, Neil E Caporaso, Robert Homer, Angela C Pesatori, Dario Consonni, Marcin Imielinski, Stephen J Chanock, David C Wedge, Dmitry A Gordenin, Ludmil B Alexandrov, Reuben S Harris and Maria Teresa Landi (2024) bioRxiv.

146. The Mutographs biorepository: A unique genomic resource to study cancer around the world

Sandra Perdomo, Behnoush Abedi-Ardekani, Ana Carolina De Carvalho, Aida Ferreiro-Iglesias, Valerie Gaborieau, Thomas Cattiaux, Helene Renard, Priscilia Chopard, Christine Carreira, Andreea Spanu, Arash Nikmanesh, Ricardo Cortez Cardoso Penha, Samuel O Antwi, Patricia Ashton-Prolla, Cristina Canova, Taned Chitapanarux, Riley Cox, Maria Paula Curado, José Carlos De Oliveira, Charles Dzamalala, Elenora Fabianova, Lorenzo Ferri, Rebecca Fitzgerald, Lenka Foretova, Steven Gallinger, Alisa M Goldstein, Ivana Holcatova, Antonio Huertas, Vladimir Janout, Sonata Jarmalaite, Radka Kaneva, Luiz Paulo Kowalski, Tomislav Kulis, Pagona Lagiou, Jolanta Lissowska, Reza Malekzadeh, Dana Mates, Valerie McCorrmack, Diana Menya, Sharayu Mhatre, Blandina Theophil Mmbaga, André De Moricz, Péter Nyirády, Miodrag Ognjanovic, Kyriaki Papadopoulou, Jerry Polesel, Mark P Purdue, Stefan Rascu, Lidia Maria Rebolho Batista, Rui Manuel Reis, Luis Felipe Ribeiro Pinto, Paula A Rodríguez-Urrego, Surasak Sangkhathat, Suleeporn Sangrajrang, Tatsuhiro Shibata, Eduard Stakhovsky, Beata Świątkowska, Carlos Vaccaro, Jose Roberto Vasconcelos de Podesta, Naveen S Vasudev, Marta Vilensky, Jonathan Yeung, David Zaridze, Kazem Zendehdel, Ghislaine Scelo, Estelle Chanudet, Jingwei Wang, Stephen Fitzgerald, Calli Latimer, Sarah Moody, Laura Humphreys, Ludmil B Alexandrov and Michael R Stratton and Paul Brennan(2024)  Cell Genomics Volume 4, Issue 3.

145. Arsenic and UVR co-exposure results in unique gene expression profile identifying key co-carcinogenic mechanisms 

Rachel M Speer, Hui Yu, Xixi Zhou, Shuvro P Nandi, Ludmil B Alexandrov, Yan Guo, Laurie G Hudson and Ke Jian Liu (2024) Toxicology and Applied Pharmacology (482): 116773.

144. Nivolumab for patients with high-risk oral leukoplakia: a nonrandomized controlled trial

Glenn J Hanna, Alessandro Villa, Shuvro P Nandi, Ruichao Shi, Anne ONeill, Mofei Liu, Charles T Quinn, Nathaniel S Treister, Herve Y Sroussi, Piamkamon Vacharotayangul, Laura A Goguen, Donald J Annino Jr, Eleni M Rettig, Vickie Y Jo, Kristine S Wong, Patrick Lizotte,  Cloud P Paweletz, Ravindra Uppaluri, Robert I Haddad, Ezra EW Cohen, Ludmil B Alexandrov, William N William Jr, Scott M Lippman and Sook-bin Woo (2024)  JAMA oncology  volume 10, Issue 1.

2023

143. Arsenic is a potent co-mutagen of ultraviolet light

Rachel M. Speer, Shuvro P. Nandi, Karen L. Cooper, Xixi Zhou, Hui Yu, Yan Guo, Laurie G. Hudson, Ludmil B. Alexandrov, and Ke Jian Liu (2023) Communications Biology, volume 6, Article number: 1273.

142. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment

Marcos Díaz-Gay, Raviteja Vangara, Mark Barnes, Xi Wang, S M Ashiqul Islam, Ian Vermes, Stephen Duke, Nithish Bharadhwaj Narasimman, Ting Yang, Zichen Jiang, Sarah Moody, Sergey Senkin, Paul Brennan, Michael R Stratton, and Ludmil B Alexandrov (2023) Bioinformatics, btad756.

141. Nivolumab for Patients With High-Risk Oral Leukoplakia

Glenn J Hanna, Alessandro Villa, Shuvro P Nandi, Ruichao Shi, Anne ONeill, Mofei Liu, Charles T Quinn, Nathaniel S Treister, Herve Y Sroussi, Piamkamon Vacharotayangul, Laura A Goguen, Donald J Annino Jr, Eleni M Rettig, Vickie Y Jo, Kristine S Wong, Patrick Lizotte, Cloud P Paweletz, Ravindra Uppaluri, Robert I  Haddad, Ezra EW Cohen, Ludmil B  Alexandrov, William N William Jr, Scott M Lippman, and Sook-bin Woo (2023) JAMA Oncology doi:10.1001/jamaoncol.2023.4853.

140. APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer

Jennifer L McCann, Agnese Cristini, Emily K Law, Seo Yun Lee, Michael Tellier, Michael A Carpenter, Chiara Beghè, Jae Jin Kim, Anthony Sanchez, Matthew C Jarvis, Bojana Stefanovska, Nuri A Temiz, Erik N Bergstrom, Daniel J Salamango, Margaret R Brown, Shona Murphy, Ludmil B Alexandrov, Kyle M Miller, Natalia Gromak, and Reuben S Harris (2023) Nature Genetics 55, 1721–1734.

139. Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

Azhar Khandekar, Raviteja Vangara, Mark Barnes, Marcos Díaz-Gay, Ammal Abbasi, Erik N Bergstrom, Christopher D Steele, Nischalan Pillay, and Ludmil B Alexandrov (2023) BMC Genomics 24(1):469.

138. Topography of mutational signatures in human cancer

Burcak Otlu, Marcos Díaz-Gay, Ian Vermes, Erik N Bergstrom, Maria Zhivagui, Mark Barnes, and Ludmil B Alexandrov (2023) Cell Reports 42 (8).

137. Mitotic tethering enables inheritance of shattered micronuclear chromosomes

Prasad Trivedi, Christopher D Steele, Franco KC Au, Ludmil B Alexandrov, and Don W Cleveland (2023) Nature 618, 1049–1056.

136. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response

Meghana Pagadala, Timothy J Sears, Victoria H Wu, Eva Pérez-Guijarro, Hyo Kim, Andrea Castro, James V Talwar, Cristian Gonzalez-Colin, Steven Cao, Benjamin J Schmiedel, Shervin Goudarzi, Divya Kirani, Jessica Au, Tongwu Zhang, Maria Teresa Landi, Rany M Salem, Gerald P Morris, Olivier Harismendy, Sandip Pravin Patel, Ludmil B Alexandrov, Jill P Mesirov, Maurizio Zanetti, Chi-Ping Day, Chun Chieh Fan, Wesley K Thompson, Glenn Merlino, J Silvio Gutkind, Pandurangan Vijayanand, and Hannah Carter (2023) Nature Communications volume 14, Article number: 2744.

135.  Chromosomal fragile site breakage by EBV-encoded EBNA1 at clustered repeats

Julia Su Zhou Li, Ammal Abbasi, Dong Hyun Kim, Scott M Lippman, Ludmil B Alexandrov, and Don W Cleveland (2023) Nature 616, 504–509.

134. Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus

Jens Luebeck, Alvin Wei Tian Ng, Patricia C Galipeau, Xiaohong Li, Carissa A Sanchez, Annalise C Katz-Summercorn, Hoon Kim, Sriganesh Jammula, Yudou He, Scott M Lippman, Roel GW Verhaak, Carlo C Maley, Ludmil B Alexandrov, Brian J Reid, Rebecca C Fitzgerald, Thomas G Paulson, Howard Y Chang, Sihan Wu, Vineet Bafna, and Paul S Mischel (2023) Nature 616, 798–805.

133. Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity

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, and Lynnette Fernandez-Cuesta (2023) Nature Genetics 55 (4), 607-618.

132. DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer

Maria Zhivagui, Areebah Hoda, Noelia Valenzuela, Yi-Yu Yeh, Jason Dai, Yudou He, Shuvro P Nandi, Burcak Otlu, Bennett Van Houten, and Ludmil B Alexandrov (2023) Nature Communications, volume 14, Article number: 276.

131. Comprehensive analysis of mutational signatures reveals distinct patterns and molecular processes across 27 pediatric cancers

Venu Thatikonda, SM Ashiqul Islam, Robert J Autry, Barbara C Jones, Susanne N Gröbner, Gregor Warsow, Barbara Hutter, Daniel Huebschmann, Stefan Fröhling, Marcel Kool, Mirjam Blattner-Johnson, David TW Jones, Ludmil B Alexandrov, Stefan M Pfister, and Natalie Jäger (2023) Nature Cancer, 4, 276-289.

130. Unraveling the impact of a germline heterozygous POLD1 frameshift variant in serrated polyposis syndrome

Laia Bonjoch, Yasmin Soares de Lima, Marcos Díaz-Gay, Isabella Dotti, Jenifer Muñoz, Leticia Moreira, Sabela Carballal, Teresa Ocaña, Miriam Cuatrecasas, Oswaldo Ortiz, Antoni Castells, Maria Pellisé, Francesc Balaguer, Azucena Salas, Ludmil B Alexandrov, and Sergi Castellví-Bel (2023) Frontiers in Molecular Biosciences, 10, 27.

129. Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis

Nicholas Light, Mehdi Layeghifard, Ayush Attery, Vallijah Subasri, Matthew Zatzman, Nathaniel D Anderson, Rupal Hatkar, Sasha Blay, David Chen, Ana Novokmet, Fabio Fuligni, James Tran, Richard de Borja, Himanshi Agarwal, Larissa Waldman, Lisa M Abegglen, Daniel Albertson, Jonathan L Finlay, Jordan R Hansford, Sam Behjati, Anita Villani, Moritz Gerstung, Ludmil B Alexandrov, Gino R Somers, Joshua D Schiffman, Varda Rotter, David Malkin, and Adam Shlien (2023) Nature Communications, volume 14, Article number: 77.

128. Control-independent mosaic single nucleotide variant detection with DeepMosaic

Xiaoxu Yang, Xin Xu, Martin W Breuss, Danny Antaki, Laurel L Ball, Changuk Chung, Jiawei Shen, Chen Li, Renee D George, Yifan Wang, Taejeong Bae, Yuhe Cheng, Alexej Abyzov, Liping Wei, Ludmil B Alexandrov, Jonathan L Sebat, NIMH Brain Somatic Mosaicism Network, and Joseph G Gleeson (2023) Nature Biotechnology, 41 (6), 870-877.

127. Ovarian and uterine carcinosarcomas are sensitive in vitro and in vivo to elimusertib, a novel ataxia-telangiectasia and Rad3-related (ATR) kinase inhibitor

Diego D Manavella, Blair McNamara, Justin Harold, Stefania Bellone, Tobias Max Philipp Hartwich, Yang Yang-Hartwich, Levent Mutlu, Margherita Zipponi, Cem Demirkiran, Miguel Skyler Verzosa, Gary Altwerger, Elena Ratner, Gloria S Huang, Mitchell Clark, Vaagn Andikyan, Masoud Azodi, Peter E Schwartz, Peter R Dottino, Jungmin Choi, Ludmil B Alexandrov, Natalia Buza, Pei Hui, and Alessandro D Santin (2023) Gynecologic Oncology, 169(4), 98-105.

2022

126. Somatic 9p24.1 alterations in HPV– head and neck squamous cancer dictate immune microenvironment and anti-PD-1 checkpoint inhibitor activity

Xin Zhao, Ezra EW Cohen, William N William Jr, Joy J Bianchi, Jim P Abraham, Daniel Magee, David B Spetzler, J Silvio Gutkind, Ludmil B Alexandrov, Webster K Cavenee, Scott M Lippman, and Teresa Davoli (2022) Proceedings of the National Academy of Sciences of the United States of America 119 (47): e2213835119.

125. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

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, and Ludmil B Alexandrov (2022) Cell Genomics 2 (11), 100179.

124. AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas

Pradipta Ghosh, Vinicius J. Campos, Daniella T. Vo, Caitlin Guccione, Vanae Goheen-Holland, Courtney Tindle, Guilherme S. Mazzini, Yudou He, Ludmil B Alexandrov, Scott M. Lippman, Richard R. Gurski, Soumita Das, Rena Yadlapati, Kit Curtius, and Debashis Sahoo (2022) JCI Insight 7(18):e161334.

123. A genetic model for central chondrosarcoma evolution correlates with patient outcome

William Cross, Iben Lyskjær, Tom Lesluyes, Steven Hargreaves, Anna-Christina Strobl, Christopher Davies, Sara Waise, Shadi Hames-Fathi, Dahmane Oukrif, Hongtao Ye, Fernanda Amary, Roberto Tirabosco, Craig Gerrand, Toby Baker, David Barnes, Christopher Steele, Ludmil B Alexandrov, Gareth Bond, Paul Cool, Nischalan Pillay, Peter Van Loo, and Adrienne M Flanagan (2022) Genome Medicine 14 (1), 1-12.

122. Mechanisms of APOBEC3 mutagenesis in human cancer cells

Mia Petljak, Alexandra Dananberg, Kevan Chu, Erik N Bergstrom, Josefine Striepen, Patrick von Morgen, Yanyang Chen, Hina Shah, Julian E Sale, Ludmil B Alexandrov, Michael R Stratton, and John Maciejowski (2022) Nature, (607), 799–807.

121. An overview of mutational and copy number signatures in human cancer

Christopher D Steele, Nischalan Pillay, and Ludmil B Alexandrov (2022) The Journal of Pathology, 257(4):454-465.

120. Signatures of copy number alterations in human cancer

Christopher D Steele, Ammal Abbasi, SM Islam, Amy L Bowes, Azhar Khandekar, Kerstin Haase, Shadi Hames-Fathi, Dolapo Ajayi, Annelien Verfaillie, Pawan Dhami, Alex McLatchie, Matt Lechner, Nicholas Light, Adam Shlien, David Malkin, Andrew Feber, Paula Proszek, Tom Lesluyes, Fredrik Mertens, Adrienne M Flanagan, Maxime Tarabichi, Peter Van Loo, Ludmil B Alexandrov, and Nischalan Pillay (2022) Nature (606), 984–991.

119. Synergistic activity of neratinib in combination with olaparib in uterine serous carcinoma overexpressing HER2/neu

Ghanshyam Yadav, Dana M Roque, Stefania Bellone, Diego D Manavella, Tobias MP Hartwich, Margherita Zipponi, Justin Harold, Joan Tymon-Rosario, Levent Mutlu, Gary Altwerger, Gulden Menderes, Elena Ratner, Natalia Buza, Pei Hui, Gloria S Huang, Vaagn Andikyan, Mitchell Clark, Masoud Azodi, Peter E Schwartz, Ludmil B Alexandrov, and Alessandro D Santin (2022) Gynecologic Oncology, 166(2), 351-357.

118. Homologous recombination deficiency (HRD) signature-3 in ovarian and uterine carcinosarcomas correlates with preclinical sensitivity to Olaparib, a poly (adenosine diphosphate [ADP]- ribose) polymerase (PARP) inhibitor

Joan R Tymon-Rosario, Paola Manara, Diego D Manavella, Stefania Bellone, Tobias Max Philipp Hartwich, Justin Harold, Yang Yang-Hartwich, Margherita Zipponi, Jungmin Choi, Kyungjo Jeong, Levent Mutlu, Kevin Yang, Gary Altwerger, Gulden Menderes, Elena Ratner, Gloria S Huang, Mitchell Clark, Vaagn Andikyan, Masoud Azodi, Peter E Schwartz, Ludmil B Alexandrov, and Alessandro D Santin (2022) Gynecologic Oncology, 166 (1), 117-125.

117. Examining clustered somatic mutations with SigProfilerClusters

Erik N Bergstrom, Mousumy Kundu, Noura Tbeileh, and Ludmil B Alexandrov (2022) Bioinformatics, 38 (13), 3470–3473.

116. Somatic mutational profiles and germline polygenic risk scores in human cancer

Yuxi Liu, Alexander Gusev, Yujing J Heng, Ludmil B Alexandrov, and Peter Kraft (2022) Genome Medicine 14 (1), 1-16.

115. Unwinding the mutational signatures of a DNA topoisomerase enzyme

Ammal Abbasi and Ludmil B Alexandrov (2022) Nature (602), 580-581.

114. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA

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, and Ludmil B Alexandrov  (2022) Nature (602), 510–517.

113. A phase 2 evaluation of pembrolizumab for recurrent Lynch-like versus sporadic endometrial cancers with microsatellite instability

Stefania Bellone, Dana M. Roque, Eric R. Siegel, Natalia Buza, Pei Hui, Elena Bonazzoli, Adele Guglielmi, Luca Zammataro, Nupur Nagarkatti, Samir Zaidi, Jungsoo Lee, Dan-Arin Silasi, Gloria S. Huang, Vaagn Andikyan, Shari Damast, Mitchell Clark, Masoud Azodi, Peter E. Schwartz, Joan R. Tymon-Rosario, Justin A Harold, Dennis Mauricio, Burak Zeybek, Gulden Menderes, Gary Altwerger, Elena Ratner, Ludmil B Alexandrov, Akiko Iwasaki, Yong Kong, Eric Song, Weilai Dong, Julia A Elvin, Jungmin Choi, and Alessandro D. Santin (2022) Cancer 128:6, 1206-1218.

2021

112. Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence

Sarah Moody, Sergey Senkin, SM Islam, Jingwei Wang, Dariush Nasrollahzadeh, Ricardo Cortez Cardoso Penha, Stephen Fitzgerald, Erik N Bergstrom, Joshua Atkins, Yudou He, Azhar Khandekar, Karl Smith-Byrne, Christine Carreira, Valerie Gaborieau, Calli Latimer, Emily Thomas, Irina Abnizova, Pauline E Bucciarelli, David Jones, Jon W Teague, Behnoush Abedi-Ardekani, Stefano Serra, Jean-Yves Scoazec, Hiva Saffar, Farid Azmoudeh-Ardalan, Masoud Sotoudeh, Arash Nikmanesh, Hossein Poustchi, Ahmadreza Niavarani, Samad Gharavi, Michael Eden, Paul Richman, Lia S Campos, Rebecca C Fitzgerald, Luis Felipe Ribeiro, Sheila Coelho Soares-Lima, Charles Dzamalala, Blandina Theophil Mmbaga, Tatsuhiro Shibata, Diana Menya, Alisa M Goldstein, Nan Hu, Reza Malekzadeh, Abdolreza Fazel, Valerie McCormack, James McKay, Sandra Perdomo, Ghislaine Scelo, Estelle Chanudet, Laura Humphreys, Ludmil B Alexandrov, Paul Brennan, and Michael R Stratton (2021) Nature Genetics 53 (11), 1553-1563.

111. Genomic and evolutionary classification of lung cancer in never smokers

Tongwu Zhang, Philippe Joubert, Naser Ansari-Pour, Wei Zhao, Phuc H Hoang, Rachel Lokanga, Aaron L Moye, Jennifer Rosenbaum, Abel Gonzalez-Perez, Francisco Martínez-Jiménez, Andrea Castro, Lucia Anna Muscarella, Paul Hofman, Dario Consonni, Angela C Pesatori, Michael Kebede, Mengying Li, Bonnie E Gould Rothberg, Iliana Peneva, Matthew B Schabath, Maria Luana Poeta, Manuela Costantini, Daniela Hirsch, Kerstin Heselmeyer-Haddad, Amy Hutchinson, Mary Olanich, Scott M Lawrence, Petra Lenz, Maire Duggan, Praphulla Bhawsar, Jian Sang, Jung Kim, Laura Mendoza, Natalie Saini, Leszek J Klimczak, SM Islam, Burcak Otlu, Azhar Khandekar, Nathan Cole, Douglas R Stewart, Jiyeon Choi, Kevin M Brown, Neil E Caporaso, Samuel H Wilson, Yves Pommier, Qing Lan, Nathaniel Rothman, Jonas S Almeida, Hannah Carter, Thomas Ried, Carla F Kim, Nuria Lopez-Bigas, Montserrat Garcia-Closas, Jianxin Shi, Yohan Bossé, Bin Zhu, Dmitry A Gordenin, Ludmil B Alexandrov, Stephen J Chanock, David C Wedge, and Maria Teresa Landi (2021) Nature Genetics 53 (9), 1348-1359.

110. Unraveling the genomic landscape of colorectal cancer through mutational signatures

Marcos Díaz-Gay and Ludmil B Alexandrov (2021) Advances in Cancer Research 151, 385-424.

109. Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures

Ammal Abbasi and Ludmil B Alexandrov (2021) DNA Repair volume 107: 103200.

108. Lineage-defined leiomyosarcoma subtypes emerge years before diagnosis and determine patient survival

Nathaniel D Anderson, Yael Babichev, Fabio Fuligni, Federico Comitani, Mehdi Layeghifard, Rosemarie E Venier, Stefan C Dentro, Anant Maheshwari, Sheena Guram, Claire Wunker, J Drew Thompson, Kyoko E Yuki, Huayun Hou, Matthew Zatzman, Nicholas Light, Marcus Q Bernardini, Jay S Wunder, Irene L Andrulis, Peter Ferguson, Albiruni R Abdul Razak, Carol J Swallow, James J Dowling, Rima S Al-Awar, Richard Marcellus, Marjan Rouzbahman, Moritz Gerstung, Daniel Durocher, Ludmil B Alexandrov, Brendan C Dickson, Rebecca A Gladdy, and Adam Shlien (2021) Nature Communications volume 12, Article number: 4496.

107. Inhibition of mTOR signaling and clinical activity of metformin in oral premalignant lesions

J. Silvio Gutkind, Alfredo Molinolo, Xingyu Wu, Zhiyong Wang, Daniela Nachmanson, Olivier Harismendy, Ludmil B Alexandrov, Beverly R. Wuertz, Frank G. Ondrey, Denise M. Laronde, Leigha D. Rock, Miriam P. Rosin, Charles S. Coffey, Valerie D. Butler, Lisa Bengtson, Chiu-Hsieh Hsu, Julie E. Bauman, Stephen M. Hewitt, Ezra E.W. Cohen, H.H. Sherry Chow, Scott M. Lippman, and Eva Szabo (2021) JCI Insight 6 (17).

106. Immune evasion in HPV− head and neck precancer–cancer transition is driven by an aneuploid switch involving chromosome 9p loss

William N William, Xin Zhao, Joy J Bianchi, Heather Y Lin, Pan Cheng, J Jack Lee, Hannah Carter, Ludmil B Alexandrov, Jim P Abraham, David B Spetzler, Steven M Dubinett, Don W Cleveland, Webster Cavenee, Teresa Davoli, and Scott M Lippman (2021) Proceedings of the National Academy of Sciences of the United States of America 118(19):e2022655118.

105. Integrated mutational landscape analysis of uterine leiomyosarcomas

Jungmin Choi, Aranzazu Manzano, Weilai Dong, Stefania Bellone, Elena Bonazzoli, Luca Zammataro, Xiaotong Yao, Aditya Deshpande, Samir Zaidi, Adele Guglielmi, Barbara Gnutti, Nupur Nagarkatti, Joan R Tymon-Rosario, Justin Harold, Dennis Mauricio, Burak Zeybek, Gulden Menderes, Gary Altwerger, Kyungjo Jeong, Siming Zhao, Natalia Buza, Pei Hui, Antonella Ravaggi, Eliana Bignotti, Chiara Romani, Paola Todeschini, Laura Zanotti, Franco Odicino, Sergio Pecorelli, Laura Ardighieri, Kaya Bilguvar, Charles M Quick, Dan-Arin Silasi, Gloria S Huang, Vaagn Andikyan, Mitchell Clark, Elena Ratner, Masoud Azodi, Marcin Imielinski, Peter E Schwartz, Ludmil B Alexandrov, Richard P Lifton, Joseph Schlessinger, and Alessandro D Santin (2021) Proceedings of the National Academy of Sciences of the United States of America 118(15):e2025182118.

104. Synchronous, Yet Genomically Distinct, GIST Offer New Insights Into Precise Targeting of Tumor Driver Mutations

Eleftherios A Makris, Ashwyn K Sharma, Erik N Bergstrom, Xiaojun Xu, Jorge de la Torre, Sudeep Banerjee, Vi Nguyen, Mojgan Hosseini, Adam Burgoyne, Olivier Harismendy, Ludmil B Alexandrov, and Jason K Sicklick (2021) JCO Precision Oncology 5, 525-532.

103. Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution

Qingfei Jiang, Jane Isquith, Luisa Ladel, Adam Mark, Frida Holm, Cayla Mason, Yudou He, Phoebe Mondala, Isabelle Oliver, Jessica Pham, Wenxue Ma, Eduardo Reynoso, Shawn Ali, Isabella Jamieson Morris, Raymond Diep, Chanond Nasamran, Guorong Xu, Roman Sasik, Sara Brin Rosenthal, Amanda Birmingham, Sanja Coso, Gabriel Pineda, Leslie Crews, Mary E Donohoe, J Craig Venter, Thomas Whisenant, Ruben A Mesa, Ludmil B Alexandrov, Kathleen M Fisch, and Catriona Jamieson (2021) Cell Reports 34 (4), 108670.

102. St. Jude Cloud-a Pediatric Cancer Genomic Data Sharing Ecosystem

Clay McLeod, Alexander M Gout, Xin Zhou, Andrew Thrasher, Delaram Rahbarinia, Samuel Warren Brady, Michael Macias, Kirby Birch, David Finkelstein, Jobin Sunny, Rahul Mudunuri, Brent A Orr, Madison Treadway, Bob Davidson, Tracy K Ard, Arthur Chiao, Andrew Swistak, Stephanie Wiggins, Scott Foy, Jian Wang, Edgar Sioson, Shuoguo Wang, J Robert Michael, Yu Liu, Xiaotu Ma, Aman Patel, Michael N Edmonson, Mark R Wilkinson, Andrew M Frantz, Ti-Cheng Chang, Liqing Tian, Shaohua Lei, SM Ashiqul Islam, Christopher Meyer, Naina Thangaraj, Pamella Tater, Vijay Kandali, Singer Ma, Tuan Nguyen, Omar Abdulgafoor Serang, Irina McGuire, Nedra Robison, Darrell Gentry, Xing Tang, Lance E Palmer, Gang Wu, Ed Suh, Leigh Tanner, James McMurry, Matthew Lear, Alberto S Pappo, Zhaoming Wang, Carmen L Wilson, Yong Cheng, Soheil Meshinchi, Ludmil B Alexandrov, Mitchell J Weiss, Gregory T Armstrong, Leslie L Robison, Yutaka Yasui, Kim E Nichols, David W Ellison, Chaitanya Bangur, Charles G Mullighan, Suzanne J Baker, Michael A Dyer, Geralyn Miller, Scott Newman, Michael Rusch, Richard Daly, Keith Perry, James R Downing, and Jinghui Zhang (2021) Cancer Discovery, 11 (5), 1082-1099. 

2020

101. Bioinformatic Methods to Identify Mutational Signatures in Cancer

SM Ashiqul Islam and Ludmil B Alexandrov (2020) Leukemia Stem Cells 447-473.

100. The mutational signature profile of known and suspected human carcinogens in mice

Laura Riva, Arun R Pandiri, Yun Rose Li, Alastair Droop, James Hewinson, Michael A Quail, Vivek Iyer, Rebecca Shepherd, Ronald A Herbert, Peter J Campbell, Robert C Sills, Ludmil B Alexandrov, Allan Balmain, and David J Adams ( 2020) Nature Genetics volume 52, pages 1189–1197.

99. Tracing Lung Cancer Risk Factors Through Mutational Signatures in Never-Smokers: The Sherlock-Lung Study

Maria Teresa Landi, Naoise C Synnott, Jennifer Rosenbaum, Tongwu Zhang, Bin Zhu, Jianxin Shi, Wei Zhao, Michael Kebede, Jian Sang, Jiyeon Choi, Laura Mendoza, Marwil Pacheco, Belynda Hicks, Neil E Caporaso, Mustapha Abubakar, Dmitry A Gordenin, David C Wedge, Ludmil B Alexandrov, Nathaniel Rothman, Qing Lan, Montserrat Garcia-Closas, and Stephen J Chanock ( 2020) American Journal of Epidemiology, 190 (6), 962-976.

98. Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator

Erik N Bergstrom, Mark Barnes, Inigo Martincorena, and Ludmil B Alexandrov ( 2020) BMC Bioinformatics 21, Article number: 438.

97. Strength of immune selection in tumors varies with sex and age

Andrea Castro, Rachel Marty Pyke, Xinlian Zhang, Wesley Kurt Thompson, Chi-Ping Day, Ludmil B Alexandrov, Maurizio Zanetti, and Hannah Carter ( 2020) Nature Communications volume 11, Article number: 4128.

96. The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

Bin Zhu, Maria Luana Poeta, Manuela Costantini, Tongwu Zhang, Jianxin Shi, Steno Sentinelli, Wei Zhao, Vincenzo Pompeo, Maurizio Cardelli, Boian S. Alexandrov, Burcak Otlu, Xing Hua, Kristine Jones, Seth Brodie, Malgorzata Ewa Dabrowska, Jorge R. Toro, Meredith Yeager, Mingyi Wang, Belynda Hicks, Ludmil B Alexandrov, Kevin M. Brown, David C. Wedge, Stephen Chanock, Vito Michele Fazio, Michele Gallucci, and Maria Teresa Landi (2020) Nature Communications volume 11, Article number: 3096.

95. Timing the initiation of multiple myeloma

Even H Rustad, Venkata Yellapantula, Daniel Leongamornlert, Niccolò Bolli, Guy Ledergor, Ferran Nadeu, Nicos Angelopoulos, Kevin J Dawson, Thomas J Mitchell, Robert J Osborne, Bachisio Ziccheddu, Cristiana Carniti, Vittorio Montefusco, Paolo Corradini, Kenneth C Anderson, Philippe Moreau, Elli Papaemmanuil, Ludmil B Alexandrov, Xose S Puente, Elias Campo, Reiner Siebert, Herve Avet-Loiseau, Ola Landgren, Nikhil Munshi, Peter J Campbell, and Francesco Maura (2020) Nature Communications volume 11, Article number: 1917.

94. The repertoire of mutational signatures in human cancer

Ludmil B Alexandrov, Jaegil Kim, Nicholas J Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R Covington, Dmitry A Gordenin, Erik N. Bergstrom, SM Ashiqul Islam, Nuria Lopez-Bigas, Leszek J Klimczak, John R. McPherson, Sandro Morganella, Radhakrishnan Sabarinathan, David A Wheeler, Ville Mustonen, PCAWG Mutational Signatures Working Group, Gad Getz, Steven G Rozen, Michael R Stratton, and PCAWG Consortium (2020) Nature (578), 94–101.

93. Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium ( 2020)  Nature (578), 82–93.

92. Mutational signatures in tumours induced by high and low energy radiation in Trp53 deficient mice

Yun Rose Li, Kyle D. Halliwill, Cassandra J. Adams, Vivek Iyer, Laura Riva, Rashid Mamunur, Kuang-Yu Jen, Reyno del Rosario, Erik Fredlund, Gillian Hirst, Ludmil B Alexandrov, David Adams, and Allan Balmain (2020) Nature Communications volume 11, Article number: 394.

91. The association of modifiable breast cancer risk factors and somatic genomic alterations in breast tumors: The Cancer Genome Atlas Network

Yujing J Heng, Susan E Hankinson, Jun Wang, Ludmil B Alexandrov, Christine B Ambrosone, Victor Piana de Andrade, Adam M Brufsky, Fergus J Couch, Tari A King, Francesmary Modugno, Celine M Vachon, A Heather Eliassen, Rulla M Tamimi, and Peter Kraft (2020) Cancer Epidemiology, Biomarkers & Prevention, 29(3):599-605.

90. Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma

Ayesha Noorani, Xiaodun Li, Martin Goddard, Jason Crawte, Ludmil B Alexandrov, Maria Secrier, Matthew D Eldridge, Lawrence Bower, Jamie Weaver, Pierre Lao-Sirieix, Inigo Martincorena, Irene Debiram-Beecham, Nicola Grehan, Shona Macrae, Shalini Malhotra, Ahmad Miremadi, Tabitha Thomas, Sarah Galbraith, Lorraine Petersen, Stephen D Preston, David Gilligan, Andrew Hindmarsh, Richard H Hardwick, Michael R Stratton, David C Wedge, and Rebecca C Fitzgerald (2020) Nature Genetics, 52:74–83.

2019

89. IL-17 signaling in steatotic hepatocytes and macrophages promotes hepatocellular carcinoma in alcohol-related liver disease

Hsiao-Yen Ma, Gen Yamamoto, Jun Xu, Xiao Liu, Daniel Karin, Ju Youn Kim, Ludmil B Alexandrov, Yukinori Koyama, Takahiro Nishio, Chris Benner, Sven Heinz, Sara B Rosenthal, Shuang Liang, Mengxi Sun, Gabriel Karin, Peng Zhao, Pnina Brodt, Iain H Mckillop, Oswald Quehenberger, Ed Dennis, Alan Saltiel, Hidekazu Tsukamoto, Bin Gao, Michael Karin, David A Brenner, and Tatiana Kisseleva (2019) Journal of Hepatology, 72(5):946-959.

88. Whole-exome sequencing reveals the impact of UVA light mutagenesis in xeroderma pigmentosum variant human cells

Natália Cestari Moreno, Tiago Antonio de Souza, Camila Carrião Machado Garcia, Nathalia Quintero Ruiz, Camila Corradi, Ligia Pereira Castro, Veridiana Munford, Susan Ienne, Ludmil B Alexandrov, and Carlos Frederico Martins Menck (2019) Nucleic Acids Research, 48(4):1941-1953.

87. Syngeneic animal models of tobacco-associated oral cancer reveal the activity of in situ anti-CTLA-4

Zhiyong Wang, Victoria H. Wu, Michael M. Allevato, Mara Gilardi, Yudou He, Juan Luis Callejas-Valera, Lynn Vitale-Cross, Daniel Martin, Panomwat Amornphimoltham, James Mcdermott, Bryan S. Yung, Yusuke Goto, Alfredo A Molinolo, Andrew B Sharabi, Ezra E W. Cohen, Qianming Chen, J Guy Lyons, Ludmil B Alexandrov, and J Silvio Gutkin (2019) Nature Communications 10 (1), 5546.

86. Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia

Benshang Li, Samuel W. Brady, Xiaotu Ma, Shuhong Shen, Yingchi Zhang, Yongjin Li, Karol Szlachta, Li Dong, Yu Liu, Fan Yang, Ningling Wang, Diane A. Flasch, Matthew A. Myers, Heather L. Mulder, Lixia Ding, Yanling Liu, Liqing Tian, Kohei Hagiwara, Ke Xu, Xin Zhou, Edgar Sioson, Tianyi Wang, Liu Yang, Jie Zhao, Hui Zhang, Ying Shao, Hongye Sun, Lele Sun, Jiaoyang Cai, Hui-ying Sun, Ting-Nien Lin, Lijuan Du, Hui Li, Michael Rusch, Michael N Edmonson, John Easton, Xiaofan Zhu, Jingliao Zhang, Cheng Cheng, Benjamin R. Raphael, Jingyan Tang, James R Downing, Ludmil B Alexandrov, Bin-Bing S Zhou, Ching-Hon Pui, Jun J Yang, and Jinghui Zhang (2019) Blood 135(1):41-55.

85. Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy

Luca Zammataro, Salvatore Lopez, Stefania Bellone, Francesca Pettinella, Elena Bonazzoli, Emanuele Perrone, Siming Zhao, Gulden Menderes, Gary Altwerger, Chanhee Han, Burak Zeybek, Anna Bianchi, Aranzazu Manzano, Paola Manara, Emiliano Cocco, Natalia Buza, Pei Hui, Serena Wong, Antonella Ravaggi, Eliana Bignotti, Chiara Romani, Paola Todeschini, Laura Zanotti, Franco Odicino, Sergio Pecorelli, Carla Donzelli, Laura Ardighieri, Roberto Angioli, Francesco Raspagliesi, Giovanni Scambia, Jungmin Choi, Weilai Dong, Kaya Bilguvar, Ludmil B Alexandrov, Dan-Arin Silasi, Gloria S. Huang, Elena Ratner, Masoud Azodi, Peter E. Schwartz, Valentina Pirazzoli, Amy L. Stiegler, Titus J. Boggon, Richard P. Lifton, Joseph Schlessinger, and Alessandro D. Santin (2019) Proceedings of the National Academy of Sciences of the United States of America 116(45):22730-22736.

84. SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events

Erik N. Bergstrom, Mi Ni Huang, Uma Mahto, Mark Barnes, Michael R. Stratton, Steven G. Rozen, and Ludmil B Alexandrov (2019) BMC Genomics 20, Article number: 685.

83. Somatic evolution and global expansion of an ancient transmissible cancer lineage

Adrian Baez-Ortega, Kevin Gori, Andrea Strakova, Castillo Domracheva, Delgadillo Keenan, Espinoza Huerta, Häfelin Manrique, Young Mi Kwon, Lopez Quintana, Martínez Castañeda, Máire Ní Leathlobhair, Rojas Gutierrez, Maximilian Stammnitz, Tapia Martínez, Thoya Ngoka, Jinhong Wang, Michael R. Stratton, Ludmil B Alexandrov, Iñigo Martincorena, and Elizabeth P. Murchison (2019) Science 365(6452):eaau9923.

82. Insights into BRCA cancer predisposition from integrated germline and somatic analyses in 7632 cancers

Shawn Yost, Elise Ruark, Ludmil B Alexandrov, and Nazneen Rahman (2019) JNCI Cancer Spectrum, 3(2):pkz028.

81. Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation

Arie B Brinkman, Serena Nik-Zainal, Femke Simmer, F German Rodriguez-Gonzalez, Marcel Smid, Ludmil B Alexandrov, Adam Butler, Sancha Martin, Helen Davies, Dominik Glodzik, Xueqing Zou, Manasa Ramakrishna, Johan Staaf, Markus Ringner, Anieta Sieuwerts, Anthony Ferrari, Sandro Morganella, Thomas Fleischer, Vessela Kristensen, Marta Gut, Marc J Van De Vijver, Anne-Lise Børresen-Dale, Andrea L Richardson, Gilles Thomas, Ivo G Gut, John WM Martens, John A Foekens, Michael R Stratton, and Hendrik G Stunnenberg (2019) Nature Communications 10 (1), 1749.

80. Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways

Christopher D Steele, Maxime Tarabichi, Dahmane Oukrif, Amy P Webster, Hongtao Ye, Matthew Fittall, Patrick Lombard, Iñigo Martincorena, Patrick S Tarpey, Grace Collord, Kerstin Haase, Sandra J Strauss, Fitim Berisha, Heli Vaikkinen, Pawan Dhami, Marnix Jansen, Sam Behjati, M Fernanda Amary, Roberto Tirabosco, Andrew Feber, Peter J Campbell, Ludmil B Alexandrov, Peter Van Loo, Adrienne M Flanagan, and Nischalan Pillay (2019) Cancer Cell 35 (3), 441-456.

79. Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

Mia Petljak, Ludmil B Alexandrov, Jonathan S Brammeld, Stacey Price, David C Wedge, Sebastian Grossmann, Kevin J Dawson, Young Seok Ju, Francesco Iorio, Jose MC Tubio, Ching Chiek Koh, Ilias Georgakopoulos-Soares, Bernardo Rodríguez–Martín, Burçak Otlu, Sarah O’Meara, Adam P Butler, Andrew Menzies, Shriram G Bhosle, Keiran Raine, David R Jones, Jon W Teague, Kathryn Beal, Calli Latimer, Laura O’Neill, Jorge Zamora, Elizabeth Anderson, Nikita Patel, Mark Maddison, Bee Ling Ng, Jennifer Graham, Mathew J Garnett, Ultan McDermott, Serena Nik-Zainal, Peter J Campbell, and Michael R Stratton (2019) Cell 176 (6), 1282-1294.

78. The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment

Samuel W Brady, Xiaotu Ma, Armita Bahrami, Gryte Satas, Gang Wu, Scott Newman, Michael Rusch, Daniel K Putnam, Heather L Mulder, Donald Yergeau, Michael N Edmonson, John Easton, Ludmil B Alexandrov, Xiang Chen, Elaine R Mardis, Richard K Wilson, James R Downing, Alberto S Pappo, Benjamin J Raphael, Michael A Dyer, and Jinghui Zhang (2019) Molecular Cancer Research, 17(4):895-906.

77. Stem cell replication, somatic mutations and role of randomness in the development of cancer

Vittorio Perduca, Ludmil B Alexandrov, Michelle Kelly-Irving, Cyrille Delpierre, Hanane Omichessan, Mark P. Little, Paolo Vineis, and Gianluca Sever (2019) Eur J Epidemiol, 34 (5) 439-445.

2018

76. Nonnegative/Binary matrix factorization with a D-Wave quantum annealer

Daniel O’Malley, Velimir V. Vesselinov, Boian S. Alexandrov, and Ludmil B Alexandrov (2018) PLoS ONE 13(12), e0206653.

75. Integrative genomic analysis of mouse and human hepatocellular carcinoma

Michelle Dow, Rachel M. Pyke, Brian Y. Tsui, Ludmil B Alexandrov, Hayato Nakagawa, Koji Taniguchi, Ekihiro Seki, Olivier Harismendy, Shabnam Shalapour, Michael Karin, Hannah Carter, and Joan Font-Burgada (2018) Proceedings of the National Academy of Sciences of the United States of America 115 (42), E9879-E9888.

74. The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature

Gareth J. Inman, Jun Wang, Ai Nagano, Ludmil B Alexandrov, Karin J. Purdie, Richard G. Taylor, Victoria Sherwood, Jason Thomson, Sarah Hogan, Lindsay C. Spender, Andrew P. South, Michael Stratton, Claude Chelala, Catherine A. Harwood, Charlotte M. Proby, and Irene M Leigh (2018) Nature Communications 9 (1), 3667.

73. Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors 

Nathaniel D Anderson, Richard de Borja, Matthew D Young, Fabio Fuligni, Andrej Rosic, Nicola D Roberts, Simon Hajjar, Mehdi Layeghifard, Ana Novokmet, Paul E Kowalski, Matthew Anaka, Scott Davidson, Mehdi Zarrei, Badr Id Said, L Christine Schreiner, Remi Marchand, Joseph Sitter, Nalan Gokgoz, Ledia Brunga, Garrett T Graham, Anthony Fullam, Nischalan Pillay, Jeffrey A Toretsky, Akihiko Yoshida, Tatsuhiro Shibata, Markus Metzler, Gino R Somers, Stephen W Scherer, Adrienne M Flanagan, Peter J Campbell, Joshua D Schiffman, Mary Shago, Ludmil B Alexandrov, Jay S Wunder, Irene L Andrulis, David Malkin, Sam Behjati, and Adam Shlien (2018) Science 361 (6405), 8419.

72. APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa 

Raymond J Cho, Ludmil B Alexandrov, Nicoline Y den Breems, Velina S Atanasova, Mehdi Farshchian, Elizabeth Purdom, Tran N Nguyen, Cristian Coarfa, Kimal Rajapakshe, Marco Prisco, Joya Sahu, Patrick Tassone, Evan J Greenawalt, Eric A Collisson, Wei Wu, Hui Yao, Xiaoping Su, Christina Guttmann-Gruber, Josefina Piñón Hofbauer, Raabia Hashmi, Ignacia Fuentes, Stephen C Benz, Justin Golovato, Erik A Ehli, Christel M Davis, Gareth E Davies, Kyle R Covington, Dedee F Murrell, Julio C Salas-Alanis, Francis Palisson, Anna L Bruckner, William Robinson, Cristina Has, Leena Bruckner-Tuderman, Matthias Titeux, Marcel F Jonkman, Elham Rashidghamat, Su M Lwin, Jemima E Mellerio, John A McGrath, Johann W Bauer, Alain Hovnanian, Kenneth Y Tsai, and Andrew P South (2018) Science Translational Medicine 10 (455), 9668.

71. Genomic patterns of progression in smoldering multiple myeloma

Niccolò Bolli, Francesco Maura, Stephane Minvielle, Dominik Gloznik, Raphael Szalat, Anthony Fullam, Inigo Martincorena, Kevin J Dawson, Mehmet Kemal Samur, Jorge Zamora, Patrick Tarpey, Helen Davies, Mariateresa Fulciniti, Masood A Shammas, Yu Tzu Tai, Florence Magrangeas, Philippe Moreau, Paolo Corradini, Kenneth Anderson, Ludmil B Alexandrov, David C Wedge, Herve Avet-Loiseau, Peter Campbell, and Nikhil Munshi (2018) Nature Communications 9 (1), 3363.

70. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets 

David C Wedge, Gunes Gundem, Thomas Mitchell, Dan J Woodcock, Inigo Martincorena, Mohammed Ghori, Jorge Zamora, Adam Butler, Hayley Whitaker, Zsofia Kote-Jarai, Ludmil B Alexandrov, Peter Loo, Charlie E Massie, Stefan Dentro, Anne Y Warren, Clare Verrill, Dan M Berney, Nening Dennis, Sue Merson, Steve Hawkins, William Howat, Yong-Jie Lu, Adam Lambert, Jonathan Kay, Barbara Kremeyer, Katalin Karaszi, Hayley Luxton, Niedzica Camacho, Luke Marsden, Sandra Edwards, Lucy Matthews, Valeria Bo, Daniel Leongamornlert, Stuart McLaren, Anthony Ng, Yongwei Yu, Hongwei Zhang, Tokhir Dadaev, Sarah Thomas, Douglas F Easton, Mahbubl Ahmed, Elizabeth Bancroft, Cyril Fisher, Naomi Livni, David Nicol, Simon Tavaré, Pelvender Gill, Christopher Greenman, Vincent Khoo, Nicholas As, Pardeep Kumar, Christopher Ogden, Declan Cahill, Alan Thompson, Erik Mayer, Edward Rowe, Tim Dudderidge, Vincent Gnanapragasam, Nimish C Shah, Keiran Raine, David Jones, Andrew Menzies, Lucy Stebbings, Jon Teague, Steven Hazell, Cathy Corbishley, Johann Bono, Gerhardt Attard, William Isaacs, Tapio Visakorpi, Michael Fraser, Paul C Boutros, Robert G Bristow, Paul Workman, Chris Sander, Freddie C Hamdy, Andrew Futreal, Ultan McDermott, Bissan Al-Lazikani, Andrew G Lynch, G Steven Bova, Christopher S Foster, Daniel S Brewer, David E Neal, Colin S Cooper, and Rosalind A Eeles (2018) Nature Genetics 50 (5), 682.

69. Intra-tumour diversification in colorectal cancer at the single-cell level

Sophie F Roerink, Nobuo Sasaki, Henry Lee-Six, Matthew D Young, Ludmil B Alexandrov, Sam Behjati, Thomas J Mitchell, Sebastian Grossmann, Howard Lightfoot, David A Egan, Apollo Pronk, Niels Smakman, Joost Gorp, Elizabeth Anderson, Stephen J Gamble, Chris Alder, Marc Wetering, Peter J Campbell, Michael R Stratton, and Hans Clevers (2018) Nature 556 (7702), 457.

68. The origins and vulnerabilities of two transmissible cancers in Tasmanian devils 

Maximilian R Stammnitz, Tim HH Coorens, Kevin C Gori, Dane Hayes, Beiyuan Fu, Jinhong Wang, Daniel E Martin-Herranz, Ludmil B Alexandrov, Adrian Baez-Ortega, Syd Barthorpe, Alexandra Beck, Francesca Giordano, Graeme W Knowles, Young Mi Kwon, George Hall, Stacey Price, Ruth J Pye, Jose MC Tubio, Hannah VT Siddle, Sukhwinder Singh Sohal, Gregory M Woods, Ultan McDermott, Fengtang Yang, Mathew J Garnett, Zemin Ning, and Elizabeth P Murchison (2018) Cancer cell 33 (4), 607-619. e15.

67. Biological and prognostic impact of APOBEC-induced mutations in the spectrum of plasma cell dyscrasias and multiple myeloma cell lines

F Maura, M Petljak, M Lionetti, I Cifola, W Liang, E Pinatel, Ludmil B Alexandrov, A Fullam, I Martincorena, KJ Dawson, N Angelopoulos, MK Samur, R Szalat, J Zamora, P Tarpey, H Davies, P Corradini, KC Anderson, S Minvielle, A Neri, H Avet-Loiseau, J Keats, PJ Campbell, NC Munshi, and N Bolli (2018) Leukemia 32 (4), 1043.

66. Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors

Julie George, Vonn Walter, Martin Peifer, Ludmil B Alexandrov, Danila Seidel, Frauke Leenders, Lukas Maas, Christian Müller, Ilona Dahmen, Tiffany M Delhomme, Maude Ardin, Noemie Leblay, Graham Byrnes, Ruping Sun, Aurélien Reynies, Anne McLeer-Florin, Graziella Bosco, Florian Malchers, Roopika Menon, Janine Altmüller, Christian Becker, Peter Nürnberg, Viktor Achter, Ulrich Lang, Peter M Schneider, Magdalena Bogus, Matthew G Soloway, Matthew D Wilkerson, Yupeng Cun, James D McKay, Denis Moro-Sibilot, Christian G Brambilla, Sylvie Lantuejoul, Nicolas Lemaitre, Alex Soltermann, Walter Weder, Verena Tischler, Odd Terje Brustugun, Marius Lund-Iversen, Åslaug Helland, Steinar Solberg, Sascha Ansén, Gavin Wright, Benjamin Solomon, Luca Roz, Ugo Pastorino, Iver Petersen, Joachim H Clement, Jörg Sänger, Jürgen Wolf, Martin Vingron, Thomas Zander, Sven Perner, William D Travis, Stefan A Haas, Magali Olivier, Matthieu Foll, Reinhard Büttner, David Neil Hayes, Elisabeth Brambilla, Lynnette Fernandez-Cuesta, and Roman K Thomas (2018) Nature Communications 9 (1), 1048.

65. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

Xiaotu Ma, Yu Liu, Yanling Liu, Ludmil B Alexandrov, Michael N Edmonson, Charles Gawad, Xin Zhou, Yongjin Li, Michael C Rusch, John Easton, Robert Huether, Veronica Gonzalez-Pena, Mark R Wilkinson, Leandro C Hermida, Sean Davis, Edgar Sioson, Stanley Pounds, Xueyuan Cao, Rhonda E Ries, Zhaoming Wang, Xiang Chen, Li Dong, Sharon J Diskin, Malcolm A Smith, Jaime M Guidry Auvil, Paul S Meltzer, Ching C Lau, Elizabeth J Perlman, John M Maris, Soheil Meshinchi, Stephen P Hunger, Daniela S Gerhard, and Jinghui Zhang (2018) Nature 555 (7696), 371.

2017

64. The driver landscape of sporadic chordoma

Patrick S Tarpey, Sam Behjati, Matthew D Young, Inigo Martincorena, Ludmil B Alexandrov, Sarah J Farndon, Charlotte Guzzo, Claire Hardy, Calli Latimer, Adam P Butler, Jon W Teague, Adam Shlien, P Andrew Futreal, Sohrab Shah, Ali Bashashati, Farzad Jamshidi, Torsten O Nielsen, David Huntsman, Daniel Baumhoer, Sebastian Brandner, Jay Wunder, Brendan Dickson, Patricia Cogswell, Josh Sommer, Joanna J Phillips, M Fernanda Amary, Roberto Tirabosco, Nischalan Pillay, Stephen Yip, Michael R Stratton, Adrienne M Flanagan, and Peter J Campbell (2017) Nature Communications 8 (1), 890.

63. Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma

Apinya Jusakul, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng, Su Pin Choo, Swe Swe Myint, Raynoo Thanan, Sanjanaa Nagarajan, Weng Khong Lim, Cedric Chuan Young Ng, Arnoud Boot, Mo Liu, Choon Kiat Ong, Vikneswari Rajasegaran, Stefanus Lie, Alvin Soon Tiong Lim, Tse Hui Lim, Jing Tan, Jia Liang Loh, John R McPherson, Narong Khuntikeo, Vajaraphongsa Bhudhisawasdi, Puangrat Yongvanit, Sopit Wongkham, Yasushi Totoki, Hiromi Nakamura, Yasuhito Arai, Satoshi Yamasaki, Pierce Kah-Hoe Chow, Alexander Yaw Fui Chung, London Lucien Peng Jin Ooi, Kiat Hon Lim, Simona Dima, Dan G Duda, Irinel Popescu, Philippe Broet, Sen-Yung Hsieh, Ming-Chin Yu, Aldo Scarpa, Jiaming Lai, Di-Xian Luo, André Lopes Carvalho, André Luiz Vettore, Hyungjin Rhee, Young Nyun Park, Ludmil B Alexandrov, Raluca Gordân, Steven G Rozen, Tatsuhiro Shibata, Chawalit Pairojkul, Bin Tean Teh, and Patrick Tan (2017) Cancer Discovery 7 (10), 1116-1135.

62. Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization

Ludmil B Alexandrov, Kim Ø Rasmussen, Alan R Bishop, and Boian S Alexandrov (2017) Scientific Reports 7, Article number: 9731.

61. Genomic evolution of breast cancer metastasis and relapse

Lucy R Yates, Stian Knappskog, David Wedge, James HR Farmery, Santiago Gonzalez, Inigo Martincorena, Ludmil B Alexandrov, Peter Van Loo, Hans Kristian Haugland, Peer Kaare Lilleng, Gunes Gundem, Moritz Gerstung, Elli Pappaemmanuil, Patrycja Gazinska, Shriram G Bhosle, David Jones, Keiran Raine, Laura Mudie, Calli Latimer, Elinor Sawyer, Christine Desmedt, Christos Sotiriou, Michael R Stratton, Anieta M Sieuwerts, Andy G Lynch, John W Martens, Andrea L Richardson, Andrew Tutt, Per Eystein Lønning, and Peter J Campbell (2017) Cancer Cell 32 (2), 169-184. e7.

60. Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1

Lene Alsøe, Antonio Sarno, Sergio Carracedo, Diana Domanska, Felix Dingler, Lisa Lirussi, Tanima SenGupta, Nuriye Basdag Tekin, Laure Jobert, Ludmil B Alexandrov, Anastasia Galashevskaya, Cristina Rada, Geir Kjetil Sandve, Torbjørn Rognes, Hans E Krokan, and Hilde Nilsen (2017) Scientific Reports 7, Article number: 7199.

59. Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma

Sam Behjati, Patrick S Tarpey, Kerstin Haase, Hongtao Ye, Matthew D Young, Ludmil B Alexandrov, Sarah J Farndon, Grace Collord, David C Wedge, Inigo Martincorena, Susanna L Cooke, Helen Davies, William Mifsud, Mathias Lidgren, Sancha Martin, Calli Latimer, Mark Maddison, Adam P Butler, Jon W Teague, Nischalan Pillay, Adam Shlien, Ultan McDermott, P Andrew Futreal, Daniel Baumhoer, Olga Zaikova, Bodil Bjerkehagen, Ola Myklebost, M Fernanda Amary, Roberto Tirabosco, Peter Van Loo, Michael R Stratton, Adrienne M Flanagan, and Peter J Campbell (2017) Nature Communications 8, 15936.

58. A specific mutational signature associated with DNA 8-oxoguanine persistence in MUTYH-defective colorectal cancer

Alessandra Viel, Alessandro Bruselles, Ettore Meccia, Mara Fornasarig, Michele Quaia, Vincenzo Canzonieri, Eleonora Policicchio, Emanuele Damiano Urso, Marco Agostini, Maurizio Genuardi, Emanuela Lucci-Cordisco, Tiziana Venesio, Aline Martayan, Maria Grazia Diodoro, Lupe Sanchez-Mete, Vittoria Stigliano, Filomena Mazzei, Francesca Grasso, Alessandro Giuliani, Marta Baiocchi, Roberta Maestro, Giuseppe Giannini, Marco Tartaglia, Ludmil B Alexandrov, and Margherita Bignami (2017) EBioMedicine 20, 39-49. 

57. Whole-genome landscapes of major melanoma subtypes

Nicholas K Hayward, James S Wilmott, Nicola Waddell, Peter A Johansson, Matthew A Field, Katia Nones, Ann-Marie Patch, Hojabr Kakavand, Ludmil B Alexandrov, Hazel Burke, Valerie Jakrot, Stephen Kazakoff, Oliver Holmes, Conrad Leonard, Radhakrishnan Sabarinathan, Loris Mularoni, Scott Wood, Qinying Xu, Nick Waddell, Varsha Tembe, Gulietta M Pupo, Ricardo De Paoli-Iseppi, Ricardo E Vilain, Ping Shang, Loretta MS Lau, Rebecca A Dagg, Sarah-Jane Schramm, Antonia Pritchard, Ken Dutton-Regester, Felicity Newell, Anna Fitzgerald, Catherine A Shang, Sean M Grimmond, Hilda A Pickett, Jean Y Yang, Jonathan R Stretch, Andreas Behren, Richard F Kefford, Peter Hersey, Georgina V Long, Jonathan Cebon, Mark Shackleton, Andrew J Spillane, Robyn PM Saw, Núria López-Bigas, John V Pearson, John F Thompson, Richard A Scolyer, and Graham J Mann (2017) Nature 545, 175–180.

56. Mutational signature analysis identifies MUTYH deficiency in colorectal cancers and adrenocortical carcinomas

Camilla Pilati, Jayendra Shinde, Ludmil B Alexandrov, Guillaume Assié, Thierry André, Zofia Hélias Rodzewicz, Romain Ducoudray, Delphine Le Corre, Jessica Zucman Rossi, Jean François Emile, Jérôme Bertherat, Eric Letouzé, and Pierre Laurent Puig (2017) The Journal of Pathology 242 (1), 10-15.

55. Precancer Atlas to Drive Precision Prevention Trials

Avrum Spira, Matthew B Yurgelun, Ludmil B Alexandrov, Anjana Rao, Rafael Bejar, Kornelia Polyak, Marios Giannakis, Ali Shilatifard, Olivera J Finn, Madhav Dhodapkar, Neil E Kay, Esteban Braggio, Eduardo Vilar, Sarah A Mazzilli, Timothy R Rebbeck, Judy E Garber, Victor E Velculescu, Mary L Disis, Douglas C Wallace, and Scott M Lippman (2017) Cancer Research 77 (7), 1510-1541.

54. Somatic mutations reveal asymmetric cellular dynamics in the early human embryo

Young Seok Ju, Inigo Martincorena, Moritz Gerstung, Mia Petljak, Ludmil B Alexandrov, Raheleh Rahbari, David C Wedge, Helen R Davies, Manasa Ramakrishna, Anthony Fullam, Sancha Martin, Christopher Alder, Nikita Patel, Steve Gamble, Sarah O’Meara, Dilip D Giri, Torril Sauer, Sarah E Pinder, Colin A Purdie, Åke Borg, Henk Stunnenberg, Marc van de Vijver, Benita KT Tan, Carlos Caldas, Andrew Tutt, Naoto T Ueno, Laura J van’t Veer, John WM Martens, Christos Sotiriou, Stian Knappskog, Paul N Span, Sunil R Lakhani, Jórunn Erla Eyfjörd, Anne-Lise Børresen-Dale, Andrea Richardson, Alastair M Thompson, Alain Viari, Matthew E Hurles, Serena Nik-Zainal, Peter J Campbell, and Michael R Stratton (2017) Nature 543, 714–718.

53. A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers

Dominik Glodzik, Sandro Morganella, Helen Davies, Peter T Simpson, Yilong Li, Xueqing Zou, Javier Diez-Perez, Johan Staaf, Ludmil B Alexandrov, Marcel Smid, Arie B Brinkman, Inga Hansine Rye, Hege Russnes, Keiran Raine, Colin A Purdie, Sunil R Lakhani, Alastair M Thompson, Ewan Birney, Hendrik G Stunnenberg, Marc J Van De Vijver, John WM Martens, Anne-Lise Børresen-Dale, Andrea L Richardson, Gu Kong, Alain Viari, Douglas Easton, Gerard Evan, Peter J Campbell, Michael R Stratton, and Serena Nik-Zainal (2017) Nature Genetics 49 (3), 341-348.

52. Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26 

Sanna Gudmundsson, Maria Wilbe, Sara Ekvall, Adam Ameur, Nicola Cahill, Ludmil B Alexandrov, Marie Virtanen, Maritta Hellström Pigg, Anders Vahlquist, Hans Törmä, and Marie-Louise Bondeson (2017) Human Molecular Genetics 26 (6), 1070-1077.

51. Base changes in tumour DNA have the power to reveal the causes and evolution of cancer

M Hollstein, Ludmil B Alexandrov, CP Wild, M Ardin, and J Zavadil (2017) Oncogene 36 (2), 158.

2016

50. Mutational signatures associated with tobacco smoking in human cancer

Ludmil B Alexandrov, Young Seok Ju, Kerstin Haase, Peter Van Loo, Inigo Martincorena, Serena Nik-Zainal, Yasushi Totoki, Akihiro Fujimoto, Hidewaki Nakagawa, Tatsuhiro Shibata, Peter J Campbell, Paolo Vineis, David H Phillips, and Michael R Stratton (2016) Science 354 (6312), 618-622.

49. Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma 

Ashton A Connor, Robert E Denroche, Gun Ho Jang, Lee Timms, Sangeetha N Kalimuthu, Iris Selander, Treasa McPherson, Gavin W Wilson, Michelle A Chan-Seng-Yue, Ivan Borozan, Vincent Ferretti, Robert C Grant, Ilinca M Lungu, Eithne Costello, William Greenhalf, Daniel Palmer, Paula Ghaneh, John P Neoptolemos, Markus Buchler, Gloria Petersen, Sarah Thayer, Michael A Hollingsworth, Alana Sherker, Daniel Durocher, Neesha Dhani, David Hedley, Stefano Serra, Aaron Pollett, Michael HA Roehrl, Prashant Bavi, John MS Bartlett, Sean Cleary, Julie M Wilson, Ludmil B Alexandrov, Malcolm Moore, Bradly G Wouters, John D McPherson, Faiyaz Notta, Lincoln D Stein, and Steven Gallinger (2016) JAMA Oncology 3(6), 774-783.

48. A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

Faiyaz Notta, Michelle Chan-Seng-Yue, Mathieu Lemire, Yilong Li, Gavin W Wilson, Ashton A Connor, Robert E Denroche, Sheng-Ben Liang, Andrew MK Brown, Jaeseung C Kim, Tao Wang, Jared T Simpson, Timothy Beck, Ayelet Borgida, Nicholas Buchner, Dianne Chadwick, Sara Hafezi-Bakhtiari, John E Dick, Lawrence Heisler, Michael A Hollingsworth, Emin Ibrahimov, Gun Ho Jang, Jeremy Johns, Lars GT Jorgensen, Calvin Law, Olga Ludkovski, Ilinca Lungu, Karen Ng, Danielle Pasternack, Gloria M Petersen, Liran I Shlush, Lee Timms, Ming-Sound Tsao, Julie M Wilson, Christina K Yung, George Zogopoulos, John MS Bartlett, Ludmil B Alexandrov, Francisco X Real, Sean P Cleary, Michael H Roehrl, John D McPherson, Lincoln D Stein, Thomas J Hudson, Peter J Campbell, and Steven Gallinger (2016) Nature 538, 378–382.

47. Mutational signatures of ionizing radiation in second malignancies 

Sam Behjati, Gunes Gundem, David C Wedge, Nicola D Roberts, Patrick S Tarpey, Susanna L Cooke, Peter Van Loo, Ludmil B Alexandrov, Manasa Ramakrishna, Helen Davies, Serena Nik-Zainal, Claire Hardy, Calli Latimer, Keiran M Raine, Lucy Stebbings, Andy Menzies, David Jones, Rebecca Shepherd, Adam P Butler, Jon W Teague, Mette Jorgensen, Bhavisha Khatri, Nischalan Pillay, Adam Shlien, P Andrew Futreal, Christophe Badie, ICGC Prostate Group, Ultan McDermott, G Steven Bova, Andrea L Richardson, Adrienne M Flanagan, Michael R Stratton, and Peter J Campbell (2016) Nature Communications 7 (12605).

46. Germline MC1R status influences somatic mutation burden in melanoma 

Carla Daniela Robles-Espinoza, Nicola D Roberts, Shuyang Chen, Finbarr P Leacy, Ludmil B Alexandrov, Natapol Pornputtapong, Ruth Halaban, Michael Krauthammer, Rutao Cui, D Timothy Bishop, and David J Adams (2016) Nature Communications 7 (12064).

45. Landscape of somatic mutations in 560 breast cancer whole-genome sequences 

Serena Nik-Zainal, Helen Davies, Johan Staaf, Manasa Ramakrishna, Dominik Glodzik, Xueqing Zou, Inigo Martincorena, Ludmil B Alexandrov, Sancha Martin, David C Wedge, Peter Van Loo, Young Seok Ju, Marcel Smid, Arie B Brinkman, Sandro Morganella, Miriam R Aure, Ole Christian Lingjærde, Anita Langerød, Markus Ringnér, Sung-Min Ahn, Sandrine Boyault, Jane E Brock, Annegien Broeks, Adam Butler, Christine Desmedt, Luc Dirix, Serge Dronov, Aquila Fatima, John A Foekens, Moritz Gerstung, Gerrit KJ Hooijer, Se Jin Jang, David R Jones, Hyung-Yong Kim, Tari A King, Savitri Krishnamurthy, Hee Jin Lee, Jeong-Yeon Lee, Yilong Li, Stuart McLaren, Andrew Menzies, Ville Mustonen, Sarah O’meara, Iris Pauporté, Xavier Pivot, Colin A Purdie, Keiran Raine, Kamna Ramakrishnan, F Germán Rodríguez-González, Gilles Romieu, Anieta M Sieuwerts, Peter T Simpson, Rebecca Shepherd, Lucy Stebbings, Olafur A Stefansson, Jon Teague, Stefania Tommasi, Isabelle Treilleux, Gert G Van den Eynden, Peter Vermeulen, Anne Vincent-Salomon, Lucy Yates, Carlos Caldas, Laura Van’t Veer, Andrew Tutt, Stian Knappskog, Benita Kiat Tee Tan, Jos Jonkers, Åke Borg, Naoto T Ueno, Christos Sotiriou, Alain Viari, P Andrew Futreal, Peter J Campbell, Paul N Span, Steven Van Laere, Sunil R Lakhani, Jorunn E Eyfjord, Alastair M Thompson, Ewan Birney, Hendrik G Stunnenberg, Marc J Van de Vijver, John WM Martens, Anne-Lise Børresen-Dale, Andrea L Richardson, Gu Kong, Gilles Thomas, and Michael R Stratton (2016) Nature 534 (7605), 47.

44. Understanding mutagenesis through delineation of mutational signatures in human cancer 

Mia Petljak and Ludmil B Alexandrov (2016) Carcinogenesis 37 (6), 531-540.

43.The topography of mutational processes in breast cancer genomes 

 Sandro Morganella, Ludmil B Alexandrov, Dominik Glodzik, Xueqing Zou, Helen Davies, Johan Staaf, Anieta M Sieuwerts, Arie B Brinkman, Sancha Martin, Manasa Ramakrishna, Adam Butler, Hyung-Yong Kim, Åke Borg, Christos Sotiriou, P Andrew Futreal, Peter J Campbell, Paul N Span, Steven Van Laere, Sunil R Lakhani, Jorunn E Eyfjord, Alastair M Thompson, Hendrik G Stunnenberg, Marc J van de Vijver, John WM Martens, Anne-Lise Børresen-Dale, Andrea L Richardson, Gu Kong, Gilles Thomas, Julian Sale, Cristina Rada, Michael R Stratton, Ewan Birney, and Serena Nik-Zainal (2016) Nature Communications 7 (11383).

42. Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents 

Jane Merlevede, Nathalie Droin, Tingting Qin, Kristen Meldi, Kenichi Yoshida, Margot Morabito, Emilie Chautard, Didier Auboeuf, Pierre Fenaux, Thorsten Braun, Raphael Itzykson, Stéphane de Botton, Bruno Quesnel, Thérèse Commes, Eric Jourdan, William Vainchenker, Olivier Bernard, Noemie Pata-Merci, Stéphanie Solier, Velimir Gayevskiy, Marcel E Dinger, Mark J Cowley, Dorothée Selimoglu-Buet, Vincent Meyer, François Artiguenave, Jean-François Deleuze, Claude Preudhomme, Michael R Stratton, Ludmil B Alexandrov, Eric Padron, Seishi Ogawa, Serge Koscielny, Maria Figueroa, and Eric Solary (2016) Nature Communications 7 (10767).

41. The role of structural parameters in DNA cyclization 

Ludmil B Alexandrov, Alan R Bishop, Kim Ø Rasmussen, and Boian S Alexandrov (2016) BMC Bioinformatics 17 (68), 1-10.

40. Timing, rates and spectra of human germline mutation 

Raheleh Rahbari, Arthur Wuster, Sarah J Lindsay, Robert J Hardwick, Ludmil B Alexandrov, Saeed Al Turki, Anna Dominiczak, Andrew Morris, David Porteous, Blair Smith, Michael R Stratton, and Matthew E Hurles, UK10K Consortium (2016) Nature Genetics 48, 126–133.

2015

39. Understanding the origins of human cancer 

Ludmil B Alexandrov (2015) Science 350 (6265), 1175-1177.

38. Clock-like mutational processes in human somatic cells 

Ludmil B Alexandrov, Philip H Jones, David C Wedge, Julian E Sale, Peter J Campbell, Serena Nik-Zainal, and Michael R Stratton (2015) Nature Genetics 47 (12), 1402–1407.

37. A mutational signature in gastric cancer suggests therapeutic strategies 

Ludmil B Alexandrov, Serena Nik-Zainal, Hoi Cheong Siu, Suet Yi Leung, and Michael R Stratton (2015) Nature Communications 6 (8683).

36. The genome as a record of environmental exposure 

Serena Nik-Zainal, Jill E Kucab, Sandro Morganella, Dominik Glodzik, Ludmil B Alexandrov, Volker M Arlt, Annette Weninger, Monica Hollstein, Michael R Stratton, and David H Phillips (2015) Mutagenesis 30 (6), 763-770.

35. Subclonal diversification of primary breast cancer revealed by multiregion sequencing 

Lucy R Yates, Moritz Gerstung, Stian Knappskog, Christine Desmedt, Gunes Gundem, Peter Van Loo, Turid Aas, Ludmil B Alexandrov, Denis Larsimont, Helen Davies, Yilong Li, Young Seok Ju, Manasa Ramakrishna, Hans Kristian Haugland, Peer Kaare Lilleng, Serena Nik-Zainal, Stuart McLaren, Adam Butler, Sancha Martin, Dominic Glodzik, Andrew Menzies, Keiran Raine, Jonathan Hinton, David Jones, Laura J Mudie, Bing Jiang, Delphine Vincent, April Greene-Colozzi, Pierre-Yves Adnet, Aquila Fatima, Marion Maetens, Michail Ignatiadis, Michael R Stratton, Christos Sotiriou, Andrea L Richardson, Per Eystein Lønning, David C Wedge, and Peter J Campbell. (2015) Nature Medicine 21 (7), 751-759.

34. High burden and pervasive positive selection of somatic mutations in normal human skin 

Iñigo Martincorena, Amit Roshan, Moritz Gerstung, Peter Ellis, Peter Van Loo, Stuart McLaren, David C Wedge, Anthony Fullam, Ludmil B Alexandrov, Jose M Tubio, Lucy Stebbings, Andrew Menzies, Sara Widaa, Michael R Stratton, Philip H Jones, and Peter J Campbell (2015) Science 348 (6237), 880-886.

33. The evolutionary history of lethal metastatic prostate cancer 

Gunes Gundem, Peter Van Loo, Barbara Kremeyer, Ludmil B Alexandrov, Jose MC Tubio, Elli Papaemmanuil, Daniel S Brewer, Heini ML Kallio, Gunilla Högnäs, Matti Annala, Kati Kivinummi, Victoria Goody, Calli Latimer, Sarah O'Meara, Kevin J Dawson, William Isaacs, Michael R Emmert-Buck, Matti Nykter, Christopher Foster, Zsofia Kote-Jarai, Douglas Easton, Hayley C Whitaker, ICGC Prostate UK Group, David E Neal, Colin S Cooper, Rosalind A Eeles, Tapio Visakorpi, Peter J Campbell, Ultan McDermott, David C Wedge, and G Steven Bova (2015) Nature 520 (7547), 353–357.

32. Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer 

Matthew KH Hong, Geoff Macintyre, David C Wedge, Peter Van Loo, Keval Patel, Sebastian Lunke, Ludmil B Alexandrov, Clare Sloggett, Marek Cmero, Francesco Marass, Dana Tsui, Stefano Mangiola, Andrew Lonie, Haroon Naeem, Nikhil Sapre, Pramit M Phal, Natalie Kurganovs, Xiaowen Chin, Michael Kerger, Anne Y Warren, David Neal, Vincent Gnanapragasam, Nitzan Rosenfeld, John S Pedersen, Andrew Ryan, Izhak Haviv, Anthony J Costello, Niall M Corcoran, and Christopher M Hovens (2015) Nature Communications 6 (6605).

31. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue 

Colin S Cooper, Rosalind Eeles, David C Wedge, Peter Van Loo, Gunes Gundem, Ludmil B Alexandrov, Barbara Kremeyer, Adam Butler, Andrew G Lynch, Niedzica Camacho, Charlie E Massie, Jonathan Kay, Hayley J Luxton, Sandra Edwards, Zsofia Kote-Jarai, Nening Dennis, Sue Merson, Daniel Leongamornlert, Jorge Zamora, Cathy Corbishley, Sarah Thomas, Serena Nik-Zainal, Sarah O'Meara, Lucy Matthews, Jeremy Clark, Rachel Hurst, Richard Mithen, Robert G Bristow, Paul C Boutros, Michael Fraser, Susanna Cooke, Keiran Raine, David Jones, Andrew Menzies, Lucy Stebbings, Jon Hinton, Jon Teague, Stuart McLaren, Laura Mudie, Claire Hardy, Elizabeth Anderson, Olivia Joseph, Victoria Goody, Ben Robinson, Mark Maddison, Stephen Gamble, Christopher Greenman, Dan Berney, Steven Hazell, Naomi Livni, Cyril Fisher, Christopher Ogden, Pardeep Kumar, Alan Thompson, Christopher Woodhouse, David Nicol, Erik Mayer, Tim Dudderidge, Nimish C Shah, Vincent Gnanapragasam, Thierry Voet, Peter Campbell, Andrew Futreal, Douglas Easton, Anne Y Warren, Christopher S Foster, Michael R Stratton, Hayley C Whitaker, Ultan McDermott, Daniel S Brewer, and David E Neal (2015) Nature Genetics 47 (4), 367-372.

30. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets 

Kornelius Schulze, Sandrine Imbeaud, Eric Letouzé, Ludmil B Alexandrov, Julien Calderaro, Sandra Rebouissou, Gabrielle Couchy, Clément Meiller, Jayendra Shinde, Frederic Soysouvanh, Anna-Line Calatayud, Roser Pinyol, Laura Pelletier, Charles Balabaud, Alexis Laurent, Jean-Frederic Blanc, Vincenzo Mazzaferro, Fabien Calvo, Augusto Villanueva, Jean-Charles Nault, Paulette Bioulac-Sage, Michael R Stratton, Josep M Llovet, and Jessica Zucman-Rossi (2015) Nature Genetics 47 (5), 505–511.

29. SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair 

N Kanu, E Grönroos, P Martinez, RA Burrell, X Yi Goh, J Bartkova, A Maya-Mendoza, M Mistrík, AJ Rowan, H Patel, A Rabinowitz, P East, G Wilson, CR Santos, N McGranahan, S Gulati, M Gerlinger, NJ Birkbak, T Joshi, Ludmil B Alexandrov, MR Stratton, T Powles, N Matthews, PA Bates, A Stewart, Z Szallasi, J Larkin, J Bartek, and C Swanton (2015) Oncogene 34, 5699-5708.

28. Analysis of mutational signatures in exomes from B-cell lymphoma cell lines suggest APOBEC3 family members to be involved in the pathogenesis of primary effusion lymphoma 

R Wagener, Ludmil B Alexandrov, M Montesinos-Rongen, M Schlesner, A Haake, HG Drexler, J Richter, GR Bignell, U McDermott, and R Siebert (2015) Leukemia 29, 1612-1615.

27. Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers 

Adam Shlien, Brittany B Campbell, Richard de Borja, Ludmil B Alexandrov, Daniele Merico, David Wedge, Peter Van Loo, Patrick S Tarpey, Paul Coupland, Sam Behjati, Aaron Pollett, Tatiana Lipman, Abolfazl Heidari, Shriya Deshmukh, Na'ama Avitzur, Bettina Meier, Moritz Gerstung, Ye Hong, Diana M Merino, Manasa Ramakrishna, Marc Remke, Roland Arnold, Gagan B Panigrahi, Neha P Thakkar, Karl P Hodel, Erin E Henninger, A Yasemin Göksenin, Doua Bakry, George S Charames, Harriet Druker, Jordan Lerner-Ellis, Matthew Mistry, Rina Dvir, Ronald Grant, Ronit Elhasid, Roula Farah, Glenn P Taylor, Paul C Nathan, Sarah Alexander, Shay Ben-Shachar, Simon C Ling, Steven Gallinger, Shlomi Constantini, Peter Dirks, Annie Huang, Stephen W Scherer, Richard G Grundy, Carol Durno, Melyssa Aronson, Anton Gartner, M Stephen Meyn, Michael D Taylor, Zachary F Pursell, Christopher E Pearson, David Malkin, P Andrew Futreal, Michael R Stratton, Eric Bouffet, Cynthia Hawkins, Peter J Campbell, and Uri Tabori, Biallelic Mismatch Repair Deficiency Consortium (2015) Nature Genetics 47 (3), 257–262.

2014

26. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer 

Young Seok Ju, Ludmil B Alexandrov, Moritz Gerstung, Inigo Martincorena, Serena Nik-Zainal, Manasa Ramakrishna, Helen R Davies, Elli Papaemmanuil, Gunes Gundem, Adam Shlien, Niccolo Bolli, Sam Behjati, Patrick S Tarpey, Jyoti Nangalia, Charles E Massie, Adam P Butler, Jon W Teague, George S Vassiliou, Anthony R Green, Ming-Qing Du, Ashwin Unnikrishnan, John E Pimanda, Bin Tean Teh, Nikhil Munshi, Mel Greaves, Paresh Vyas, Adel K El-Naggar, Tom Santarius, V Peter Collins, Richard Grundy, Jack A Taylor, D Neil Hayes, David Malkin, Christopher S Foster, Anne Y Warren, Hayley C Whitaker, Daniel Brewer, Rosalind Eeles, Colin Cooper, David Neal, Tapio Visakorpi, William B Isaacs, G Steven Bova, Adrienne M Flanagan, P Andrew Futreal, Andy G Lynch, Patrick F Chinnery, Ultan McDermott, Michael R Stratton, and Peter J Campbell, ICGC Breast Cancer Group, ICGC Chronic Myeloid Disorders Group, ICGC Prostate Cancer Group (2014) eLife 3, e02935.

25. C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency 

Bettina Meier, Susanna L Cooke, Joerg Weiss, Aymeric P Bailly, Ludmil B Alexandrov, John Marshall, Keiran Raine, Mark Maddison, Elizabeth Anderson, Michael R Stratton, Anton Gartner, and Peter J Campbell (2014) Genome Research 24 (10), 1624-1636.

24. Genome sequencing of normal cells reveals developmental lineages and mutational processes 

Sam Behjati, Meritxell Huch, Ruben van Boxtel, Wouter Karthaus, David C Wedge, Asif U Tamuri, Inigo Martincorena, Mia Petljak, Ludmil B Alexandrov, Gunes Gundem, Patrick S Tarpey, Sophie Roerink, Joyce Blokker, Mark Maddison, Laura Mudie, Ben Robinson, Serena Nik-Zainal, Peter Campbell, Nick Goldman, Marc van de Wetering, Edwin Cuppen, Hans Clevers, and Michael R Stratton (2014) Nature 513 (7518), 422.

23. Fast randomization of large genomic datasets while preserving alteration counts 

Andrea Gobbi, Francesco Iorio, Kevin J Dawson, David C Wedge, David Tamborero, Ludmil B Alexandrov, Nuria Lopez-Bigas, Mathew J Garnett, Giuseppe Jurman, and Julio Saez-Rodriguez (2014) Bioinformatics 30 (17), i617-i623.

22. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes 

Jose MC Tubio, Yilong Li, Young Seok Ju, Inigo Martincorena, Susanna L Cooke, Marta Tojo, Gunes Gundem, Christodoulos P Pipinikas, Jorge Zamora, Keiran Raine, Andrew Menzies, Pablo Roman-Garcia, Anthony Fullam, Moritz Gerstung, Adam Shlien, Patrick S Tarpey, Elli Papaemmanuil, Stian Knappskog, Peter Van Loo, Manasa Ramakrishna, Helen R Davies, John Marshall, David C Wedge, Jon W Teague, Adam P Butler, Serena Nik-Zainal, Ludmil B Alexandrov, Sam Behjati, Lucy R Yates, Niccolo Bolli, Laura Mudie, Claire Hardy, Sancha Martin, Stuart McLaren, Sarah O’Meara, Elizabeth Anderson, Mark Maddison, Stephen Gamble, Christopher Foster, Anne Y Warren, Hayley Whitaker, Daniel Brewer, Rosalind Eeles, Colin Cooper, David Neal, Andy G Lynch, Tapio Visakorpi, William B Isaacs, Laura van't Veer, Carlos Caldas, Christine Desmedt, Christos Sotiriou, Sam Aparicio, John A Foekens, Jórunn Erla Eyfjörd, Sunil R Lakhani, Gilles Thomas, Ola Myklebost, Paul N Span, Anne-Lise Børresen-Dale, Andrea L Richardson, Marc Van de Vijver, Anne Vincent-Salomon, Gert G Van den Eynden, Adrienne M Flanagan, P Andrew Futreal, Sam M Janes, G Steven Bova, Michael R Stratton, Ultan McDermott, and Peter J Campbell (2014) Science 345 (6196), 1251343.

21. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer 

Serena Nik-Zainal, David C Wedge, Ludmil B Alexandrov, Mia Petljak, Adam P Butler, Niccolo Bolli, Helen R Davies, Stian Knappskog, Sancha Martin, Elli Papaemmanuil, Manasa Ramakrishna, Adam Shlien, Ingrid Simonic, Yali Xue, Chris Tyler-Smith, Peter J Campbell, and Michael R Stratton (2014) Nature Genetics 46 (5), 487–491.

20. Mutational signatures: the patterns of somatic mutations hidden in cancer genomes 

Ludmil B Alexandrov and Michael R Stratton. (2014) Current Opinion in Genetics & Development 24, 52-60.

19. Transmissable Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage 

Elizabeth P Murchison, David C Wedge, Ludmil B Alexandrov, Beiyuan Fu, Inigo Martincorena, Zemin Ning, Jose MC Tubio, Emma I Werner, Jan Allen, Andrigo Barboza De Nardi, Edward M Donelan, Gabriele Marino, Ariberto Fassati, Peter J Campbell, Fengtang Yang, Austin Burt, Robin A Weiss, and Michael R Stratton (2014) Science 343 (6169), 437-440.

18. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma 

Niccolo Bolli, Hervé Avet-Loiseau, David C Wedge, Peter Van Loo, Ludmil B Alexandrov, Inigo Martincorena, Kevin J Dawson, Francesco Iorio, Serena Nik-Zainal, Graham R Bignell, Jonathan W Hinton, Yilong Li, Jose MC Tubio, Stuart McLaren, Sarah O'Meara, Adam P Butler, Jon W Teague, Laura Mudie, Elizabeth Anderson, Naim Rashid, Yu-Tzu Tai, Masood A Shammas, Adam S Sperling, Mariateresa Fulciniti, Paul G Richardson, Giovanni Parmigiani, Florence Magrangeas, Stephane Minvielle, Philippe Moreau, Michel Attal, Thierry Facon, P Andrew Futreal, Kenneth C Anderson, Peter J Campbell, and Nikhil C Munshi. (2014) Nature Communications 5 (2997).

17. RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia 

Elli Papaemmanuil, Inmaculada Rapado, Yilong Li, Nicola E Potter, David C Wedge, Jose Tubio, Ludmil B Alexandrov, Peter Van Loo, Susanna L Cooke, John Marshall, Inigo Martincorena, Jonathan Hinton, Gunes Gundem, Frederik W van Delft, Serena Nik-Zainal, David R Jones, Manasa Ramakrishna, Ian Titley, Lucy Stebbings, Catherine Leroy, Andrew Menzies, John Gamble, Ben Robinson, Laura Mudie, Keiran Raine, Sarah O'Meara, Jon W Teague, Adam P Butler, Giovanni Cazzaniga, Andrea Biondi, Jan Zuna, Helena Kempski, Markus Muschen, Anthony M Ford, Michael R Stratton, Mel Greaves, and Peter J Campbell. (2014) Nature Genetics 46 (2), 116–125.

2013

16. Inactivating CUX1 mutations promote tumorigenesis 

Chi C Wong, Inigo Martincorena, Alistair G Rust, Mamunur Rashid, Constantine Alifrangis, Ludmil B Alexandrov, Jessamy C Tiffen, Christina Kober, Anthony R Green, Charles E Massie, Jyoti Nangalia, Stella Lempidaki, Hartmut Döhner, Konstanze Döhner, Sarah J Bray, Ultan McDermott, Elli Papaemmanuil, Peter J Campbell, and David J Adams, Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium (2013) Nature Genetics 46 (1), 33-38.

15. Signatures of mutational processes in human cancer 

Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel AJR Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale, Sandrine Boyault, Birgit Burkhardt, Adam P Butler, Carlos Caldas, Helen R Davies, Christine Desmedt, Roland Eils, Jórunn Erla Eyfjörd, John A Foekens, Mel Greaves, Fumie Hosoda, Barbara Hutter, Tomislav Ilicic, Sandrine Imbeaud, Marcin Imielinsk, Natalie Jäger, David TW Jones, David Jones, Stian Knappskog, Marcel Kool, Sunil R Lakhani, Carlos López-Otín, Sancha Martin, Nikhil C Munshi, Hiromi Nakamura, Paul A Northcott, Marina Pajic, Elli Papaemmanuil, Angelo Paradiso, John V Pearson, Xose S Puente, Keiran Raine, Manasa Ramakrishna, Andrea L Richardson, Julia Richter, Philip Rosenstiel, Matthias Schlesner, Ton N Schumacher, Paul N Span, Jon W Teague, Yasushi Totoki, Andrew NJ Tutt, Rafael Valdés-Mas, Marit M van Buuren, Laura van’t Veer, Anne Vincent-Salomon, Nicola Waddell, Lucy R Yates, ICGC PedBrain, Jessica Zucman-Rossi, P Andrew Futreal, Ultan McDermott, Peter Lichter, Matthew Meyerson, Sean M Grimmond, Reiner Siebert, Elías Campo, Tatsuhiro Shibata, Stefan M Pfister, Peter J Campbell, and Michael R Stratton, Australian Pancreatic Cancer Genome Initiative, ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium (2013) Nature 500 (7463), 415-421.

14. Specificity and Heterogeneity of Terahertz Radiation Effect on Gene Expression in Mouse Mesenchymal Stem Cells 

Boian S Alexandrov, M Lisa Phipps, Ludmil B Alexandrov, Layla G Booshehri, Anna Erat, Janice Zabolotny, Charles H Mielke, Hou-Tong Chen, George Rodriguez, Kim Ø Rasmussen, Jennifer S Martinez, Alan R Bishop, and Anny Usheva (2013) Scientific Reports 3, Article number: 1184.

13. Binding of nucleoid-associated protein Fis to DNA is regulated by DNA breathing dynamics 

Kristy Nowak-Lovato, Ludmil B Alexandrov, Afsheen Banisadr, Amy L Bauer, Alan R Bishop, Anny Usheva, Fangping Mu, Elizabeth Hong-Geller, Kim Ø Rasmussen, William S Hlavacek, and Boian S Alexandrov (2013) PLOS Computational Biology 9 (1), e1002881.

12. Deciphering Signatures of Mutational Processes Operative in Human Cancer 

Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Peter J Campbell, and Michael R Stratton. (2013) Cell Reports 3 (1), 246-259.

2012

11. Mutational Processes Molding the Genomes of 21 Breast Cancers 

Serena Nik-Zainal, Ludmil B Alexandrov, David C Wedge, Peter Van Loo, Christopher D Greenman, Keiran Raine, David Jones, Jonathan Hinton, John Marshall, Lucy A Stebbings, Andrew Menzies, Sancha Martin, Kenric Leung, Lina Chen, Catherine Leroy, Manasa Ramakrishna, Richard Rance, King Wai Lau, Laura J Mudie, Ignacio Varela, David J McBride, Graham R Bignell, Susanna L Cooke, Adam Shlien, John Gamble, Ian Whitmore, Mark Maddison, Patrick S Tarpey, Helen R Davies, Elli Papaemmanuil, Philip J Stephens, Stuart McLaren, Adam P Butler, Jon W Teague, Göran Jönsson, Judy E Garber, Daniel Silver, Penelope Miron, Aquila Fatima, Sandrine Boyault, Anita Langerød, Andrew Tutt, John WM Martens, Samuel AJR Aparicio, Åke Borg, Anne Vincent Salomon, Gilles Thomas, Anne-Lise Børresen-Dale, Andrea L Richardson, Michael S Neuberger, P Andrew Futreal, Peter J Campbell, and Michael R Stratton (2012) Cell 149 (5), 979-993.

10. The Life History of 21 Breast Cancers 

Serena Nik-Zainal, Peter Van Loo, David C Wedge, Ludmil B Alexandrov, Christopher D Greenman, King Wai Lau, Keiran Raine, David Jones, John Marshall, Manasa Ramakrishna, Adam Shlien, Susanna L Cooke, Jonathan Hinton, Andrew Menzies, Lucy A Stebbings, Catherine Leroy, Mingming Jia, Richard Rance, Laura J Mudie, Stephen J Gamble, Philip J Stephens, Stuart McLaren, Patrick S Tarpey, Elli Papaemmanuil, Helen R Davies, Ignacio Varela, David J McBride, Graham R Bignell, Kenric Leung, Adam P Butler, Jon W Teague, Sancha Martin, Goran Jönsson, Odette Mariani, Sandrine Boyault, Penelope Miron, Aquila Fatima, Anita Langerød, Samuel AJR Aparicio, Andrew Tutt, Anieta M Sieuwerts, Åke Borg, Gilles Thomas, Anne Vincent Salomon, Andrea L Richardson, Anne-Lise Børresen-Dale, P Andrew Futreal, Michael R Stratton, and Peter J Campbell (2012) Cell 149 (5), 994-1007.

9. Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer 

Elizabeth P Murchison, Ole B Schulz-Trieglaff, Zemin Ning, Ludmil B Alexandrov, Markus J Bauer, Beiyuan Fu, Matthew Hims, Zhihao Ding, Sergii Ivakhno, Caitlin Stewart, Bee Ling Ng, Wendy Wong, Bronwen Aken, Simon White, Amber Alsop, Jennifer Becq, Graham R Bignell, R Keira Cheetham, William Cheng, Thomas R Connor, Anthony J Cox, Zhi-Ping Feng, Yong Gu, Russell J Grocock, Simon R Harris, Irina Khrebtukova, Zoya Kingsbury, Mark Kowarsky, Alexandre Kreiss, Shujun Luo, John Marshall, David J McBride, Lisa Murray, Anne-Maree Pearse, Keiran Raine, Isabelle Rasolonjatovo, Richard Shaw, Philip Tedder, Carolyn Tregidgo, Albert J Vilella, David C Wedge, Gregory M Woods, Niall Gormley, Sean Humphray, Gary Schroth, Geoffrey Smith, Kevin Hall, Stephen MJ Searle, Nigel P Carter, Anthony T Papenfuss, P Andrew Futreal, Peter J Campbell, Fengtang Yang, David R Bentley, Dirk J Evers, and Michael R Stratton (2012) Cell 148 (4), 780-791.

2011

8. Non-thermal effects of terahertz radiation on gene expression in mouse stem cells 

Boian S Alexandrov, Kim Ø Rasmussen, Alan R Bishop, Anny Usheva, Ludmil B Alexandrov, Shou Chong, Yossi Dagon, Layla G Booshehri, Charles H Mielke, M Lisa Phipps, Jennifer S Martinez, Hou-Tong Chen, and George Rodriguez (2011) Biomedical Optics Express 2 (9), 2679-2689.

7. DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases 

Boian S Alexandrov, Vlad I Valtchinov, Ludmil B Alexandrov, Vladimir Gelev, Yossi Dagon, Jonathan Bock, Isaac S Kohane, Kim Ø Rasmussen, Alan R Bishop, and Anny Usheva (2011) PLoS ONE 6 (5), e19800.

2010

6. Mammalian stem cells reprogramming in response to terahertz radiation 

Jonathan Bock, Yayoi Fukuyo, Sona Kang, M Lisa Phipps, Ludmil B Alexandrov, Kim Ø Rasmussen, Alan R Bishop, Evan D Rosen, Jennifer S Martinez, Hou-Tong Chen, George Rodriguez, Boian S Alexandrov, and Anny Usheva. (2010) PLoS ONE 5 (12), e15806.

5. DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation 

Boian S Alexandrov, Vladimir Gelev, Sang Wook Yoo, Ludmil B Alexandrov, Yayoi Fukuyo, Alan R Bishop, Kim Ø Rasmussen, and Anny Usheva (2010) Nucleic Acids Research (12), e15806.

2009

4. Computer Modeling Describes Gravity-Related Adaptation in Cell Cultures 

Ludmil B Alexandrov, Stoyana Alexandrova, and Anny Usheva (2009) PLoS ONE 4 (12), e8332.

3. A nonlinear dynamic model of DNA with a sequence-dependent stacking term 

Boian S Alexandrov, Vladimir Gelev, Yevgeniya Monisova, Ludmil B Alexandrov, Alan R Bishop, Kim Ø Rasmussen, and Anny Usheva (2009) Nucleic Acids Research 37 (7), 2405-2410.

2007

2. Modelling the magnetic signature of neuronal tissue 

KB Blagoev, B Mihaila, BJ Travis, Ludmil B Alexandrov, AR Bishop, D Ranken, S Posse, C Gasparovic, A Mayer, CJ Aine, I Ulbert, M Morita, W Müller, J Connor, and E Halgren (2007) NeuroImage 37 (1), 137-148.

2005

1. MRI of neural currents: numerical study

KB Blagoev, B Mihaila, Ludmil B Alexandrov, BJ Travis, I Ulbert, E Halgren, and VJ Wedeen (2005) Proc Int Soc Magn Reson Med 13, 1425.