Publications by authors named "Ludmil Alexandrov"

99Publications

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

Authors:
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 S M 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 Jinghui Zhang

Cancer Discov 2021 Jan 6. Epub 2021 Jan 6.

Department of Computational Biology, St. Jude Children's Research Hospital

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January 2021

Bioinformatic Methods to Identify Mutational Signatures in Cancer.

Authors:
S M Ashiqul Islam Ludmil B Alexandrov

Methods Mol Biol 2021 ;2185:447-473

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

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January 2021

Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator.

Authors:
Erik N Bergstrom Mark Barnes Iñigo Martincorena Ludmil B Alexandrov

BMC Bioinformatics 2020 Oct 7;21(1):438. Epub 2020 Oct 7.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.

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October 2020

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

Authors:
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 David J Adams

Nat Genet 2020 11 28;52(11):1189-1197. Epub 2020 Sep 28.

Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.

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November 2020

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

Authors:
Andrea Castro Rachel Marty Pyke Xinlian Zhang Wesley Kurt Thompson Chi-Ping Day Ludmil B Alexandrov Maurizio Zanetti Hannah Carter

Nat Commun 2020 08 17;11(1):4128. Epub 2020 Aug 17.

Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.

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August 2020

Author Correction: The evolutionary history of lethal metastatic prostate cancer.

Authors:
Gunes Gundem Peter Van Loo Barbara Kremeyer Ludmil B Alexandrov Jose M C Tubio Elli Papaemmanuil Daniel S Brewer Heini M L Kallio Gunilla Hägnäs 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 David E Neal Colin S Cooper Rosalind A Eeles Tapio Visakorpi Peter J Campbell Ultan McDermott David C Wedge G Steven Bova

Nature 2020 Aug;584(7820):E18

Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland.

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August 2020

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

Authors:
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 Maria Teresa Landi

Nat Commun 2020 06 18;11(1):3096. Epub 2020 Jun 18.

Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, 20892, USA.

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June 2020

Timing the initiation of multiple myeloma.

Authors:
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 Francesco Maura

Nat Commun 2020 04 21;11(1):1917. Epub 2020 Apr 21.

Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

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April 2020

The repertoire of mutational signatures in human cancer.

Authors:
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 S M Ashiqul Islam Nuria Lopez-Bigas Leszek J Klimczak John R McPherson Sandro Morganella Radhakrishnan Sabarinathan David A Wheeler Ville Mustonen Gad Getz Steven G Rozen Michael R Stratton

Nature 2020 02 5;578(7793):94-101. Epub 2020 Feb 5.

Wellcome Sanger Institute, Hinxton, UK.

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February 2020

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

Authors:
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 Allan Balmain

Nat Commun 2020 01 20;11(1):394. Epub 2020 Jan 20.

UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA.

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January 2020

The Association of Modifiable Breast Cancer Risk Factors and Somatic Genomic Alterations in Breast Tumors: The Cancer Genome Atlas Network.

Authors:
Yujing J Heng Susan E Hankinson Jun Wang Ludmil B Alexandrov Christine B Ambrosone Victor P de Andrade Adam M Brufsky Fergus J Couch Tari A King Francesmary Modugno Celine M Vachon A Heather Eliassen Rulla M Tamimi Peter Kraft

Cancer Epidemiol Biomarkers Prev 2020 03 13;29(3):599-605. Epub 2020 Jan 13.

Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts.

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March 2020

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

Authors:
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 Rebecca C Fitzgerald

Nat Genet 2020 01 6;52(1):74-83. Epub 2020 Jan 6.

MRC Cancer Unit, University of Cambridge, Cambridge, UK.

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January 2020

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

Authors:
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 Tatiana Kisseleva

J Hepatol 2020 05 31;72(5):946-959. Epub 2019 Dec 31.

Department of Surgery, University of California San Diego, La Jolla, CA, USA. Electronic address:

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May 2020

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

Authors:
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 Carlos Frederico Martins Menck

Nucleic Acids Res 2020 02;48(4):1941-1953

Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil.

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February 2020

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

Authors:
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 J Silvio Gutkind

Nat Commun 2019 12 5;10(1):5546. Epub 2019 Dec 5.

Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA, USA.

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December 2019

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

Authors:
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 J Raphael Jingyan Tang James R Downing Ludmil B Alexandrov Bin-Bing S Zhou Ching-Hon Pui Jun J Yang Jinghui Zhang

Blood 2020 01;135(1):41-55

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN.

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January 2020

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

Authors:
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 Alessandro D Santin

Proc Natl Acad Sci U S A 2019 11 17;116(45):22730-22736. Epub 2019 Oct 17.

Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510.

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November 2019

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

Authors:
Erik N Bergstrom Mi Ni Huang Uma Mahto Mark Barnes Michael R Stratton Steven G Rozen Ludmil B Alexandrov

BMC Genomics 2019 Aug 30;20(1):685. Epub 2019 Aug 30.

Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.

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August 2019

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

Authors:
Adrian Baez-Ortega Kevin Gori Andrea Strakova Janice L Allen Karen M Allum Leontine Bansse-Issa Thinlay N Bhutia Jocelyn L Bisson Cristóbal Briceño Artemio Castillo Domracheva Anne M Corrigan Hugh R Cran Jane T Crawford Eric Davis Karina F de Castro Andrigo B de Nardi Anna P de Vos Laura Delgadillo Keenan Edward M Donelan Adela R Espinoza Huerta Ibikunle A Faramade Mohammed Fazil Eleni Fotopoulou Skye N Fruean Fanny Gallardo-Arrieta Olga Glebova Pagona G Gouletsou Rodrigo F Häfelin Manrique Joaquim J G P Henriques Rodrigo S Horta Natalia Ignatenko Yaghouba Kane Cathy King Debbie Koenig Ada Krupa Steven J Kruzeniski Young-Mi Kwon Marta Lanza-Perea Mihran Lazyan Adriana M Lopez Quintana Thibault Losfelt Gabriele Marino Simón Martínez Castañeda Mayra F Martínez-López Michael Meyer Edward J Migneco Berna Nakanwagi Karter B Neal Winifred Neunzig Máire Ní Leathlobhair Sally J Nixon Antonio Ortega-Pacheco Francisco Pedraza-Ordoñez Maria C Peleteiro Katherine Polak Ruth J Pye John F Reece Jose Rojas Gutierrez Haleema Sadia Sheila K Schmeling Olga Shamanova Alan G Sherlock Maximilian Stammnitz Audrey E Steenland-Smit Alla Svitich Lester J Tapia Martínez Ismail Thoya Ngoka Cristian G Torres Elizabeth M Tudor Mirjam G van der Wel Bogdan A Viţălaru Sevil A Vural Oliver Walkinton Jinhong Wang Alvaro S Wehrle-Martinez Sophie A E Widdowson Michael R Stratton Ludmil B Alexandrov Iñigo Martincorena Elizabeth P Murchison

Science 2019 08;365(6452)

Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.

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August 2019

Insights into BRCA Cancer Predisposition from Integrated Germline and Somatic Analyses in 7632 Cancers.

Authors:
Shawn Yost Elise Ruark Ludmil B Alexandrov Nazneen Rahman

JNCI Cancer Spectr 2019 Jun 19;3(2):pkz028. Epub 2019 Apr 19.

Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.

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June 2019