A citation-based method for searching scientific literature

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 W M Martens, Samuel A J R Aparicio, Åke Borg, Anne Vincent Salomon, Gilles Thomas, Anne-Lise Børresen-Dale, Andrea L Richardson, Michael S Neuberger, P Andrew Futreal, Peter J Campbell, Michael R Stratton. Cell 2012
Times Cited: 1105







List of co-cited articles
855 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Signatures of mutational processes in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel A J R Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale,[...]. Nature 2013
62

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,[...]. Nature 2020
555
33

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,[...]. Nature 2016
998
24

Deciphering signatures of mutational processes operative in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Peter J Campbell, Michael R Stratton. Cell Rep 2013
609
22

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers.
Steven A Roberts, Michael S Lawrence, Leszek J Klimczak, Sara A Grimm, David Fargo, Petar Stojanov, Adam Kiezun, Gregory V Kryukov, Scott L Carter, Gordon Saksena,[...]. Nat Genet 2013
677
20


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 M C Tubio,[...]. Cell 2019
124
18

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Helen Davies, Dominik Glodzik, Sandro Morganella, Lucy R Yates, Johan Staaf, Xueqing Zou, Manasa Ramakrishna, Sancha Martin, Sandrine Boyault, Anieta M Sieuwerts,[...]. Nat Med 2017
344
17

MutationalPatterns: comprehensive genome-wide analysis of mutational processes.
Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen. Genome Med 2018
197
16

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, Michael R Stratton. Nat Genet 2015
422
14

Mechanisms underlying mutational signatures in human cancers.
Thomas Helleday, Saeed Eshtad, Serena Nik-Zainal. Nat Rev Genet 2014
448
12

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
12

DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.
Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S Taylor, Charles Swanton. Genome Biol 2016
478
12

APOBEC3B is an enzymatic source of mutation in breast cancer.
Michael B Burns, Lela Lackey, Michael A Carpenter, Anurag Rathore, Allison M Land, Brandon Leonard, Eric W Refsland, Delshanee Kotandeniya, Natalia Tretyakova, Jason B Nikas,[...]. Nature 2013
512
11

Patterns of somatic structural variation in human cancer genomes.
Yilong Li, Nicola D Roberts, Jeremiah A Wala, Ofer Shapira, Steven E Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O Korbel, James E Haber,[...]. Nature 2020
144
11

COSMIC: the Catalogue Of Somatic Mutations In Cancer.
John G Tate, Sally Bamford, Harry C Jubb, Zbyslaw Sondka, David M Beare, Nidhi Bindal, Harry Boutselakis, Charlotte G Cole, Celestino Creatore, Elisabeth Dawson,[...]. Nucleic Acids Res 2019
11

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
11

Mutational signatures associated with tobacco smoking in human cancer.
Ludmil B Alexandrov, Young Seok Ju, Kerstin Haase, Peter Van Loo, Iñigo Martincorena, Serena Nik-Zainal, Yasushi Totoki, Akihiro Fujimoto, Hidewaki Nakagawa, Tatsuhiro Shibata,[...]. Science 2016
455
10

Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution.
S Kasar, J Kim, R Improgo, G Tiao, P Polak, N Haradhvala, M S Lawrence, A Kiezun, S M Fernandes, S Bahl,[...]. Nat Commun 2015
108
10

Universal Patterns of Selection in Cancer and Somatic Tissues.
Iñigo Martincorena, Keiran M Raine, Moritz Gerstung, Kevin J Dawson, Kerstin Haase, Peter Van Loo, Helen Davies, Michael R Stratton, Peter J Campbell. Cell 2017
411
10

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers.
Kin Chan, Steven A Roberts, Leszek J Klimczak, Joan F Sterling, Natalie Saini, Ewa P Malc, Jaegil Kim, David J Kwiatkowski, David C Fargo, Piotr A Mieczkowski,[...]. Nat Genet 2015
205
10

A Compendium of Mutational Signatures of Environmental Agents.
Jill E Kucab, Xueqing Zou, Sandro Morganella, Madeleine Joel, A Scott Nanda, Eszter Nagy, Celine Gomez, Andrea Degasperi, Rebecca Harris, Stephen P Jackson,[...]. Cell 2019
173
10

Somatic mutant clones colonize the human esophagus with age.
Iñigo Martincorena, Joanna C Fowler, Agnieszka Wabik, Andrew R J Lawson, Federico Abascal, Michael W J Hall, Alex Cagan, Kasumi Murai, Krishnaa Mahbubani, Michael R Stratton,[...]. Science 2018
342
10

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.
Kristian Cibulskis, Michael S Lawrence, Scott L Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S Lander, Gad Getz. Nat Biotechnol 2013
10

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,[...]. Nat Commun 2016
142
9

Evidence for APOBEC3B mutagenesis in multiple human cancers.
Michael B Burns, Nuri A Temiz, Reuben S Harris. Nat Genet 2013
458
9

Mechanisms generating cancer genome complexity from a single cell division error.
Neil T Umbreit, Cheng-Zhong Zhang, Luke D Lynch, Logan J Blaine, Anna M Cheng, Richard Tourdot, Lili Sun, Hannah F Almubarak, Kim Judge, Thomas J Mitchell,[...]. Science 2020
93
9

Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions.
Steven A Roberts, Joan Sterling, Cole Thompson, Shawn Harris, Deepak Mav, Ruchir Shah, Leszek J Klimczak, Gregory V Kryukov, Ewa Malc, Piotr A Mieczkowski,[...]. Mol Cell 2012
270
9

Massive genomic rearrangement acquired in a single catastrophic event during cancer development.
Philip J Stephens, Chris D Greenman, Beiyuan Fu, Fengtang Yang, Graham R Bignell, Laura J Mudie, Erin D Pleasance, King Wai Lau, David Beare, Lucy A Stebbings,[...]. Cell 2011
9

Mutational signatures are jointly shaped by DNA damage and repair.
Nadezda V Volkova, Bettina Meier, Víctor González-Huici, Simone Bertolini, Santiago Gonzalez, Harald Vöhringer, Federico Abascal, Iñigo Martincorena, Peter J Campbell, Anton Gartner,[...]. Nat Commun 2020
52
17

The mutational landscape of normal human endometrial epithelium.
Luiza Moore, Daniel Leongamornlert, Tim H H Coorens, Mathijs A Sanders, Peter Ellis, Stefan C Dentro, Kevin J Dawson, Tim Butler, Raheleh Rahbari, Thomas J Mitchell,[...]. Nature 2020
100
9

The landscape of somatic mutation in normal colorectal epithelial cells.
Henry Lee-Six, Sigurgeir Olafsson, Peter Ellis, Robert J Osborne, Mathijs A Sanders, Luiza Moore, Nikitas Georgakopoulos, Franco Torrente, Ayesha Noorani, Martin Goddard,[...]. Nature 2019
152
9

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,[...]. Cell 2012
833
9

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair.
Nicholas J Haradhvala, Paz Polak, Petar Stojanov, Kyle R Covington, Eve Shinbrot, Julian M Hess, Esther Rheinbay, Jaegil Kim, Yosef E Maruvka, Lior Z Braunstein,[...]. Cell 2016
204
8

Chromothripsis from DNA damage in micronuclei.
Cheng-Zhong Zhang, Alexander Spektor, Hauke Cornils, Joshua M Francis, Emily K Jackson, Shiwei Liu, Matthew Meyerson, David Pellman. Nature 2015
535
8

Chromothripsis and Kataegis Induced by Telomere Crisis.
John Maciejowski, Yilong Li, Nazario Bosco, Peter J Campbell, Titia de Lange. Cell 2015
321
8


Pan-cancer landscape of homologous recombination deficiency.
Luan Nguyen, John W M Martens, Arne Van Hoeck, Edwin Cuppen. Nat Commun 2020
37
21

Homologous Recombination Deficiency (HRD) Score Predicts Response to Platinum-Containing Neoadjuvant Chemotherapy in Patients with Triple-Negative Breast Cancer.
Melinda L Telli, Kirsten M Timms, Julia Reid, Bryan Hennessy, Gordon B Mills, Kristin C Jensen, Zoltan Szallasi, William T Barry, Eric P Winer, Nadine M Tung,[...]. Clin Cancer Res 2016
338
8

Detecting the mutational signature of homologous recombination deficiency in clinical samples.
Doga C Gulhan, Jake June-Koo Lee, Giorgio E M Melloni, Isidro Cortés-Ciriano, Peter J Park. Nat Genet 2019
62
12

Tissue-specific mutation accumulation in human adult stem cells during life.
Francis Blokzijl, Joep de Ligt, Myrthe Jager, Valentina Sasselli, Sophie Roerink, Nobuo Sasaki, Meritxell Huch, Sander Boymans, Ewart Kuijk, Pjotr Prins,[...]. Nature 2016
429
8

5-Fluorouracil treatment induces characteristic T>G mutations in human cancer.
Sharon Christensen, Bastiaan Van der Roest, Nicolle Besselink, Roel Janssen, Sander Boymans, John W M Martens, Marie-Laure Yaspo, Peter Priestley, Ewart Kuijk, Edwin Cuppen,[...]. Nat Commun 2019
55
14

Molecular portraits of human breast tumours.
C M Perou, T Sørlie, M B Eisen, M van de Rijn, S S Jeffrey, C A Rees, J R Pollack, D T Ross, H Johnsen, L A Akslen,[...]. Nature 2000
7

APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis.
John Maciejowski, Aikaterini Chatzipli, Alexandra Dananberg, Kevan Chu, Eleonore Toufektchan, Leszek J Klimczak, Dmitry A Gordenin, Peter J Campbell, Titia de Lange. Nat Genet 2020
36
19

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.
Jianjiong Gao, Bülent Arman Aksoy, Ugur Dogrusoz, Gideon Dresdner, Benjamin Gross, S Onur Sumer, Yichao Sun, Anders Jacobsen, Rileen Sinha, Erik Larsson,[...]. Sci Signal 2013
7

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
7


A practical guide for mutational signature analysis in hematological malignancies.
Francesco Maura, Andrea Degasperi, Ferran Nadeu, Daniel Leongamornlert, Helen Davies, Luiza Moore, Romina Royo, Bachisio Ziccheddu, Xose S Puente, Herve Avet-Loiseau,[...]. Nat Commun 2019
60
11

Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase.
Helen E Bryant, Niklas Schultz, Huw D Thomas, Kayan M Parker, Dan Flower, Elena Lopez, Suzanne Kyle, Mark Meuth, Nicola J Curtin, Thomas Helleday. Nature 2005
7

Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer.
V Abkevich, K M Timms, B T Hennessy, J Potter, M S Carey, L A Meyer, K Smith-McCune, R Broaddus, K H Lu, J Chen,[...]. Br J Cancer 2012
318
7


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.