A citation-based method for searching scientific literature

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 A J R 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, Peter J Campbell. Cell 2012
Times Cited: 867







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



Times Cited
  Times     Co-cited
Similarity


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
811
29

The evolutionary history of 2,658 cancers.
Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu,[...]. Nature 2020
292
25

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
24

PyClone: statistical inference of clonal population structure in cancer.
Andrew Roth, Jaswinder Khattra, Damian Yap, Adrian Wan, Emma Laks, Justina Biele, Gavin Ha, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P Shah. Nat Methods 2014
520
23



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,[...]. Nat Med 2015
477
19

Absolute quantification of somatic DNA alterations in human cancer.
Scott L Carter, Kristian Cibulskis, Elena Helman, Aaron McKenna, Hui Shen, Travis Zack, Peter W Laird, Robert C Onofrio, Wendy Winckler, Barbara A Weir,[...]. Nat Biotechnol 2012
18

Tracking the Evolution of Non-Small-Cell Lung Cancer.
Mariam Jamal-Hanjani, Gareth A Wilson, Nicholas McGranahan, Nicolai J Birkbak, Thomas B K Watkins, Selvaraju Veeriah, Seema Shafi, Diana H Johnson, Richard Mitter, Rachel Rosenthal,[...]. N Engl J Med 2017
18

The evolutionary history of lethal metastatic prostate cancer.
Gunes Gundem, Peter Van Loo, Barbara Kremeyer, Ludmil B Alexandrov, Jose M C Tubio, Elli Papaemmanuil, Daniel S Brewer, Heini M L Kallio, Gunilla Högnäs, Matti Annala,[...]. Nature 2015
808
18

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
Marco Gerlinger, Andrew J Rowan, Stuart Horswell, M Math, James Larkin, David Endesfelder, Eva Gronroos, Pierre Martinez, Nicholas Matthews, Aengus Stewart,[...]. N Engl J Med 2012
17

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
15

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
15

Clonal evolution in cancer.
Mel Greaves, Carlo C Maley. Nature 2012
15

Allele-specific copy number analysis of tumors.
Peter Van Loo, Silje H Nordgard, Ole Christian Lingjærde, Hege G Russnes, Inga H Rye, Wei Sun, Victor J Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume,[...]. Proc Natl Acad Sci U S A 2010
631
15


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
493
15

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,[...]. Cell 2012
15

SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.
Christopher A Miller, Brian S White, Nathan D Dees, Malachi Griffith, John S Welch, Obi L Griffith, Ravi Vij, Michael H Tomasson, Timothy A Graubert, Matthew J Walter,[...]. PLoS Comput Biol 2014
267
14

PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.
Amit G Deshwar, Shankar Vembu, Christina K Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris. Genome Biol 2015
195
13

Principles of Reconstructing the Subclonal Architecture of Cancers.
Stefan C Dentro, David C Wedge, Peter Van Loo. Cold Spring Harb Perspect Med 2017
46
28

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity.
Noemi Andor, Trevor A Graham, Marnix Jansen, Li C Xia, C Athena Aktipis, Claudia Petritsch, Hanlee P Ji, Carlo C Maley. Nat Med 2016
429
13

Evolution and impact of subclonal mutations in chronic lymphocytic leukemia.
Dan A Landau, Scott L Carter, Petar Stojanov, Aaron McKenna, Kristen Stevenson, Michael S Lawrence, Carrie Sougnez, Chip Stewart, Andrey Sivachenko, Lili Wang,[...]. Cell 2013
952
13

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing.
Emma Laks, Andrew McPherson, Hans Zahn, Daniel Lai, Adi Steif, Jazmine Brimhall, Justina Biele, Beixi Wang, Tehmina Masud, Jerome Ting,[...]. Cell 2019
63
19

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
12

Identification of neutral tumor evolution across cancer types.
Marc J Williams, Benjamin Werner, Chris P Barnes, Trevor A Graham, Andrea Sottoriva. Nat Genet 2016
312
12

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
12

Tumour evolution inferred by single-cell sequencing.
Nicholas Navin, Jude Kendall, Jennifer Troge, Peter Andrews, Linda Rodgers, Jeanne McIndoo, Kerry Cook, Asya Stepansky, Dan Levy, Diane Esposito,[...]. Nature 2011
11

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer.
Ruli Gao, Alexander Davis, Thomas O McDonald, Emi Sei, Xiuqing Shi, Yong Wang, Pei-Ching Tsai, Anna Casasent, Jill Waters, Hong Zhang,[...]. Nat Genet 2016
252
11

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution.
Nicholas McGranahan, Francesco Favero, Elza C de Bruin, Nicolai Juul Birkbak, Zoltan Szallasi, Charles Swanton. Sci Transl Med 2015
399
11

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
11


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
479
10

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
423
10

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
199
10

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.
Yong Wang, Jill Waters, Marco L Leung, Anna Unruh, Whijae Roh, Xiuqing Shi, Ken Chen, Paul Scheet, Selina Vattathil, Han Liang,[...]. Nature 2014
627
10

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.
Charissa Kim, Ruli Gao, Emi Sei, Rachel Brandt, Johan Hartman, Thomas Hatschek, Nicola Crosetto, Theodoros Foukakis, Nicholas E Navin. Cell 2018
386
10

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
Sohrab P Shah, Andrew Roth, Rodrigo Goya, Arusha Oloumi, Gavin Ha, Yongjun Zhao, Gulisa Turashvili, Jiarui Ding, Kane Tse, Gholamreza Haffari,[...]. Nature 2012
10

Genomic Evolution of Breast Cancer Metastasis and Relapse.
Lucy R Yates, Stian Knappskog, David Wedge, James H R Farmery, Santiago Gonzalez, Inigo Martincorena, Ludmil B Alexandrov, Peter Van Loo, Hans Kristian Haugland, Peer Kaare Lilleng,[...]. Cancer Cell 2017
324
10

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.
Andrew McPherson, Andrew Roth, Emma Laks, Tehmina Masud, Ali Bashashati, Allen W Zhang, Gavin Ha, Justina Biele, Damian Yap, Adrian Wan,[...]. Nat Genet 2016
179
10

A Big Bang model of human colorectal tumor growth.
Andrea Sottoriva, Haeyoun Kang, Zhicheng Ma, Trevor A Graham, Matthew P Salomon, Junsong Zhao, Paul Marjoram, Kimberly Siegmund, Michael F Press, Darryl Shibata,[...]. Nat Genet 2015
578
10

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
10

Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
9

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
205
9

A community effort to create standards for evaluating tumor subclonal reconstruction.
Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G Espiritu, Amit G Deshwar, Matei David, Nathan M Wilson, Stefan Dentro, Jeff A Wintersinger, Lydia Y Liu, Minjeong Ko,[...]. Nat Biotechnol 2020
31
29

Comprehensive Characterization of Cancer Driver Genes and Mutations.
Matthew H Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C Wendl, Jaegil Kim, Brendan Reardon,[...]. Cell 2018
798
9

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.
Elza C de Bruin, Nicholas McGranahan, Richard Mitter, Max Salm, David C Wedge, Lucy Yates, Mariam Jamal-Hanjani, Seema Shafi, Nirupa Murugaesu, Andrew J Rowan,[...]. Science 2014
709
9

Intra-tumour heterogeneity: a looking glass for cancer?
Andriy Marusyk, Vanessa Almendro, Kornelia Polyak. Nat Rev Cancer 2012
9

Genomic basis for RNA alterations in cancer.
Claudia Calabrese, Natalie R Davidson, Deniz Demircioğlu, Nuno A Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M Soulette,[...]. Nature 2020
141
9

Tumor evolution. 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,[...]. Science 2015
866
9


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.