A citation-based method for searching scientific literature

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 K J 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 W M Martens, Anne-Lise Børresen-Dale, Andrea L Richardson, Gu Kong, Gilles Thomas, Michael R Stratton. Nature 2016
Times Cited: 1182







List of co-cited articles
882 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
27


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
26

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
473
23


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

A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer.
Paz Polak, Jaegil Kim, Lior Z Braunstein, Rosa Karlic, Nicholas J Haradhavala, Grace Tiao, Daniel Rosebrock, Dimitri Livitz, Kirsten Kübler, Kent W Mouw,[...]. Nat Genet 2017
286
13

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
260
12

Pan-cancer whole-genome analyses of metastatic solid tumours.
Peter Priestley, Jonathan Baber, Martijn P Lolkema, Neeltje Steeghs, Ewart de Bruijn, Charles Shale, Korneel Duyvesteyn, Susan Haidari, Arne van Hoeck, Wendy Onstenk,[...]. Nature 2019
354
11

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.
Isidro Cortés-Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L Jung, Lixing Yang, Dmitry Gordenin, Leszek J Klimczak, Cheng-Zhong Zhang, David S Pellman,[...]. Nat Genet 2020
200
10

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
10

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
Christina Curtis, Sohrab P Shah, Suet-Feung Chin, Gulisa Turashvili, Oscar M Rueda, Mark J Dunning, Doug Speed, Andy G Lynch, Shamith Samarajiwa, Yinyin Yuan,[...]. Nature 2012
10

Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study.
Johan Staaf, Dominik Glodzik, Ana Bosch, Johan Vallon-Christersson, Christel Reuterswärd, Jari Häkkinen, Andrea Degasperi, Tauanne Dias Amarante, Lao H Saal, Cecilia Hegardt,[...]. Nat Med 2019
117
10


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

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M Hess, Randi Istrup Juul, Ziao Lin,[...]. Nature 2020
226
9

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
9

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
610
9

Carboplatin in BRCA1/2-mutated and triple-negative breast cancer BRCAness subgroups: the TNT Trial.
Andrew Tutt, Holly Tovey, Maggie Chon U Cheang, Sarah Kernaghan, Lucy Kilburn, Patrycja Gazinska, Julie Owen, Jacinta Abraham, Sophie Barrett, Peter Barrett-Lee,[...]. Nat Med 2018
450
9

Olaparib for Metastatic Breast Cancer in Patients with a Germline BRCA Mutation.
Mark Robson, Seock-Ah Im, Elżbieta Senkus, Binghe Xu, Susan M Domchek, Norikazu Masuda, Suzette Delaloge, Wei Li, Nadine Tung, Anne Armstrong,[...]. N Engl J Med 2017
9

A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies.
Andrea Degasperi, Tauanne Dias Amarante, Jan Czarnecki, Scott Shooter, Xueqing Zou, Dominik Glodzik, Sandro Morganella, Arjun S Nanda, Cherif Badja, Gene Koh,[...]. Nat Cancer 2020
74
12

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
150
8

The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations.
Francesca Menghi, Floris P Barthel, Vinod Yadav, Ming Tang, Bo Ji, Zhonghui Tang, Gregory W Carter, Yijun Ruan, Ralph Scully, Roel G W Verhaak,[...]. Cancer Cell 2018
90
8

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.
Kevin Hadi, Xiaotong Yao, Julie M Behr, Aditya Deshpande, Charalampos Xanthopoulakis, Huasong Tian, Sarah Kudman, Joel Rosiene, Madison Darmofal, Joseph DeRose,[...]. Cell 2020
62
12

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
891
8

Whole-genome characterization of chemoresistant ovarian cancer.
Ann-Marie Patch, Elizabeth L Christie, Dariush Etemadmoghadam, Dale W Garsed, Joshy George, Sian Fereday, Katia Nones, Prue Cowin, Kathryn Alsop, Peter J Bailey,[...]. Nature 2015
888
8

Pan-cancer landscape of homologous recombination deficiency.
Luan Nguyen, John W M Martens, Arne Van Hoeck, Edwin Cuppen. Nat Commun 2020
119
8

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
404
8

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
473
8

The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers.
Pedram Razavi, Matthew T Chang, Guotai Xu, Chaitanya Bandlamudi, Dara S Ross, Neil Vasan, Yanyan Cai, Craig M Bielski, Mark T A Donoghue, Philip Jonsson,[...]. Cancer Cell 2018
402
8

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
8

Punctuated evolution of prostate cancer genomes.
Sylvan C Baca, Davide Prandi, Michael S Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y MacDonald, Mahmoud Ghandi,[...]. Cell 2013
810
7

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies.
Brian D Lehmann, Joshua A Bauer, Xi Chen, Melinda E Sanders, A Bapsi Chakravarthy, Yu Shyr, Jennifer A Pietenpol. J Clin Invest 2011
7

The landscape of cancer genes and mutational processes in breast cancer.
Philip J Stephens, Patrick S Tarpey, Helen Davies, Peter Van Loo, Chris Greenman, David C Wedge, Serena Nik-Zainal, Sancha Martin, Ignacio Varela, Graham R Bignell,[...]. Nature 2012
7

Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer.
Neha Chopra, Holly Tovey, Alex Pearson, Ros Cutts, Christy Toms, Paula Proszek, Michael Hubank, Mitch Dowsett, Andrew Dodson, Frances Daley,[...]. Nat Commun 2020
95
7

Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation.
Tatiana Popova, Elodie Manié, Guillaume Rieunier, Virginie Caux-Moncoutier, Carole Tirapo, Thierry Dubois, Olivier Delattre, Brigitte Sigal-Zafrani, Marc Bollet, Michel Longy,[...]. Cancer Res 2012
363
7

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
112
7

TBCRC 048: Phase II Study of Olaparib for Metastatic Breast Cancer and Mutations in Homologous Recombination-Related Genes.
Nadine M Tung, Mark E Robson, Steffen Ventz, Cesar A Santa-Maria, Rita Nanda, Paul K Marcom, Payal D Shah, Tarah J Ballinger, Eddy S Yang, Shaveta Vinayak,[...]. J Clin Oncol 2020
134
7

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
7

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes.
Bernard Pereira, Suet-Feung Chin, Oscar M Rueda, Hans-Kristian Moen Vollan, Elena Provenzano, Helen A Bardwell, Michelle Pugh, Linda Jones, Roslin Russell, Stephen-John Sammut,[...]. Nat Commun 2016
846
7

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Morten Källberg, Anthony J Cox, Semyon Kruglyak, Christopher T Saunders. Bioinformatics 2016
715
7

Copy number signatures and mutational processes in ovarian carcinoma.
Geoff Macintyre, Teodora E Goranova, Dilrini De Silva, Darren Ennis, Anna M Piskorz, Matthew Eldridge, Daoud Sie, Liz-Anne Lewsley, Aishah Hanif, Cheryl Wilson,[...]. Nat Genet 2018
169
7

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
7

Criteria for inference of chromothripsis in cancer genomes.
Jan O Korbel, Peter J Campbell. Cell 2013
327
6

Genomic characterization of metastatic breast cancers.
François Bertucci, Charlotte K Y Ng, Anne Patsouris, Nathalie Droin, Salvatore Piscuoglio, Nadine Carbuccia, Jean Charles Soria, Alicia Tran Dien, Yahia Adnani, Maud Kamal,[...]. Nature 2019
305
6

BRCAness revisited.
Christopher J Lord, Alan Ashworth. Nat Rev Cancer 2016
715
6

Genomic analyses identify molecular subtypes of pancreatic cancer.
Peter Bailey, David K Chang, Katia Nones, Amber L Johns, Ann-Marie Patch, Marie-Claude Gingras, David K Miller, Angelika N Christ, Tim J C Bruxner, Michael C Quinn,[...]. Nature 2016
6

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
341
6

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade.
Dung T Le, Jennifer N Durham, Kellie N Smith, Hao Wang, Bjarne R Bartlett, Laveet K Aulakh, Steve Lu, Holly Kemberling, Cara Wilt, Brandon S Luber,[...]. Science 2017
6

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
231
6


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.