A citation-based method for searching scientific literature

Jaegil Kim, Kent W Mouw, Paz Polak, Lior Z Braunstein, Atanas Kamburov, David J Kwiatkowski, Jonathan E Rosenberg, Eliezer M Van Allen, Alan D'Andrea, Gad Getz. Nat Genet 2016
Times Cited: 173







List of co-cited articles
786 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
54

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
581
22

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
948
20

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.
A Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, Joaquim Bellmunt, Guangwu Guo, Andrew D Cherniack, Toshinori Hinoue, Peter W Laird, Katherine A Hoadley, Rehan Akbani,[...]. Cell 2017
768
20

Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma.
Eliezer M Van Allen, Kent W Mouw, Philip Kim, Gopa Iyer, Nikhil Wagle, Hikmat Al-Ahmadie, Cong Zhu, Irina Ostrovnaya, Gregory V Kryukov, Kevin W O'Connor,[...]. Cancer Discov 2014
309
19

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
443
18

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
17

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
17

Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts,[...]. Nature 2013
17

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
99
16

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

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
437
15

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
399
15

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
136
14

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
306
14

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
415
14


GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz. Genome Biol 2011
13

Comprehensive Analysis of Hypermutation in Human Cancer.
Brittany B Campbell, Nicholas Light, David Fabrizio, Matthew Zatzman, Fabio Fuligni, Richard de Borja, Scott Davidson, Melissa Edwards, Julia A Elvin, Karl P Hodel,[...]. Cell 2017
316
13

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
13

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
647
13

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
144
13

Mechanisms underlying mutational signatures in human cancers.
Thomas Helleday, Saeed Eshtad, Serena Nik-Zainal. Nat Rev Genet 2014
432
12

Impact of Molecular Subtypes in Muscle-invasive Bladder Cancer on Predicting Response and Survival after Neoadjuvant Chemotherapy.
Roland Seiler, Hussam Al Deen Ashab, Nicholas Erho, Bas W G van Rhijn, Brian Winters, James Douglas, Kim E Van Kessel, Elisabeth E Fransen van de Putte, Matthew Sommerlad, Natalie Q Wang,[...]. Eur Urol 2017
348
12

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial.
Jonathan E Rosenberg, Jean Hoffman-Censits, Tom Powles, Michiel S van der Heijden, Arjun V Balar, Andrea Necchi, Nancy Dawson, Peter H O'Donnell, Ani Balmanoukian, Yohann Loriot,[...]. Lancet 2016
12


Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
12

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
206
12

Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy.
Woonyoung Choi, Sima Porten, Seungchan Kim, Daniel Willis, Elizabeth R Plimack, Jean Hoffman-Censits, Beat Roth, Tiewei Cheng, Mai Tran, I-Ling Lee,[...]. Cancer Cell 2014
849
11

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
192
11

MutationalPatterns: comprehensive genome-wide analysis of mutational processes.
Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen. Genome Med 2018
173
11

SomaticSignatures: inferring mutational signatures from single-nucleotide variants.
Julian S Gehring, Bernd Fischer, Michael Lawrence, Wolfgang Huber. Bioinformatics 2015
163
10

EMu: probabilistic inference of mutational processes and their localization in the cancer genome.
Andrej Fischer, Christopher J R Illingworth, Peter J Campbell, Ville Mustonen. Genome Biol 2013
56
17

The cancer genome.
Michael R Stratton, Peter J Campbell, P Andrew Futreal. Nature 2009
10

A flexible R package for nonnegative matrix factorization.
Renaud Gaujoux, Cathal Seoighe. BMC Bioinformatics 2010
454
10

Automatic relevance determination in nonnegative matrix factorization with the β-divergence.
Vincent Y F Tan, Cédric Févotte. IEEE Trans Pattern Anal Mach Intell 2013
55
18

DNA Damage Response and Repair Gene Alterations Are Associated with Improved Survival in Patients with Platinum-Treated Advanced Urothelial Carcinoma.
Min Yuen Teo, Richard M Bambury, Emily C Zabor, Emmet Jordan, Hikmat Al-Ahmadie, Mariel E Boyd, Nancy Bouvier, Stephanie A Mullane, Eugene K Cha, Nitin Roper,[...]. Clin Cancer Res 2017
119
10

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
10

Detecting presence of mutational signatures in cancer with confidence.
Xiaoqing Huang, Damian Wojtowicz, Teresa M Przytycka. Bioinformatics 2018
28
35

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer.
Jarno Drost, Ruben van Boxtel, Francis Blokzijl, Tomohiro Mizutani, Nobuo Sasaki, Valentina Sasselli, Joep de Ligt, Sam Behjati, Judith E Grolleman, Tom van Wezel,[...]. Science 2017
175
10

Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.
Naiyer A Rizvi, Matthew D Hellmann, Alexandra Snyder, Pia Kvistborg, Vladimir Makarov, Jonathan J Havel, William Lee, Jianda Yuan, Phillip Wong, Teresa S Ho,[...]. Science 2015
10

Validating the concept of mutational signatures with isogenic cell models.
Xueqing Zou, Michel Owusu, Rebecca Harris, Stephen P Jackson, Joanna I Loizou, Serena Nik-Zainal. Nat Commun 2018
50
20

Oncotator: cancer variant annotation tool.
Alex H Ramos, Lee Lichtenstein, Manaswi Gupta, Michael S Lawrence, Trevor J Pugh, Gordon Saksena, Matthew Meyerson, Gad Getz. Hum Mutat 2015
278
10

signeR: an empirical Bayesian approach to mutational signature discovery.
Rafael A Rosales, Rodrigo D Drummond, Renan Valieris, Emmanuel Dias-Neto, Israel T da Silva. Bioinformatics 2017
40
22

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
395
9

Defects in DNA Repair Genes Predict Response to Neoadjuvant Cisplatin-based Chemotherapy in Muscle-invasive Bladder Cancer.
Elizabeth R Plimack, Roland L Dunbrack, Timothy A Brennan, Mark D Andrake, Yan Zhou, Ilya G Serebriiskii, Michael Slifker, Katherine Alpaugh, Essel Dulaimi, Norma Palma,[...]. Eur Urol 2015
244
9

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
9

Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair.
N J Haradhvala, J Kim, Y E Maruvka, P Polak, D Rosebrock, D Livitz, J M Hess, I Leshchiner, A Kamburov, K W Mouw,[...]. Nat Commun 2018
59
15

Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis.
Eric Letouzé, Jayendra Shinde, Victor Renault, Gabrielle Couchy, Jean-Frédéric Blanc, Emmanuel Tubacher, Quentin Bayard, Delphine Bacq, Vincent Meyer, Jérémy Semhoun,[...]. Nat Commun 2017
99
9

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
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.