A citation-based method for searching scientific literature

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, Atanas Kamburov, Philip C Hanawalt, David A Wheeler, Amnon Koren, Michael S Lawrence, Gad Getz. Cell 2016
Times Cited: 220







List of co-cited articles
903 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
942
40

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
32

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
159
29


APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication.
Vladimir B Seplyarskiy, Ruslan A Soldatov, Konstantin Y Popadin, Stylianos E Antonarakis, Georgii A Bazykin, Sergey I Nikolaev. Genome Res 2016
104
26

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
746
26

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
26

APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication.
James I Hoopes, Luis M Cortez, Tony M Mertz, Ewa P Malc, Piotr A Mieczkowski, Steven A Roberts. Cell Rep 2016
113
24

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
226
22

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
228
21

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
164
19

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
287
18

Mechanisms underlying mutational signatures in human cancers.
Thomas Helleday, Saeed Eshtad, Serena Nik-Zainal. Nat Rev Genet 2014
497
18

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
547
18

Evidence for APOBEC3B mutagenesis in multiple human cancers.
Michael B Burns, Nuri A Temiz, Reuben S Harris. Nat Genet 2013
486
18

Transcription-coupled DNA repair: two decades of progress and surprises.
Philip C Hanawalt, Graciela Spivak. Nat Rev Mol Cell Biol 2008
728
18

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
693
18


Mutational signature distribution varies with DNA replication timing and strand asymmetry.
Marketa Tomkova, Jakub Tomek, Skirmantas Kriaucionis, Benjamin Schuster-Böckler. Genome Biol 2018
56
30

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
17

Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features.
Rémi Buisson, Adam Langenbucher, Danae Bowen, Eugene E Kwan, Cyril H Benes, Lee Zou, Michael S Lawrence. Science 2019
122
17

MutationalPatterns: comprehensive genome-wide analysis of mutational processes.
Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen. Genome Med 2018
272
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
509
14

APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions.
Marat D Kazanov, Steven A Roberts, Paz Polak, John Stamatoyannopoulos, Leszek J Klimczak, Dmitry A Gordenin, Shamil R Sunyaev. Cell Rep 2015
53
26

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
77
18

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
14

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis.
Benjamin Jm Taylor, Serena Nik-Zainal, Yee Ling Wu, Lucy A Stebbings, Keiran Raine, Peter J Campbell, Cristina Rada, Michael R Stratton, Michael S Neuberger. Elife 2013
243
13

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
534
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
239
13

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors.
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
219
12

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity.
Charles Swanton, Nicholas McGranahan, Gabriel J Starrett, Reuben S Harris. Cancer Discov 2015
264
12

Differential relationship of DNA replication timing to different forms of human mutation and variation.
Amnon Koren, Paz Polak, James Nemesh, Jacob J Michaelson, Jonathan Sebat, Shamil R Sunyaev, Steven A McCarroll. Am J Hum Genet 2012
161
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
584
12

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
71
16

Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes.
Christina L Zheng, Nicholas J Wang, Jongsuk Chung, Homayoun Moslehi, J Zachary Sanborn, Joseph S Hur, Eric A Collisson, Swapna S Vemula, Agne Naujokas, Kami E Chiotti,[...]. Cell Rep 2014
71
15

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
235
11

The genome as a record of environmental exposure.
Serena Nik-Zainal, Jill E Kucab, Sandro Morganella, Dominik Glodzik, Ludmil B Alexandrov, Volker M Arlt, Annette Weninger, Monica Hollstein, Michael R Stratton, David H Phillips. Mutagenesis 2015
116
11

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
11


Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli.
Ashok S Bhagwat, Weilong Hao, Jesse P Townes, Heewook Lee, Haixu Tang, Patricia L Foster. Proc Natl Acad Sci U S A 2016
55
18

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Ke Shi, Michael A Carpenter, Surajit Banerjee, Nadine M Shaban, Kayo Kurahashi, Daniel J Salamango, Jennifer L McCann, Gabriel J Starrett, Justin V Duffy, Özlem Demir,[...]. Nat Struct Mol Biol 2017
133
10

Nucleotide excision repair is impaired by binding of transcription factors to DNA.
Radhakrishnan Sabarinathan, Loris Mularoni, Jordi Deu-Pons, Abel Gonzalez-Perez, Núria López-Bigas. Nature 2016
169
10


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
503
10

APOBEC3A is a prominent cytidine deaminase in breast cancer.
Luis M Cortez, Amber L Brown, Madeline A Dennis, Christopher D Collins, Alexander J Brown, Debra Mitchell, Tony M Mertz, Steven A Roberts. PLoS Genet 2019
38
26

Human mutation rate associated with DNA replication timing.
John A Stamatoyannopoulos, Ivan Adzhubei, Robert E Thurman, Gregory V Kryukov, Sergei M Mirkin, Shamil R Sunyaev. Nat Genet 2009
268
10

Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.
Sheera Adar, Jinchuan Hu, Jason D Lieb, Aziz Sancar. Proc Natl Acad Sci U S A 2016
105
9


Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication.
Eve Shinbrot, Erin E Henninger, Nils Weinhold, Kyle R Covington, A Yasemin Göksenin, Nikolaus Schultz, Hsu Chao, HarshaVardhan Doddapaneni, Donna M Muzny, Richard A Gibbs,[...]. Genome Res 2014
176
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.