A citation-based method for searching scientific literature

Hoon Kim, Nam-Phuong Nguyen, Kristen Turner, Sihan Wu, Amit D Gujar, Jens Luebeck, Jihe Liu, Viraj Deshpande, Utkrisht Rajkumar, Sandeep Namburi, Samirkumar B Amin, Eunhee Yi, Francesca Menghi, Johannes H Schulte, Anton G Henssen, Howard Y Chang, Christine R Beck, Paul S Mischel, Vineet Bafna, Roel G W Verhaak. Nat Genet 2020
Times Cited: 69







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



Times Cited
  Times     Co-cited
Similarity


Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity.
Kristen M Turner, Viraj Deshpande, Doruk Beyter, Tomoyuki Koga, Jessica Rusert, Catherine Lee, Bin Li, Karen Arden, Bing Ren, David A Nathanson,[...]. Nature 2017
244
65

Circular ecDNA promotes accessible chromatin and high oncogene expression.
Sihan Wu, Kristen M Turner, Nam Nguyen, Ramya Raviram, Marcella Erb, Jennifer Santini, Jens Luebeck, Utkrisht Rajkumar, Yarui Diao, Bin Li,[...]. Nature 2019
123
63

Functional Enhancers Shape Extrachromosomal Oncogene Amplifications.
Andrew R Morton, Nergiz Dogan-Artun, Zachary J Faber, Graham MacLeod, Cynthia F Bartels, Megan S Piazza, Kevin C Allan, Stephen C Mack, Xiuxing Wang, Ryan C Gimple,[...]. Cell 2019
88
52

Extrachromosomal oncogene amplification in tumour pathogenesis and evolution.
Roel G W Verhaak, Vineet Bafna, Paul S Mischel. Nat Rev Cancer 2019
93
50

Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA.
David A Nathanson, Beatrice Gini, Jack Mottahedeh, Koppany Visnyei, Tomoyuki Koga, German Gomez, Ascia Eskin, Kiwook Hwang, Jun Wang, Kenta Masui,[...]. Science 2014
296
46

Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Richard P Koche, Elias Rodriguez-Fos, Konstantin Helmsauer, Martin Burkert, Ian C MacArthur, Jesper Maag, Rocio Chamorro, Natalia Munoz-Perez, Montserrat Puiggròs, Heathcliff Dorado Garcia,[...]. Nat Genet 2020
74
46

Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma.
Ana C deCarvalho, Hoon Kim, Laila M Poisson, Mary E Winn, Claudius Mueller, David Cherba, Julie Koeman, Sahil Seth, Alexei Protopopov, Michelle Felicella,[...]. Nat Genet 2018
108
39

Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.
Viraj Deshpande, Jens Luebeck, Nam-Phuong D Nguyen, Mehrdad Bakhtiari, Kristen M Turner, Richard Schwab, Hannah Carter, Paul S Mischel, Vineet Bafna. Nat Commun 2019
55
47

MINUTE CHROMATIN BODIES IN MALIGNANT TUMOURS OF CHILDHOOD.
D COX, C YUNCKEN, A I SPRIGGS. Lancet 1965
200
31

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
28

Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma.
Konstantin Helmsauer, Maria E Valieva, Salaheddine Ali, Rocío Chamorro González, Robert Schöpflin, Claudia Röefzaad, Yi Bei, Heathcliff Dorado Garcia, Elias Rodriguez-Fos, Montserrat Puiggròs,[...]. Nat Commun 2020
40
50

Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure.
Clelia Tiziana Storlazzi, Angelo Lonoce, Maria C Guastadisegni, Domenico Trombetta, Pietro D'Addabbo, Giulia Daniele, Alberto L'Abbate, Gemma Macchia, Cecilia Surace, Klaas Kok,[...]. Genome Res 2010
117
26

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.
Yanfen Zhu, Amit D Gujar, Chee-Hong Wong, Harianto Tjong, Chew Yee Ngan, Liang Gong, Yi-An Chen, Hoon Kim, Jihe Liu, Meihong Li,[...]. Cancer Cell 2021
26
69


Extrachromosomal DNA-relieving heredity constraints, accelerating tumour evolution.
C Bailey, M J Shoura, P S Mischel, C Swanton. Ann Oncol 2020
29
55

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
168
21

Double minute chromosomes can be produced from precursors derived from a chromosomal deletion.
S M Carroll, M L DeRose, P Gaudray, C M Moore, D R Needham-Vandevanter, D D Von Hoff, G M Wahl. Mol Cell Biol 1988
181
21

Structure and evolution of double minutes in diagnosis and relapse brain tumors.
Ke Xu, Liang Ding, Ti-Cheng Chang, Ying Shao, Jason Chiang, Heather Mulder, Shuoguo Wang, Tim I Shaw, Ji Wen, Laura Hover,[...]. Acta Neuropathol 2019
32
46

Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation.
Pankaj Kumar, Laura W Dillon, Yoshiyuki Shibata, Amir A Jazaeri, David R Jones, Anindya Dutta. Mol Cancer Res 2017
80
20

Chromothripsis drives the evolution of gene amplification in cancer.
Ofer Shoshani, Simon F Brunner, Rona Yaeger, Peter Ly, Yael Nechemia-Arbely, Dong Hyun Kim, Rongxin Fang, Guillaume A Castillon, Miao Yu, Julia S Z Li,[...]. Nature 2021
59
23

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
586
18


Inhibiting homologous recombination decreases extrachromosomal amplification but has no effect on intrachromosomal amplification in methotrexate-resistant colon cancer cells.
Mengdi Cai, Huishu Zhang, Liqing Hou, Wei Gao, Ying Song, Xiaobo Cui, Chunxiang Li, Rongwei Guan, Jinfa Ma, Xu Wang,[...]. Int J Cancer 2019
24
54

Transposition and amplification of oncogene-related sequences in human neuroblastomas.
N E Kohl, N Kanda, R R Schreck, G Bruns, S A Latt, F Gilbert, F W Alt. Cell 1983
654
18


Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer.
Alberto L'Abbate, Gemma Macchia, Pietro D'Addabbo, Angelo Lonoce, Doron Tolomeo, Domenico Trombetta, Klaas Kok, Christoph Bartenhagen, Christopher W Whelan, Orazio Palumbo,[...]. Nucleic Acids Res 2014
66
19

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
120
17

Molecular structure of double-minute chromosomes bearing amplified copies of the epidermal growth factor receptor gene in gliomas.
Nicolas Vogt, Sandrine-Hélène Lefèvre, Françoise Apiou, Anne-Marie Dutrillaux, Andrej Cör, Pascal Leuraud, Marie-France Poupon, Bernard Dutrillaux, Michelle Debatisse, Bernard Malfoy. Proc Natl Acad Sci U S A 2004
102
17

Circular DNA elements of chromosomal origin are common in healthy human somatic tissue.
Henrik Devitt Møller, Marghoob Mohiyuddin, Iñigo Prada-Luengo, M Reza Sailani, Jens Frey Halling, Peter Plomgaard, Lasse Maretty, Anders Johannes Hansen, Michael P Snyder, Henriette Pilegaard,[...]. Nat Commun 2018
92
17

ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines.
Pankaj Kumar, Shashi Kiran, Shekhar Saha, Zhangli Su, Teressa Paulsen, Ajay Chatrath, Yoshiyuki Shibata, Etsuko Shibata, Anindya Dutta. Sci Adv 2020
29
41

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
15

Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma.
Nicolas Vogt, Anne Gibaud, Frédéric Lemoine, Pierre de la Grange, Michelle Debatisse, Bernard Malfoy. Nucleic Acids Res 2014
27
40

Extrachromosomal circular DNA is common in yeast.
Henrik D Møller, Lance Parsons, Tue S Jørgensen, David Botstein, Birgitte Regenberg. Proc Natl Acad Sci U S A 2015
102
15

Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells.
Teressa Paulsen, Pankaj Kumar, M Murat Koseoglu, Anindya Dutta. Trends Genet 2018
63
17

Criteria for inference of chromothripsis in cancer genomes.
Jan O Korbel, Peter J Campbell. Cell 2013
317
15

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
14

Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues.
Yoshiyuki Shibata, Pankaj Kumar, Ryan Layer, Smaranda Willcox, Jeffrey R Gagan, Jack D Griffith, Anindya Dutta. Science 2012
124
14

Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements.
Peter Ly, Simon F Brunner, Ofer Shoshani, Dong Hyun Kim, Weijie Lan, Tatyana Pyntikova, Adrienne M Flanagan, Sam Behjati, David C Page, Peter J Campbell,[...]. Nat Genet 2019
69
14

AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications.
Jens Luebeck, Ceyda Coruh, Siavash R Dehkordi, Joshua T Lange, Kristen M Turner, Viraj Deshpande, Dave A Pai, Chao Zhang, Utkrisht Rajkumar, Julie A Law,[...]. Nat Commun 2020
14
71

Chromothripsis and Kataegis Induced by Telomere Crisis.
John Maciejowski, Yilong Li, Nazario Bosco, Peter J Campbell, Titia de Lange. Cell 2015
354
13

Novel role for non-homologous end joining in the formation of double minutes in methotrexate-resistant colon cancer cells.
Xiangning Meng, Xiuying Qi, Huanhuan Guo, Mengdi Cai, Chunxiang Li, Jing Zhu, Feng Chen, Huan Guo, Jie Li, Yuzhen Zhao,[...]. J Med Genet 2015
33
27

Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity.
Laura W Dillon, Pankaj Kumar, Yoshiyuki Shibata, Yuh-Hwa Wang, Smaranda Willcox, Jack D Griffith, Yves Pommier, Shunichi Takeda, Anindya Dutta. Cell Rep 2015
65
13

MYC-containing double minutes in hematologic malignancies: evidence in favor of the episome model and exclusion of MYC as the target gene.
Clelia Tiziana Storlazzi, Thoas Fioretos, Cecilia Surace, Angelo Lonoce, Angela Mastrorilli, Bodil Strömbeck, Pietro D'Addabbo, Francesco Iacovelli, Crescenzio Minervini, Anna Aventin,[...]. Hum Mol Genet 2006
87
13

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations.
Tobias Rausch, David T W Jones, Marc Zapatka, Adrian M Stütz, Thomas Zichner, Joachim Weischenfeldt, Natalie Jäger, Marc Remke, David Shih, Paul A Northcott,[...]. Cell 2012
557
13

The chromatin accessibility landscape of primary human cancers.
M Ryan Corces, Jeffrey M Granja, Shadi Shams, Bryan H Louie, Jose A Seoane, Wanding Zhou, Tiago C Silva, Clarice Groeneveld, Christopher K Wong, Seung Woo Cho,[...]. Science 2018
355
13

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
46
19


ecDNA hubs drive cooperative intermolecular oncogene expression.
King L Hung, Kathryn E Yost, Liangqi Xie, Quanming Shi, Konstantin Helmsauer, Jens Luebeck, Robert Schöpflin, Joshua T Lange, Rocío Chamorro González, Natasha E Weiser,[...]. Nature 2021
17
52

Classification of extrachromosomal circular DNA with a focus on the role of extrachromosomal DNA (ecDNA) in tumor heterogeneity and progression.
Zhenyu Liao, Wang Jiang, Longyun Ye, Tianjiao Li, Xianjun Yu, Liang Liu. Biochim Biophys Acta Rev Cancer 2020
21
38



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.