A citation-based method for searching scientific literature


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



Times Cited
  Times     Co-cited
Similarity


Effect of fixatives and tissue processing on the content and integrity of nucleic acids.
Mythily Srinivasan, Daniel Sedmak, Scott Jewell. Am J Pathol 2002
746
14

Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing.
Stephen Q Wong, Jason Li, Angela Y-C Tan, Ravikiran Vedururu, Jia-Min B Pang, Hongdo Do, Jason Ellul, Ken Doig, Anthony Bell, Grant A MacArthur,[...]. BMC Med Genomics 2014
150
13

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
12

Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue.
Jakob Hedegaard, Kasper Thorsen, Mette Katrine Lund, Anne-Mette K Hein, Stephen Jacques Hamilton-Dutoit, Søren Vang, Iver Nordentoft, Karin Birkenkamp-Demtröder, Mogens Kruhøffer, Henrik Hager,[...]. PLoS One 2014
189
11

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.
Pauline Robbe, Niko Popitsch, Samantha J L Knight, Pavlos Antoniou, Jennifer Becq, Miao He, Alexander Kanapin, Anastasia Samsonova, Dimitrios V Vavoulis, Mark T Ross,[...]. Genet Med 2018
60
16

A high frequency of sequence alterations is due to formalin fixation of archival specimens.
C Williams, F Pontén, C Moberg, P Söderkvist, M Uhlén, J Pontén, G Sitbon, J Lundeberg. Am J Pathol 1999
368
9

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.
Eliezer M Van Allen, Nikhil Wagle, Petar Stojanov, Danielle L Perrin, Kristian Cibulskis, Sara Marlow, Judit Jane-Valbuena, Dennis C Friedrich, Gregory Kryukov, Scott L Carter,[...]. Nat Med 2014
343
9

Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation.
Naoki Einaga, Akio Yoshida, Hiroko Noda, Masaaki Suemitsu, Yuki Nakayama, Akihisa Sakurada, Yoshiko Kawaji, Hiromi Yamaguchi, Yasushi Sasaki, Takashi Tokino,[...]. PLoS One 2017
42
21

Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.
Martin Kerick, Melanie Isau, Bernd Timmermann, Holger Sültmann, Ralf Herwig, Sylvia Krobitsch, Georg Schaefer, Irmgard Verdorfer, Georg Bartsch, Helmut Klocker,[...]. BMC Med Genomics 2011
124
9

Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists.
Lawrence J Jennings, Maria E Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M Lubin, John Pfeifer, Robyn L Temple-Smolkin, Karl V Voelkerding, Marina N Nikiforova. J Mol Diagn 2017
228
9

Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples.
Ensel Oh, Yoon-La Choi, Mi Jeong Kwon, Ryong Nam Kim, Yu Jin Kim, Ji-Young Song, Kyung Soo Jung, Young Kee Shin. PLoS One 2015
52
17

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
8

Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue.
Danielle Mercatante Carrick, Michele G Mehaffey, Michael C Sachs, Sean Altekruse, Corinne Camalier, Rodrigo Chuaqui, Wendy Cozen, Biswajit Das, Brenda Y Hernandez, Chih-Jian Lih,[...]. PLoS One 2015
56
14

Detection of circulating tumor DNA in early- and late-stage human malignancies.
Chetan Bettegowda, Mark Sausen, Rebecca J Leary, Isaac Kinde, Yuxuan Wang, Nishant Agrawal, Bjarne R Bartlett, Hao Wang, Brandon Luber, Rhoda M Alani,[...]. Sci Transl Med 2014
8

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden.
Zachary R Chalmers, Caitlin F Connelly, David Fabrizio, Laurie Gay, Siraj M Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki,[...]. Genome Med 2017
8

The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine.
Andrea Garofalo, Lynette Sholl, Brendan Reardon, Amaro Taylor-Weiner, Ali Amin-Mansour, Diana Miao, David Liu, Nelly Oliver, Laura MacConaill, Matthew Ducar,[...]. Genome Med 2016
99
8

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
8


PD-1 Blockade in Tumors with Mismatch-Repair Deficiency.
Dung T Le, Jennifer N Uram, Hao Wang, Bjarne R Bartlett, Holly Kemberling, Aleksandra D Eyring, Andrew D Skora, Brandon S Luber, Nilofer S Azad, Dan Laheru,[...]. N Engl J Med 2015
7

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
7

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
6

Detection and localization of surgically resectable cancers with a multi-analyte blood test.
Joshua D Cohen, Lu Li, Yuxuan Wang, Christopher Thoburn, Bahman Afsari, Ludmila Danilova, Christopher Douville, Ammar A Javed, Fay Wong, Austin Mattox,[...]. Science 2018
853
6

Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS): Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE) Samples.
Gladys Arreaza, Ping Qiu, Ling Pang, Andrew Albright, Lewis Z Hong, Matthew J Marton, Diane Levitan. Int J Mol Sci 2016
30
20

Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens.
David H Spencer, Jennifer K Sehn, Haley J Abel, Mark A Watson, John D Pfeifer, Eric J Duncavage. J Mol Diagn 2013
109
6

Cytosine deamination is a major cause of baseline noise in next-generation sequencing.
Guoli Chen, Stacy Mosier, Christopher D Gocke, Ming-Tseh Lin, James R Eshleman. Mol Diagn Ther 2014
69
8


Detection and quantification of rare mutations with massively parallel sequencing.
Isaac Kinde, Jian Wu, Nick Papadopoulos, Kenneth W Kinzler, Bert Vogelstein. Proc Natl Acad Sci U S A 2011
667
6

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage.
Aaron M Newman, Scott V Bratman, Jacqueline To, Jacob F Wynne, Neville C W Eclov, Leslie A Modlin, Chih Long Liu, Joel W Neal, Heather A Wakelee, Robert E Merritt,[...]. Nat Med 2014
6

Detection of ultra-rare mutations by next-generation sequencing.
Michael W Schmitt, Scott R Kennedy, Jesse J Salk, Edward J Fox, Joseph B Hiatt, Lawrence A Loeb. Proc Natl Acad Sci U S A 2012
515
6

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Daniel C Koboldt, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, Richard K Wilson. Genome Res 2012
6


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
6

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.
Sarah Munchel, Yen Hoang, Yue Zhao, Joseph Cottrell, Brandy Klotzle, Andrew K Godwin, Devin Koestler, Peter Beyerlein, Jian-Bing Fan, Marina Bibikova,[...]. Oncotarget 2015
42
14

Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples.
Simon Haile, Richard D Corbett, Steve Bilobram, Morgan H Bye, Heather Kirk, Pawan Pandoh, Eva Trinh, Tina MacLeod, Helen McDonald, Miruna Bala,[...]. Nucleic Acids Res 2019
13
46

Tumor mutational load predicts survival after immunotherapy across multiple cancer types.
Robert M Samstein, Chung-Han Lee, Alexander N Shoushtari, Matthew D Hellmann, Ronglai Shen, Yelena Y Janjigian, David A Barron, Ahmet Zehir, Emmet J Jordan, Antonio Omuro,[...]. Nat Genet 2019
864
6



Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.
Ahmet Zehir, Ryma Benayed, Ronak H Shah, Aijazuddin Syed, Sumit Middha, Hyunjae R Kim, Preethi Srinivasan, Jianjiong Gao, Debyani Chakravarty, Sean M Devlin,[...]. Nat Med 2017
5

A straightforward assay to evaluate DNA integrity and optimize next-generation sequencing for clinical diagnosis in oncology.
Fabiana Bettoni, Fernanda Christtanini Koyama, Paola de Avelar Carpinetti, Pedro Alexandre Favoretto Galante, Anamaria Aranha Camargo, Paula Fontes Asprino. Exp Mol Pathol 2017
8
62

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
5

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
Garrett M Frampton, Alex Fichtenholtz, Geoff A Otto, Kai Wang, Sean R Downing, Jie He, Michael Schnall-Levin, Jared White, Eric M Sanford, Peter An,[...]. Nat Biotechnol 2013
5

Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden.
Matthew D Hellmann, Tudor-Eliade Ciuleanu, Adam Pluzanski, Jong Seok Lee, Gregory A Otterson, Clarisse Audigier-Valette, Elisa Minenza, Helena Linardou, Sjaak Burgers, Pamela Salman,[...]. N Engl J Med 2018
5

DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification.
Lixin Chen, Pingfang Liu, Thomas C Evans, Laurence M Ettwiller. Science 2017
113
5

Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues.
Burcu Sengüven, Emre Baris, Tulin Oygur, Mehmet Berktas. Int J Med Sci 2014
52
9

Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis.
Michal R Schweiger, Martin Kerick, Bernd Timmermann, Marcus W Albrecht, Tatjana Borodina, Dmitri Parkhomchuk, Kurt Zatloukal, Hans Lehrach. PLoS One 2009
126
5

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
5

DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks.
Alice Guyard, Alice Boyez, Anaïs Pujals, Cyrielle Robe, Jeanne Tran Van Nhieu, Yves Allory, Julien Moroch, Odette Georges, Jean-Christophe Fournet, Elie-Serge Zafrani,[...]. Virchows Arch 2017
34
14


Tumor Mutational Burden and Response Rate to PD-1 Inhibition.
Mark Yarchoan, Alexander Hopkins, Elizabeth M Jaffee. N Engl J Med 2017
944
5

Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses.
Natalie Ludyga, Barbara Grünwald, Omid Azimzadeh, Sonja Englert, Heinz Höfler, Soile Tapio, Michaela Aubele. Virchows Arch 2012
104
5


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.