A citation-based method for searching scientific literature

Rick Kamps, Rita D Brandão, Bianca J van den Bosch, Aimee D C Paulussen, Sofia Xanthoulea, Marinus J Blok, Andrea Romano. Int J Mol Sci 2017
Times Cited: 181







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



Times Cited
  Times     Co-cited
Similarity


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
15

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
7

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
7

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
6

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
5

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
5

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.
Marilyn M Li, Michael Datto, Eric J Duncavage, Shashikant Kulkarni, Neal I Lindeman, Somak Roy, Apostolia M Tsimberidou, Cindy L Vnencak-Jones, Daynna J Wolff, Anas Younes,[...]. J Mol Diagn 2017
590
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

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
5


KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
4

Next-generation sequencing: advances and applications in cancer diagnosis.
Simona Serratì, Simona De Summa, Brunella Pilato, Daniela Petriella, Rosanna Lacalamita, Stefania Tommasi, Rosamaria Pinto. Onco Targets Ther 2016
76
5

Gefitinib or carboplatin-paclitaxel in pulmonary adenocarcinoma.
Tony S Mok, Yi-Long Wu, Sumitra Thongprasert, Chih-Hsin Yang, Da-Tong Chu, Nagahiro Saijo, Patrapim Sunpaweravong, Baohui Han, Benjamin Margono, Yukito Ichinose,[...]. N Engl J Med 2009
4

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
4

OncoKB: A Precision Oncology Knowledge Base.
Debyani Chakravarty, Jianjiong Gao, Sarah M Phillips, Ritika Kundra, Hongxin Zhang, Jiaojiao Wang, Julia E Rudolph, Rona Yaeger, Tara Soumerai, Moriah H Nissan,[...]. JCO Precis Oncol 2017
720
4

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology.
Donavan T Cheng, Talia N Mitchell, Ahmet Zehir, Ronak H Shah, Ryma Benayed, Aijazuddin Syed, Raghu Chandramohan, Zhen Yu Liu, Helen H Won, Sasinya N Scott,[...]. J Mol Diagn 2015
948
4

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.
Malachi Griffith, Nicholas C Spies, Kilannin Krysiak, Joshua F McMichael, Adam C Coffman, Arpad M Danos, Benjamin J Ainscough, Cody A Ramirez, Damian T Rieke, Lynzey Kujan,[...]. Nat Genet 2017
227
4

A survey of best practices for RNA-seq data analysis.
Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J Gaffney, Laura L Elo, Xuegong Zhang,[...]. Genome Biol 2016
937
4

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
4

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
4

The hallmarks of cancer.
D Hanahan, R A Weinberg. Cell 2000
4


Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer.
Manabu Soda, Young Lim Choi, Munehiro Enomoto, Shuji Takada, Yoshihiro Yamashita, Shunpei Ishikawa, Shin-ichiro Fujiwara, Hideki Watanabe, Kentaro Kurashina, Hisashi Hatanaka,[...]. Nature 2007
4

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
4

Cancer statistics, 2020.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2020
4

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
3

Prevalence and detection of low-allele-fraction variants in clinical cancer samples.
Hyun-Tae Shin, Yoon-La Choi, Jae Won Yun, Nayoung K D Kim, Sook-Young Kim, Hyo Jeong Jeon, Jae-Yong Nam, Chung Lee, Daeun Ryu, Sang Cheol Kim,[...]. Nat Commun 2017
82
3

Mutational landscape and significance across 12 major cancer types.
Cyriac Kandoth, Michael D McLellan, Fabio Vandin, Kai Ye, Beifang Niu, Charles Lu, Mingchao Xie, Qunyuan Zhang, Joshua F McMichael, Matthew A Wyczalkowski,[...]. Nature 2013
3

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
3

Hereditary breast and ovarian cancer: new genes in confined pathways.
Finn Cilius Nielsen, Thomas van Overeem Hansen, Claus Storgaard Sørensen. Nat Rev Cancer 2016
186
3


Next generation sequencing-based gene panel tests for the management of solid tumors.
Masayuki Nagahashi, Yoshifumi Shimada, Hiroshi Ichikawa, Hitoshi Kameyama, Kazuaki Takabe, Shujiro Okuda, Toshifumi Wakai. Cancer Sci 2019
37
8

Erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non-small-cell lung cancer (EURTAC): a multicentre, open-label, randomised phase 3 trial.
Rafael Rosell, Enric Carcereny, Radj Gervais, Alain Vergnenegre, Bartomeu Massuti, Enriqueta Felip, Ramon Palmero, Ramon Garcia-Gomez, Cinta Pallares, Jose Miguel Sanchez,[...]. Lancet Oncol 2012
3


TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg. Genome Biol 2013
3

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.
Eric Talevich, A Hunter Shain, Thomas Botton, Boris C Bastian. PLoS Comput Biol 2016
546
3

Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests.
Jihun Kim, Woong-Yang Park, Nayoung K D Kim, Se Jin Jang, Sung-Min Chun, Chang-Ohk Sung, Jene Choi, Young-Hyeh Ko, Yoon-La Choi, Hyo Sup Shim,[...]. J Pathol Transl Med 2017
20
15

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
3

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
3

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.
Brian J Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet, Aviv Regev. Genome Biol 2019
124
3

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
3

Improved survival with vemurafenib in melanoma with BRAF V600E mutation.
Paul B Chapman, Axel Hauschild, Caroline Robert, John B Haanen, Paolo Ascierto, James Larkin, Reinhard Dummer, Claus Garbe, Alessandro Testori, Michele Maio,[...]. N Engl J Med 2011
3

Review of Clinical Next-Generation Sequencing.
Sophia Yohe, Bharat Thyagarajan. Arch Pathol Lab Med 2017
111
3

The current state of molecular testing in the treatment of patients with solid tumors, 2019.
Wafik S El-Deiry, Richard M Goldberg, Heinz-Josef Lenz, Anthony F Shields, Geoffrey T Gibney, Antoinette R Tan, Jubilee Brown, Burton Eisenberg, Elisabeth I Heath, Surasak Phuphanich,[...]. CA Cancer J Clin 2019
85
3

Cancer Statistics, 2017.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2017
3

RNA sequencing: the teenage years.
Rory Stark, Marta Grzelak, James Hadfield. Nat Rev Genet 2019
326
3

RNA-Seq differential expression analysis: An extended review and a software tool.
Juliana Costa-Silva, Douglas Domingues, Fabricio Martins Lopes. PLoS One 2017
178
3

RNA-Seq methods for transcriptome analysis.
Radmila Hrdlickova, Masoud Toloue, Bin Tian. Wiley Interdiscip Rev RNA 2017
206
3

Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib.
Thomas J Lynch, Daphne W Bell, Raffaella Sordella, Sarada Gurubhagavatula, Ross A Okimoto, Brian W Brannigan, Patricia L Harris, Sara M Haserlat, Jeffrey G Supko, Frank G Haluska,[...]. N Engl J Med 2004
3

Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial.
Jordi Rodon, Jean-Charles Soria, Raanan Berger, Wilson H Miller, Eitan Rubin, Aleksandra Kugel, Apostolia Tsimberidou, Pierre Saintigny, Aliza Ackerstein, Irene Braña,[...]. Nat Med 2019
160
3


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.