A citation-based method for searching scientific literature

Amy S Gargis, Lisa Kalman, Meredith W Berry, David P Bick, David P Dimmock, Tina Hambuch, Fei Lu, Elaine Lyon, Karl V Voelkerding, Barbara A Zehnbauer, Richa Agarwala, Sarah F Bennett, Bin Chen, Ephrem L H Chin, John G Compton, Soma Das, Daniel H Farkas, Matthew J Ferber, Birgit H Funke, Manohar R Furtado, Lilia M Ganova-Raeva, Ute Geigenmüller, Sandra J Gunselman, Madhuri R Hegde, Philip L F Johnson, Andrew Kasarskis, Shashikant Kulkarni, Thomas Lenk, C S Jonathan Liu, Megan Manion, Teri A Manolio, Elaine R Mardis, Jason D Merker, Mangalathu S Rajeevan, Martin G Reese, Heidi L Rehm, Birgitte B Simen, Joanne M Yeakley, Justin M Zook, Ira M Lubin. Nat Biotechnol 2012
Times Cited: 295







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



Times Cited
  Times     Co-cited
Similarity


ACMG clinical laboratory standards for next-generation sequencing.
Heidi L Rehm, Sherri J Bale, Pinar Bayrak-Toydemir, Jonathan S Berg, Kerry K Brown, Joshua L Deignan, Michael J Friez, Birgit H Funke, Madhuri R Hegde, Elaine Lyon. Genet Med 2013
508
38

College of American Pathologists' laboratory standards for next-generation sequencing clinical tests.
Nazneen Aziz, Qin Zhao, Lynn Bry, Denise K Driscoll, Birgit Funke, Jane S Gibson, Wayne W Grody, Madhuri R Hegde, Gerald A Hoeltge, Debra G B Leonard,[...]. Arch Pathol Lab Med 2015
184
26

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
24

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
210
16

Guidelines for diagnostic next-generation sequencing.
Gert Matthijs, Erika Souche, Mariëlle Alders, Anniek Corveleyn, Sebastian Eck, Ilse Feenstra, Valérie Race, Erik Sistermans, Marc Sturm, Marjan Weiss,[...]. Eur J Hum Genet 2016
212
13

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
13

Good laboratory practice for clinical next-generation sequencing informatics pipelines.
Amy S Gargis, Lisa Kalman, David P Bick, Cristina da Silva, David P Dimmock, Birgit H Funke, Sivakumar Gowrisankar, Madhuri R Hegde, Shashikant Kulkarni, Christopher E Mason,[...]. Nat Biotechnol 2015
80
16

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
Michael A Quail, Miriam Smith, Paul Coupland, Thomas D Otto, Simon R Harris, Thomas R Connor, Anna Bertoni, Harold P Swerdlow, Yong Gu. BMC Genomics 2012
971
11

Standardization and quality management in next-generation sequencing.
Christoph Endrullat, Jörn Glökler, Philipp Franke, Marcus Frohme. Appl Transl Genom 2016
80
13

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
468
11

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.
Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S Kip, Eric W Klee, Stephen E Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L Temple-Smolkin, Karl V Voelkerding,[...]. J Mol Diagn 2018
127
11

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.
Justin M Zook, Brad Chapman, Jason Wang, David Mittelman, Oliver Hofmann, Winston Hide, Marc Salit. Nat Biotechnol 2014
400
10

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
10

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
808
10

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
10

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
Robert C Green, Jonathan S Berg, Wayne W Grody, Sarah S Kalia, Bruce R Korf, Christa L Martin, Amy L McGuire, Robert L Nussbaum, Julianne M O'Daniel, Kelly E Ormond,[...]. Genet Med 2013
9


Reference standards for next-generation sequencing.
Simon A Hardwick, Ira W Deveson, Tim R Mercer. Nat Rev Genet 2017
88
10

Next-Generation Sequencing in Clinical Molecular Diagnostics of Cancer: Advantages and Challenges.
Rajyalakshmi Luthra, Hui Chen, Sinchita Roy-Chowdhuri, R Rajesh Singh. Cancers (Basel) 2015
72
11

Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Justin M Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E Mason, Noah Alexander,[...]. Sci Data 2016
221
8

Validation of a next-generation sequencing assay for clinical molecular oncology.
Catherine E Cottrell, Hussam Al-Kateb, Andrew J Bredemeyer, Eric J Duncavage, David H Spencer, Haley J Abel, Christina M Lockwood, Ian S Hagemann, Stephanie M O'Guin, Lauren C Burcea,[...]. J Mol Diagn 2014
131
8

Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL.
Zandra C Deans, Jose Luis Costa, Ian Cree, Els Dequeker, Anders Edsjö, Shirley Henderson, Michael Hummel, Marjolijn Jl Ligtenberg, Marco Loddo, Jose Carlos Machado,[...]. Virchows Arch 2017
48
16

Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology.
Iris Schrijver, Nazneen Aziz, Daniel H Farkas, Manohar Furtado, Andrea Ferreira Gonzalez, Timothy C Greiner, Wayne W Grody, Tina Hambuch, Lisa Kalman, Jeffrey A Kant,[...]. J Mol Diagn 2012
98
7

A standardized framework for the validation and verification of clinical molecular genetic tests.
Christopher J Mattocks, Michael A Morris, Gert Matthijs, Elfriede Swinnen, Anniek Corveleyn, Els Dequeker, Clemens R Müller, Victoria Pratt, Andrew Wallace. Eur J Hum Genet 2010
104
7

Sequencing technologies - the next generation.
Michael L Metzker. Nat Rev Genet 2010
7


Analytical Validation and Application of a Targeted Next-Generation Sequencing Mutation-Detection Assay for Use in Treatment Assignment in the NCI-MPACT Trial.
Chih-Jian Lih, David J Sims, Robin D Harrington, Eric C Polley, Yingdong Zhao, Michele G Mehaffey, Thomas D Forbes, Biswajit Das, William D Walsh, Vivekananda Datta,[...]. J Mol Diagn 2016
31
19

A map of human genome variation from population-scale sequencing.
Gonçalo R Abecasis, David Altshuler, Adam Auton, Lisa D Brooks, Richard M Durbin, Richard A Gibbs, Matt E Hurles, Gil A McVean. Nature 2010
6

ClinVar: public archive of interpretations of clinically relevant variants.
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Jeffrey Hoover,[...]. Nucleic Acids Res 2016
6

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
330
6

Guidance for laboratories performing molecular pathology for cancer patients.
Ian A Cree, Zandra Deans, Marjolijn J L Ligtenberg, Nicola Normanno, Anders Edsjö, Etienne Rouleau, Francesc Solé, Erik Thunnissen, Wim Timens, Ed Schuuring,[...]. J Clin Pathol 2014
95
6

Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays.
David J Sims, Robin D Harrington, Eric C Polley, Thomas D Forbes, Michele G Mehaffey, Paul M McGregor, Corinne E Camalier, Kneshay N Harper, Courtney H Bouk, Biswajit Das,[...]. J Mol Diagn 2016
21
28

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
6

Performance comparison of benchtop high-throughput sequencing platforms.
Nicholas J Loman, Raju V Misra, Timothy J Dallman, Chrystala Constantinidou, Saheer E Gharbia, John Wain, Mark J Pallen. Nat Biotechnol 2012
757
6

Clinical validation of a next-generation sequencing screen for mutational hotspots in 46 cancer-related genes.
Rajesh R Singh, Keyur P Patel, Mark J Routbort, Neelima G Reddy, Bedia A Barkoh, Brian Handal, Rashmi Kanagal-Shamanna, Wesley O Greaves, L Jeffrey Medeiros, Kenneth D Aldape,[...]. J Mol Diagn 2013
237
6

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
6

Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants.
Tyler F Beck, James C Mullikin, Leslie G Biesecker. Clin Chem 2016
83
7

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
Marco Gerlinger, Andrew J Rowan, Stuart Horswell, M Math, James Larkin, David Endesfelder, Eva Gronroos, Pierre Martinez, Nicholas Matthews, Aengus Stewart,[...]. N Engl J Med 2012
6

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
Geraldine A Van der Auwera, Mauricio O Carneiro, Christopher Hartl, Ryan Poplin, Guillermo Del Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault,[...]. Curr Protoc Bioinformatics 2013
6

Analysis of protein-coding genetic variation in 60,706 humans.
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings,[...]. Nature 2016
6

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
6

Synthetic Circulating Cell-free DNA as Quality Control Materials for Somatic Mutation Detection in Liquid Biopsy for Cancer.
Rui Zhang, Rongxue Peng, Ziyang Li, Peng Gao, Shiyu Jia, Xin Yang, Jiansheng Ding, Yanxi Han, Jiehong Xie, Jinming Li. Clin Chem 2017
23
26

A general framework for estimating the relative pathogenicity of human genetic variants.
Martin Kircher, Daniela M Witten, Preti Jain, Brian J O'Roak, Gregory M Cooper, Jay Shendure. Nat Genet 2014
5

Clinical whole-exome sequencing for the diagnosis of mendelian disorders.
Yaping Yang, Donna M Muzny, Jeffrey G Reid, Matthew N Bainbridge, Alecia Willis, Patricia A Ward, Alicia Braxton, Joke Beuten, Fan Xia, Zhiyv Niu,[...]. N Engl J Med 2013
5

Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis.
Clare M McCourt, Darragh G McArt, Ken Mills, Mark A Catherwood, Perry Maxwell, David J Waugh, Peter Hamilton, Joe M O'Sullivan, Manuel Salto-Tellez. PLoS One 2013
72
6

Representing genetic variation with synthetic DNA standards.
Ira W Deveson, Wendy Y Chen, Ted Wong, Simon A Hardwick, Stacey B Andersen, Lars K Nielsen, John S Mattick, Tim R Mercer. Nat Methods 2016
17
29

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

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
5

Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics.
Sarah S Kalia, Kathy Adelman, Sherri J Bale, Wendy K Chung, Christine Eng, James P Evans, Gail E Herman, Sophia B Hufnagel, Teri E Klein, Bruce R Korf,[...]. Genet Med 2017
740
5

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
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.