A citation-based method for searching scientific literature

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, Chen Wang, Alexis B Carter. J Mol Diagn 2018
Times Cited: 139







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



Times Cited
  Times     Co-cited
Similarity


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
31

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
29

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
525
23

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
188
19

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
510
19

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
13

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
12

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
12

Reference standards for next-generation sequencing.
Simon A Hardwick, Ira W Deveson, Tim R Mercer. Nat Rev Genet 2017
94
10

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
221
10

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
410
10

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
10

The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
10

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
9

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
81
11

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
783
9

Assuring the quality of next-generation sequencing in clinical laboratory practice.
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,[...]. Nat Biotechnol 2012
308
8

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna,[...]. Nat Genet 2011
8

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants.
Aziz Belkadi, Alexandre Bolze, Yuval Itan, Aurélie Cobat, Quentin B Vincent, Alexander Antipenko, Lei Shang, Bertrand Boisson, Jean-Laurent Casanova, Laurent Abel. Proc Natl Acad Sci U S A 2015
241
8

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
8

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
7

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
7

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
7

Molecular findings among patients referred for clinical whole-exome sequencing.
Yaping Yang, Donna M Muzny, Fan Xia, Zhiyv Niu, Richard Person, Yan Ding, Patricia Ward, Alicia Braxton, Min Wang, Christian Buhay,[...]. JAMA 2014
783
7

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
229
7

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.
Michael A Eberle, Epameinondas Fritzilas, Peter Krusche, Morten Källberg, Benjamin L Moore, Mitchell A Bekritsky, Zamin Iqbal, Han-Yu Chuang, Sean J Humphray, Aaron L Halpern,[...]. Genome Res 2017
149
7

An open resource for accurately benchmarking small variant and reference calls.
Justin M Zook, Jennifer McDaniel, Nathan D Olson, Justin Wagner, Hemang Parikh, Haynes Heaton, Sean A Irvine, Len Trigg, Rebecca Truty, Cory Y McLean,[...]. Nat Biotechnol 2019
62
11


ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
7

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

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
6

Sequencing technologies - the next generation.
Michael L Metzker. Nat Rev Genet 2010
6

Circulating Tumor DNA Analysis in Patients With Cancer: American Society of Clinical Oncology and College of American Pathologists Joint Review.
Jason D Merker, Geoffrey R Oxnard, Carolyn Compton, Maximilian Diehn, Patricia Hurley, Alexander J Lazar, Neal Lindeman, Christina M Lockwood, Alex J Rai, Richard L Schilsky,[...]. J Clin Oncol 2018
339
6

Best practices for benchmarking germline small-variant calls in human genomes.
Peter Krusche, Len Trigg, Paul C Boutros, Christopher E Mason, Francisco M De La Vega, Benjamin L Moore, Mar Gonzalez-Porta, Michael A Eberle, Zivana Tezak, Samir Lababidi,[...]. Nat Biotechnol 2019
59
10

Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants.
Tyler F Beck, James C Mullikin, Leslie G Biesecker. Clin Chem 2016
88
6

Targeted capture and massively parallel sequencing of 12 human exomes.
Sarah B Ng, Emily H Turner, Peggy D Robertson, Steven D Flygare, Abigail W Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E Eichler,[...]. Nature 2009
6

Sequencing depth and coverage: key considerations in genomic analyses.
David Sims, Ian Sudbery, Nicholas E Ilott, Andreas Heger, Chris P Ponting. Nat Rev Genet 2014
611
6

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
6

Genomic Classification and Prognosis in Acute Myeloid Leukemia.
Elli Papaemmanuil, Moritz Gerstung, Lars Bullinger, Verena I Gaidzik, Peter Paschka, Nicola D Roberts, Nicola E Potter, Michael Heuser, Felicitas Thol, Niccolo Bolli,[...]. N Engl J Med 2016
6


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
855
5

A Model Study of In Silico Proficiency Testing for Clinical Next-Generation Sequencing.
Eric J Duncavage, Haley J Abel, Jason D Merker, John B Bodner, Qin Zhao, Karl V Voelkerding, John D Pfeifer. Arch Pathol Lab Med 2016
19
26

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.
Robert Schlaberg, Charles Y Chiu, Steve Miller, Gary W Procop, George Weinstock. Arch Pathol Lab Med 2017
143
5

Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
Michael R Wilson, Samia N Naccache, Erik Samayoa, Mark Biagtan, Hiba Bashir, Guixia Yu, Shahriar M Salamat, Sneha Somasekar, Scot Federman, Steve Miller,[...]. N Engl J Med 2014
369
5

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
110
5

Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory.
Samuel P Strom, Hane Lee, Kingshuk Das, Eric Vilain, Stanley F Nelson, Wayne W Grody, Joshua L Deignan. Genet Med 2014
86
5

Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing.
Diana Mandelker, Ryan J Schmidt, Arunkanth Ankala, Kristin McDonald Gibson, Mark Bowser, Himanshu Sharma, Elizabeth Duffy, Madhuri Hegde, Avni Santani, Matthew Lebo,[...]. Genet Med 2016
68
7

Sanger Confirmation Is Required to Achieve Optimal Sensitivity and Specificity in Next-Generation Sequencing Panel Testing.
Wenbo Mu, Hsiao-Mei Lu, Jefferey Chen, Shuwei Li, Aaron M Elliott. J Mol Diagn 2016
91
5

DNA sequencing with chain-terminating inhibitors.
F Sanger, S Nicklen, A R Coulson. Proc Natl Acad Sci U S A 1977
5

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
52
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.