A citation-based method for searching scientific literature

Amy S Gargis, Lisa Kalman, Ira M Lubin. J Clin Microbiol 2016
Times Cited: 53







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



Times Cited
  Times     Co-cited
Similarity


Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
20

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities.
Jacob Moran-Gilad, Vitali Sintchenko, Susanne Karlsmose Pedersen, William J Wolfgang, James Pettengill, Errol Strain, Rene S Hendriksen. BMC Infect Dis 2015
35
28

Application of next generation sequencing in clinical microbiology and infection prevention.
Ruud H Deurenberg, Erik Bathoorn, Monika A Chlebowicz, Natacha Couto, Mithila Ferdous, Silvia García-Cobos, Anna M D Kooistra-Smid, Erwin C Raangs, Sigrid Rosema, Alida C M Veloo,[...]. J Biotechnol 2017
159
18

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.
Varvara K Kozyreva, Chau-Linda Truong, Alexander L Greninger, John Crandall, Rituparna Mukhopadhyay, Vishnu Chaturvedi. J Clin Microbiol 2017
40
25

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
16

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
295
16


Next-Generation Sequencing for Infectious Disease Diagnosis and Management: A Report of the Association for Molecular Pathology.
Martina I Lefterova, Carlos J Suarez, Niaz Banaei, Benjamin A Pinsky. J Mol Diagn 2015
77
15

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
15

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
15

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
15

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
Susannah J Salter, Michael J Cox, Elena M Turek, Szymon T Calus, William O Cookson, Miriam F Moffatt, Paul Turner, Julian Parkhill, Nicholas J Loman, Alan W Walker. BMC Biol 2014
15

Real-time, portable genome sequencing for Ebola surveillance.
Joshua Quick, Nicholas J Loman, Sophie Duraffour, Jared T Simpson, Ettore Severi, Lauren Cowley, Joseph Akoi Bore, Raymond Koundouno, Gytis Dudas, Amy Mikhail,[...]. Nature 2016
538
15

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
129
15

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
13

Transforming clinical microbiology with bacterial genome sequencing.
Xavier Didelot, Rory Bowden, Daniel J Wilson, Tim E A Peto, Derrick W Crook. Nat Rev Genet 2012
393
13

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.
Phelim Bradley, N Claire Gordon, Timothy M Walker, Laura Dunn, Simon Heys, Bill Huang, Sarah Earle, Louise J Pankhurst, Luke Anson, Mariateresa de Cesare,[...]. Nat Commun 2015
245
13

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
13

Bioinformatics for clinical next generation sequencing.
Gavin R Oliver, Steven N Hart, Eric W Klee. Clin Chem 2015
49
12

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
11

Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study.
Louise J Pankhurst, Carlos Del Ojo Elias, Antonina A Votintseva, Timothy M Walker, Kevin Cole, Jim Davies, Jilles M Fermont, Deborah M Gascoyne-Binzi, Thomas A Kohl, Clare Kong,[...]. Lancet Respir Med 2016
167
11

Whole genome sequencing in clinical and public health microbiology.
J C Kwong, N McCallum, V Sintchenko, B P Howden. Pathology 2015
129
11

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
11

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.
Claudio U Köser, Matthew T G Holden, Matthew J Ellington, Edward J P Cartwright, Nicholas M Brown, Amanda L Ogilvy-Stuart, Li Yang Hsu, Claire Chewapreecha, Nicholas J Croucher, Simon R Harris,[...]. N Engl J Med 2012
408
11

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
Baofeng Jia, Amogelang R Raphenya, Brian Alcock, Nicholas Waglechner, Peiyao Guo, Kara K Tsang, Briony A Lago, Biren M Dave, Sheldon Pereira, Arjun N Sharma,[...]. Nucleic Acids Res 2017
834
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

Reference standards for next-generation sequencing.
Simon A Hardwick, Ira W Deveson, Tim R Mercer. Nat Rev Genet 2017
88
11

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
349
11

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
11

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
9

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.
Simon R Harris, Edward J P Cartwright, M Estée Török, Matthew T G Holden, Nicholas M Brown, Amanda L Ogilvy-Stuart, Matthew J Ellington, Michael A Quail, Stephen D Bentley, Julian Parkhill,[...]. Lancet Infect Dis 2013
324
9

Identification of acquired antimicrobial resistance genes.
Ea Zankari, Henrik Hasman, Salvatore Cosentino, Martin Vestergaard, Simon Rasmussen, Ole Lund, Frank M Aarestrup, Mette Voldby Larsen. J Antimicrob Chemother 2012
9

Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing.
N C Gordon, J R Price, K Cole, R Everitt, M Morgan, J Finney, A M Kearns, B Pichon, B Young, D J Wilson,[...]. J Clin Microbiol 2014
165
9

High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial.
Alexander Mellmann, Paal Skytt Andersen, Stefan Bletz, Alexander W Friedrich, Thomas A Kohl, Berit Lilje, Stefan Niemann, Karola Prior, John W Rossen, Dag Harmsen. J Clin Microbiol 2017
41
12

Standardization and quality management in next-generation sequencing.
Christoph Endrullat, Jörn Glökler, Philipp Franke, Marcus Frohme. Appl Transl Genom 2016
80
9

Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples.
Henrik Hasman, Dhany Saputra, Thomas Sicheritz-Ponten, Ole Lund, Christina Aaby Svendsen, Niels Frimodt-Møller, Frank M Aarestrup. J Clin Microbiol 2014
175
9

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.
Nicholas J Loman, Chrystala Constantinidou, Martin Christner, Holger Rohde, Jacqueline Z-M Chan, Joshua Quick, Jacqueline C Weir, Christopher Quince, Geoffrey P Smith, Jason R Betley,[...]. JAMA 2013
170
9

The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.
M J Ellington, O Ekelund, F M Aarestrup, R Canton, M Doumith, C Giske, H Grundman, H Hasman, M T G Holden, K L Hopkins,[...]. Clin Microbiol Infect 2017
176
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
210
9

Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.
Erin H Graf, Keith E Simmon, Keith D Tardif, Weston Hymas, Steven Flygare, Karen Eilbeck, Mark Yandell, Robert Schlaberg. J Clin Microbiol 2016
81
9

DNA sequencing with chain-terminating inhibitors.
F Sanger, S Nicklen, A R Coulson. Proc Natl Acad Sci U S A 1977
9


Towards a genomics-informed, real-time, global pathogen surveillance system.
Jennifer L Gardy, Nicholas J Loman. Nat Rev Genet 2018
172
9

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.
Steve Miller, Samia N Naccache, Erik Samayoa, Kevin Messacar, Shaun Arevalo, Scot Federman, Doug Stryke, Elizabeth Pham, Becky Fung, William J Bolosky,[...]. Genome Res 2019
85
9

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
7

Comparison of next-generation sequencing systems.
Lin Liu, Yinhu Li, Siliang Li, Ni Hu, Yimin He, Ray Pong, Danni Lin, Lihua Lu, Maggie Law. J Biomed Biotechnol 2012
593
7

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.
Timothy M Walker, Thomas A Kohl, Shaheed V Omar, Jessica Hedge, Carlos Del Ojo Elias, Phelim Bradley, Zamin Iqbal, Silke Feuerriegel, Katherine E Niehaus, Daniel J Wilson,[...]. Lancet Infect Dis 2015
283
7


Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.
Marc W Allard, Errol Strain, David Melka, Kelly Bunning, Steven M Musser, Eric W Brown, Ruth Timme. J Clin Microbiol 2016
144
7


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.