A citation-based method for searching scientific literature

Tehmina Bharucha, Clarissa Oeser, Francois Balloux, Julianne R Brown, Ellen C Carbo, Andre Charlett, Charles Y Chiu, Eric C J Claas, Marcus C de Goffau, Jutte J C de Vries, Marc Eloit, Susan Hopkins, Jim F Huggett, Duncan MacCannell, Sofia Morfopoulou, Avindra Nath, Denise M O'Sullivan, Lauren B Reoma, Liam P Shaw, Igor Sidorov, Patricia J Simner, Le Van Tan, Emma C Thomson, Lucy van Dorp, Michael R Wilson, Judith Breuer, Nigel Field. Lancet Infect Dis 2020
Times Cited: 5







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



Times Cited
  Times     Co-cited
Similarity


Clinical metagenomics.
Charles Y Chiu, Steven A Miller. Nat Rev Genet 2019
169
40

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
94
40

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.
Michael R Wilson, Hannah A Sample, Kelsey C Zorn, Shaun Arevalo, Guixia Yu, John Neuhaus, Scot Federman, Doug Stryke, Benjamin Briggs, Charles Langelier,[...]. N Engl J Med 2019
184
40

The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease.
Anneloes L van Rijn, Sander van Boheemen, Igor Sidorov, Ellen C Carbo, Nikos Pappas, Hailiang Mei, Mariet Feltkamp, Marianne Aanerud, Per Bakke, Eric C J Claas,[...]. PLoS One 2019
17
40

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
40

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
40

A pneumonia outbreak associated with a new coronavirus of probable bat origin.
Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang,[...]. Nature 2020
20

Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing.
Chao Qi, Peter Hountras, Chiagozie Ononye Pickens, James M Walter, Jacqueline M Kruser, Benjamin D Singer, Patrick Seed, Stefan J Green, Richard G Wunderink. J Med Microbiol 2019
9
20


The Next Pandemic: Prepare for "Disease X".
Kenneth V Iserson. West J Emerg Med 2020
3
33

A novel rhabdovirus associated with acute hemorrhagic fever in central Africa.
Gilda Grard, Joseph N Fair, Deanna Lee, Elizabeth Slikas, Imke Steffen, Jean-Jacques Muyembe, Taylor Sittler, Narayanan Veeraraghavan, J Graham Ruby, Chunlin Wang,[...]. PLoS Pathog 2012
126
20

Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018.
B Bas Oude Munnink, E Münger, D F Nieuwenhuijse, R Kohl, A van der Linden, C M E Schapendonk, H van der Jeugd, M Kik, J M Rijks, C B E M Reusken,[...]. Sci Rep 2020
11
20

Lessons from the Nipah virus outbreak in Malaysia.
Lai-Meng Looi, Kaw-Bing Chua. Malays J Pathol 2007
35
20

Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing.
Samia N Naccache, Karl S Peggs, Frank M Mattes, Rahul Phadke, Jeremy A Garson, Paul Grant, Erik Samayoa, Scot Federman, Steve Miller, Michael P Lunn,[...]. Clin Infect Dis 2015
169
20

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand.
Jemma L Geoghegan, Xiaoyun Ren, Matthew Storey, James Hadfield, Lauren Jelley, Sarah Jefferies, Jill Sherwood, Shevaun Paine, Sue Huang, Jordan Douglas,[...]. Nat Commun 2020
25
20

Tracking COVID-19 with wastewater.
David A Larsen, Krista R Wigginton. Nat Biotechnol 2020
36
20

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.
L E Kafetzopoulou, S T Pullan, P Lemey, M A Suchard, D U Ehichioya, M Pahlmann, A Thielebein, J Hinzmann, L Oestereich, D M Wozniak,[...]. Science 2019
93
20

Sequencing-based methods and resources to study antimicrobial resistance.
Manish Boolchandani, Alaric W D'Souza, Gautam Dantas. Nat Rev Genet 2019
93
20

Global trends in emerging infectious diseases.
Kate E Jones, Nikkita G Patel, Marc A Levy, Adam Storeygard, Deborah Balk, John L Gittleman, Peter Daszak. Nature 2008
20

Diagnostic strategy used to establish etiologies of encephalitis in a prospective cohort of patients in England.
H E Ambrose, J Granerod, J P Clewley, N W S Davies, G Keir, R Cunningham, M Zuckerman, K J Mutton, K N Ward, S Ijaz,[...]. J Clin Microbiol 2011
43
20

The waiting time for inter-country spread of pandemic influenza.
Peter Caley, Niels G Becker, David J Philp. PLoS One 2007
34
20

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
571
20

Towards a genomics-informed, real-time, global pathogen surveillance system.
Jennifer L Gardy, Nicholas J Loman. Nat Rev Genet 2018
187
20

Genomic and epidemiological monitoring of yellow fever virus transmission potential.
N R Faria, M U G Kraemer, S C Hill, J Goes de Jesus, R S Aguiar, F C M Iani, J Xavier, J Quick, L du Plessis, S Dellicour,[...]. Science 2018
126
20

Metagenomic analysis of human diarrhea: viral detection and discovery.
Stacy R Finkbeiner, Adam F Allred, Phillip I Tarr, Eileen J Klein, Carl D Kirkwood, David Wang. PLoS Pathog 2008
230
20

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study.
Luke W Meredith, William L Hamilton, Ben Warne, Charlotte J Houldcroft, Myra Hosmillo, Aminu S Jahun, Martin D Curran, Surendra Parmar, Laura G Caller, Sarah L Caddy,[...]. Lancet Infect Dis 2020
94
20

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.
Roujian Lu, Xiang Zhao, Juan Li, Peihua Niu, Bo Yang, Honglong Wu, Wenling Wang, Hao Song, Baoying Huang, Na Zhu,[...]. Lancet 2020
20

From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics.
Augusto Dulanto Chiang, John P Dekker. J Infect Dis 2020
14
20

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.
Chaolin Huang, Yeming Wang, Xingwang Li, Lili Ren, Jianping Zhao, Yi Hu, Li Zhang, Guohui Fan, Jiuyang Xu, Xiaoying Gu,[...]. Lancet 2020
20

New approaches for metagenome assembly with short reads.
Martin Ayling, Matthew D Clark, Richard M Leggett. Brief Bioinform 2020
36
20

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
371
20

Recombinant origin of the retrovirus XMRV.
Tobias Paprotka, Krista A Delviks-Frankenberry, Oya Cingöz, Anthony Martinez, Hsing-Jien Kung, Clifford G Tepper, Wei-Shau Hu, Matthew J Fivash, John M Coffin, Vinay K Pathak. Science 2011
188
20

The challenge of diagnostic metagenomics.
Alexander L Greninger. Expert Rev Mol Diagn 2018
51
20

The Global Virome Project.
Dennis Carroll, Peter Daszak, Nathan D Wolfe, George F Gao, Carlos M Morel, Subhash Morzaria, Ariel Pablos-Méndez, Oyewale Tomori, Jonna A K Mazet. Science 2018
132
20

Zika virus in the Americas: Early epidemiological and genetic findings.
Nuno Rodrigues Faria, Raimunda do Socorro da Silva Azevedo, Moritz U G Kraemer, Renato Souza, Mariana Sequetin Cunha, Sarah C Hill, Julien Thézé, Michael B Bonsall, Thomas A Bowden, Ilona Rissanen,[...]. Science 2016
621
20

Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology.
Robert Schlaberg, Krista Queen, Keith Simmon, Keith Tardif, Chris Stockmann, Steven Flygare, Brett Kennedy, Karl Voelkerding, Anna Bramley, Jing Zhang,[...]. J Infect Dis 2017
37
20

Clinical metagenomics of bone and joint infections: a proof of concept study.
Etienne Ruppé, Vladimir Lazarevic, Myriam Girard, William Mouton, Tristan Ferry, Frédéric Laurent, Jacques Schrenzel. Sci Rep 2017
35
20

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.
Themoula Charalampous, Gemma L Kay, Hollian Richardson, Alp Aydin, Rossella Baldan, Christopher Jeanes, Duncan Rae, Sara Grundy, Daniel J Turner, John Wain,[...]. Nat Biotechnol 2019
84
20

Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study.
P Parize, E Muth, C Richaud, M Gratigny, B Pilmis, A Lamamy, J-L Mainardi, J Cheval, L de Visser, F Jagorel,[...]. Clin Microbiol Infect 2017
50
20

Noninvasive Diagnosis of Infection Using Plasma Next-Generation Sequencing: A Single-Center Experience.
Jenna Rossoff, Sonali Chaudhury, Maulin Soneji, Sameer J Patel, Soyang Kwon, Amy Armstrong, William J Muller. Open Forum Infect Dis 2019
25
20

Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing.
Ronan M Doyle, Carrie Burgess, Rachel Williams, Rebecca Gorton, Helen Booth, James Brown, Josephine M Bryant, Jackie Chan, Dean Creer, Jolyon Holdstock,[...]. J Clin Microbiol 2018
53
20

Community-acquired pneumonia in children: cell-free plasma sequencing for diagnosis and management.
Lauge Farnaes, Julianne Wilke, Kathleen Ryan Loker, John S Bradley, Christopher R Cannavino, David K Hong, Alice Pong, Jennifer Foley, Nicole G Coufal. Diagn Microbiol Infect Dis 2019
17
20

Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach.
Matthew J Thoendel, Patricio R Jeraldo, Kerryl E Greenwood-Quaintance, Janet Z Yao, Nicholas Chia, Arlen D Hanssen, Matthew P Abdel, Robin Patel. Clin Infect Dis 2018
61
20

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing.
Teresa L Street, Nicholas D Sanderson, Bridget L Atkins, Andrew J Brent, Kevin Cole, Dona Foster, Martin A McNally, Sarah Oakley, Leon Peto, Adrian Taylor,[...]. J Clin Microbiol 2017
77
20

Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease.
Timothy A Blauwkamp, Simone Thair, Michael J Rosen, Lily Blair, Martin S Lindner, Igor D Vilfan, Trupti Kawli, Fred C Christians, Shivkumar Venkatasubrahmanyam, Gregory D Wall,[...]. Nat Microbiol 2019
164
20

Library construction for next-generation sequencing: overviews and challenges.
Steven R Head, H Kiyomi Komori, Sarah A LaMere, Thomas Whisenant, Filip Van Nieuwerburgh, Daniel R Salomon, Phillip Ordoukhanian. Biotechniques 2014
244
20

Cost-effectiveness of blood cultures for adult patients with cellulitis.
B Perl, N P Gottehrer, D Raveh, Y Schlesinger, B Rudensky, A M Yinnon. Clin Infect Dis 1999
113
20

DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing.
Luke W Anson, Kevin Chau, Nicholas Sanderson, Sarah Hoosdally, Phelim Bradley, Zamin Iqbal, Hang Phan, Dona Foster, Sarah Oakley, Marcus Morgan,[...]. J Med Microbiol 2018
10
20

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products.
J Handelsman, M R Rondon, S F Brady, J Clardy, R M Goodman. Chem Biol 1998
692
20

Viral Surveillance in Serum Samples From Patients With Acute Liver Failure By Metagenomic Next-Generation Sequencing.
Sneha Somasekar, Deanna Lee, Jody Rule, Samia N Naccache, Mars Stone, Michael P Busch, Corron Sanders, William M Lee, Charles Y Chiu. Clin Infect Dis 2017
46
20


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.