A citation-based method for searching scientific literature

Themoula Charalampous, Gemma L Kay, Hollian Richardson, Alp Aydin, Rossella Baldan, Christopher Jeanes, Duncan Rae, Sara Grundy, Daniel J Turner, John Wain, Richard M Leggett, David M Livermore, Justin O'Grady. Nat Biotechnol 2019
Times Cited: 161







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



Times Cited
  Times     Co-cited
Similarity


Clinical metagenomics.
Charles Y Chiu, Steven A Miller. Nat Rev Genet 2019
290
23


Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
Wei Gu, Xianding Deng, Marco Lee, Yasemin D Sucu, Shaun Arevalo, Doug Stryke, Scot Federman, Allan Gopez, Kevin Reyes, Kelsey Zorn,[...]. Nat Med 2021
79
27

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing.
K Schmidt, S Mwaigwisya, L C Crossman, M Doumith, D Munroe, C Pires, A M Khan, N Woodford, N J Saunders, J Wain,[...]. J Antimicrob Chemother 2017
152
19

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
297
18

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
157
18

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
649
16

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.
Wei Gu, Steve Miller, Charles Y Chiu. Annu Rev Pathol 2019
284
15

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.
Alexander L Greninger, Samia N Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, Jerome Bouquet, Sneha Somasekar, Jeffrey M Linnen,[...]. Genome Med 2015
267
15

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
14

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices.
Nicholas D Sanderson, Teresa L Street, Dona Foster, Jeremy Swann, Bridget L Atkins, Andrew J Brent, Martin A McNally, Sarah Oakley, Adrian Taylor, Tim E A Peto,[...]. BMC Genomics 2018
62
22

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
235
12

Centrifuge: rapid and sensitive classification of metagenomic sequences.
Daehwan Kim, Li Song, Florian P Breitwieser, Steven L Salzberg. Genome Res 2016
429
12

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
11

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
185
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
444
11

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.
Sam Kovaka, Yunfan Fan, Bohan Ni, Winston Timp, Michael C Schatz. Nat Biotechnol 2021
44
25

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
11

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler,[...]. Nat Protoc 2017
434
11

Readfish enables targeted nanopore sequencing of gigabase-sized genomes.
Alexander Payne, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat J Debebe, Matthew Loose. Nat Biotechnol 2021
41
26

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.
Franka J Rang, Wigard P Kloosterman, Jeroen de Ridder. Genome Biol 2018
213
10

Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens.
Richard M Leggett, Cristina Alcon-Giner, Darren Heavens, Shabhonam Caim, Thomas C Brook, Magdalena Kujawska, Samuel Martin, Ned Peel, Holly Acford-Palmer, Lesley Hoyles,[...]. Nat Microbiol 2020
46
21

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
9

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
90
10


Improving saliva shotgun metagenomics by chemical host DNA depletion.
Clarisse A Marotz, Jon G Sanders, Cristal Zuniga, Livia S Zaramela, Rob Knight, Karsten Zengler. Microbiome 2018
98
9

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
92
9

A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
595
9

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
9

Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing.
Arne M Taxt, Ekaterina Avershina, Stephan A Frye, Umaer Naseer, Rafi Ahmad. Sci Rep 2020
26
34

MetaPhlAn2 for enhanced metagenomic taxonomic profiling.
Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, Nicola Segata. Nat Methods 2015
934
8

Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
797
8

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island.
Philip M Ashton, Satheesh Nair, Tim Dallman, Salvatore Rubino, Wolfgang Rabsch, Solomon Mwaigwisya, John Wain, Justin O'Grady. Nat Biotechnol 2015
246
8

Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples.
Kuiama Lewandowski, Yifei Xu, Steven T Pullan, Sheila F Lumley, Dona Foster, Nicholas Sanderson, Alison Vaughan, Marcus Morgan, Nicole Bright, James Kavanagh,[...]. J Clin Microbiol 2019
57
14


Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice.
Qing Miao, Yuyan Ma, Qingqing Wang, Jue Pan, Yao Zhang, Wenting Jin, Yumeng Yao, Yi Su, Yingnan Huang, Mengran Wang,[...]. Clin Infect Dis 2018
166
8

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing.
Mohammad R Hasan, Arun Rawat, Patrick Tang, Puthen V Jithesh, Eva Thomas, Rusung Tan, Peter Tilley. J Clin Microbiol 2016
90
8

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
7

metaSPAdes: a new versatile metagenomic assembler.
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A Pevzner. Genome Res 2017
7

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
114
7

Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing.
Morgan I Ivy, Matthew J Thoendel, Patricio R Jeraldo, Kerryl E Greenwood-Quaintance, Arlen D Hanssen, Matthew P Abdel, Nicholas Chia, Janet Z Yao, Aaron J Tande, Jayawant N Mandrekar,[...]. J Clin Microbiol 2018
68
10

Nanopore sequencing and assembly of a human genome with ultra-long reads.
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes,[...]. Nat Biotechnol 2018
728
7

Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study.
Libing Yang, Ghady Haidar, Haris Zia, Rachel Nettles, Shulin Qin, Xiaohong Wang, Faraaz Shah, Sarah F Rapport, Themoula Charalampous, Barbara Methé,[...]. Respir Res 2019
24
29

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
482
7

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
47
14

Three decades of nanopore sequencing.
David Deamer, Mark Akeson, Daniel Branton. Nat Biotechnol 2016
363
7

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes.
Denis Bertrand, Jim Shaw, Manesh Kalathiyappan, Amanda Hui Qi Ng, M Senthil Kumar, Chenhao Li, Mirta Dvornicic, Janja Paliska Soldo, Jia Yu Koh, Chengxuan Tong,[...]. Nat Biotechnol 2019
75
8

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
6

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
6

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.
Charles Langelier, Katrina L Kalantar, Farzad Moazed, Michael R Wilson, Emily D Crawford, Thomas Deiss, Annika Belzer, Samaneh Bolourchi, Saharai Caldera, Monica Fung,[...]. Proc Natl Acad Sci U S A 2018
123
6


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.