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
Times Cited: 161
Times Cited
Times Co-cited
Similarity
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
Wei Gu, Xianding Deng, Marco Lee, Yasemin D Sucu, Shaun Arevalo, Doug Stryke, Scot Federman, Allan Gopez, Kevin Reyes, Kelsey Zorn,[...]. Nat Med 2021
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
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
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
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
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
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
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
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
16
Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.
Wei Gu, Steve Miller, Charles Y Chiu. Annu Rev Pathol 2019
Wei Gu, Steve Miller, Charles Y Chiu. Annu Rev Pathol 2019
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
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
15
Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
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
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
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
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
12
Centrifuge: rapid and sensitive classification of metagenomic sequences.
Daehwan Kim, Li Song, Florian P Breitwieser, Steven L Salzberg. Genome Res 2016
Daehwan Kim, Li Song, Florian P Breitwieser, Steven L Salzberg. Genome Res 2016
12
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
Robert Schlaberg, Charles Y Chiu, Steve Miller, Gary W Procop, George Weinstock. Arch Pathol Lab Med 2017
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
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
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
Sam Kovaka, Yunfan Fan, Bohan Ni, Winston Timp, Michael C Schatz. Nat Biotechnol 2021
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
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
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
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
Alexander Payne, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat J Debebe, Matthew Loose. Nat Biotechnol 2021
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
Franka J Rang, Wigard P Kloosterman, Jeroen de Ridder. Genome Biol 2018
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
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
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
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
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
10
Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases.
Patricia J Simner, Steven Miller, Karen C Carroll. Clin Infect Dis 2018
Patricia J Simner, Steven Miller, Karen C Carroll. Clin Infect Dis 2018
9
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
Clarisse A Marotz, Jon G Sanders, Cristal Zuniga, Livia S Zaramela, Rob Knight, Karsten Zengler. Microbiome 2018
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
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
9
A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
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
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
Arne M Taxt, Ekaterina Avershina, Stephan A Frye, Umaer Naseer, Rafi Ahmad. Sci Rep 2020
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
Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, Nicola Segata. Nat Methods 2015
8
Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
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
Philip M Ashton, Satheesh Nair, Tim Dallman, Salvatore Rubino, Wolfgang Rabsch, Solomon Mwaigwisya, John Wain, Justin O'Grady. Nat Biotechnol 2015
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
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
14
Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
8
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
Qing Miao, Yuyan Ma, Qingqing Wang, Jue Pan, Yao Zhang, Wenting Jin, Yumeng Yao, Yi Su, Yingnan Huang, Mengran Wang,[...]. Clin Infect Dis 2018
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
Mohammad R Hasan, Arun Rawat, Patrick Tang, Puthen V Jithesh, Eva Thomas, Rusung Tan, Peter Tilley. J Clin Microbiol 2016
8
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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
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
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
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
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
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
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
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
Libing Yang, Ghady Haidar, Haris Zia, Rachel Nettles, Shulin Qin, Xiaohong Wang, Faraaz Shah, Sarah F Rapport, Themoula Charalampous, Barbara Methé,[...]. Respir Res 2019
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
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
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
Etienne Ruppé, Vladimir Lazarevic, Myriam Girard, William Mouton, Tristan Ferry, Frédéric Laurent, Jacques Schrenzel. Sci Rep 2017
14
Three decades of nanopore sequencing.
David Deamer, Mark Akeson, Daniel Branton. Nat Biotechnol 2016
David Deamer, Mark Akeson, Daniel Branton. Nat Biotechnol 2016
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
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
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
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
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
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
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.