Real-time, portable genome sequencing for Ebola surveillance

David A. Matthews | Jared T. Simpson | C. V. Williams | Andrew Rambaut | Oumar Faye | Marc Mertens | Abdoulaye Camara | Joshua Quick | Cecelia V. Williams | Gytis Dudas | Nicholas J. Loman | Ousmane Faye | Amadou Alpha Sall | Martin Gabriel | Lauren A. Cowley | Sophie Duraffour | Julian A. Hiscox | Georgios Pollakis | Kilian Stoecker | Miles W. Carroll | N. Loman | J. Quick | O. Faye | J. Simpson | D. Turner | P. Formenty | D. Matthews | A. Rambaut | A. Bello | A. di Caro | M. O’Shea | Abdoulaye Camara | A. M. Johnston | R. Woelfel | M. Carroll | J. Hiscox | J. Boettcher | A. Sall | A. Camara | A. Diarra | J. Gerlach | A. Sachse | B. Diallo | S. Keita | C. Logue | S. Weller | J. Portmann | G. Gutierrez | Martin Gabriel | K. Nebie | G. Dudas | Marianne Gérard | O. Faye | N. Magassouba | E. Hutley | J. Hinzmann | K. Stoecker | L. Koivogui | E. Fleischmann | S. Duraffour | S. Gunther | Eeva Kuisma | E. Severi | J. A. Bore | Raymond Koundouno | A. Mikhail | N. Ouédraogo | B. Afrough | A. Bah | Jonathan HJ Baum | B. Becker-Ziaja | Mar Cabeza-Cabrerizo | Alvaro Camino-Sanchez | Lisa L. Carter | J. Doerrbecker | T. Enkirch | Isabel Graciela García Dorival | Nicole Hetzelt | Tobias Holm | L. Kafetzopoulou | Michel Koropogui | Abigail Kosgey | A. Mazzarelli | S. Meisel | M. Mertens | J. Michel | D. Ngabo | K. Nitzsche | Elisa Pallash | L. Patrono | Johanna Repits | Natasha Y. Rickett | K. Singethan | I. Vitoriano | Rahel L Yemanaberhan | E. Zekeng | Racine Trina | Victoria Amburgey | L. Winona | E. Davis | F. Washington | V. Monteil | M. Jourdain | M. Bererd | H. Somlaré | G. Bado | B. Baillet | D. Delaune | Yacouba Savane | R. Pallawo | N. Milhano | Isabelle Roger | Christopher J. Williams | Facinet Yattara | K. Lewandowski | Jamie Taylor | P. Rachwal | G. Pollakis | Duncan R. Wilson | E. Smit | Pierre Formenty | Sakoba Keita | Ettore Severi | Lauren Cowley | Joseph Akoi Bore | Raymond Koundouno | Amy Mikhail | Nobila Ouédraogo | Babak Afrough | Amadou Bah | Beate Becker-Ziaja | Jan-Peter Boettcher | Mar Cabeza-Cabrerizo | Alvaro Camino-Sanchez | Juiliane Doerrbecker | Theresa Enkirch | Nicole Hetzelt | Julia Hinzmann | Tobias Holm | Liana Eleni Kafetzopoulou | Michel Koropogui | Abigail Kosgey | Eeva Kuisma | Christopher H Logue | Antonio Mazzarelli | Sarah Meisel | Janine Michel | Didier Ngabo | Katja Nitzsche | Elisa Pallash | Livia Victoria Patrono | Jasmine Portmann | Johanna Gabriella Repits | Natasha Yasmin Rickett | Andrea Sachse | Katrin Singethan | Inês Vitoriano | Elsa G Zekeng | Racine Trina | Alexander Bello | N’Faly Magassouba | Victoria Amburgey | Linda Winona | Emily Davis | Jon Gerlach | Franck Washington | Vanessa Monteil | Marine Jourdain | Marion Bererd | Alimou Camara | Hermann Somlare | Marianne Gerard | Guillaume Bado | Bernard Baillet | Déborah Delaune | Koumpingnin Yacouba Nebie | Abdoulaye Diarra | Yacouba Savane | Raymond Bernard Pallawo | Giovanna Jaramillo Gutierrez | Natacha Milhano | Isabelle Roger | Christopher J Williams | Facinet Yattara | Kuiama Lewandowski | Jamie Taylor | Philip Rachwal | Daniel Turner | Matthew K. O’Shea | Andrew McD Johnston | Duncan Wilson | Emma Hutley | Erasmus Smit | Antonino Di Caro | Roman Woelfel | Erna Fleischmann | Simon A. Weller | Lamine Koivogui | Boubacar Diallo | Stephan Gunther | Christopher Williams | L. Cowley | J. A. Boré | Abdoulaye Camara | J. H. Baum | Rahel L Yemanaberhan | A. Johnston | Katrin Singethan

[1]  B. Avraham.  Biosensors and Biodetection , 2017, Methods in Molecular Biology.

[2]  Jens H Kuhn,et al.  Molecular Evidence of Sexual Transmission of Ebola Virus. , 2015, The New England journal of medicine.

[3]  Di Liu,et al.  Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone , 2015, Nature.

[4]  Claudia Kohl,et al.  Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa , 2015, Nature.

[5]  Pardis C Sabeti,et al.  Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic , 2015, Nature.

[6]  Andrew Rambaut,et al.  Real-time digital pathogen surveillance — the time is now , 2015, Genome Biology.

[7]  S. Weller,et al.  Buffer AVL Alone Does Not Inactivate Ebola Virus in a Representative Clinical Sample Type , 2015, Journal of Clinical Microbiology.

[8]  Pardis C. Sabeti,et al.  Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia , 2015, Emerging infectious diseases.

[9]  Trevor Bedford,et al.  Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone , 2015, Cell.

[10]  Doug Stryke,et al.  Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis , 2015, Genome Medicine.

[11]  Joshua Quick,et al.  Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella , 2015, Genome Biology.

[12]  Charles E. Lawrence,et al.  Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION , 2015, bioRxiv.

[13]  Pardis C. Sabeti,et al.  Data sharing: Make outbreak research open access , 2015, Nature.

[14]  N. Loman,et al.  A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.

[15]  Benedict Paten,et al.  Improved data analysis for the MinION nanopore sequencer , 2015, Nature Methods.

[16]  Aaron R Quinlan,et al.  Erratum: A reference bacterial genome dataset generated on the MinIONTM portable single-molecule nanopore sequencer , 2015, GigaScience.

[17]  P. Horby,et al.  Recent evolution patterns of Ebola virus inferred from patient samples collected from February-May 2015 with direct deep sequencing in Sierra Leone. , 2015 .

[18]  Aaron R Quinlan,et al.  A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer , 2014, GigaScience.

[19]  Rachel S. G. Sealfon,et al.  Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak , 2014, Science.

[20]  Aaron R. Quinlan,et al.  Poretools: a toolkit for analyzing nanopore sequence data , 2014, bioRxiv.

[21]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[22]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[23]  Mandev S. Gill,et al.  Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. , 2013, Molecular biology and evolution.

[24]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[25]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[26]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[27]  Avraham Rasooly,et al.  Rapid DNA amplification using a battery-powered thin-film resistive thermocycler. , 2009, Methods in molecular biology.

[28]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[29]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[30]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.

[31]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[32]  Ziheng Yang.  Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

[33]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.