M
Matthew Loose
Researcher at University of Nottingham
Publications - 97
Citations - 6923
Matthew Loose is an academic researcher from University of Nottingham. The author has contributed to research in topics: Nanopore sequencing & Medicine. The author has an hindex of 28, co-authored 74 publications receiving 5058 citations. Previous affiliations of Matthew Loose include Queen's University.
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Journal ArticleDOI
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,Sunir Malla,Hannah Marriott,Tom Nieto,Justin O'Grady,Hugh E. Olsen,Brent S. Pedersen,Arang Rhie,Hollian Richardson,Aaron R. Quinlan,Terrance P. Snutch,Louise Tee,Benedict Paten,Adam M. Phillippy,Jared T. Simpson,Jared T. Simpson,Nicholas J. Loman,Matthew Loose +26 more
TL;DR: Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.
Journal ArticleDOI
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 Morales Claro,Andrew D. Smith,Karthik Gangavarapu,Glenn Oliveira,Refugio Robles-Sikisaka,Thomas F. Rogers,Thomas F. Rogers,Nathan Beutler,Dennis R. Burton,Lia Laura Lewis-Ximenez,Jaqueline Goes de Jesus,Marta Giovanetti,Marta Giovanetti,Sarah C. Hill,Allison Black,Allison Black,Trevor Bedford,Miles W. Carroll,Márcio Roberto Teixeira Nunes,Luiz Carlos Junior Alcantara,Ester Cerdeira Sabino,Sally A. Baylis,Nuno R. Faria,Matthew Loose,Jared T. Simpson,Oliver G. Pybus,Kristian G. Andersen,Kristian G. Andersen,Nicholas J. Loman +31 more
TL;DR: A protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences.
Journal ArticleDOI
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Nuno R. Faria,Joshua Quick,Ingra Morales Claro,Julien Thézé,J G de Jesus,Marta Giovanetti,Moritz U. G. Kraemer,Sarah C. Hill,Allison Black,Allison Black,A. C. da Costa,L. C Franco,Sandro Patroca da Silva,C-H Wu,Jayna Raghwani,Simon Cauchemez,L. du Plessis,M. P Verotti,W. K. de Oliveira,Eduardo Hage Carmo,Giovanini E. Coelho,A. C. F. S Santelli,L. C Vinhal,Cláudio Maierovitch Pessanha Henriques,Jared T. Simpson,Matthew Loose,Kristian G. Andersen,Nathan D. Grubaugh,Sneha Somasekar,Charles Y. Chiu,José Esteban Muñoz-Medina,César González-Bonilla,Carlos F. Arias,Lia Laura Lewis-Ximenez,Sally A. Baylis,Alexandre Otavio Chieppe,Shirlei Ferreira Aguiar,Carlos Fernandes,Poliana da Silva Lemos,B. L. S Nascimento,Hamilton Antônio de Oliveira Monteiro,Isadora Cristina de Siqueira,M. G. de Queiroz,T. R. de Souza,João Felipe Bezerra,M. R Lemos,Gavin Pereira,D Loudal,L. C Moura,Rafael Dhalia,Rafael F. O. França,T Magalhães,T Magalhães,T Magalhães,Ernesto T. A. Marques,Thomas Jaenisch,Gabriel Luz Wallau,M. C. de Lima,Vitor H. Nascimento,E. M. de Cerqueira,M. M. de Lima,D. L Mascarenhas,J. P Moura Neto,Anna S. Levin,Tania Regina Tozetto-Mendoza,Silvia Nunes Szente Fonseca,Maria Cassia Mendes-Correa,Flavio Augusto de Pádua Milagres,Aluísio Augusto Cotrim Segurado,Edward C. Holmes,Andrew Rambaut,Andrew Rambaut,Trevor Bedford,Márcio Roberto Teixeira Nunes,Márcio Roberto Teixeira Nunes,Ester Cerdeira Sabino,Luiz Carlos Junior Alcantara,Nicholas J. Loman,Oliver G. Pybus +78 more
TL;DR: The origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly and other birth defects as mentioned in this paper.
Journal ArticleDOI
Nanopore native RNA sequencing of a human poly(A) transcriptome.
Rachael E. Workman,Alison D. Tang,Paul S. Tang,Miten Jain,John R. Tyson,Roham Razaghi,Philip C. Zuzarte,Timothy Gilpatrick,Alexander Payne,Joshua Quick,Norah Sadowski,Nadine Holmes,Jaqueline Goes de Jesus,Karen Jones,Cameron M. Soulette,Terrance P. Snutch,Nicholas J. Loman,Benedict Paten,Matthew Loose,Jared T. Simpson,Jared T. Simpson,Hugh E. Olsen,Angela N. Brooks,Mark Akeson,Winston Timp +24 more
TL;DR: This study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions to identify 33,984 plausible RNA isoforms and describes strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes.
Posted ContentDOI
Nanopore sequencing and assembly of a human genome with ultra-long reads
Miten Jain,Sergey Koren,Josh Quick,Arthur C Rand,Thomas A Sasani,John R. Tyson,Andrew D Beggs,Alexander T. Dilthey,Ian T. Fiddes,Sunir Malla,Hannah Marriott,Karen H. Miga,Tom Nieto,Justin O'Grady,Hugh E. Olsen,Brent S. Pedersen,Arang Rhie,Hollian Richardson,Aaron R. Quinlan,Terrance P. Snutch,Louise Tee,Benedict Paten,Adam M. Phillippy,Jared T. Simpson,Nicholas J. Loman,Matthew Loose +25 more
TL;DR: Modelling the repeat structure of the human genome predicts extraordinarily contiguous assemblies may be possible using nanopore reads alone, and it is found that adding an additional 5×-coverage of ‘ultra-long’ reads more than doubled the assembly contiguity.