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James Bonfield
James Bonfield
Verified email at sanger.ac.uk
Title
Cited by
Cited by
Year
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium
Nature 431 (7011), 931-945, 2004
51572004
Twelve years of SAMtools and BCFtools
P Danecek, JK Bonfield, J Liddle, J Marshall, V Ohan, MO Pollard, ...
Gigascience 10 (2), giab008, 2021
47992021
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Project management: Fulton Lucinda A. 1 Mardis Elaine R. 1 Wilson Richard K. 1
Nature 432 (7018), 695-716, 2004
29352004
2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans
R Wilson, R Ainscough, K Anderson, C Baynes, M Berks, J Bonfield, ...
Nature 368 (6466), 32-38, 1994
18421994
The staden package, 1998
R Staden, KF Beal, JK Bonfield
Bioinformatics methods and protocols, 115-130, 1999
17141999
A new DNA sequence assembly program
JK Bonfield, KF Smith, R Staden
Nucleic acids research 23 (24), 4992-4999, 1995
11951995
Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B. 1.617. 2) compared with alpha (B. 1.1. 7) variants of concern: a cohort study
KA Twohig, T Nyberg, A Zaidi, S Thelwall, MA Sinnathamby, S Aliabadi, ...
The Lancet Infectious Diseases 22 (1), 35-42, 2022
7922022
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B. 1.1. 7
B Meng, SA Kemp, G Papa, R Datir, IATM Ferreira, S Marelli, WT Harvey, ...
Cell reports 35 (13), 2021
4162021
Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B. 1.1. 7: an ecological study
MS Graham, CH Sudre, A May, M Antonelli, B Murray, T Varsavsky, ...
The Lancet Public Health 6 (5), e335-e345, 2021
3362021
Compression of FASTQ and SAM format sequencing data
JK Bonfield, MV Mahoney
PloS one 8 (3), e59190, 2013
2392013
Gap5—editing the billion fragment sequence assembly
JK Bonfield, A Whitwham
Bioinformatics 26 (14), 1699-1703, 2010
2162010
Analyzing sequences using the Staden package and EMBOSS
R Staden, DP Judge, JK Bonfield
Introduction to bioinformatics: a theoretical and practical approach, 393-410, 2003
205*2003
HTSlib: C library for reading/writing high-throughput sequencing data
JK Bonfield, J Marshall, P Danecek, H Li, V Ohan, A Whitwham, T Keane, ...
Gigascience 10 (2), giab007, 2021
1882021
De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
F Giordano, L Aigrain, MA Quail, P Coupland, JK Bonfield, RM Davies, ...
Scientific reports 7 (1), 3935, 2017
1762017
A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction
DJ Adams, MA Quail, T Cox, L Van Der Weyden, BD Gorick, Q Su, ...
Genomics 86 (6), 753-758, 2005
1682005
Petabyte-scale innovations at the European Nucleotide Archive
G Cochrane, R Akhtar, J Bonfield, L Bower, F Demiralp, N Faruque, ...
Nucleic acids research 37 (suppl_1), D19-D25, 2009
1302009
GA4GH: International policies and standards for data sharing across genomic research and healthcare
HL Rehm, AJH Page, L Smith, JB Adams, G Alterovitz, LJ Babb, ...
Cell genomics 1 (2), 2021
1262021
Comparison of high-throughput sequencing data compression tools
I Numanagić, JK Bonfield, F Hach, J Voges, J Ostermann, C Alberti, ...
nature methods 13 (12), 1005-1008, 2016
1132016
Experiment files and their application during large-scale sequencing projects
JK Bonfield, R Staden
DNA sequence 6 (2), 109-117, 1996
1111996
Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant
P Elliott, D Haw, H Wang, O Eales, CE Walters, KEC Ainslie, C Atchison, ...
Science 374 (6574), eabl9551, 2021
1102021
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