James Bonfield
James Bonfield
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Cited by
Twelve years of SAMtools and BCFtools
P Danecek, JK Bonfield, J Liddle, J Marshall, V Ohan, MO Pollard, ...
Gigascience 10 (2), giab008, 2021
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium
Nature 431 (7011), 931-945, 2004
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
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
The staden package, 1998
R Staden, KF Beal, JK Bonfield
Bioinformatics methods and protocols, 115-130, 1999
A new DNA sequence assembly program
JK Bonfield, KF Smith, R Staden
Nucleic acids research 23 (24), 4992-4999, 1995
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
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
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
Compression of FASTQ and SAM format sequencing data
JK Bonfield, MV Mahoney
PloS one 8 (3), e59190, 2013
Gap5—editing the billion fragment sequence assembly
JK Bonfield, A Whitwham
Bioinformatics 26 (14), 1699-1703, 2010
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
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
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
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
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
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
Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10 (2): giab008
P Danecek, JK Bonfield, J Liddle, J Marshall, V Ohan, MO Pollard, ...
PubMed Abstract| Publisher Full Text, 0
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
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
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