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Dog as an outgroup to human and mouse.
Lunter G. Lunter G. PLoS Comput Biol. 2007 Apr 27;3(4):e74. doi: 10.1371/journal.pcbi.0030074. PLoS Comput Biol. 2007. PMID: 17465673 Free PMC article. No abstract available.
Genome-wide identification of human functional DNA using a neutral indel model.
Lunter G, Ponting CP, Hein J. Lunter G, et al. PLoS Comput Biol. 2006 Jan;2(1):e5. doi: 10.1371/journal.pcbi.0020005. Epub 2006 Jan 13. PLoS Comput Biol. 2006. PMID: 16410828 Free PMC article.
Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.
Lunter G. Lunter G. Bioinformatics. 2007 Jul 1;23(13):i289-96. doi: 10.1093/bioinformatics/btm185. Bioinformatics. 2007. PMID: 17646308
Applying the method to these species, I show that indel rates are up to twice higher than is apparent from alignments, and depend strongly on the local G + C content. ...
Applying the method to these species, I show that indel rates are up to twice higher than is apparent from alignments, and depend strongly o …
CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.
Münz M, Ruark E, Renwick A, Ramsay E, Clarke M, Mahamdallie S, Cloke V, Seal S, Strydom A, Lunter G, Rahman N. Münz M, et al. Genome Med. 2015 Jul 28;7(1):76. doi: 10.1186/s13073-015-0195-6. Genome Med. 2015. PMID: 26315209 Free PMC article.
A systematic survey of loss-of-function variants in human protein-coding genes.
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG; 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. MacArthur DG, et al. Science. 2012 Feb 17;335(6070):823-8. doi: 10.1126/science.1215040. Science. 2012. PMID: 22344438 Free PMC article.
A nucleotide substitution model with nearest-neighbour interactions.
Lunter G, Hein J. Lunter G, et al. Bioinformatics. 2004 Aug 4;20 Suppl 1:i216-23. doi: 10.1093/bioinformatics/bth901. Bioinformatics. 2004. PMID: 15262802
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
Dindel: accurate indel calls from short-read data.
Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R. Albers CA, et al. Genome Res. 2011 Jun;21(6):961-73. doi: 10.1101/gr.112326.110. Epub 2010 Oct 27. Genome Res. 2011. PMID: 20980555 Free PMC article.
Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.
Lunter G, Goodson M. Lunter G, et al. Genome Res. 2011 Jun;21(6):936-9. doi: 10.1101/gr.111120.110. Epub 2010 Oct 27. Genome Res. 2011. PMID: 20980556 Free PMC article.
Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. ...
Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in b …
Haplotype matching in large cohorts using the Li and Stephens model.
Lunter G. Lunter G. Bioinformatics. 2019 Mar 1;35(5):798-806. doi: 10.1093/bioinformatics/bty735. Bioinformatics. 2019. PMID: 30165547 Free PMC article.
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