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Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.

Hoehn KB, Vander Heiden JA, Zhou JQ, Lunter G, Pybus OG, Kleinstein SH.

Proc Natl Acad Sci U S A. 2019 Nov 5;116(45):22664-22672. doi: 10.1073/pnas.1906020116. Epub 2019 Oct 21.


Sequencing of human genomes with nanopore technology.

Bowden R, Davies RW, Heger A, Pagnamenta AT, de Cesare M, Oikkonen LE, Parkes D, Freeman C, Dhalla F, Patel SY, Popitsch N, Ip CLC, Roberts HE, Salatino S, Lockstone H, Lunter G, Taylor JC, Buck D, Simpson MA, Donnelly P.

Nat Commun. 2019 Apr 23;10(1):1869. doi: 10.1038/s41467-019-09637-5.


An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs.

Brown RC, Lunter G.

Bioinformatics. 2019 Jul 1;35(13):2177-2184. doi: 10.1093/bioinformatics/bty964.


Haplotype matching in large cohorts using the Li and Stephens model.

Lunter G.

Bioinformatics. 2019 Mar 1;35(5):798-806. doi: 10.1093/bioinformatics/bty735.


A high throughput screen for active human transposable elements.

Kvikstad EM, Piazza P, Taylor JC, Lunter G.

BMC Genomics. 2018 Feb 1;19(1):115. doi: 10.1186/s12864-018-4485-4.


Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN.

Fowler A, Mahamdallie S, Ruark E, Seal S, Ramsay E, Clarke M, Uddin I, Wylie H, Strydom A, Lunter G, Rahman N.

Wellcome Open Res. 2016 Nov 25;1:20. doi: 10.12688/wellcomeopenres.10069.1.


A Phylogenetic Codon Substitution Model for Antibody Lineages.

Hoehn KB, Lunter G, Pybus OG.

Genetics. 2017 May;206(1):417-427. doi: 10.1534/genetics.116.196303. Epub 2017 Mar 17.


Erratum to: B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation.

Galson JD, Trück J, Clutterbuck EA, Fowler A, Cerundolo V, Pollard AJ, Lunter G, Kelly DF.

Genome Med. 2016 Aug 3;8(1):81. No abstract available.


OpEx - a validated, automated pipeline optimised for clinical exome sequence analysis.

Ruark E, Münz M, Clarke M, Renwick A, Ramsay E, Elliott A, Seal S, Lunter G, Rahman N.

Sci Rep. 2016 Aug 3;6:31029. doi: 10.1038/srep31029.


B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation.

Galson JD, Trück J, Clutterbuck EA, Fowler A, Cerundolo V, Pollard AJ, Lunter G, Kelly DF.

Genome Med. 2016 Jun 16;8(1):68. doi: 10.1186/s13073-016-0322-z. Erratum in: Genome Med. 2016;8(1):81.


Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences.

Galson JD, Trück J, Fowler A, Clutterbuck EA, Münz M, Cerundolo V, Reinhard C, van der Most R, Pollard AJ, Lunter G, Kelly DF.

EBioMedicine. 2015 Nov 24;2(12):2070-9. doi: 10.1016/j.ebiom.2015.11.034. eCollection 2015 Dec.


The Diversity and Molecular Evolution of B-Cell Receptors during Infection.

Hoehn KB, Fowler A, Lunter G, Pybus OG.

Mol Biol Evol. 2016 May;33(5):1147-57. doi: 10.1093/molbev/msw015. Epub 2016 Jan 22. Review.


In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire.

Galson JD, Trück J, Fowler A, Münz M, Cerundolo V, Pollard AJ, Lunter G, Kelly DF.

Front Immunol. 2015 Oct 12;6:531. doi: 10.3389/fimmu.2015.00531. eCollection 2015.


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.

Genome Med. 2015 Jul 28;7:76. doi: 10.1186/s13073-015-0195-6.


Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.

Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G.

Nat Genet. 2015 Jul;47(7):717-726. doi: 10.1038/ng.3304. Epub 2015 May 18.


BCR repertoire sequencing: different patterns of B-cell activation after two Meningococcal vaccines.

Galson JD, Clutterbuck EA, Trück J, Ramasamy MN, Münz M, Fowler A, Cerundolo V, Pollard AJ, Lunter G, Kelly DF.

Immunol Cell Biol. 2015 Nov;93(10):885-95. doi: 10.1038/icb.2015.57. Epub 2015 May 15.


High-throughput DNA Sequencing Identifies Novel CtIP (RBBP8) Variants in Muscle-invasive Bladder Cancer Patients.

Jevons SJ, Green A, Lunter G, Kartsonaki C, Buck D, Piazza P, Kiltie AE.

Bladder Cancer. 2015 Apr 30;1(1):31-44. doi: 10.3233/BLC-150007.


scrm: efficiently simulating long sequences using the approximated coalescent with recombination.

Staab PR, Zhu S, Metzler D, Lunter G.

Bioinformatics. 2015 May 15;31(10):1680-2. doi: 10.1093/bioinformatics/btu861. Epub 2015 Jan 8.


Identification of antigen-specific B cell receptor sequences using public repertoire analysis.

Trück J, Ramasamy MN, Galson JD, Rance R, Parkhill J, Lunter G, Pollard AJ, Kelly DF.

J Immunol. 2015 Jan 1;194(1):252-261. doi: 10.4049/jimmunol.1401405. Epub 2014 Nov 12.


8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage.

Rands CM, Meader S, Ponting CP, Lunter G.

PLoS Genet. 2014 Jul 24;10(7):e1004525. doi: 10.1371/journal.pgen.1004525. eCollection 2014 Jul.


Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.

Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SRF; WGS500 Consortium, Wilkie AOM, McVean G, Lunter G.

Nat Genet. 2014 Aug;46(8):912-918. doi: 10.1038/ng.3036. Epub 2014 Jul 13.


Improved workflows for high throughput library preparation using the transposome-based Nextera system.

Lamble S, Batty E, Attar M, Buck D, Bowden R, Lunter G, Crook D, El-Fahmawi B, Piazza P.

BMC Biotechnol. 2013 Nov 20;13:104. doi: 10.1186/1472-6750-13-104.


GAT: a simulation framework for testing the association of genomic intervals.

Heger A, Webber C, Goodson M, Ponting CP, Lunter G.

Bioinformatics. 2013 Aug 15;29(16):2046-8. doi: 10.1093/bioinformatics/btt343. Epub 2013 Jun 18.


The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J; 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.

Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11.


Unlocking the bottleneck in forward genetics using whole-genome sequencing and identity by descent to isolate causative mutations.

Bull KR, Rimmer AJ, Siggs OM, Miosge LA, Roots CM, Enders A, Bertram EM, Crockford TL, Whittle B, Potter PK, Simon MM, Mallon AM, Brown SD, Beutler B, Goodnow CC, Lunter G, Cornall RJ.

PLoS Genet. 2013;9(1):e1003219. doi: 10.1371/journal.pgen.1003219. Epub 2013 Jan 31.


A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.

Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH.

PLoS Genet. 2012;8(12):e1003125. doi: 10.1371/journal.pgen.1003125. Epub 2012 Dec 20.


Recessive mutations in SPTBN2 implicate β-III spectrin in both cognitive and motor development.

Lise S, Clarkson Y, Perkins E, Kwasniewska A, Sadighi Akha E, Schnekenberg RP, Suminaite D, Hope J, Baker I, Gregory L, Green A, Allan C, Lamble S, Jayawant S, Quaghebeur G, Cader MZ, Hughes S, Armstrong RJ, Kanapin A, Rimmer A, Lunter G, Mathieson I, Cazier JB, Buck D, Taylor JC, Bentley D, McVean G, Donnelly P, Knight SJ, Jackson M, Ragoussis J, Németh AH.

PLoS Genet. 2012;8(12):e1003074. doi: 10.1371/journal.pgen.1003074. Epub 2012 Dec 6.


The bonobo genome compared with the chimpanzee and human genomes.

Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S.

Nature. 2012 Jun 28;486(7404):527-31. doi: 10.1038/nature11128.


Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.

Westesson O, Lunter G, Paten B, Holmes I.

PLoS One. 2012;7(4):e34572. doi: 10.1371/journal.pone.0034572. Epub 2012 Apr 20.


A fine-scale chimpanzee genetic map from population sequencing.

Auton A, Fledel-Alon A, Pfeifer S, Venn O, Ségurel L, Street T, Leffler EM, Bowden R, Aneas I, Broxholme J, Humburg P, Iqbal Z, Lunter G, Maller J, Hernandez RD, Melton C, Venkat A, Nobrega MA, Bontrop R, Myers S, Donnelly P, Przeworski M, McVean G.

Science. 2012 Apr 13;336(6078):193-8. doi: 10.1126/science.1216872. Epub 2012 Mar 15.


The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines.

Eizirik DL, Sammeth M, Bouckenooghe T, Bottu G, Sisino G, Igoillo-Esteve M, Ortis F, Santin I, Colli ML, Barthson J, Bouwens L, Hughes L, Gregory L, Lunter G, Marselli L, Marchetti P, McCarthy MI, Cnop M.

PLoS Genet. 2012;8(3):e1002552. doi: 10.1371/journal.pgen.1002552. Epub 2012 Mar 8.


Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R.

Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.


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.

Science. 2012 Feb 17;335(6070):823-8. doi: 10.1126/science.1215040. Erratum in: Science. 2012 Apr 20;336(6079):296.


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.

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.


Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model.

Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH.

PLoS Genet. 2011 Mar;7(3):e1001319. doi: 10.1371/journal.pgen.1001319. Epub 2011 Mar 3.


Comparative and demographic analysis of orang-utan genomes.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.


Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.

Lunter G, Goodson M.

Genome Res. 2011 Jun;21(6):936-9. doi: 10.1101/gr.111120.110. Epub 2010 Oct 27.


Dindel: accurate indel calls from short-read data.

Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R.

Genome Res. 2011 Jun;21(6):961-73. doi: 10.1101/gr.112326.110. Epub 2010 Oct 27.


Massive turnover of functional sequence in human and other mammalian genomes.

Meader S, Ponting CP, Lunter G.

Genome Res. 2010 Oct;20(10):1335-43. doi: 10.1101/gr.108795.110. Epub 2010 Aug 6.


Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.

Satija R, Hein J, Lunter GA.

Bioinformatics. 2010 Sep 1;26(17):2116-20. doi: 10.1093/bioinformatics/btq360. Epub 2010 Jul 7.


Genome assembly quality: assessment and improvement using the neutral indel model.

Meader S, Hillier LW, Locke D, Ponting CP, Lunter G.

Genome Res. 2010 May;20(5):675-84. doi: 10.1101/gr.096966.109. Epub 2010 Mar 19.


Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa.

Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, Phadnis N, Beatson SA, Lunter G, Malik HS, Ponting CP.

PLoS Genet. 2009 Dec;5(12):e1000753. doi: 10.1371/journal.pgen.1000753. Epub 2009 Dec 4.


Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain.

Ponjavic J, Oliver PL, Lunter G, Ponting CP.

PLoS Genet. 2009 Aug;5(8):e1000617. doi: 10.1371/journal.pgen.1000617. Epub 2009 Aug 21.


Evolution of primate gene expression: drift and corrective sweeps?

Chaix R, Somel M, Kreil DP, Khaitovich P, Lunter GA.

Genetics. 2008 Nov;180(3):1379-89. doi: 10.1534/genetics.108.089623. Epub 2008 Sep 14.


Investigating selection on viruses: a statistical alignment approach.

de Groot S, Mailund T, Lunter G, Hein J.

BMC Bioinformatics. 2008 Jul 10;9:304. doi: 10.1186/1471-2105-9-304.


Uncertainty in homology inferences: assessing and improving genomic sequence alignment.

Lunter G, Rocco A, Mimouni N, Heger A, Caldeira A, Hein J.

Genome Res. 2008 Feb;18(2):298-309. Epub 2007 Dec 11.


HMMoC--a compiler for hidden Markov models.

Lunter G.

Bioinformatics. 2007 Sep 15;23(18):2485-7. Epub 2007 Jul 10.


Dog as an outgroup to human and mouse.

Lunter G.

PLoS Comput Biol. 2007 Apr 27;3(4):e74. No abstract available.


Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs.

Ponjavic J, Ponting CP, Lunter G.

Genome Res. 2007 May;17(5):556-65. Epub 2007 Mar 26.

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