Gerton Lunter

Gerton Lunter

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Gerton Lunter

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Inferring B cell specificity for vaccines using a Bayesian mixture model.

BMC Genomics 2020 Feb 22;21(1):176. Epub 2020 Feb 22.

MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.

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http://dx.doi.org/10.1186/s12864-020-6571-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036227PMC
February 2020

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

Proc Natl Acad Sci U S A 2019 11 21;116(45):22664-22672. Epub 2019 Oct 21.

Department of Pathology, Yale School of Medicine, New Haven, CT 06520;

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http://dx.doi.org/10.1073/pnas.1906020116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842591PMC
November 2019

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

Authors:
Gerton Lunter

Bioinformatics 2019 03;35(5):798-806

University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394399PMC
March 2019

A high throughput screen for active human transposable elements.

BMC Genomics 2018 02 1;19(1):115. Epub 2018 Feb 1.

Wellcome Trust Centre for Human Genetics, Oxford, UK.

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http://dx.doi.org/10.1186/s12864-018-4485-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5796560PMC
February 2018

A Phylogenetic Codon Substitution Model for Antibody Lineages.

Genetics 2017 05 17;206(1):417-427. Epub 2017 Mar 17.

Department of Zoology, University of Oxford, OX1 3PS, United Kingdom

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http://dx.doi.org/10.1534/genetics.116.196303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5419485PMC
May 2017

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

Sci Rep 2016 08 3;6:31029. Epub 2016 Aug 3.

The Institute of Cancer Research, London, Division of Genetics &Epidemiology, Sutton SM2 5NG, UK.

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http://dx.doi.org/10.1038/srep31029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971567PMC
August 2016

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

Genome Med 2016 Aug 3;8(1):81. Epub 2016 Aug 3.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, OX3 7LE, UK.

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http://dx.doi.org/10.1186/s13073-016-0337-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973058PMC
August 2016

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

Genome Med 2016 06 16;8(1):68. Epub 2016 Jun 16.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, OX3 7LE, UK.

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http://dx.doi.org/10.1186/s13073-016-0322-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910312PMC
June 2016

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

Mol Biol Evol 2016 05 22;33(5):1147-57. Epub 2016 Jan 22.

Department of Zoology, University of Oxford, Oxford, United Kingdom

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http://dx.doi.org/10.1093/molbev/msw015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839220PMC
May 2016

The ICR1000 UK exome series: a resource of gene variation in an outbred population.

F1000Res 2015 22;4:883. Epub 2015 Sep 22.

Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK; Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK.

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http://dx.doi.org/10.12688/f1000research.7049.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706061PMC
February 2016

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

EBioMedicine 2015 Dec 24;2(12):2070-9. Epub 2015 Nov 24.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford OX3 7LE, United Kingdom.

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http://dx.doi.org/10.1016/j.ebiom.2015.11.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703725PMC
December 2015

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

Immunol Cell Biol 2015 Nov 15;93(10):885-95. Epub 2015 May 15.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, UK.

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http://dx.doi.org/10.1038/icb.2015.57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551417PMC
November 2015

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

Front Immunol 2015 12;6:531. Epub 2015 Oct 12.

Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford , Oxford , UK.

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http://dx.doi.org/10.3389/fimmu.2015.00531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4601265PMC
November 2015

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

Authors:
Jenny C Taylor Hilary C Martin Stefano Lise John Broxholme Jean-Baptiste Cazier Andy Rimmer Alexander Kanapin Gerton Lunter Simon Fiddy Chris Allan A Radu Aricescu Moustafa Attar Christian Babbs Jennifer Becq David Beeson Celeste Bento Patricia Bignell Edward Blair Veronica J Buckle Katherine Bull Ondrej Cais Holger Cario Helen Chapel Richard R Copley Richard Cornall Jude Craft Karin Dahan Emma E Davenport Calliope Dendrou Olivier Devuyst Aimée L Fenwick Jonathan Flint Lars Fugger Rodney D Gilbert Anne Goriely Angie Green Ingo H Greger Russell Grocock Anja V Gruszczyk Robert Hastings Edouard Hatton Doug Higgs Adrian Hill Chris Holmes Malcolm Howard Linda Hughes Peter Humburg David Johnson Fredrik Karpe Zoya Kingsbury Usha Kini Julian C Knight Jonathan Krohn Sarah Lamble Craig Langman Lorne Lonie Joshua Luck Davis McCarthy Simon J McGowan Mary Frances McMullin Kerry A Miller Lisa Murray Andrea H Németh M Andrew Nesbit David Nutt Elizabeth Ormondroyd Annette Bang Oturai Alistair Pagnamenta Smita Y Patel Melanie Percy Nayia Petousi Paolo Piazza Sian E Piret Guadalupe Polanco-Echeverry Niko Popitsch Fiona Powrie Chris Pugh Lynn Quek Peter A Robbins Kathryn Robson Alexandra Russo Natasha Sahgal Pauline A van Schouwenburg Anna Schuh Earl Silverman Alison Simmons Per Soelberg Sørensen Elizabeth Sweeney John Taylor Rajesh V Thakker Ian Tomlinson Amy Trebes Stephen Rf Twigg Holm H Uhlig Paresh Vyas Tim Vyse Steven A Wall Hugh Watkins Michael P Whyte Lorna Witty Ben Wright Chris Yau David Buck Sean Humphray Peter J Ratcliffe John I Bell Andrew Om Wilkie David Bentley Peter Donnelly Gilean McVean

Nat Genet 2015 Jul 18;47(7):717-726. Epub 2015 May 18.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/ng.3304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4601524PMC
July 2015

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

Bioinformatics 2015 May 8;31(10):1680-2. Epub 2015 Jan 8.

Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btu861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426833PMC
May 2015

High-throughput DNA Sequencing Identifies Novel Variants in Muscle-invasive Bladder Cancer Patients.

Bladder Cancer 2015 Apr 30;1(1):31-44. Epub 2015 Apr 30.

CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.3233/BLC-150007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218178PMC
April 2015

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

J Immunol 2015 Jan 12;194(1):252-261. Epub 2014 Nov 12.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, United Kingdom.

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http://dx.doi.org/10.4049/jimmunol.1401405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272858PMC
January 2015

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

PLoS Genet 2014 Jul 24;10(7):e1004525. Epub 2014 Jul 24.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109858PMC
July 2014

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

Bioinformatics 2013 Aug 18;29(16):2046-8. Epub 2013 Jun 18.

MRC CGAT Programme and Functional Genomics Unit, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722528PMC
August 2013

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.

PLoS One 2012 20;7(4):e34572. Epub 2012 Apr 20.

University of California Berkeley and University of California San Francisco Graduate Program in Bioengineering, University of California, Berkeley, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034572PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335033PMC
August 2012

Dindel: accurate indel calls from short-read data.

Genome Res 2011 Jun 27;21(6):961-73. Epub 2010 Oct 27.

Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, United Kingdom.

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http://dx.doi.org/10.1101/gr.112326.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106329PMC
June 2011

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

Genome Res 2011 Jun 27;21(6):936-9. Epub 2010 Oct 27.

Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.111120.110
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http://dx.doi.org/10.1101/gr.111120.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106326PMC
June 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

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

Genome Res 2010 Oct 6;20(10):1335-43. Epub 2010 Aug 6.

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.108795.110
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http://dx.doi.org/10.1101/gr.108795.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945182PMC
October 2010

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

Genome Res 2010 May 19;20(5):675-84. Epub 2010 Mar 19.

Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

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http://dx.doi.org/10.1101/gr.096966.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860169PMC
May 2010

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

PLoS Genet 2009 Dec 4;5(12):e1000753. Epub 2009 Dec 4.

Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.

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http://flygenetics.com/assets/oliver2009.pdf
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http://dx.plos.org/10.1371/journal.pgen.1000753
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.1000753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779102PMC
December 2009

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

PLoS Genet 2009 Aug 21;5(8):e1000617. Epub 2009 Aug 21.

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1000617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722021PMC
August 2009

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

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

MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

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http://dx.doi.org/10.1101/gr.6725608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203628PMC
February 2008

HMMoC--a compiler for hidden Markov models.

Authors:
Gerton Lunter

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

MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, South Parks Road, OX1 3TG, University of Oxford, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btm350DOI Listing
September 2007

Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.

Authors:
Gerton Lunter

Bioinformatics 2007 Jul;23(13):i289-96

MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, United Kingdom.

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https://academic.oup.com/bioinformatics/article/23/13/i289/2
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http://dx.doi.org/10.1093/bioinformatics/btm185DOI Listing
July 2007

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

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

MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

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http://www.genome.org/cgi/doi/10.1101/gr.6036807
Publisher Site
http://dx.doi.org/10.1101/gr.6036807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855172PMC
May 2007

Novel type IV secretion system involved in propagation of genomic islands.

J Bacteriol 2007 Feb 22;189(3):761-71. Epub 2006 Nov 22.

Clinical Microbiology and Infectious Diseases, Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Headington, OX3 9DU Oxford, United Kingdom.

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http://dx.doi.org/10.1128/JB.01327-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797279PMC
February 2007

Signatures of adaptive evolution within human non-coding sequence.

Hum Mol Genet 2006 Oct;15 Spec No 2:R170-5

MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK.

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http://academic.oup.com/hmg/article/15/suppl_2/R170/622182/S
Publisher Site
http://dx.doi.org/10.1093/hmg/ddl182DOI Listing
October 2006

Evolutionary biology: human brain gene wins genome race.

Nature 2006 Sep 16;443(7108):149-50. Epub 2006 Aug 16.

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http://www.nature.com/doifinder/10.1038/nature05154
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http://dx.doi.org/10.1038/nature05154DOI Listing
September 2006

Genome-wide identification of human functional DNA using a neutral indel model.

PLoS Comput Biol 2006 Jan 13;2(1):e5. Epub 2006 Jan 13.

MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.

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http://dx.plos.org/10.1371/journal.pcbi.0020005
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http://dx.doi.org/10.1371/journal.pcbi.0020005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326222PMC
January 2006

Bayesian coestimation of phylogeny and sequence alignment.

BMC Bioinformatics 2005 Apr 1;6:83. Epub 2005 Apr 1.

Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.

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http://dx.doi.org/10.1186/1471-2105-6-83DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087833PMC
April 2005

A nucleotide substitution model with nearest-neighbour interactions.

Bioinformatics 2004 Aug;20 Suppl 1:i216-23

Bioinformatics group, Department of Statistics, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/bth901DOI Listing
August 2004