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Items: 19

1.

AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes.

Lee W, Plant K, Humburg P, Knight JC.

Bioinformatics. 2018 Jul 15;34(14):2401-2408. doi: 10.1093/bioinformatics/bty125.

2.

Synergistic cooperation and crosstalk between MYD88L265P and mutations that dysregulate CD79B and surface IgM.

Wang JQ, Jeelall YS, Humburg P, Batchelor EL, Kaya SM, Yoo HM, Goodnow CC, Horikawa K.

J Exp Med. 2017 Sep 4;214(9):2759-2776. doi: 10.1084/jem.20161454. Epub 2017 Jul 12.

3.

An image-processing methodology for extracting bloodstain pattern features.

Arthur RM, Humburg PJ, Hoogenboom J, Baiker M, Taylor MC, de Bruin KG.

Forensic Sci Int. 2017 Aug;277:122-132. doi: 10.1016/j.forsciint.2017.05.022. Epub 2017 Jun 3.

PMID:
28646752
4.

High resolution HLA haplotyping by imputation for a British population bioresource.

Neville MJ, Lee W, Humburg P, Wong D, Barnardo M, Karpe F, Knight JC.

Hum Immunol. 2017 Mar;78(3):242-251. doi: 10.1016/j.humimm.2017.01.006. Epub 2017 Jan 19.

5.

Shared and Distinct Aspects of the Sepsis Transcriptomic Response to Fecal Peritonitis and Pneumonia.

Burnham KL, Davenport EE, Radhakrishnan J, Humburg P, Gordon AC, Hutton P, Svoren-Jabalera E, Garrard C, Hill AVS, Hinds CJ, Knight JC.

Am J Respir Crit Care Med. 2017 Aug 1;196(3):328-339. doi: 10.1164/rccm.201608-1685OC.

6.

IgD attenuates the IgM-induced anergy response in transitional and mature B cells.

Sabouri Z, Perotti S, Spierings E, Humburg P, Yabas M, Bergmann H, Horikawa K, Roots C, Lambe S, Young C, Andrews TD, Field M, Enders A, Reed JH, Goodnow CC.

Nat Commun. 2016 Nov 10;7:13381. doi: 10.1038/ncomms13381.

7.

Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation.

Humburg P, Maugeri N, Lee W, Mohr B, Knight JC.

Genome Med. 2016 Aug 24;8(1):87. doi: 10.1186/s13073-016-0345-5.

8.

Genomic landscape of the individual host response and outcomes in sepsis: a prospective cohort study.

Davenport EE, Burnham KL, Radhakrishnan J, Humburg P, Hutton P, Mills TC, Rautanen A, Gordon AC, Garrard C, Hill AV, Hinds CJ, Knight JC.

Lancet Respir Med. 2016 Apr;4(4):259-71. doi: 10.1016/S2213-2600(16)00046-1. Epub 2016 Feb 23.

9.

Genomic modulators of gene expression in human neutrophils.

Naranbhai V, Fairfax BP, Makino S, Humburg P, Wong D, Ng E, Hill AV, Knight JC.

Nat Commun. 2015 Jul 7;6:7545. doi: 10.1038/ncomms8545.

10.

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.

11.

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach.

Wong D, Lee W, Humburg P, Makino S, Lau E, Naranbhai V, Fairfax BP, Chan K, Plant K, Knight JC.

Genome Biol. 2014;15(10):494.

12.

Choice of transcripts and software has a large effect on variant annotation.

McCarthy DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, Cazier JB, Donnelly P.

Genome Med. 2014 Mar 31;6(3):26. doi: 10.1186/gm543. eCollection 2014.

13.

Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression.

Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, Jostins L, Plant K, Andrews R, McGee C, Knight JC.

Science. 2014 Mar 7;343(6175):1246949. doi: 10.1126/science.1246949.

14.

Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer.

Ruark E, Snape K, Humburg P, Loveday C, Bajrami I, Brough R, Rodrigues DN, Renwick A, Seal S, Ramsay E, Duarte Sdel V, Rivas MA, Warren-Perry M, Zachariou A, Campion-Flora A, Hanks S, Murray A, Ansari Pour N, Douglas J, Gregory L, Rimmer A, Walker NM, Yang TP, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Brice G, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Eccles D, Evans DG, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Shanley S, Walker L, Gore M, Houlston R, Brown MA, Caufield MJ, Deloukas P, McCarthy MI, Todd JA; Breast and Ovarian Cancer Susceptibility Collaboration; Wellcome Trust Case Control Consortium, Turnbull C, Reis-Filho JS, Ashworth A, Antoniou AC, Lord CJ, Donnelly P, Rahman N.

Nature. 2013 Jan 17;493(7432):406-10. doi: 10.1038/nature11725. Epub 2012 Dec 16.

15.

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.

16.

Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits.

Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk M, Angelov D, Dimitrov S, Udalova IA, Ragoussis J.

Genome Biol. 2011 Jul 29;12(7):R70. doi: 10.1186/gb-2011-12-7-r70.

17.

ChIPseqR: analysis of ChIP-seq experiments.

Humburg P, Helliwell CA, Bulger D, Stone G.

BMC Bioinformatics. 2011 Jan 31;12:39. doi: 10.1186/1471-2105-12-39.

18.

Parameter estimation for robust HMM analysis of ChIP-chip data.

Humburg P, Bulger D, Stone G.

BMC Bioinformatics. 2008 Aug 18;9:343. doi: 10.1186/1471-2105-9-343.

19.

Validation and functional annotation of expression-based clusters based on gene ontology.

Steuer R, Humburg P, Selbig J.

BMC Bioinformatics. 2006 Aug 15;7:380.

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