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Items: 34

1.

Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation.

Diesch J, Bywater MJ, Sanij E, Cameron DP, Schierding W, Brajanovski N, Son J, Sornkom J, Hein N, Evers M, Pearson RB, McArthur GA, Ganley ARD, O'Sullivan JM, Hannan RD, Poortinga G.

Commun Biol. 2019 Jan 28;2(1):39. doi: 10.1038/s42003-019-0284-y.

PMID:
31924928
2.

GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI.

Couto Alves A, De Silva NMG, Karhunen V, Sovio U, Das S, Taal HR, Warrington NM, Lewin AM, Kaakinen M, Cousminer DL, Thiering E, Timpson NJ, Bond TA, Lowry E, Brown CD, Estivill X, Lindi V, Bradfield JP, Geller F, Speed D, Coin LJM, Loh M, Barton SJ, Beilin LJ, Bisgaard H, Bønnelykke K, Alili R, Hatoum IJ, Schramm K, Cartwright R, Charles MA, Salerno V, Clément K, Claringbould AAJ; BIOS Consortium, van Duijn CM, Moltchanova E, Eriksson JG, Elks C, Feenstra B, Flexeder C, Franks S, Frayling TM, Freathy RM, Elliott P, Widén E, Hakonarson H, Hattersley AT, Rodriguez A, Banterle M, Heinrich J, Heude B, Holloway JW, Hofman A, Hyppönen E, Inskip H, Kaplan LM, Hedman AK, Läärä E, Prokisch H, Grallert H, Lakka TA, Lawlor DA, Melbye M, Ahluwalia TS, Marinelli M, Millwood IY, Palmer LJ, Pennell CE, Perry JR, Ring SM, Savolainen MJ, Rivadeneira F, Standl M, Sunyer J, Tiesler CMT, Uitterlinden AG, Schierding W, O'Sullivan JM, Prokopenko I, Herzig KH, Smith GD, O'Reilly P, Felix JF, Buxton JL, Blakemore AIF, Ong KK, Jaddoe VWV, Grant SFA, Sebert S, McCarthy MI, Järvelin MR; Early Growth Genetics (EGG) Consortium.

Sci Adv. 2019 Sep 4;5(9):eaaw3095. doi: 10.1126/sciadv.aaw3095. eCollection 2019 Sep.

3.

Transcriptional profiling of the zebrafish proximal tubule.

Sander V, Salleh L, Naylor RW, Schierding W, Sontam DM, O'Sullivan JM, Davidson AJ.

Am J Physiol Renal Physiol. 2019 Jun 12. doi: 10.1152/ajprenal.00174.2019. [Epub ahead of print]

PMID:
31188030
4.

Corrigendum: Functional Urate-Associated Genetic Variants Influence Expression of lincRNAs LINC01229 and MAFTRR.

Leask M, Dowdle A, Salvesen H, Topless R, Fadason T, Wei W, Schierding W, Marsman J, Antony J, O'Sullivan JM, Merriman TR, Horsfield JA.

Front Genet. 2019 Apr 24;10:382. doi: 10.3389/fgene.2019.00382. eCollection 2019.

5.

Protocol for the Gut Bugs Trial: a randomised double-blind placebo-controlled trial of gut microbiome transfer for the treatment of obesity in adolescents.

Leong KSW, Jayasinghe TN, Derraik JGB, Albert BB, Chiavaroli V, Svirskis DM, Beck KL, Conlon CA, Jiang Y, Schierding W, Vatanen T, Holland DJ, O'Sullivan JM, Cutfield WS.

BMJ Open. 2019 Apr 20;9(4):e026174. doi: 10.1136/bmjopen-2018-026174.

6.

Machine Learning SNP Based Prediction for Precision Medicine.

Ho DSW, Schierding W, Wake M, Saffery R, O'Sullivan J.

Front Genet. 2019 Mar 27;10:267. doi: 10.3389/fgene.2019.00267. eCollection 2019. Review.

7.

Comprehensive Profiling of the Circulatory miRNAome Response to a High Protein Diet in Elderly Men: A Potential Role in Inflammatory Response Modulation.

Ramzan F, Mitchell CJ, Milan AM, Schierding W, Zeng N, Sharma P, Mitchell SM, D'Souza RF, Knowles SO, Roy NC, Sjödin A, Wagner KH, Cameron-Smith D.

Mol Nutr Food Res. 2019 Apr;63(8):e1800811. doi: 10.1002/mnfr.201800811. Epub 2019 Apr 1.

PMID:
30892810
8.

Functional Urate-Associated Genetic Variants Influence Expression of lincRNAs LINC01229 and MAFTRR.

Leask M, Dowdle A, Salvesen H, Topless R, Fadason T, Wei W, Schierding W, Marsman J, Antony J, O'Sullivan JM, Merriman TR, Horsfield JA.

Front Genet. 2019 Jan 21;9:733. doi: 10.3389/fgene.2018.00733. eCollection 2018. Erratum in: Front Genet. 2019 Apr 24;10:382.

9.

Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation.

Diesch J, Bywater MJ, Sanij E, Cameron DP, Schierding W, Brajanovski N, Son J, Sornkom J, Hein N, Evers M, Pearson RB, McArthur GA, Ganley ARD, O'Sullivan JM, Hannan RD, Poortinga G.

Commun Biol. 2019 Jan 28;2:39. doi: 10.1038/s42003-019-0284-y. eCollection 2019.

10.

Chromatin interactions and expression quantitative trait loci reveal genetic drivers of multimorbidities.

Fadason T, Schierding W, Lumley T, O'Sullivan JM.

Nat Commun. 2018 Dec 5;9(1):5198. doi: 10.1038/s41467-018-07692-y.

11.

The role of DNA methylation in human trophoblast differentiation.

Gamage TKJB, Schierding W, Hurley D, Tsai P, Ludgate JL, Bhoothpur C, Chamley LW, Weeks RJ, Macaulay EC, James JL.

Epigenetics. 2018;13(12):1154-1173. doi: 10.1080/15592294.2018.1549462. Epub 2018 Dec 5.

PMID:
30475094
12.

Human trophoblasts are primarily distinguished from somatic cells by differences in the pattern rather than the degree of global CpG methylation.

Gamage TKJB, Schierding W, Tsai P, Ludgate JL, Chamley LW, Weeks RJ, Macaulay EC, James JL.

Biol Open. 2018 Aug 8;7(8). pii: bio034884. doi: 10.1242/bio.034884.

13.

Identification of human skeletal muscle miRNA related to strength by high-throughput sequencing.

Mitchell CJ, D'Souza RF, Schierding W, Zeng N, Ramzan F, O'Sullivan JM, Poppitt SD, Cameron-Smith D.

Physiol Genomics. 2018 Jun 1;50(6):416-424. doi: 10.1152/physiolgenomics.00112.2017. Epub 2018 Mar 30.

PMID:
29602299
14.

Physical Interactions and Expression Quantitative Traits Loci Identify Regulatory Connections for Obesity and Type 2 Diabetes Associated SNPs.

Fadason T, Ekblad C, Ingram JR, Schierding WS, O'Sullivan JM.

Front Genet. 2017 Oct 13;8:150. doi: 10.3389/fgene.2017.00150. eCollection 2017.

15.

GWAS on prolonged gestation (post-term birth): analysis of successive Finnish birth cohorts.

Schierding W, Antony J, Karhunen V, Vääräsmäki M, Franks S, Elliott P, Kajantie E, Sebert S, Blakemore A, Horsfield JA, Järvelin MR, O'Sullivan JM, Cutfield WS.

J Med Genet. 2018 Jan;55(1):55-63. doi: 10.1136/jmedgenet-2017-104880. Epub 2017 Oct 10.

16.

Intergenic GWAS SNPs are key components of the spatial and regulatory network for human growth.

Schierding W, Antony J, Cutfield WS, Horsfield JA, O'Sullivan JM.

Hum Mol Genet. 2016 Aug 1;25(15):3372-3382. doi: 10.1093/hmg/ddw165. Epub 2016 Jun 10.

PMID:
27288450
17.

A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe.

Pichugina T, Sugawara T, Kaykov A, Schierding W, Masuda K, Uewaki J, Grand RS, Allison JR, Martienssen RA, Nurse P, Ueno M, O'Sullivan JM.

Sci Rep. 2016 Jan 5;6:18757. doi: 10.1038/srep18757.

18.

Connecting SNPs in Diabetes: A Spatial Analysis of Meta-GWAS Loci.

Schierding W, O'Sullivan JM.

Front Endocrinol (Lausanne). 2015 Jul 3;6:102. doi: 10.3389/fendo.2015.00102. eCollection 2015. Review.

19.

Genome Modeling System: A Knowledge Management Platform for Genomics.

Griffith M, Griffith OL, Smith SM, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK.

PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015 Jul.

20.

Genes and post-term birth: late for delivery.

Schierding W, O'Sullivan JM, Derraik JG, Cutfield WS.

BMC Res Notes. 2014 Oct 14;7:720. doi: 10.1186/1756-0500-7-720.

21.

SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.

Miller CA, White BS, Dees ND, Griffith M, Welch JS, Griffith OL, Vij R, Tomasson MH, Graubert TA, Walter MJ, Ellis MJ, Schierding W, DiPersio JF, Ley TJ, Mardis ER, Wilson RK, Ding L.

PLoS Comput Biol. 2014 Aug 7;10(8):e1003665. doi: 10.1371/journal.pcbi.1003665. eCollection 2014 Aug.

22.

The missing story behind Genome Wide Association Studies: single nucleotide polymorphisms in gene deserts have a story to tell.

Schierding W, Cutfield WS, O'Sullivan JM.

Front Genet. 2014 Feb 18;5:39. doi: 10.3389/fgene.2014.00039. eCollection 2014. Review.

23.

Smooth muscle cells from abdominal aortic aneurysms are unique and can independently and synergistically degrade insoluble elastin.

Airhart N, Brownstein BH, Cobb JP, Schierding W, Arif B, Ennis TL, Thompson RW, Curci JA.

J Vasc Surg. 2014 Oct;60(4):1033-41; discussion 1041-2. doi: 10.1016/j.jvs.2013.07.097. Epub 2013 Sep 27.

24.

MuSiC: identifying mutational significance in cancer genomes.

Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L.

Genome Res. 2012 Aug;22(8):1589-98. doi: 10.1101/gr.134635.111. Epub 2012 Jul 3.

25.

Whole-genome analysis informs breast cancer response to aromatase inhibition.

Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER.

Nature. 2012 Jun 10;486(7403):353-60. doi: 10.1038/nature11143.

26.

Preliminary evidence for leukocyte transcriptional signatures for pediatric ventilator-associated pneumonia.

Werner JA, Schierding W, Dixon D, MacMillan S, Oppedal D, Muenzer J, Cobb JP, Checchia PA.

J Intensive Care Med. 2012 Nov-Dec;27(6):362-9. doi: 10.1177/0885066611406835. Epub 2011 May 23.

PMID:
21606059
27.

Estimating sparse gene regulatory networks using a bayesian linear regression.

Sarder P, Schierding W, Cobb JP, Nehorai A.

IEEE Trans Nanobioscience. 2010 Jun;9(2):121-31. doi: 10.1109/TNB.2010.2043444.

PMID:
20650703
28.

Evidence for a novel blood RNA diagnostic for pediatric appendicitis: the riboleukogram.

Muenzer JT, Jaffe DM, Schwulst SJ, Dixon DJ, Schierding WS, Li Q, MacMillan SK, Oppedal D, Warner BW, Dillon PA, Lin N, Checchia PA, Cobb JP.

Pediatr Emerg Care. 2010 May;26(5):333-8. doi: 10.1097/PEC.0b013e3181db1de3.

PMID:
20404783
29.

Genome remodelling in a basal-like breast cancer metastasis and xenograft.

Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM Jr, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER.

Nature. 2010 Apr 15;464(7291):999-1005. doi: 10.1038/nature08989.

30.

Validation of the riboleukogram to detect ventilator-associated pneumonia after severe injury.

Cobb JP, Moore EE, Hayden DL, Minei JP, Cuschieri J, Yang J, Li Q, Lin N, Brownstein BH, Hennessy L, Mason PH, Schierding WS, Dixon DJ, Tompkins RG, Warren HS, Schoenfeld DA, Maier RV.

Ann Surg. 2009 Oct;250(4):531-9. doi: 10.1097/SLA.0b013e3181b8fbd5. Review.

31.

Differences in outcome between obese and nonobese patients following severe blunt trauma are not consistent with an early inflammatory genomic response.

Winfield RD, Delano MJ, Dixon DJ, Schierding WS, Cendan JC, Lottenberg L, Lopez MC, Baker HV, Cobb JP, Moldawer LL, Maier RV, Cuschieri J.

Crit Care Med. 2010 Jan;38(1):51-8. doi: 10.1097/CCM.0b013e3181b08089.

32.

Targeted delivery of siRNA to cell death proteins in sepsis.

Brahmamdam P, Watanabe E, Unsinger J, Chang KC, Schierding W, Hoekzema AS, Zhou TT, McDonough JS, Holemon H, Heidel JD, Coopersmith CM, McDunn JE, Hotchkiss RS.

Shock. 2009 Aug;32(2):131-9. doi: 10.1097/SHK.0b013e318194bcee.

33.

Myocardial transcriptional profiles in a murine model of sepsis: evidence for the importance of age.

Checchia PA, Schierding W, Polpitiya A, Dixon D, Macmillan S, Muenzer J, Stromberg P, Coopersmith CM, Buchman TG, Cobb JP.

Pediatr Crit Care Med. 2008 Sep;9(5):530-5. doi: 10.1097/PCC.0b013e3181849a2f.

PMID:
18679145
34.

Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram.

McDunn JE, Husain KD, Polpitiya AD, Burykin A, Ruan J, Li Q, Schierding W, Lin N, Dixon D, Zhang W, Coopersmith CM, Dunne WM, Colonna M, Ghosh BK, Cobb JP.

PLoS One. 2008 Feb 13;3(2):e1564. doi: 10.1371/journal.pone.0001564.

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