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Items: 30

1.

Molecular Profiling of Ulcerative Colitis Subjects from the TURANDOT Trial Reveals Novel Pharmacodynamic/Efficacy Biomarkers.

Zhou H, Xi L, Ziemek D, O'Neil S, Lee J, Stewart Z, Zhan Y, Zhao S, Zhang Y, Page K, Huang A, Maciejewski M, Zhang B, Gorelick KJ, Fitz L, Pradhan V, Cataldi F, Vincent M, Von Schack D, Hung K, Hassan-Zahraee M.

J Crohns Colitis. 2019 May 27;13(6):702-713. doi: 10.1093/ecco-jcc/jjy217.

2.

An Unbiased Lipid Phenotyping Approach To Study the Genetic Determinants of Lipids and Their Association with Coronary Heart Disease Risk Factors.

Harshfield EL, Koulman A, Ziemek D, Marney L, Fauman EB, Paul DS, Stacey D, Rasheed A, Lee JJ, Shah N, Jabeen S, Imran A, Abbas S, Hina Z, Qamar N, Mallick NH, Yaqoob Z, Saghir T, Rizvi SNH, Memon A, Rasheed SZ, Memon FU, Qureshi IH, Ishaq M, Frossard P, Danesh J, Saleheen D, Butterworth AS, Wood AM, Griffin JL.

J Proteome Res. 2019 Jun 7;18(6):2397-2410. doi: 10.1021/acs.jproteome.8b00786. Epub 2019 Apr 26.

3.

SUBSTRA: Supervised Bayesian Patient Stratification.

Khakabimamaghani S, Kelkar YD, Grande BM, Morin RD, Ester M, Ziemek D.

Bioinformatics. 2019 Feb 15. pii: btz112. doi: 10.1093/bioinformatics/btz112. [Epub ahead of print]

PMID:
30768166
4.

Profiling of Gene Expression Biomarkers as a Classifier of Methotrexate Nonresponse in Patients With Rheumatoid Arthritis.

Plant D, Maciejewski M, Smith S, Nair N; Maximising Therapeutic Utility in Rheumatoid Arthritis Consortium, the RAMS Study Group, Hyrich K, Ziemek D, Barton A, Verstappen S.

Arthritis Rheumatol. 2019 May;71(5):678-684. doi: 10.1002/art.40810. Epub 2019 Mar 19.

PMID:
30615300
5.

ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci.

Stacey D, Fauman EB, Ziemek D, Sun BB, Harshfield EL, Wood AM, Butterworth AS, Suhre K, Paul DS.

Nucleic Acids Res. 2019 Jan 10;47(1):e3. doi: 10.1093/nar/gky837.

6.

From hype to reality: data science enabling personalized medicine.

Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B.

BMC Med. 2018 Aug 27;16(1):150. doi: 10.1186/s12916-018-1122-7.

7.

A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes.

van Zuydam NR, Ahlqvist E, Sandholm N, Deshmukh H, Rayner NW, Abdalla M, Ladenvall C, Ziemek D, Fauman E, Robertson NR, McKeigue PM, Valo E, Forsblom C, Harjutsalo V; Finnish Diabetic Nephropathy Study (FinnDiane), Perna A, Rurali E, Marcovecchio ML, Igo RP Jr, Salem RM, Perico N, Lajer M, Käräjämäki A, Imamura M, Kubo M, Takahashi A, Sim X, Liu J, van Dam RM, Jiang G, Tam CHT, Luk AOY, Lee HM, Lim CKP, Szeto CC, So WY, Chan JCN; Hong Kong Diabetes Registry Theme-based Research Scheme Project Group, Ang SF, Dorajoo R, Wang L, Clara TSH, McKnight AJ, Duffy S; Warren 3 and Genetics of Kidneys in Diabetes (GoKinD) Study Group, Pezzolesi MG; GENIE (GEnetics of Nephropathy an International Effort) Consortium, Marre M, Gyorgy B, Hadjadj S, Hiraki LT; Diabetes Control and Complications Trial (DCCT)/Epidemiology of Diabetes Interventions and Complications (EDIC) Research Group, Ahluwalia TS, Almgren P, Schulz CA, Orho-Melander M, Linneberg A, Christensen C, Witte DR, Grarup N, Brandslund I, Melander O, Paterson AD, Tregouet D, Maxwell AP, Lim SC, Ma RCW, Tai ES, Maeda S, Lyssenko V, Tuomi T, Krolewski AS, Rich SS, Hirschhorn JN, Florez JC, Dunger D, Pedersen O, Hansen T, Rossing P, Remuzzi G; SUrrogate markers for Micro- and Macrovascular hard endpoints for Innovative diabetes Tools (SUMMIT) Consortium, Brosnan MJ, Palmer CNA, Groop PH, Colhoun HM, Groop LC, McCarthy MI.

Diabetes. 2018 Jul;67(7):1414-1427. doi: 10.2337/db17-0914. Epub 2018 Apr 27.

8.

Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes.

Zarringhalam K, Degras D, Brockel C, Ziemek D.

Sci Rep. 2018 Jan 19;8(1):1237. doi: 10.1038/s41598-018-19635-0.

9.

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

Kang T, Ding W, Zhang L, Ziemek D, Zarringhalam K.

BMC Bioinformatics. 2017 Dec 19;18(1):565. doi: 10.1186/s12859-017-1984-2.

10.

From the Cover: Fenretinide, Troglitazone, and Elmiron Add to Weight of Evidence Support for Hemangiosarcoma Mode-of-Action From Studies in Mice.

Cook JC, Obert LA, Koza-Taylor P, Coskran TM, Opsahl AC, Ziemek D, Roy M, Qian J, Lawton MP, Criswell KA.

Toxicol Sci. 2018 Jan 1;161(1):58-75. doi: 10.1093/toxsci/kfx195.

PMID:
28973697
11.

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease.

Folkersen L, Fauman E, Sabater-Lleal M, Strawbridge RJ, Frånberg M, Sennblad B, Baldassarre D, Veglia F, Humphries SE, Rauramaa R, de Faire U, Smit AJ, Giral P, Kurl S, Mannarino E, Enroth S, Johansson Å, Enroth SB, Gustafsson S, Lind L, Lindgren C, Morris AP, Giedraitis V, Silveira A, Franco-Cereceda A, Tremoli E; IMPROVE study group, Gyllensten U, Ingelsson E, Brunak S, Eriksson P, Ziemek D, Hamsten A, Mälarstig A.

PLoS Genet. 2017 Apr 3;13(4):e1006706. doi: 10.1371/journal.pgen.1006706. eCollection 2017 Apr.

12.

GWAS of self-reported mosquito bite size, itch intensity and attractiveness to mosquitoes implicates immune-related predisposition loci.

Jones AV, Tilley M, Gutteridge A, Hyde C, Nagle M, Ziemek D, Gorman D, Fauman EB, Chen X, Miller MR, Tian C, Hu Y, Hinds DA, Cox P, Scollen S.

Hum Mol Genet. 2017 Apr 1;26(7):1391-1406. doi: 10.1093/hmg/ddx036.

13.

The Genetic Landscape of Renal Complications in Type 1 Diabetes.

Sandholm N, Van Zuydam N, Ahlqvist E, Juliusdottir T, Deshmukh HA, Rayner NW, Di Camillo B, Forsblom C, Fadista J, Ziemek D, Salem RM, Hiraki LT, Pezzolesi M, Trégouët D, Dahlström E, Valo E, Oskolkov N, Ladenvall C, Marcovecchio ML, Cooper J, Sambo F, Malovini A, Manfrini M, McKnight AJ, Lajer M, Harjutsalo V, Gordin D, Parkkonen M; The FinnDiane Study Group, Tuomilehto J, Lyssenko V, McKeigue PM, Rich SS, Brosnan MJ, Fauman E, Bellazzi R, Rossing P, Hadjadj S, Krolewski A, Paterson AD; The DCCT/EDIC Study Group, Florez JC, Hirschhorn JN, Maxwell AP; GENIE Consortium, Dunger D, Cobelli C, Colhoun HM, Groop L, McCarthy MI, Groop PH; SUMMIT Consortium.

J Am Soc Nephrol. 2017 Feb;28(2):557-574. doi: 10.1681/ASN.2016020231. Epub 2016 Sep 19.

14.

Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks.

Fakhry CT, Choudhary P, Gutteridge A, Sidders B, Chen P, Ziemek D, Zarringhalam K.

BMC Bioinformatics. 2016 Aug 24;17(1):318. doi: 10.1186/s12859-016-1181-8.

15.

Genome-wide association analysis of self-reported events in 6135 individuals and 252 827 controls identifies 8 loci associated with thrombosis.

Hinds DA, Buil A, Ziemek D, Martinez-Perez A, Malik R, Folkersen L, Germain M, Mälarstig A, Brown A, Soria JM, Dichgans M, Bing N, Franco-Cereceda A, Souto JC, Dermitzakis ET, Hamsten A, Worrall BB, Tung JY; METASTROKE Consortium, INVENT Consortium, Sabater-Lleal M.

Hum Mol Genet. 2016 May 1;25(9):1867-74. doi: 10.1093/hmg/ddw037. Epub 2016 Feb 9.

16.

Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks.

Zarringhalam K, Enayetallah A, Reddy P, Ziemek D.

Bioinformatics. 2014 Jun 15;30(12):i69-77. doi: 10.1093/bioinformatics/btu272.

17.

An atlas of genetic influences on human blood metabolites.

Shin SY, Fauman EB, Petersen AK, Krumsiek J, Santos R, Huang J, Arnold M, Erte I, Forgetta V, Yang TP, Walter K, Menni C, Chen L, Vasquez L, Valdes AM, Hyde CL, Wang V, Ziemek D, Roberts P, Xi L, Grundberg E; Multiple Tissue Human Expression Resource (MuTHER) Consortium, Waldenberger M, Richards JB, Mohney RP, Milburn MV, John SL, Trimmer J, Theis FJ, Overington JP, Suhre K, Brosnan MJ, Gieger C, Kastenmüller G, Spector TD, Soranzo N.

Nat Genet. 2014 Jun;46(6):543-550. doi: 10.1038/ng.2982. Epub 2014 May 11.

18.

Brown fat determination and development from muscle precursor cells by novel action of bone morphogenetic protein 6.

Sharma A, Huard C, Vernochet C, Ziemek D, Knowlton KM, Tyminski E, Paradis T, Zhang Y, Jones JE, von Schack D, Brown CT, Milos PM, Coyle AJ, Tremblay F, Martinez RV.

PLoS One. 2014 Mar 21;9(3):e92608. doi: 10.1371/journal.pone.0092608. eCollection 2014.

19.

GeneTopics--interpretation of gene sets via literature-driven topic models.

Wang V, Xi L, Enayetallah A, Fauman E, Ziemek D.

BMC Syst Biol. 2013;7 Suppl 5:S10. doi: 10.1186/1752-0509-7-S5-S10. Epub 2013 Dec 9.

20.

Molecular causes of transcriptional response: a Bayesian prior knowledge approach.

Zarringhalam K, Enayetallah A, Gutteridge A, Sidders B, Ziemek D.

Bioinformatics. 2013 Dec 15;29(24):3167-73. doi: 10.1093/bioinformatics/btt557. Epub 2013 Sep 26.

21.

Assessing the translatability of in vivo cardiotoxicity mechanisms to in vitro models using causal reasoning.

Enayetallah AE, Puppala D, Ziemek D, Fischer JE, Kantesaria S, Pletcher MT.

BMC Pharmacol Toxicol. 2013 Sep 6;14:46. doi: 10.1186/2050-6511-14-46.

22.

HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain.

Denk F, Huang W, Sidders B, Bithell A, Crow M, Grist J, Sharma S, Ziemek D, Rice AS, Buckley NJ, McMahon SB.

Pain. 2013 Sep;154(9):1668-79. doi: 10.1016/j.pain.2013.05.021. Epub 2013 May 18.

23.

Novel pancreatic endocrine maturation pathways identified by genomic profiling and causal reasoning.

Gutteridge A, Rukstalis JM, Ziemek D, Tié M, Ji L, Ramos-Zayas R, Nardone NA, Norquay LD, Brenner MB, Tang K, McNeish JD, Rowntree RK.

PLoS One. 2013;8(2):e56024. doi: 10.1371/journal.pone.0056024. Epub 2013 Feb 13.

24.

Genes contributing to pain sensitivity in the normal population: an exome sequencing study.

Williams FM, Scollen S, Cao D, Memari Y, Hyde CL, Zhang B, Sidders B, Ziemek D, Shi Y, Harris J, Harrow I, Dougherty B, Malarstig A, McEwen R, Stephens JC, Patel K, Menni C, Shin SY, Hodgkiss D, Surdulescu G, He W, Jin X, McMahon SB, Soranzo N, John S, Wang J, Spector TD.

PLoS Genet. 2012;8(12):e1003095. doi: 10.1371/journal.pgen.1003095. Epub 2012 Dec 20.

25.

Silencing of enzymes involved in ceramide biosynthesis causes distinct global alterations of lipid homeostasis and gene expression.

Ruangsiriluk W, Grosskurth SE, Ziemek D, Kuhn M, des Etages SG, Francone OL.

J Lipid Res. 2012 Aug;53(8):1459-71. doi: 10.1194/jlr.M020941. Epub 2012 May 23.

26.

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge.

Huang CL, Lamb J, Chindelevitch L, Kostrowicki J, Guinney J, Delisi C, Ziemek D.

BMC Bioinformatics. 2012 Mar 23;13:46. doi: 10.1186/1471-2105-13-46.

27.

Causal reasoning on biological networks: interpreting transcriptional changes.

Chindelevitch L, Ziemek D, Enayetallah A, Randhawa R, Sidders B, Brockel C, Huang ES.

Bioinformatics. 2012 Apr 15;28(8):1114-21. doi: 10.1093/bioinformatics/bts090. Epub 2012 Feb 21.

PMID:
22355083
28.

Assessing statistical significance in causal graphs.

Chindelevitch L, Loh PR, Enayetallah A, Berger B, Ziemek D.

BMC Bioinformatics. 2012 Feb 20;13:35. doi: 10.1186/1471-2105-13-35.

29.

Modeling the mechanism of action of a DGAT1 inhibitor using a causal reasoning platform.

Enayetallah AE, Ziemek D, Leininger MT, Randhawa R, Yang J, Manion TB, Mather DE, Zavadoski WJ, Kuhn M, Treadway JL, des Etages SA, Gibbs EM, Greene N, Steppan CM.

PLoS One. 2011;6(11):e27009. doi: 10.1371/journal.pone.0027009. Epub 2011 Nov 4.

30.

Characterization of human cardiac Kv1.5 inhibition by the novel atrial-selective antiarrhythmic compound AVE1231.

Ehrlich JR, Ocholla H, Ziemek D, Rütten H, Hohnloser SH, Gögelein H.

J Cardiovasc Pharmacol. 2008 Apr;51(4):380-7. doi: 10.1097/FJC.0b013e3181669030.

PMID:
18427281

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