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Items: 1 to 50 of 84

1.

Using Machine Learning to Predict Sensorineural Hearing Loss Based on Perilymph Micro RNA Expression Profile.

Shew M, New J, Wichova H, Koestler DC, Staecker H.

Sci Rep. 2019 Mar 4;9(1):3393. doi: 10.1038/s41598-019-40192-7.

2.

Subject level clustering using a negative binomial model for small transcriptomic studies.

Li Q, Noel-MacDonnell JR, Koestler DC, Goode EL, Fridley BL.

BMC Bioinformatics. 2018 Dec 12;19(1):474. doi: 10.1186/s12859-018-2556-9.

3.

O-GlcNAc homeostasis contributes to cell fate decisions during hematopoiesis.

Zhang Z, Parker MP, Graw S, Novikova LV, Fedosyuk H, Fontes JD, Koestler DC, Peterson KR, Slawson C.

J Biol Chem. 2019 Jan 25;294(4):1363-1379. doi: 10.1074/jbc.RA118.005993. Epub 2018 Dec 6.

PMID:
30523150
4.

A Curated Cancer Clinical Outcomes Database (C3OD) for accelerating patient recruitment in cancer clinical trials.

Mudaranthakam DP, Thompson J, Hu J, Pei D, Chintala SR, Park M, Fridley BL, Gajewski B, Koestler DC, Mayo MS.

JAMIA Open. 2018 Oct;1(2):166-171. doi: 10.1093/jamiaopen/ooy023. Epub 2018 Jul 10.

5.

The Microbiomes of Pancreatic and Duodenum Tissue Overlap and Are Highly Subject Specific but Differ between Pancreatic Cancer and Noncancer Subjects.

Del Castillo E, Meier R, Chung M, Koestler DC, Chen T, Paster BJ, Charpentier KP, Kelsey KT, Izard J, Michaud DS.

Cancer Epidemiol Biomarkers Prev. 2019 Feb;28(2):370-383. doi: 10.1158/1055-9965.EPI-18-0542. Epub 2018 Oct 29.

PMID:
30373903
6.

Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array.

Zaimi I, Pei D, Koestler DC, Marsit CJ, De Vivo I, Tworoger SS, Shields AE, Kelsey KT, Michaud DS.

Epigenetics. 2018;13(10-11):1056-1071. doi: 10.1080/15592294.2018.1530008. Epub 2018 Oct 21.

PMID:
30270718
7.

Methylation-derived Neutrophil-to-Lymphocyte Ratio and Lung Cancer Risk in Heavy Smokers.

Grieshober L, Graw S, Barnett MJ, Thornquist MD, Goodman GE, Chen C, Koestler DC, Marsit CJ, Doherty JA.

Cancer Prev Res (Phila). 2018 Nov;11(11):727-734. doi: 10.1158/1940-6207.CAPR-18-0111. Epub 2018 Sep 25.

PMID:
30254071
8.

DNA methylation derived systemic inflammation indices are associated with head and neck cancer development and survival.

Ambatipudi S, Langdon R, Richmond RC, Suderman M, Koestler DC, Kelsey KT, Kazmi N, Penfold C, Ho KM, McArdle W, Ring SM, Pring M, Waterboer T, Pawlita M, Gaunt TR, Davey Smith G, Thomas S, Ness AR, Relton CL.

Oral Oncol. 2018 Oct;85:87-94. doi: 10.1016/j.oraloncology.2018.08.021. Epub 2018 Sep 5.

9.

Reduced mitochondrial reactive oxygen species production in peripheral nerves of mice fed a ketogenic diet.

Cooper MA, McCoin C, Pei D, Thyfault JP, Koestler D, Wright DE.

Exp Physiol. 2018 Sep;103(9):1206-1212. doi: 10.1113/EP087083. Epub 2018 Aug 8.

PMID:
30088302
10.

Tracing human stem cell lineage during development using DNA methylation.

Salas LA, Wiencke JK, Koestler DC, Zhang Z, Christensen BC, Kelsey KT.

Genome Res. 2018 Sep;28(9):1285-1295. doi: 10.1101/gr.233213.117. Epub 2018 Aug 2.

11.

Licofelone Enhances the Efficacy of Paclitaxel in Ovarian Cancer by Reversing Drug Resistance and Tumor Stem-like Properties.

Hirst J, Pathak HB, Hyter S, Pessetto ZY, Ly T, Graw S, Koestler DC, Krieg AJ, Roby KF, Godwin AK.

Cancer Res. 2018 Aug 1;78(15):4370-4385. doi: 10.1158/0008-5472.CAN-17-3993. Epub 2018 Jun 11.

PMID:
29891506
12.

An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray.

Salas LA, Koestler DC, Butler RA, Hansen HM, Wiencke JK, Kelsey KT, Christensen BC.

Genome Biol. 2018 May 29;19(1):64. doi: 10.1186/s13059-018-1448-7.

13.

Association of Neutrophil-to-Lymphocyte Ratio With Mortality and Cardiovascular Disease in the Jackson Heart Study and Modification by the Duffy Antigen Variant.

Kim S, Eliot M, Koestler DC, Wu WC, Kelsey KT.

JAMA Cardiol. 2018 Jun 1;3(6):455-462. doi: 10.1001/jamacardio.2018.1042.

PMID:
29801037
14.

Developing a genetic signature to predict drug response in ovarian cancer.

Hyter S, Hirst J, Pathak H, Pessetto ZY, Koestler DC, Raghavan R, Pei D, Godwin AK.

Oncotarget. 2017 Dec 26;9(19):14828-14848. doi: 10.18632/oncotarget.23663. eCollection 2018 Mar 13.

15.

Mediation analysis of alcohol consumption, DNA methylation, and epithelial ovarian cancer.

Wu D, Yang H, Winham SJ, Natanzon Y, Koestler DC, Luo T, Fridley BL, Goode EL, Zhang Y, Cui Y.

J Hum Genet. 2018 Mar;63(3):339-348. doi: 10.1038/s10038-017-0385-8. Epub 2018 Jan 10.

16.

VaDiR: an integrated approach to Variant Detection in RNA.

Neums L, Suenaga S, Beyerlein P, Anders S, Koestler D, Mariani A, Chien J.

Gigascience. 2018 Feb 1;7(2). doi: 10.1093/gigascience/gix122.

17.

A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.

Seyednasrollah F, Koestler DC, Wang T, Piccolo SR, Vega R, Greiner R, Fuchs C, Gofer E, Kumar L, Wolfinger RD, Kanigel Winner K, Bare C, Neto EC, Yu T, Shen L, Abdallah K, Norman T, Stolovitzky G, Soule HR, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Elo LL, Zhou FL, Guinney J, Costello JC; Prostate Cancer DREAM Challenge Community.

JCO Clin Cancer Inform. 2017 Nov;1:1-15. doi: 10.1200/CCI.17.00018.

18.

Mitochondrial Haplotype Alters Mammary Cancer Tumorigenicity and Metastasis in an Oncogenic Driver-Dependent Manner.

Brinker AE, Vivian CJ, Koestler DC, Tsue TT, Jensen RA, Welch DR.

Cancer Res. 2017 Dec 15;77(24):6941-6949. doi: 10.1158/0008-5472.CAN-17-2194. Epub 2017 Oct 25.

19.

Sustained O-GlcNAcylation reprograms mitochondrial function to regulate energy metabolism.

Tan EP, McGreal SR, Graw S, Tessman R, Koppel SJ, Dhakal P, Zhang Z, Machacek M, Zachara NE, Koestler DC, Peterson KR, Thyfault JP, Swerdlow RH, Krishnamurthy P, DiTacchio L, Apte U, Slawson C.

J Biol Chem. 2017 Sep 8;292(36):14940-14962. doi: 10.1074/jbc.M117.797944. Epub 2017 Jul 24.

20.

Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression.

Vivian CJ, Brinker AE, Graw S, Koestler DC, Legendre C, Gooden GC, Salhia B, Welch DR.

Cancer Res. 2017 Nov 15;77(22):6202-6214. doi: 10.1158/0008-5472.CAN-17-1473. Epub 2017 Jun 29.

21.

Maternal serum PFOA concentration and DNA methylation in cord blood: A pilot study.

Kingsley SL, Kelsey KT, Butler R, Chen A, Eliot MN, Romano ME, Houseman A, Koestler DC, Lanphear BP, Yolton K, Braun JM.

Environ Res. 2017 Oct;158:174-178. doi: 10.1016/j.envres.2017.06.013. Epub 2017 Jun 20.

22.

The aquaglyceroporin AQP9 contributes to the sex-specific effects of in utero arsenic exposure on placental gene expression.

Winterbottom EF, Koestler DC, Fei DL, Wika E, Capobianco AJ, Marsit CJ, Karagas MR, Robbins DJ.

Environ Health. 2017 Jun 14;16(1):59. doi: 10.1186/s12940-017-0267-8.

23.

Integrative epigenetic and genetic pan-cancer somatic alteration portraits.

Salas LA, Johnson KC, Koestler DC, O'Sullivan DE, Christensen BC.

Epigenetics. 2017 Jul 3;12(7):561-574. doi: 10.1080/15592294.2017.1319043. Epub 2017 Apr 20.

24.

An ensemble-based Cox proportional hazards regression framework for predicting survival in metastatic castration-resistant prostate cancer (mCRPC) patients.

Meier R, Graw S, Usset J, Raghavan R, Dai J, Chalise P, Ellis S, Fridley B, Koestler D.

F1000Res. 2016 Nov 16;5:2677. doi: 10.12688/f1000research.8226.1. eCollection 2016.

25.

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Zheng SC, Beck S, Jaffe AE, Koestler DC, Hansen KD, Houseman AE, Irizarry RA, Teschendorff AE.

Nat Methods. 2017 Feb 28;14(3):216-217. doi: 10.1038/nmeth.4187. No abstract available.

PMID:
28245219
26.

Immunomethylomic approach to explore the blood neutrophil lymphocyte ratio (NLR) in glioma survival.

Wiencke JK, Koestler DC, Salas LA, Wiemels JL, Roy RP, Hansen HM, Rice T, McCoy LS, Bracci PM, Molinaro AM, Kelsey KT, Wrensch MR, Christensen BC.

Clin Epigenetics. 2017 Feb 2;9:10. doi: 10.1186/s13148-017-0316-8. eCollection 2017.

27.

digit-a tool for detection and identification of genomic interchromosomal translocations.

Meier R, Graw S, Beyerlein P, Koestler D, Molina JR, Chien J.

Nucleic Acids Res. 2017 May 19;45(9):e72. doi: 10.1093/nar/gkx010.

28.

DNA Methylation-Derived Neutrophil-to-Lymphocyte Ratio: An Epigenetic Tool to Explore Cancer Inflammation and Outcomes.

Koestler DC, Usset J, Christensen BC, Marsit CJ, Karagas MR, Kelsey KT, Wiencke JK.

Cancer Epidemiol Biomarkers Prev. 2017 Mar;26(3):328-338. doi: 10.1158/1055-9965.EPI-16-0461. Epub 2016 Dec 13.

29.

Enlarged leukocyte referent libraries can explain additional variance in blood-based epigenome-wide association studies.

Kim S, Eliot M, Koestler DC, Houseman EA, Wetmur JG, Wiencke JK, Kelsey KT.

Epigenomics. 2016 Sep;8(9):1185-92. doi: 10.2217/epi-2016-0037. Epub 2016 Aug 16.

30.

Epigenetic and genetic burden measures are associated with tumor characteristics in invasive breast carcinoma.

O'Sullivan DE, Johnson KC, Skinner L, Koestler DC, Christensen BC.

Epigenetics. 2016 May 3;11(5):344-53. doi: 10.1080/15592294.2016.1168673. Epub 2016 Apr 12.

31.

Prenatal Programming of Infant Neurobehaviour in a Healthy Population.

Appleton AA, Murphy MA, Koestler DC, Lesseur C, Paquette AG, Padbury JF, Lester BM, Marsit CJ.

Paediatr Perinat Epidemiol. 2016 Jul;30(4):367-75. doi: 10.1111/ppe.12294. Epub 2016 Mar 23.

32.

Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL).

Koestler DC, Jones MJ, Usset J, Christensen BC, Butler RA, Kobor MS, Wiencke JK, Kelsey KT.

BMC Bioinformatics. 2016 Mar 8;17:120. doi: 10.1186/s12859-016-0943-7.

33.

CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma.

Langevin SM, Eliot M, Butler RA, Cheong A, Zhang X, McClean MD, Koestler DC, Kelsey KT.

Clin Epigenetics. 2015 Dec 3;7:125. doi: 10.1186/s13148-015-0160-7. eCollection 2015.

34.

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

Munchel S, Hoang Y, Zhao Y, Cottrell J, Klotzle B, Godwin AK, Koestler D, Beyerlein P, Fan JB, Bibikova M, Chien J.

Oncotarget. 2015 Sep 22;6(28):25943-61. doi: 10.18632/oncotarget.4671.

35.

GLI3 Links Environmental Arsenic Exposure and Human Fetal Growth.

Winterbottom EF, Fei DL, Koestler DC, Giambelli C, Wika E, Capobianco AJ, Lee E, Marsit CJ, Karagas MR, Robbins DJ.

EBioMedicine. 2015 May 1;2(6):536-43. doi: 10.1016/j.ebiom.2015.04.019. eCollection 2015 Jun.

36.

DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer.

Johnson KC, Koestler DC, Fleischer T, Chen P, Jenson EG, Marotti JD, Onega T, Kristensen VN, Christensen BC.

Clin Epigenetics. 2015 Jul 25;7:75. doi: 10.1186/s13148-015-0094-0. eCollection 2015.

37.

DNA methylation changes in the placenta are associated with fetal manganese exposure.

Maccani JZ, Koestler DC, Houseman EA, Armstrong DA, Marsit CJ, Kelsey KT.

Reprod Toxicol. 2015 Nov;57:43-9. doi: 10.1016/j.reprotox.2015.05.002. Epub 2015 May 15.

38.

Differential DNA methylation in umbilical cord blood of infants exposed to mercury and arsenic in utero.

Cardenas A, Koestler DC, Houseman EA, Jackson BP, Kile ML, Karagas MR, Marsit CJ.

Epigenetics. 2015;10(6):508-15. doi: 10.1080/15592294.2015.1046026. Epub 2015 Apr 29.

39.

Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors.

Rijlaarsdam MA, Tax DM, Gillis AJ, Dorssers LC, Koestler DC, de Ridder J, Looijenga LH.

PLoS One. 2015 Apr 10;10(4):e0122146. doi: 10.1371/journal.pone.0122146. eCollection 2015. Erratum in: PLoS One. 2015;10(7):e0132981.

40.

Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis.

Hoen AG, Li J, Moulton LA, O'Toole GA, Housman ML, Koestler DC, Guill MF, Moore JH, Hibberd PL, Morrison HG, Sogin ML, Karagas MR, Madan JC.

J Pediatr. 2015 Jul;167(1):138-47.e1-3. doi: 10.1016/j.jpeds.2015.02.049. Epub 2015 Mar 26.

41.

Placental DNA Methylation Related to Both Infant Toenail Mercury and Adverse Neurobehavioral Outcomes.

Maccani JZ, Koestler DC, Lester B, Houseman EA, Armstrong DA, Kelsey KT, Marsit CJ.

Environ Health Perspect. 2015 Jul;123(7):723-9. doi: 10.1289/ehp.1408561. Epub 2015 Mar 6.

42.

Improving NCLeX-RN First-Time Pass Rates with a Balanced Curriculum.

Koestler DL.

Nurs Educ Perspect. 2015 Jan/Feb;36(1):55-57. doi: 10.5480/11-591.1.

PMID:
29194160
43.

The era of integrative genomics: more data or better methods?

Koestler DC, Jones MJ, Kobor MS.

Epigenomics. 2014;6(5):463-7. doi: 10.2217/epi.14.44. No abstract available. Erratum in: Epigenomics. 2014;6(6):690. Jones, Meaghan [corrected to Jones, Meaghan J]; Kobor, Michael [corrected to Kobor, Michael S].

44.

Fetal exposures and perinatal influences on the stool microbiota of premature infants.

Chernikova DA, Koestler DC, Hoen AG, Housman ML, Hibberd PL, Moore JH, Morrison HG, Sogin ML, Zain-Ul-Abideen M, Madan JC.

J Matern Fetal Neonatal Med. 2016;29(1):99-105. doi: 10.3109/14767058.2014.987748. Epub 2015 Sep 4.

45.

A recursively partitioned mixture model for clustering time-course gene expression data.

Koestler DC, Marsit CJ, Christensen BC, Kelsey KT, Houseman EA.

Transl Cancer Res. 2014;3(3):217-232.

46.

Integrative clustering methods for high-dimensional molecular data.

Chalise P, Koestler DC, Bimali M, Yu Q, Fridley BL.

Transl Cancer Res. 2014 Jun 1;3(3):202-216.

47.

In utero arsenic exposure and fetal immune repertoire in a US pregnancy cohort.

Nadeau KC, Li Z, Farzan S, Koestler D, Robbins D, Fei DL, Malipatlolla M, Maecker H, Enelow R, Korrick S, Karagas MR.

Clin Immunol. 2014 Dec;155(2):188-97. doi: 10.1016/j.clim.2014.09.004. Epub 2014 Sep 16.

48.

Placental FKBP5 genetic and epigenetic variation is associated with infant neurobehavioral outcomes in the RICHS cohort.

Paquette AG, Lester BM, Koestler DC, Lesseur C, Armstrong DA, Marsit CJ.

PLoS One. 2014 Aug 12;9(8):e104913. doi: 10.1371/journal.pone.0104913. eCollection 2014.

49.

Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome.

Fridley BL, Armasu SM, Cicek MS, Larson MC, Wang C, Winham SJ, Kalli KR, Koestler DC, Rider DN, Shridhar V, Olson JE, Cunningham JM, Goode EL.

BMC Med Genomics. 2014 Apr 28;7:21. doi: 10.1186/1755-8794-7-21.

50.

Individualizing care for ovarian cancer patients using big data.

Fridley BL, Koestler DC, Godwin AK.

J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju080. doi: 10.1093/jnci/dju080. No abstract available. Erratum in: J Natl Cancer Inst. 2014 Aug;106(8):dju234 doi:10.1093/jnci/dju234. Devin C. Koeslter [corrected to Devin C. Koestler].

PMID:
24700802

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