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Items: 1 to 50 of 111

1.

IFNL4-ΔG allele is associated with an interferon signature in tumors and survival of African-American men with prostate cancer.

Tang W, Wallace TA, Yi M, Magi-Galluzzi C, Dorsey TH, Onabajo OO, Obajemu A, Jordan SV, Loffredo CA, Stephens RM, Silverman RH, Stark GR, Klein EA, Prokunina-Olsson L, Ambs S.

Clin Cancer Res. 2018 Jul 16. pii: clincanres.1060.2018. doi: 10.1158/1078-0432.CCR-18-1060. [Epub ahead of print]

PMID:
30012562
2.

The Drosophila simulans Y chromosome interacts with the autosomes to influence male fitness.

Archer CR, Stephens RM, Sharma MD, Hosken DJ.

J Evol Biol. 2017 Oct;30(10):1821-1825. doi: 10.1111/jeb.13141. Epub 2017 Aug 4.

PMID:
28703322
3.

Tumor RAS Gene Expression Levels Are Influenced by the Mutational Status of RAS Genes and Both Upstream and Downstream RAS Pathway Genes.

Stephens RM, Yi M, Kessing B, Nissley DV, McCormick F.

Cancer Inform. 2017 Jun 8;16:1176935117711944. doi: 10.1177/1176935117711944. eCollection 2017.

4.

Comparative proteomics of a model MCF10A-KRasG12V cell line reveals a distinct molecular signature of the KRasG12V cell surface.

Ye X, Chan KC, Waters AM, Bess M, Harned A, Wei BR, Loncarek J, Luke BT, Orsburn BC, Hollinger BD, Stephens RM, Bagni R, Martinko A, Wells JA, Nissley DV, McCormick F, Whiteley G, Blonder J.

Oncotarget. 2016 Dec 27;7(52):86948-86971. doi: 10.18632/oncotarget.13566.

5.

An Immune-Inflammation Gene Expression Signature in Prostate Tumors of Smokers.

Prueitt RL, Wallace TA, Glynn SA, Yi M, Tang W, Luo J, Dorsey TH, Stagliano KE, Gillespie JW, Hudson RS, Terunuma A, Shoe JL, Haines DC, Yfantis HG, Han M, Martin DN, Jordan SV, Borin JF, Naslund MJ, Alexander RB, Stephens RM, Loffredo CA, Lee DH, Putluri N, Sreekumar A, Hurwitz AA, Ambs S.

Cancer Res. 2016 Mar 1;76(5):1055-1065. doi: 10.1158/0008-5472.CAN-14-3630. Epub 2015 Dec 30.

6.

Erratum to: The somatic autosomal mutation matrix in cancer genomes.

Temiz NA, Donohue DE, Bacolla A, Vasquez KM, Cooper DN, Mudunuri U, Ivanic J, Cer RZ, Yi M, Stephens RM, Collins JR, Luke BT.

Hum Genet. 2015 Aug;134(8):865-7. doi: 10.1007/s00439-015-1576-z. No abstract available.

7.

The somatic autosomal mutation matrix in cancer genomes.

Temiz NA, Donohue DE, Bacolla A, Vasquez KM, Cooper DN, Mudunuri U, Ivanic J, Cer RZ, Yi M, Stephens RM, Collins JR, Luke BT.

Hum Genet. 2015 Aug;134(8):851-64. doi: 10.1007/s00439-015-1566-1. Epub 2015 May 23. Erratum in: Hum Genet. 2015 Aug;134(8):865-7.

8.

A new non-surgical technique for management of high condylar neck fractures.

Stephens RM, Naini FB.

Ann R Coll Surg Engl. 2014 Sep;96(6):482-3. doi: 10.1308/rcsann.2014.96.6.482. No abstract available.

9.

Performance comparison of SNP detection tools with illumina exome sequencing data--an assessment using both family pedigree information and sample-matched SNP array data.

Yi M, Zhao Y, Jia L, He M, Kebebew E, Stephens RM.

Nucleic Acids Res. 2014 Jul;42(12):e101. doi: 10.1093/nar/gku392. Epub 2014 May 15.

10.

Pathway-specific engineered mouse allograft models functionally recapitulate human serous epithelial ovarian cancer.

Szabova L, Bupp S, Kamal M, Householder DB, Hernandez L, Schlomer JJ, Baran ML, Yi M, Stephens RM, Annunziata CM, Martin PL, Van Dyke TA, Weaver Ohler Z, Difilippantonio S.

PLoS One. 2014 Apr 18;9(4):e95649. doi: 10.1371/journal.pone.0095649. eCollection 2014.

11.

miR-126 contributes to Parkinson's disease by dysregulating the insulin-like growth factor/phosphoinositide 3-kinase signaling.

Kim W, Lee Y, McKenna ND, Yi M, Simunovic F, Wang Y, Kong B, Rooney RJ, Seo H, Stephens RM, Sonntag KC.

Neurobiol Aging. 2014 Jul;35(7):1712-21. doi: 10.1016/j.neurobiolaging.2014.01.021. Epub 2014 Jan 24.

12.

MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis.

Terunuma A, Putluri N, Mishra P, Mathé EA, Dorsey TH, Yi M, Wallace TA, Issaq HJ, Zhou M, Killian JK, Stevenson HS, Karoly ED, Chan K, Samanta S, Prieto D, Hsu TY, Kurley SJ, Putluri V, Sonavane R, Edelman DC, Wulff J, Starks AM, Yang Y, Kittles RA, Yfantis HG, Lee DH, Ioffe OB, Schiff R, Stephens RM, Meltzer PS, Veenstra TD, Westbrook TF, Sreekumar A, Ambs S.

J Clin Invest. 2014 Jan;124(1):398-412. doi: 10.1172/JCI71180. Epub 2013 Dec 9.

13.

Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data.

Mudunuri US, Khouja M, Repetski S, Venkataraman G, Che A, Luke BT, Girard FP, Stephens RM.

PLoS One. 2013 Dec 2;8(12):e80503. doi: 10.1371/journal.pone.0080503. eCollection 2013.

14.

AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations.

Vuong H, Stephens RM, Volfovsky N.

Bioinformatics. 2014 Apr 1;30(7):1013-4. doi: 10.1093/bioinformatics/btt655. Epub 2013 Nov 9.

15.

Guanine holes are prominent targets for mutation in cancer and inherited disease.

Bacolla A, Temiz NA, Yi M, Ivanic J, Cer RZ, Donohue DE, Ball EV, Mudunuri US, Wang G, Jain A, Volfovsky N, Luke BT, Stephens RM, Cooper DN, Collins JR, Vasquez KM.

PLoS Genet. 2013;9(9):e1003816. doi: 10.1371/journal.pgen.1003816. Epub 2013 Sep 26.

16.

Transcription signatures encoded by ultraconserved genomic regions in human prostate cancer.

Hudson RS, Yi M, Volfovsky N, Prueitt RL, Esposito D, Volinia S, Liu CG, Schetter AJ, Van Roosbroeck K, Stephens RM, Calin GA, Croce CM, Ambs S.

Mol Cancer. 2013 Feb 14;12:13. doi: 10.1186/1476-4598-12-13.

17.

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.

Retrovirology. 2013 Feb 13;10:18. doi: 10.1186/1742-4690-10-18.

18.

SRAdb: query and use public next-generation sequencing data from within R.

Zhu Y, Stephens RM, Meltzer PS, Davis SR.

BMC Bioinformatics. 2013 Jan 17;14:19. doi: 10.1186/1471-2105-14-19.

19.

An integrated understanding of the physiological response to elevated extracellular phosphate.

Camalier CE, Yi M, Yu LR, Hood BL, Conrads KA, Lee YJ, Lin Y, Garneys LM, Bouloux GF, Young MR, Veenstra TD, Stephens RM, Colburn NH, Conrads TP, Beck GR Jr.

J Cell Physiol. 2013 Jul;228(7):1536-50. doi: 10.1002/jcp.24312.

20.

Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia.

Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M, Bethell D, Se Y, Lon C, Tyner SD, Saunders DL, Socheat D, Ariey F, Phyo AP, Starzengruber P, Fuehrer HP, Swoboda P, Stepniewska K, Flegg J, Arze C, Cerqueira GC, Silva JC, Ricklefs SM, Porcella SF, Stephens RM, Adams M, Kenefic LJ, Campino S, Auburn S, MacInnis B, Kwiatkowski DP, Su XZ, White NJ, Ringwald P, Plowe CV.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):240-5. doi: 10.1073/pnas.1211205110. Epub 2012 Dec 17.

21.

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.

Cer RZ, Donohue DE, Mudunuri US, Temiz NA, Loss MA, Starner NJ, Halusa GN, Volfovsky N, Yi M, Luke BT, Bacolla A, Collins JR, Stephens RM.

Nucleic Acids Res. 2013 Jan;41(Database issue):D94-D100. doi: 10.1093/nar/gks955. Epub 2012 Nov 3.

22.

MicroRNA-106b-25 cluster expression is associated with early disease recurrence and targets caspase-7 and focal adhesion in human prostate cancer.

Hudson RS, Yi M, Esposito D, Glynn SA, Starks AM, Yang Y, Schetter AJ, Watkins SK, Hurwitz AA, Dorsey TH, Stephens RM, Croce CM, Ambs S.

Oncogene. 2013 Aug 29;32(35):4139-47. doi: 10.1038/onc.2012.424. Epub 2012 Sep 17.

23.

Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool).

Cer RZ, Bruce KH, Donohue DE, Temiz NA, Mudunuri US, Yi M, Volfovsky N, Bacolla A, Luke BT, Collins JR, Stephens RM.

Curr Protoc Hum Genet. 2012 Apr;Chapter 18:Unit 18.7.1-22. doi: 10.1002/0471142905.hg1807s73.

24.

MiR-1 and miR-200 inhibit EMT via Slug-dependent and tumorigenesis via Slug-independent mechanisms.

Liu YN, Yin JJ, Abou-Kheir W, Hynes PG, Casey OM, Fang L, Yi M, Stephens RM, Seng V, Sheppard-Tillman H, Martin P, Kelly K.

Oncogene. 2013 Jan 17;32(3):296-306. doi: 10.1038/onc.2012.58. Epub 2012 Feb 27.

PMID:
22370643
25.

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance.

Li J, Akagi K, Hu Y, Trivett AL, Hlynialuk CJ, Swing DA, Volfovsky N, Morgan TC, Golubeva Y, Stephens RM, Smith DE, Symer DE.

Genome Res. 2012 May;22(5):870-84. doi: 10.1101/gr.130740.111. Epub 2012 Feb 23.

26.

MicroRNA-1 is a candidate tumor suppressor and prognostic marker in human prostate cancer.

Hudson RS, Yi M, Esposito D, Watkins SK, Hurwitz AA, Yfantis HG, Lee DH, Borin JF, Naslund MJ, Alexander RB, Dorsey TH, Stephens RM, Croce CM, Ambs S.

Nucleic Acids Res. 2012 Apr;40(8):3689-703. doi: 10.1093/nar/gkr1222. Epub 2011 Dec 30.

27.

Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage.

Zhu M, Yi M, Kim CH, Deng C, Li Y, Medina D, Stephens RM, Green JE.

Genome Biol. 2011 Aug 16;12(8):R77. doi: 10.1186/gb-2011-12-8-r77.

28.

Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants.

Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Kolokotronis SO, Roca AL.

PLoS One. 2011;6(6):e20642. doi: 10.1371/journal.pone.0020642. Epub 2011 Jun 8.

29.

Human glioma growth is controlled by microRNA-10b.

Gabriely G, Yi M, Narayan RS, Niers JM, Wurdinger T, Imitola J, Ligon KL, Kesari S, Esau C, Stephens RM, Tannous BA, Krichevsky AM.

Cancer Res. 2011 May 15;71(10):3563-72. doi: 10.1158/0008-5472.CAN-10-3568. Epub 2011 Apr 6.

30.

Impact of chromatin structure on sequence variability in the human genome.

Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ.

Nat Struct Mol Biol. 2011 Apr;18(4):510-5. doi: 10.1038/nsmb.2012. Epub 2011 Mar 13.

31.

miRNA-7 attenuation in Schwannoma tumors stimulates growth by upregulating three oncogenic signaling pathways.

Saydam O, Senol O, Würdinger T, Mizrak A, Ozdener GB, Stemmer-Rachamimov AO, Yi M, Stephens RM, Krichevsky AM, Saydam N, Brenner GJ, Breakefield XO.

Cancer Res. 2011 Feb 1;71(3):852-61. doi: 10.1158/0008-5472.CAN-10-1219. Epub 2010 Dec 13.

32.

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes.

Cer RZ, Bruce KH, Mudunuri US, Yi M, Volfovsky N, Luke BT, Bacolla A, Collins JR, Stephens RM.

Nucleic Acids Res. 2011 Jan;39(Database issue):D383-91. doi: 10.1093/nar/gkq1170. Epub 2010 Nov 21.

33.

Increased NOS2 predicts poor survival in estrogen receptor-negative breast cancer patients.

Glynn SA, Boersma BJ, Dorsey TH, Yi M, Yfantis HG, Ridnour LA, Martin DN, Switzer CH, Hudson RS, Wink DA, Lee DH, Stephens RM, Ambs S.

J Clin Invest. 2010 Nov;120(11):3843-54. doi: 10.1172/JCI42059. Epub 2010 Oct 18.

34.

Long-range enhancers on 8q24 regulate c-Myc.

Sotelo J, Esposito D, Duhagon MA, Banfield K, Mehalko J, Liao H, Stephens RM, Harris TJ, Munroe DJ, Wu X.

Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3001-5. doi: 10.1073/pnas.0906067107. Epub 2010 Jan 26.

35.

Temporal characteristics of botulinum neurotoxin therapy.

Lebeda FJ, Cer RZ, Stephens RM, Mudunuri U.

Expert Rev Neurother. 2010 Jan;10(1):93-103. doi: 10.1586/ern.09.134. Review.

36.

MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains.

Akagi K, Stephens RM, Li J, Evdokimov E, Kuehn MR, Volfovsky N, Symer DE.

Nucleic Acids Res. 2010 Jan;38(Database issue):D600-6. doi: 10.1093/nar/gkp1046. Epub 2009 Nov 20.

37.

RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy.

Shao W, Kearney M, Maldarelli F, Mellors JW, Stephens RM, Lifson JD, KewalRamani VN, Ambrose Z, Coffin JM, Palmer SE.

Retrovirology. 2009 Nov 4;6:101. doi: 10.1186/1742-4690-6-101.

38.

Downregulated microRNA-200a in meningiomas promotes tumor growth by reducing E-cadherin and activating the Wnt/beta-catenin signaling pathway.

Saydam O, Shen Y, Würdinger T, Senol O, Boke E, James MF, Tannous BA, Stemmer-Rachamimov AO, Yi M, Stephens RM, Fraefel C, Gusella JF, Krichevsky AM, Breakefield XO.

Mol Cell Biol. 2009 Nov;29(21):5923-40. doi: 10.1128/MCB.00332-09. Epub 2009 Aug 24.

39.

Predictors of Outpatient Mental Health Service Use by American Youth.

Alexandre PK, Stephens RM, Laris AS, Dowling K, Rely K.

Psychol Serv. 2008 Aug 1;5(3):251-261.

40.
41.

Large-scale genotyping and genetic mapping in Plasmodium parasites.

Su XZ, Jiang H, Yi M, Mu J, Stephens RM.

Korean J Parasitol. 2009 Jun;47(2):83-91. doi: 10.3347/kjp.2009.47.2.83. Epub 2009 May 26. Review.

42.

Differences in the tumor microenvironment between African-American and European-American breast cancer patients.

Martin DN, Boersma BJ, Yi M, Reimers M, Howe TM, Yfantis HG, Tsai YC, Williams EH, Lee DH, Stephens RM, Weissman AM, Ambs S.

PLoS One. 2009;4(2):e4531. doi: 10.1371/journal.pone.0004531. Epub 2009 Feb 19.

43.

Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22.

Volfovsky N, Oleksyk TK, Cruz KC, Truelove AL, Stephens RM, Smith MW.

BMC Genomics. 2009 Jan 26;10:51. doi: 10.1186/1471-2164-10-51.

44.

bioDBnet: the biological database network.

Mudunuri U, Che A, Yi M, Stephens RM.

Bioinformatics. 2009 Feb 15;25(4):555-6. doi: 10.1093/bioinformatics/btn654. Epub 2009 Jan 7.

45.

Gene expression profiling of substantia nigra dopamine neurons: further insights into Parkinson's disease pathology.

Simunovic F, Yi M, Wang Y, Macey L, Brown LT, Krichevsky AM, Andersen SL, Stephens RM, Benes FM, Sonntag KC.

Brain. 2009 Jul;132(Pt 7):1795-809. doi: 10.1093/brain/awn323. Epub 2008 Dec 3.

46.

Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi.

Anderson SJ, Stone CL, Posada-Buitrago ML, Boore JL, Neelam BA, Stephens RM, Luster DG, Frederick RD, Pedley KF.

Mol Ecol Resour. 2008 Nov;8(6):1310-2. doi: 10.1111/j.1755-0998.2008.02272.x.

PMID:
21586030
47.

Altered gene expression profiles define pathways in colorectal cancer cell lines affected by celecoxib.

Fatima N, Yi M, Ajaz S, Stephens RM, Stauffer S, Greenwald P, Munroe DJ, Ali IU.

Cancer Epidemiol Biomarkers Prev. 2008 Nov;17(11):3051-61. doi: 10.1158/1055-9965.EPI-08-0261. Epub 2008 Oct 28.

48.
49.

Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray.

Jiang H, Yi M, Mu J, Zhang L, Ivens A, Klimczak LJ, Huyen Y, Stephens RM, Su XZ.

BMC Genomics. 2008 Aug 25;9:398. doi: 10.1186/1471-2164-9-398.

50.

Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

Ambs S, Prueitt RL, Yi M, Hudson RS, Howe TM, Petrocca F, Wallace TA, Liu CG, Volinia S, Calin GA, Yfantis HG, Stephens RM, Croce CM.

Cancer Res. 2008 Aug 1;68(15):6162-70. doi: 10.1158/0008-5472.CAN-08-0144.

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