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Integrated copy number and miRNA expression analysis in triple negative breast cancer of Latin American patients.

Sugita BM, Pereira SR, de Almeida RC, Gill M, Mahajan A, Duttargi A, Kirolikar S, Fadda P, de Lima RS, Urban CA, Makambi K, Madhavan S, Boca SM, Gusev Y, Cavalli IJ, Ribeiro EMSF, Cavalli LR.

Oncotarget. 2019 Oct 22;10(58):6184-6203. doi: 10.18632/oncotarget.27250. eCollection 2019 Oct 22.


Agrobacterial, Single-Stranded DNA-Binding Protein VirE2 and Its Complexes.

Gusev Y, Mazilov S, Volokhina I, Chumakov M.

J Comput Biol. 2019 Sep 5. doi: 10.1089/cmb.2019.0243. [Epub ahead of print]


Genome sequencing analysis of blood cells identifies germline haplotypes strongly associated with drug resistance in osteosarcoma patients.

Bhuvaneshwar K, Harris M, Gusev Y, Madhavan S, Iyer R, Vilboux T, Deeken J, Yang E, Shankar S.

BMC Cancer. 2019 Apr 16;19(1):357. doi: 10.1186/s12885-019-5474-y.


The quasi-low temperature behaviour of specific heat.

Gusev YV.

R Soc Open Sci. 2019 Jan 30;6(1):171285. doi: 10.1098/rsos.171285. eCollection 2019 Jan.


The REMBRANDT study, a large collection of genomic data from brain cancer patients.

Gusev Y, Bhuvaneshwar K, Song L, Zenklusen JC, Fine H, Madhavan S.

Sci Data. 2018 Aug 14;5:180158. doi: 10.1038/sdata.2018.158.


Molecular structure and properties of κ-carrageenan-gelatin gels.

Derkach SR, Voron'ko NG, Kuchina YA, Kolotova DS, Gordeeva AM, Faizullin DA, Gusev YA, Zuev YF, Makshakova ON.

Carbohydr Polym. 2018 Oct 1;197:66-74. doi: 10.1016/j.carbpol.2018.05.063. Epub 2018 May 23.


viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors.

Bhuvaneshwar K, Song L, Madhavan S, Gusev Y.

Front Microbiol. 2018 Jun 5;9:1172. doi: 10.3389/fmicb.2018.01172. eCollection 2018.


CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data.

Song L, Bhuvaneshwar K, Wang Y, Feng Y, Shih IM, Madhavan S, Gusev Y.

Cancer Inform. 2017 Dec 13;16:1176935117746637. doi: 10.1177/1176935117746637. eCollection 2017.


EGR1 regulates cellular metabolism and survival in endocrine resistant breast cancer.

Shajahan-Haq AN, Boca SM, Jin L, Bhuvaneshwar K, Gusev Y, Cheema AK, Demas DD, Raghavan KS, Michalek R, Madhavan S, Clarke R.

Oncotarget. 2017 May 30;8(57):96865-96884. doi: 10.18632/oncotarget.18292. eCollection 2017 Nov 14.


Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors.

Mahajan AS, Sugita BM, Duttargi AN, Saenz F, Krawczyk E, McCutcheon JN, Fonseca AS, Kallakury B, Pohlmann P, Gusev Y, Cavalli LR.

PLoS One. 2017 Oct 19;12(10):e0186190. doi: 10.1371/journal.pone.0186190. eCollection 2017.


The low-temperature dynamic crossover in the dielectric relaxation of ice Ih.

Popov I, Lunev I, Khamzin A, Greenbaum Gutina A, Gusev Y, Feldman Y.

Phys Chem Chem Phys. 2017 Nov 1;19(42):28610-28620. doi: 10.1039/c7cp05731h.


[Analysis of the Gamete-Fusion Genes in the Haploid-inducing ZMS-P Maize Line].

Volokhina IV, Moiseeva YM, Gusev YS, Gutorova OV, Chumakov MI.

Ontogenez. 2017 Mar-Apr;48(2):134-9. Russian.


Computer evaluation of VirE2 protein complexes for ssDNA transfer ability.

Volokhina I, Gusev Y, Mazilov S, Moiseeva Y, Chumakov M.

Comput Biol Chem. 2017 Jun;68:64-70. doi: 10.1016/j.compbiolchem.2017.01.016. Epub 2017 Feb 9.


Differentially expressed miRNAs in triple negative breast cancer between African-American and non-Hispanic white women.

Sugita B, Gill M, Mahajan A, Duttargi A, Kirolikar S, Almeida R, Regis K, Oluwasanmi OL, Marchi F, Marian C, Makambi K, Kallakury B, Sheahan L, Cavalli IJ, Ribeiro EM, Madhavan S, Boca S, Gusev Y, Cavalli LR.

Oncotarget. 2016 Nov 29;7(48):79274-79291. doi: 10.18632/oncotarget.13024.


Globally increased ultraconserved noncoding RNA expression in pancreatic adenocarcinoma.

Jiang J, Azevedo-Pouly AC, Redis RS, Lee EJ, Gusev Y, Allard D, Sutaria DS, Badawi M, Elgamal OA, Lerner MR, Brackett DJ, Calin GA, Schmittgen TD.

Oncotarget. 2016 Aug 16;7(33):53165-53177. doi: 10.18632/oncotarget.10242.


Ly6E/K Signaling to TGFβ Promotes Breast Cancer Progression, Immune Escape, and Drug Resistance.

AlHossiny M, Luo L, Frazier WR, Steiner N, Gusev Y, Kallakury B, Glasgow E, Creswell K, Madhavan S, Kumar R, Upadhyay G.

Cancer Res. 2016 Jun 1;76(11):3376-86. doi: 10.1158/0008-5472.CAN-15-2654. Epub 2016 Apr 11.


G-DOC Plus - an integrative bioinformatics platform for precision medicine.

Bhuvaneshwar K, Belouali A, Singh V, Johnson RM, Song L, Alaoui A, Harris MA, Clarke R, Weiner LM, Gusev Y, Madhavan S.

BMC Bioinformatics. 2016 Apr 30;17(1):193. doi: 10.1186/s12859-016-1010-0.


MicroRNA analysis of breast ductal fluid in breast cancer patients.

Do Canto LM, Marian C, Willey S, Sidawy M, Da Cunha PA, Rone JD, Li X, Gusev Y, Haddad BR.

Int J Oncol. 2016 May;48(5):2071-8. doi: 10.3892/ijo.2016.3435. Epub 2016 Mar 10.


A case study for cloud based high throughput analysis of NGS data using the globus genomics system.

Bhuvaneshwar K, Sulakhe D, Gauba R, Rodriguez A, Madduri R, Dave U, Lacinski L, Foster I, Gusev Y, Madhavan S.

Comput Struct Biotechnol J. 2014 Nov 7;13:64-74. doi: 10.1016/j.csbj.2014.11.001. eCollection 2015.


Distinct lymphocyte antigens 6 (Ly6) family members Ly6D, Ly6E, Ly6K and Ly6H drive tumorigenesis and clinical outcome.

Luo L, McGarvey P, Madhavan S, Kumar R, Gusev Y, Upadhyay G.

Oncotarget. 2016 Mar 8;7(10):11165-93. doi: 10.18632/oncotarget.7163.


ERRγ target genes are poor prognostic factors in Tamoxifen-treated breast cancer.

Madhavan S, Gusev Y, Singh S, Riggins RB.

J Exp Clin Cancer Res. 2015 May 15;34:45. doi: 10.1186/s13046-015-0150-9.


βII-Spectrin (SPTBN1) suppresses progression of hepatocellular carcinoma and Wnt signaling by regulation of Wnt inhibitor kallistatin.

Zhi X, Lin L, Yang S, Bhuvaneshwar K, Wang H, Gusev Y, Lee MH, Kallakury B, Shivapurkar N, Cahn K, Tian X, Marshall JL, Byers SW, He AR.

Hepatology. 2015 Feb;61(2):598-612. doi: 10.1002/hep.27558.


Transcriptional regulation of STAT3 by SPTBN1 and SMAD3 in HCC through cAMP-response element-binding proteins ATF3 and CREB2.

Lin L, Yao Z, Bhuvaneshwar K, Gusev Y, Kallakury B, Yang S, Shetty K, He AR.

Carcinogenesis. 2014 Nov;35(11):2393-403. doi: 10.1093/carcin/bgu163. Epub 2014 Aug 5.


Increased copy number of the DLX4 homeobox gene in breast axillary lymph node metastasis.

Torresan C, Oliveira MM, Pereira SR, Ribeiro EM, Marian C, Gusev Y, Lima RS, Urban CA, Berg PE, Haddad BR, Cavalli IJ, Cavalli LR.

Cancer Genet. 2014 May;207(5):177-87. doi: 10.1016/j.cancergen.2014.04.007. Epub 2014 May 2.


Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse.

Madhavan S, Gusev Y, Natarajan TG, Song L, Bhuvaneshwar K, Gauba R, Pandey A, Haddad BR, Goerlitz D, Cheema AK, Juhl H, Kallakury B, Marshall JL, Byers SW, Weiner LM.

Front Genet. 2013 Nov 20;4:236. doi: 10.3389/fgene.2013.00236. eCollection 2013.


Platform for Personalized Oncology: Integrative analyses reveal novel molecular signatures associated with colorectal cancer relapse.

Madhavan S, Gauba R, Song L, Bhuvaneshwar K, Gusev Y, Byers S, Juhl H, Weiner L.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:118. eCollection 2013.


Tumor suppressive function of mir-205 in breast cancer is linked to HMGB3 regulation.

Elgamal OA, Park JK, Gusev Y, Azevedo-Pouly AC, Jiang J, Roopra A, Schmittgen TD.

PLoS One. 2013 Oct 2;8(10):e76402. doi: 10.1371/journal.pone.0076402. eCollection 2013.


In silico discovery of mitosis regulation networks associated with early distant metastases in estrogen receptor positive breast cancers.

Gusev Y, Riggins RB, Bhuvaneshwar K, Gauba R, Sheahan L, Clarke R, Madhavan S.

Cancer Inform. 2013;12:31-51. doi: 10.4137/CIN.S10329. Epub 2013 Feb 13.


Preclinical magnetic resonance imaging and systems biology in cancer research: current applications and challenges.

Albanese C, Rodriguez OC, VanMeter J, Fricke ST, Rood BR, Lee Y, Wang SS, Madhavan S, Gusev Y, Petricoin EF 3rd, Wang Y.

Am J Pathol. 2013 Feb;182(2):312-8. doi: 10.1016/j.ajpath.2012.09.024. Epub 2012 Dec 4. Review.


VirE2-dependent pores for ssDNA transfer across artificial and cell membranes.

Volokhina I, Gusev Y, Mazilov S, Chumakov M.

J Bioinform Comput Biol. 2012 Apr;10(2):1241009. doi: 10.1142/S0219720012410090.


Supramolecular complexes of the Agrobacterium tumefaciens virulence protein VirE2.

Volokhina IV, Gusev YS, Mazilov SI, Chumakov MI.

Biochemistry (Mosc). 2011 Nov;76(11):1270-5. doi: 10.1134/S0006297911110095.


G-DOC: a systems medicine platform for personalized oncology.

Madhavan S, Gusev Y, Harris M, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet LA, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, Weiner LM.

Neoplasia. 2011 Sep;13(9):771-83.


miR-132 and miR-212 are increased in pancreatic cancer and target the retinoblastoma tumor suppressor.

Park JK, Henry JC, Jiang J, Esau C, Gusev Y, Lerner MR, Postier RG, Brackett DJ, Schmittgen TD.

Biochem Biophys Res Commun. 2011 Mar 25;406(4):518-23. doi: 10.1016/j.bbrc.2011.02.065. Epub 2011 Feb 15.


MicroRNAs are mediators of androgen action in prostate and muscle.

Narayanan R, Jiang J, Gusev Y, Jones A, Kearbey JD, Miller DD, Schmittgen TD, Dalton JT.

PLoS One. 2010 Oct 27;5(10):e13637. doi: 10.1371/journal.pone.0013637.


Magnetized boxes for housing polarized spins in homogeneous fields.

Hiebel S, Grossmann T, Kiselev D, Schmiedeskamp J, Gusev Y, Heil W, Karpuk S, Krimmer J, Otten EW, Salhi Z.

J Magn Reson. 2010 May;204(1):37-49. doi: 10.1016/j.jmr.2010.01.017. Epub 2010 Feb 14.


Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction.

Wren JD, Gusev Y, Isokpehi RD, Berleant D, Braga-Neto U, Wilkins D, Bridges S.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S1. doi: 10.1186/1471-2105-10-S11-S1. No abstract available.


Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Wren JD, Wilkins D, Fuscoe JC, Bridges S, Winters-Hilt S, Gusev Y.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S1. doi: 10.1186/1471-2105-9-S9-S1. No abstract available.


Microarray analysis of choroid/RPE gene expression in marmoset eyes undergoing changes in ocular growth and refraction.

Shelton L, Troilo D, Lerner MR, Gusev Y, Brackett DJ, Rada JS.

Mol Vis. 2008 Aug 11;14:1465-79.


Dr. Andrei Yakovlev: visionary, leader, iconoclast.

Gusev Y, Hanin L, Klebanov L, Tsodikov A, Yanev NM, Zorin A.

Biol Direct. 2008 Mar 26;3:10. doi: 10.1186/1745-6150-3-10. No abstract available.


Association of MicroRNA expression in hepatocellular carcinomas with hepatitis infection, cirrhosis, and patient survival.

Jiang J, Gusev Y, Aderca I, Mettler TA, Nagorney DM, Brackett DJ, Roberts LR, Schmittgen TD.

Clin Cancer Res. 2008 Jan 15;14(2):419-27. doi: 10.1158/1078-0432.CCR-07-0523.


Biomarker identification in human pancreatic cancer sera.

Hanas JS, Hocker JR, Cheung JY, Larabee JL, Lerner MR, Lightfoot SA, Morgan DL, Denson KD, Prejeant KC, Gusev Y, Smith BJ, Hanas RJ, Postier RG, Brackett DJ.

Pancreas. 2008 Jan;36(1):61-9. doi: 10.1097/mpa.0b013e3180d0a738.


Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer.

Gusev Y, Schmittgen TD, Lerner M, Postier R, Brackett D.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S16.


Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.

Wilkins D, Gusev Y, Loganantharaj R, Bridges S, Winters-Hilt S, Wren JD.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S1. No abstract available.


Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors.

Lee EJ, Baek M, Gusev Y, Brackett DJ, Nuovo GJ, Schmittgen TD.

RNA. 2008 Jan;14(1):35-42. Epub 2007 Nov 19.


MicroRNA expression profiling in cancer from a bioinformatics prospective.

Gusev Y, Brackett DJ.

Expert Rev Mol Diagn. 2007 Nov;7(6):787-92. Review.


Expression profiling identifies microRNA signature in pancreatic cancer.

Lee EJ, Gusev Y, Jiang J, Nuovo GJ, Lerner MR, Frankel WL, Morgan DL, Postier RG, Brackett DJ, Schmittgen TD.

Int J Cancer. 2007 Mar 1;120(5):1046-54.


Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction.

Wren JD, Gusev Y, Ptitsyn A, Winters-Hilt S.

BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S1. No abstract available.


Real-time expression profiling of microRNA precursors in human cancer cell lines.

Jiang J, Lee EJ, Gusev Y, Schmittgen TD.

Nucleic Acids Res. 2005 Sep 28;33(17):5394-403. Print 2005.


Expression of pp32 gene family members in breast cancer.

Kadkol SS, El Naga GA, Brody JR, Bai J, Gusev Y, Dooley WC, Pasternack GR.

Breast Cancer Res Treat. 2001 Jul;68(1):65-73.


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