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Items: 1 to 50 of 57

1.

An ErbB2/c-Src axis links bioenergetics with PRC2 translation to drive epigenetic reprogramming and mammary tumorigenesis.

Smith HW, Hirukawa A, Sanguin-Gendreau V, Nandi I, Dufour CR, Zuo D, Tandoc K, Leibovitch M, Singh S, Rennhack JP, Swiatnicki M, Lavoie C, Papavasiliou V, Temps C, Carragher NO, Unciti-Broceta A, Savage P, Basik M, van Hoef V, Larsson O, Cooper CL, Vargas Calderon AC, Beith J, Millar E, Selinger C, Giguère V, Park M, Harris LN, Varadan V, Andrechek ER, O'Toole SA, Topisirovic I, Muller WJ.

Nat Commun. 2019 Jul 1;10(1):2901. doi: 10.1038/s41467-019-10681-4.

2.

Association of Peritumoral Radiomics With Tumor Biology and Pathologic Response to Preoperative Targeted Therapy for HER2 (ERBB2)-Positive Breast Cancer.

Braman N, Prasanna P, Whitney J, Singh S, Beig N, Etesami M, Bates DDB, Gallagher K, Bloch BN, Vulchi M, Turk P, Bera K, Abraham J, Sikov WM, Somlo G, Harris LN, Gilmore H, Plecha D, Varadan V, Madabhushi A.

JAMA Netw Open. 2019 Apr 5;2(4):e192561. doi: 10.1001/jamanetworkopen.2019.2561.

3.

Systems Biology Analyses Show Hyperactivation of Transforming Growth Factor-β and JNK Signaling Pathways in Esophageal Cancer.

Blum AE, Venkitachalam S, Ravillah D, Chelluboyina AK, Kieber-Emmons AM, Ravi L, Kresak A, Chandar AK, Markowitz SD, Canto MI, Wang JS, Shaheen NJ, Guo Y, Shyr Y, Willis JE, Chak A, Varadan V, Guda K.

Gastroenterology. 2019 May;156(6):1761-1774. doi: 10.1053/j.gastro.2019.01.263. Epub 2019 Feb 12.

PMID:
30768984
4.

The DNMT1-associated lincRNA DACOR1 reprograms genome-wide DNA methylation in colon cancer.

Somasundaram S, Forrest ME, Moinova H, Cohen A, Varadan V, LaFramboise T, Markowitz S, Khalil AM.

Clin Epigenetics. 2018 Oct 22;10(1):127. doi: 10.1186/s13148-018-0555-3.

5.

Clinicopathological, immunohistochemical and molecular correlation of neural crest transcription factor SOX10 expression in triple-negative breast carcinoma.

Harbhajanka A, Chahar S, Miskimen K, Silverman P, Harris L, Williams N, Varadan V, Gilmore H.

Hum Pathol. 2018 Oct;80:163-169. doi: 10.1016/j.humpath.2018.06.007. Epub 2018 Jun 9.

PMID:
29894722
6.

Radiogenomic analysis of hypoxia pathway is predictive of overall survival in Glioblastoma.

Beig N, Patel J, Prasanna P, Hill V, Gupta A, Correa R, Bera K, Singh S, Partovi S, Varadan V, Ahluwalia M, Madabhushi A, Tiwari P.

Sci Rep. 2018 Jan 8;8(1):7. doi: 10.1038/s41598-017-18310-0.

7.

Interferon-beta represses cancer stem cell properties in triple-negative breast cancer.

Doherty MR, Cheon H, Junk DJ, Vinayak S, Varadan V, Telli ML, Ford JM, Stark GR, Jackson MW.

Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13792-13797. doi: 10.1073/pnas.1713728114. Epub 2017 Dec 11.

8.

Mitotic Vulnerability in Triple-Negative Breast Cancer Associated with LIN9 Is Targetable with BET Inhibitors.

Sahni JM, Gayle SS, Webb BM, Weber-Bonk KL, Seachrist DD, Singh S, Sizemore ST, Restrepo NA, Bebek G, Scacheri PC, Varadan V, Summers MK, Keri RA.

Cancer Res. 2017 Oct 1;77(19):5395-5408. doi: 10.1158/0008-5472.CAN-17-1571. Epub 2017 Aug 14.

9.

Erratum to: Global DNA methylation patterns in Barrett's esophagus, dysplastic Barrett's, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use.

Kaz AM, Wong CJ, Varadan V, Willis JE, Chak A, Grady WM.

Clin Epigenetics. 2017 Mar 1;9:23. doi: 10.1186/s13148-017-0324-8. eCollection 2017.

10.

InFlo: a novel systems biology framework identifies cAMP-CREB1 axis as a key modulator of platinum resistance in ovarian cancer.

Dimitrova N, Nagaraj AB, Razi A, Singh S, Kamalakaran S, Banerjee N, Joseph P, Mankovich A, Mittal P, DiFeo A, Varadan V.

Oncogene. 2017 Apr 27;36(17):2472-2482. doi: 10.1038/onc.2016.398. Epub 2016 Nov 7.

11.
12.

RNA Sequencing Identifies Transcriptionally Viable Gene Fusions in Esophageal Adenocarcinomas.

Blum AE, Venkitachalam S, Guo Y, Kieber-Emmons AM, Ravi L, Chandar AK, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Barnholtz-Sloan JS, Markowitz SD, Willis JE, Shyr Y, Chak A, Varadan V, Guda K.

Cancer Res. 2016 Oct 1;76(19):5628-5633. Epub 2016 Aug 8.

13.

Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach.

Razi A, Afghah F, Singh S, Varadan V.

Biomed Eng Comput Biol. 2016 Apr 5;7(Suppl 2):1-14. doi: 10.4137/BECB.S38244. eCollection 2016.

14.

Biochemical and functional characterization of glycosylation-associated mutational landscapes in colon cancer.

Venkitachalam S, Revoredo L, Varadan V, Fecteau RE, Ravi L, Lutterbaugh J, Markowitz SD, Willis JE, Gerken TA, Guda K.

Sci Rep. 2016 Mar 23;6:23642. doi: 10.1038/srep23642.

15.

Biomarkers for Predicting Response to Anti-HER2 Agents.

Varadan V, Sandoval M, Harris LN.

Adv Exp Med Biol. 2016;882:155-67. doi: 10.1007/978-3-319-22909-6_6. Review.

PMID:
26987534
16.

Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors.

Goel S, Wang Q, Watt AC, Tolaney SM, Dillon DA, Li W, Ramm S, Palmer AC, Yuzugullu H, Varadan V, Tuck D, Harris LN, Wong KK, Liu XS, Sicinski P, Winer EP, Krop IE, Zhao JJ.

Cancer Cell. 2016 Mar 14;29(3):255-269. doi: 10.1016/j.ccell.2016.02.006.

17.

Immune Signatures Following Single Dose Trastuzumab Predict Pathologic Response to PreoperativeTrastuzumab and Chemotherapy in HER2-Positive Early Breast Cancer.

Varadan V, Gilmore H, Miskimen KL, Tuck D, Parsai S, Awadallah A, Krop IE, Winer EP, Bossuyt V, Somlo G, Abu-Khalaf MM, Fenton MA, Sikov W, Harris LN.

Clin Cancer Res. 2016 Jul 1;22(13):3249-59. doi: 10.1158/1078-0432.CCR-15-2021. Epub 2016 Feb 3.

18.

Non-linear Bayesian framework to determine the transcriptional effects of cancer-associated genomic aberrations.

Razi A, Banerjee N, Dimitrova N, Varadan V.

Conf Proc IEEE Eng Med Biol Soc. 2015;2015:6514-8. doi: 10.1109/EMBC.2015.7319885.

19.

Identifying gene subnetworks associated with clinical outcome in ovarian cancer using Network Based Coalition Game.

Razi A, Afghah F, Varadan V.

Conf Proc IEEE Eng Med Biol Soc. 2015;2015:6509-13. doi: 10.1109/EMBC.2015.7319884.

PMID:
26737784
20.

Brief-exposure to preoperative bevacizumab reveals a TGF-β signature predictive of response in HER2-negative breast cancers.

Varadan V, Kamalakaran S, Gilmore H, Banerjee N, Janevski A, Miskimen KL, Williams N, Basavanhalli A, Madabhushi A, Lezon-Geyda K, Bossuyt V, Lannin DR, Abu-Khalaf M, Sikov W, Dimitrova N, Harris LN.

Int J Cancer. 2016 Feb 1;138(3):747-57. doi: 10.1002/ijc.29808. Epub 2015 Aug 31.

21.

ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients.

Varadan V, Singh S, Nosrati A, Ravi L, Lutterbaugh J, Barnholtz-Sloan JS, Markowitz SD, Willis JE, Guda K.

Genome Med. 2015 Jul 20;7:69. doi: 10.1186/s13073-015-0192-9. eCollection 2015.

22.

Reply to Ashktorab et al.: Mutational landscape of colon cancers in African Americans.

Guda K, Veigl ML, Varadan V, Nosrati A, Ravi L, Lutterbaugh J, Beard L, Willson JK, Sedwick WD, Wang ZJ, Molyneaux N, Miron A, Adams MD, Elston RC, Markowitz SD, Willis JE.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2853. doi: 10.1073/pnas.1505059112. Epub 2015 May 4. No abstract available.

23.

Novel recurrently mutated genes in African American colon cancers.

Guda K, Veigl ML, Varadan V, Nosrati A, Ravi L, Lutterbaugh J, Beard L, Willson JK, Sedwick WD, Wang ZJ, Molyneaux N, Miron A, Adams MD, Elston RC, Markowitz SD, Willis JE.

Proc Natl Acad Sci U S A. 2015 Jan 27;112(4):1149-54. doi: 10.1073/pnas.1417064112. Epub 2015 Jan 12.

24.

Mechanical properties of carbon nanotube/polymer composites.

Arash B, Wang Q, Varadan VK.

Sci Rep. 2014 Oct 1;4:6479. doi: 10.1038/srep06479.

25.

Integrative prediction of gene function and platinum-free survival from genomic and epigenetic features in ovarian cancer.

Wrzeszczynski KO, Varadan V, Kamalakaran S, Levine DA, Dimitrova N, Lucito R.

Methods Mol Biol. 2013;1049:35-51. doi: 10.1007/978-1-62703-547-7_4.

PMID:
23913207
26.

Translating next generation sequencing to practice: opportunities and necessary steps.

Kamalakaran S, Varadan V, Janevski A, Banerjee N, Tuck D, McCombie WR, Dimitrova N, Harris LN.

Mol Oncol. 2013 Aug;7(4):743-55. doi: 10.1016/j.molonc.2013.04.008. Epub 2013 May 15. Review.

27.

Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions.

Tang MH, Varadan V, Kamalakaran S, Zhang MQ, Dimitrova N, Hicks J.

Front Oncol. 2012 Dec 27;2:197. doi: 10.3389/fonc.2012.00197. eCollection 2012.

28.

Effective normalization for copy number variation detection from whole genome sequencing.

Janevski A, Varadan V, Kamalakaran S, Banerjee N, Dimitrova N.

BMC Genomics. 2012;13 Suppl 6:S16. doi: 10.1186/1471-2164-13-S6-S16. Epub 2012 Oct 26.

29.

A microRNA panel to discriminate carcinomas from high-grade intraepithelial neoplasms in colonoscopy biopsy tissue.

Wang S, Wang L, Bayaxi N, Li J, Verhaegh W, Janevski A, Varadan V, Ren Y, Merkle D, Meng X, Gao X, Wang H, Ren J, Kuo WP, Dimitrova N, Wu Y, Zhu H.

Gut. 2013 Feb;62(2):280-9. doi: 10.1136/gutjnl-2011-301554. Epub 2012 Apr 25. Erratum in: Gut. 2013 Feb;62(2):288.

PMID:
22535378
30.

Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer.

Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, Kamalakaran S, Levine DA, Dimitrova N, Zhang MQ, Lucito R.

PLoS One. 2011;6(12):e28503. doi: 10.1371/journal.pone.0028503. Epub 2011 Dec 8.

31.

DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables.

Kamalakaran S, Varadan V, Giercksky Russnes HE, Levy D, Kendall J, Janevski A, Riggs M, Banerjee N, Synnestvedt M, Schlichting E, Kåresen R, Shama Prasada K, Rotti H, Rao R, Rao L, Eric Tang MH, Satyamoorthy K, Lucito R, Wigler M, Dimitrova N, Naume B, Borresen-Dale AL, Hicks JB.

Mol Oncol. 2011 Feb;5(1):77-92. doi: 10.1016/j.molonc.2010.11.002. Epub 2010 Dec 2.

32.

Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1.

Kim H, Watkinson J, Varadan V, Anastassiou D.

BMC Med Genomics. 2010 Nov 3;3:51. doi: 10.1186/1755-8794-3-51.

33.

PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment.

Janevski A, Kamalakaran S, Banerjee N, Varadan V, Dimitrova N.

BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S7. doi: 10.1186/1471-2105-10-S9-S7.

34.

Process synthesis and optimization for the production of carbon nanostructures.

Iyuke SE, Mamvura TA, Liu K, Sibanda V, Meyyappan M, Varadan VK.

Nanotechnology. 2009 Sep 16;20(37):375602. doi: 10.1088/0957-4484/20/37/375602. Epub 2009 Aug 26.

PMID:
19706958
35.

The role of the concentration and distribution of water in the complex permittivity of breast fat tissue.

Said T, Varadan VV.

Bioelectromagnetics. 2009 Dec;30(8):669-77. doi: 10.1002/bem.20512. Review.

PMID:
19479938
36.

Nanoelectronic interface for lab-on-a-chip devices.

Abraham JK, Yoon H, Chintakuntla R, Kavdia M, Varadan VK.

IET Nanobiotechnol. 2008 Sep;2(3):55-61. doi: 10.1049/iet-nbt:20070030.

PMID:
19045838
37.

The effects of functional magnetic nanotubes with incorporated nerve growth factor in neuronal differentiation of PC12 cells.

Xie J, Chen L, Varadan VK, Yancey J, Srivatsan M.

Nanotechnology. 2008 Mar 12;19(10):105101. doi: 10.1088/0957-4484/19/10/105101. Epub 2008 Feb 13.

PMID:
21817692
38.

Aligned nanowire growth using lithography-assisted bonding of a polycarbonate template for neural probe electrodes.

Yoon H, Deshpande DC, Ramachandran V, Varadan VK.

Nanotechnology. 2008 Jan 16;19(2):025304. doi: 10.1088/0957-4484/19/02/025304. Epub 2007 Dec 6.

PMID:
21817541
39.

Evaluation of a new self-contained, ambulatory, objective cough monitor.

Paul IM, Wai K, Jewell SJ, Shaffer ML, Varadan VV.

Cough. 2006 Sep 27;2:7.

40.

Computational inference of the molecular logic for synaptic connectivity in C. elegans.

Varadan V, Miller DM 3rd, Anastassiou D.

Bioinformatics. 2006 Jul 15;22(14):e497-506.

PMID:
16873513
41.

Inference of disease-related molecular logic from systems-based microarray analysis.

Varadan V, Anastassiou D.

PLoS Comput Biol. 2006 Jun 16;2(6):e68. Epub 2006 Jun 16.

42.

Variable window binding for mutually exclusive alternative splicing.

Anastassiou D, Liu H, Varadan V.

Genome Biol. 2006;7(1):R2. Epub 2006 Jan 13.

43.

Shape identification of underwater objects using backscattered frequency signals.

Liu GR, Li W, Zhang XM, Varadan VK.

J Acoust Soc Am. 2003 Jun;113(6):3146-54.

PMID:
12822786
44.

Characterization of all the elastic, dielectric, and piezoelectric constants of uniaxially oriented poled PVDF films.

Roh Y, Varadan VV, Varadan VK.

IEEE Trans Ultrason Ferroelectr Freq Control. 2002 Jun;49(6):836-47.

PMID:
12075977
45.

Linear scanning array with bulk ferroelectric-integrated feed network.

Teo PT, Jose KA, Wang YJ, Lee CK, Varadan VK.

IEEE Trans Ultrason Ferroelectr Freq Control. 2002 May;49(5):558-64.

PMID:
12046931
46.

Simple expressions for scattering by a chiral elliptic cylinder of small cross-sectional dimensions.

Lakhtakia A, Varadan VK, Varadan VV.

J Opt Soc Am A. 1991 Sep;8(9):1421-4.

PMID:
1941298
47.

Dilute random distribution of small chiral spheres.

Lakhtakia A, Varadan VK, Varadan VV.

Appl Opt. 1990 Sep 1;29(25):3627-32. doi: 10.1364/AO.29.003627.

PMID:
20567462
48.

Time-harmonic and time-dependent dyadic Green's functions for some uniaxial gyroelectromagnetic media.

Lakhtakia A, Varadan VV, Varadan VK.

Appl Opt. 1989 Mar 15;28(6):1049-52. doi: 10.1364/AO.28.001049.

PMID:
20548616
49.

Scattered intensity of a wave propagating in a discrete random medium.

Ma Y, Varadan VV, Varadan VK.

Appl Opt. 1988 Jun 15;27(12):2469-77. doi: 10.1364/AO.27.002469.

PMID:
20531779
50.

Erratum: Use of combinatorial algebra for diffusion on fractals

Lakhtakia A, Messier R, Varadan VK, Varadan VV.

Phys Rev A Gen Phys. 1987 Feb 1;35(3):1445. No abstract available.

PMID:
9898294

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