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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. An ErbB2/c-Src axis links bioenergetics with PRC2 translation to drive epigenetic reprogramming and mammary tumorigenesis. Nat Commun. 2019 Jul 1;10(1):2901. doi: 10.1038/s41467-019-10681-4. PubMed PMID: 31263101; PubMed Central PMCID: PMC6603039.
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. Systems Biology Analyses Show Hyperactivation of Transforming Growth Factor-β and JNK Signaling Pathways in Esophageal Cancer. Gastroenterology. 2019 May;156(6):1761-1774. doi: 10.1053/j.gastro.2019.01.263. Epub 2019 Feb 12. PubMed PMID: 30768984; PubMed Central PMCID: PMC6701681.
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. Association of Peritumoral Radiomics With Tumor Biology and Pathologic Response to Preoperative Targeted Therapy for HER2 (ERBB2)-Positive Breast Cancer. JAMA Netw Open. 2019 Apr 5;2(4):e192561. doi: 10.1001/jamanetworkopen.2019.2561. PubMed PMID: 31002322; PubMed Central PMCID: PMC6481453.
Somasundaram S, Forrest ME, Moinova H, Cohen A, Varadan V, LaFramboise T, Markowitz S, Khalil AM. The DNMT1-associated lincRNA DACOR1 reprograms genome-wide DNA methylation in colon cancer. Clin Epigenetics. 2018 Oct 22;10(1):127. doi: 10.1186/s13148-018-0555-3. PubMed PMID: 30348202; PubMed Central PMCID: PMC6196572.
Harbhajanka A, Chahar S, Miskimen K, Silverman P, Harris L, Williams N, Varadan V, Gilmore H. Clinicopathological, immunohistochemical and molecular correlation of neural crest transcription factor SOX10 expression in triple-negative breast carcinoma. Hum Pathol. 2018 Oct;80:163-169. doi: 10.1016/j.humpath.2018.06.007. Epub 2018 Jun 9. PubMed PMID: 29894722.
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. Radiogenomic analysis of hypoxia pathway is predictive of overall survival in Glioblastoma. Sci Rep. 2018 Jan 8;8(1):7. doi: 10.1038/s41598-017-18310-0. PubMed PMID: 29311558; PubMed Central PMCID: PMC5758516.
Doherty MR, Cheon H, Junk DJ, Vinayak S, Varadan V, Telli ML, Ford JM, Stark GR, Jackson MW. Interferon-beta represses cancer stem cell properties in triple-negative breast cancer. Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13792-13797. doi: 10.1073/pnas.1713728114. Epub 2017 Dec 11. PubMed PMID: 29229854; PubMed Central PMCID: PMC5748193.
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. Mitotic Vulnerability in Triple-Negative Breast Cancer Associated with LIN9 Is Targetable with BET Inhibitors. Cancer Res. 2017 Oct 1;77(19):5395-5408. doi: 10.1158/0008-5472.CAN-17-1571. Epub 2017 Aug 14. PubMed PMID: 28807940; PubMed Central PMCID: PMC5626629.
Dimitrova N, Nagaraj AB, Razi A, Singh S, Kamalakaran S, Banerjee N, Joseph P, Mankovich A, Mittal P, DiFeo A, Varadan V. InFlo: a novel systems biology framework identifies cAMP-CREB1 axis as a key modulator of platinum resistance in ovarian cancer. Oncogene. 2017 Apr 27;36(17):2472-2482. doi: 10.1038/onc.2016.398. Epub 2016 Nov 7. PubMed PMID: 27819677; PubMed Central PMCID: PMC5415943.
Kaz AM, Wong CJ, Varadan V, Willis JE, Chak A, Grady WM. Erratum to: Global DNA methylation patterns in Barrett's esophagus, dysplastic Barrett's, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use. Clin Epigenetics. 2017;9:23. doi: 10.1186/s13148-017-0324-8. eCollection 2017. PubMed PMID: 28265303; PubMed Central PMCID: PMC5333432.
Kaz AM, Wong CJ, Varadan V, Willis JE, Chak A, Grady WM. Global DNA methylation patterns in Barrett's esophagus, dysplastic Barrett's, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use. Clin Epigenetics. 2016;8:111. doi: 10.1186/s13148-016-0273-7. eCollection 2016. PubMed PMID: 27795744; PubMed Central PMCID: PMC5082363.
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. RNA Sequencing Identifies Transcriptionally Viable Gene Fusions in Esophageal Adenocarcinomas. Cancer Res. 2016 Oct 1;76(19):5628-5633. doi: 10.1158/0008-5472.CAN-16-0979. Epub 2016 Aug 8. PubMed PMID: 27503924; PubMed Central PMCID: PMC5050127.
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. Immune Signatures Following Single Dose Trastuzumab Predict Pathologic Response to PreoperativeTrastuzumab and Chemotherapy in HER2-Positive Early Breast Cancer. Clin Cancer Res. 2016 Jul 1;22(13):3249-59. doi: 10.1158/1078-0432.CCR-15-2021. Epub 2016 Feb 3. PubMed PMID: 26842237; PubMed Central PMCID: PMC5439498.
Razi A, Afghah F, Singh S, Varadan V. Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach. Biomed Eng Comput Biol. 2016;7(Suppl 2):1-14. doi: 10.4137/BECB.S38244. eCollection 2016. PubMed PMID: 27081328; PubMed Central PMCID: PMC4822726.
Venkitachalam S, Revoredo L, Varadan V, Fecteau RE, Ravi L, Lutterbaugh J, Markowitz SD, Willis JE, Gerken TA, Guda K. Biochemical and functional characterization of glycosylation-associated mutational landscapes in colon cancer. Sci Rep. 2016 Mar 23;6:23642. doi: 10.1038/srep23642. PubMed PMID: 27004849; PubMed Central PMCID: PMC4804330.
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. Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors. Cancer Cell. 2016 Mar 14;29(3):255-269. doi: 10.1016/j.ccell.2016.02.006. PubMed PMID: 26977878; PubMed Central PMCID: PMC4794996.
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. Brief-exposure to preoperative bevacizumab reveals a TGF-β signature predictive of response in HER2-negative breast cancers. Int J Cancer. 2016 Feb 1;138(3):747-57. doi: 10.1002/ijc.29808. Epub 2015 Aug 31. PubMed PMID: 26284485.
Varadan V, Sandoval M, Harris LN. Biomarkers for Predicting Response to Anti-HER2 Agents. Adv Exp Med Biol. 2016;882:155-67. doi: 10.1007/978-3-319-22909-6_6. Review. PubMed PMID: 26987534.
Varadan V, Singh S, Nosrati A, Ravi L, Lutterbaugh J, Barnholtz-Sloan JS, Markowitz SD, Willis JE, Guda K. ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients. Genome Med. 2015;7:69. doi: 10.1186/s13073-015-0192-9. eCollection 2015. PubMed PMID: 26269717; PubMed Central PMCID: PMC4534088.
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. Reply to Ashktorab et al.: Mutational landscape of colon cancers in African Americans. Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2853. doi: 10.1073/pnas.1505059112. Epub 2015 May 4. PubMed PMID: 25941411; PubMed Central PMCID: PMC4460466.
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. Novel recurrently mutated genes in African American colon cancers. Proc Natl Acad Sci U S A. 2015 Jan 27;112(4):1149-54. doi: 10.1073/pnas.1417064112. Epub 2015 Jan 12. PubMed PMID: 25583493; PubMed Central PMCID: PMC4313860.
Razi A, Afghah F, Varadan V. Identifying gene subnetworks associated with clinical outcome in ovarian cancer using Network Based Coalition Game. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:6509-13. doi: 10.1109/EMBC.2015.7319884. PubMed PMID: 26737784.
Razi A, Banerjee N, Dimitrova N, Varadan V. Non-linear Bayesian framework to determine the transcriptional effects of cancer-associated genomic aberrations. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:6514-8. doi: 10.1109/EMBC.2015.7319885. PubMed PMID: 26737785; PubMed Central PMCID: PMC5341149.
Kamalakaran S, Varadan V, Janevski A, Banerjee N, Tuck D, McCombie WR, Dimitrova N, Harris LN. Translating next generation sequencing to practice: opportunities and necessary steps. Mol Oncol. 2013 Aug;7(4):743-55. doi: 10.1016/j.molonc.2013.04.008. Epub 2013 May 15. Review. PubMed PMID: 23769412; PubMed Central PMCID: PMC5528427.
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. A microRNA panel to discriminate carcinomas from high-grade intraepithelial neoplasms in colonoscopy biopsy tissue. Gut. 2013 Feb;62(2):280-9. doi: 10.1136/gutjnl-2011-301554. Epub 2012 Apr 25. PubMed PMID: 22535378.
Wrzeszczynski KO, Varadan V, Kamalakaran S, Levine DA, Dimitrova N, Lucito R. Integrative prediction of gene function and platinum-free survival from genomic and epigenetic features in ovarian cancer. Methods Mol Biol. 2013;1049:35-51. doi: 10.1007/978-1-62703-547-7_4. PubMed PMID: 23913207.
Tang MH, Varadan V, Kamalakaran S, Zhang MQ, Dimitrova N, Hicks J. Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Front Oncol. 2012;2:197. doi: 10.3389/fonc.2012.00197. eCollection 2012. PubMed PMID: 23293768; PubMed Central PMCID: PMC3530719.
Janevski A, Varadan V, Kamalakaran S, Banerjee N, Dimitrova N. Effective normalization for copy number variation detection from whole genome sequencing. BMC Genomics. 2012;13 Suppl 6:S16. doi: 10.1186/1471-2164-13-S6-S16. Epub 2012 Oct 26. PubMed PMID: 23134596; PubMed Central PMCID: PMC3481445.
Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, Kamalakaran S, Levine DA, Dimitrova N, Zhang MQ, Lucito R. Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PLoS One. 2011;6(12):e28503. doi: 10.1371/journal.pone.0028503. Epub 2011 Dec 8. PubMed PMID: 22174824; PubMed Central PMCID: PMC3234280.
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. DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables. Mol Oncol. 2011 Feb;5(1):77-92. doi: 10.1016/j.molonc.2010.11.002. Epub 2010 Dec 2. PubMed PMID: 21169070; PubMed Central PMCID: PMC5528275.
Kim H, Watkinson J, Varadan V, Anastassiou D. Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1. BMC Med Genomics. 2010 Nov 3;3:51. doi: 10.1186/1755-8794-3-51. PubMed PMID: 21047417; PubMed Central PMCID: PMC2988703.
Janevski A, Kamalakaran S, Banerjee N, Varadan V, Dimitrova N. PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment. BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S7. doi: 10.1186/1471-2105-10-S9-S7. PubMed PMID: 19761577; PubMed Central PMCID: PMC2745694.
Varadan V, Miller DM 3rd, Anastassiou D. Computational inference of the molecular logic for synaptic connectivity in C. elegans. Bioinformatics. 2006 Jul 15;22(14):e497-506. doi: 10.1093/bioinformatics/btl224. PubMed PMID: 16873513.
Varadan V, Anastassiou D. Inference of disease-related molecular logic from systems-based microarray analysis. PLoS Comput Biol. 2006 Jun 16;2(6):e68. doi: 10.1371/journal.pcbi.0020068. Epub 2006 Jun 16. PubMed PMID: 16789819; PubMed Central PMCID: PMC1479089.
Anastassiou D, Liu H, Varadan V. Variable window binding for mutually exclusive alternative splicing. Genome Biol. 2006;7(1):R2. doi: 10.1186/gb-2006-7-1-r2. Epub 2006 Jan 13. PubMed PMID: 16507134; PubMed Central PMCID: PMC1431710.
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