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Journal Publications

• Baslan T, Kendall J, Volyanskyy K, McNamara K, Cox H, D'Italia S, Ambrosio F, Riggs M, Rodgers L, Leotta A, Song J, Mao Y, Wu J, Shah R, Gularte-Mérida R, Chadalavada K, Nanjangud G, Varadan V, Gordon A, Curtis C, Krasnitz A, Dimitrova N, Harris L, Wigler M, Hicks J., "Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing," Elife. 2020 May 13;9. pii: e51480. [PMID: 32401198]
  
• Das Purkayastha BP, Chan ER, Ravillah D, Ravi L, Gupta R, Canto MI, Wang JS, Shaheen NJ, Willis JE, Chak A, Varadan V, Guda K., "Genome-Scale Analysis Identifies Novel Transcript-Variants in Esophageal Adenocarcinoma," Cell Mol Gastroenterol Hepatol. 2020 Apr 25. pii: S2352-345X(20)30061-8. [PMID: 32344180]
  
• Beig N, Bera K, Prasanna P, Antunes J, Correa R, Singh S, Saeed Bamashmos A, Ismail M, Braman N, Verma R, Hill VB, Statsevych V, Ahluwalia MS, Varadan V, Madabhushi A, Tiwari P., "Radiogenomic-Based Survival Risk Stratification of Tumor Habitat on Gd-T1w MRI Is Associated with Biological Processes in Glioblastoma," Clinical Cancer Research. 2020 Apr 15;26(8):1866-1876. [PMID: 32079590]
  
• Roberts MS, Sahni JM, Schrock MS, Piemonte KM, Weber-Bonk KL, Seachrist DD, Avril S, Anstine LJ, Singh S, Sizemore ST, Varadan V, Summers MK, Keri RA., "LIN9 and NEK2 Are Core Regulators of Mitotic Fidelity That Can Be Therapeutically Targeted to Overcome Taxane Resistance," Cancer Research, 2020 Apr 15;80(8):1693-1706. [PMID: 32054769].
  
• Hirukawa A, Singh S, Wang J, Rennhack JP, Swiatnicki M, Sanguin-Gendreau V, Zuo D, Daldoul K, Lavoie C, Park M, Andrechek ER, Westbrook TF, Harris LN, Varadan V, Smith HW, Muller WJ., "Reduction of Global H3K27me(3) Enhances HER2/ErbB2 Targeted Therapy," Cell Reports, 2019 Oct 8;29(2):249-257.e8. [PMID: 31597089]
  
• 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," Nature Communications. 2019 Jul 1;10(1):2901. [PMID: 31263101]
  
• 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 Network Open. 2019 Apr 5;2(4):e192561. [PMID: 31002322] (# corresponding author)
  
• 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 Reveal Hyperactivation of Transforming Growth Factor beta and JNK Signaling pathways in Esophageal Cancer,” Gastroenterology, 156(6):1761-1774, 2019. [PMID: 30768984] (* co-senior author)
  
• Harbhajanka A, Chahar S, Miskimen K, Silverman P, Harris L, Williams N, Varadan V, Gilmore H "Clinicopathological, ummunohistochemical and molecular correlation of neural crest transcription factor SOX10 expression in Triple-Negative Breast Carcinoma," Human Pathology, Jun 9. pii: S0046-8177(18)30213-2, 2018. [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", Scientific Reports, 8(1):7, 2018. [PMID: 29311558]
  
• 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. Sciences, 114(52):13792-13797, 2017. [PMID: 29229854]
  
• Sahni JM, Gayle SS, Webb B, Weber-Bonk KL, Seachrist DD, Singh S, Sizemore ST, Restrepo NA, Bebek G, Scacheri P, Varadan V, Summers MK, Keri RA "Mitotic vulnerability in triple-negative breast cancer associated with LIN9 is targetable with BET inhibitors", Cancer Research, 77(19):5395-5408, 2017. [PMID: 28807940]
  
• 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, 36(17):2472-2482, 2017. [PMID: 27819677] (#Corresponding author)
  
• 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”, Clinical Epigenetics, 8:111, 2016. [PMID: 27795744]
  
• Blum A, 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 Research, 76(19):5628-5633, 2016. [PMID: 27503924]
  
• Razi A, Afghah F, Singh S, Varadan V#, “Network-based enriched gene subnetwork identification: a game-theoretic approach,” Biomed Eng Comput Biol., 7:1-4, 2016. [PMID: 27081328] (# corresponding author)
  
• 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,” Scientific Reports, 6:23642, 2016. [PMID: 27004849]
  
• Varadan V, Sandoval M, Harris LN, "Biomarkers for Predicting Response to Anti-HER2 Agents," Adv. Exp. Med. Biol., 882:155-167, 2016. [PMID: 26987534]
  
• Varadan V#, Gilmore H, Miskimen KLS, Tuck D, Parsai S, Awadallal A, Krop IE, Winer EP, Bossuyt V, Somlo G, Abu-Khalaf M, Sikov W, Harris LN#, “Immune Signatures Following Single Dose Trastuzumab Predict Pathologic Response to Preoperative Trastuzumab and Chemotherapy in HER2-Positive Early Breast Cancer,” Clinical Cancer Research, 22:3249-3259, 2016. [PMID: 26842237] (# corresponding author)
  
• 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 K, Liu S, Sicinski P, Winer EP, Krop IE & Zhao JJ. Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors. Cancer Cell, 29(3):255-69, 2016. [PMID: 26977878].
  
• Varadan V#, Kamalakaran S, Gilmore H, Banerjee N, Janevski A, Miskimen KLS, 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. Journal of Cancer, 2015. [PMID: 26284485] (# corresponding author)
  
• 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 African American colon cancers,” Genome Medicine, 7(1): 69, 2015. [PMID: 26269717] (# corresponding author)
  
• Guda K, Veigl ML*, Varadan V*, Nosrati A, Ravi L, Lutterbaugh J, Beard L, Willson JKV, 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. Sciences, 112(4):1149-54, 2015.  [PMID: 25583493] (*equal contribution)
  
• 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., 1049:35-51, 2013. [PMID: 23769412]
  
• Kamalakaran S, Varadan V, Janevski A, Banerjee N, Tuck D, McCombie R, Dimitrova N, Harris LN, “Translating Next Generation Sequencing to practice: opportunities and necessary steps,” Molecular Oncology, 2013. [PMID: 23769412]
  
• Wang S, Wang L, Bayaxi N, Li J, Verhaegh W, Janevski A, Varadan V, et al, “A microRNA panel to discriminate carcinomas from high-grade intraepithelial neoplasms in colonoscopy biopsy tissue”, Gut, 62(2):280-9, 2013. [PMID: 22535378]
• 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”, Frontiers in Oncology, 2:197, 2012. [PMID: 23293768]
  
• Janevski A, Varadan V, Kamalakaran S, et.al, “Effective normalization for copy number variation detection from whole genome sequencing”, BMC Genomics, 13 Suppl 6:S16, 2012. [PMID: 23134596]
  
• Varadan V, Mittal P, Vaske CJ, Benz SC, “The integration of biological pathway knowledge in cancer genomics: a review of existing computational approaches”, IEEE Signal Processing Magazine, 29(1):35-50, 2012.
  
• Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, et al, “Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer”, PLoS One, 6(12):e28503, 2011. [PMID: 22174824]
  
• Kamalakaran S, Varadan V, Giercksky Russnes HE, Levy D, Kendall J, Janevski A et al. DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables, Molecular Oncology, 2011. [PMID: 21169070]
  
• 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 Medical Genomics, 3:51, 2010. [PMID: 21047417]