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CSCB - Selected Publications

Balaparya A, De S. Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data. Nat Genet. 2018 Sep 24. PMID:30250123.

Chan CS, Laddha SV, Lewis PW, Koletsky MS, Robzyk K, Da Silva E, Torres PJ, Untch BR, Li J, Bose P, Chan TA, Klimstra DS, Allis CD, Tang LH. ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup. Nat Commun. 2018 Oct 12;9(1):4158. PMID:30315258.

Panda A, de Cubas AA, Stein M, Riedlinger G, Kra J, Mayer T, Smith CC, Vincent BG, Serody JS, Beckermann KE, Ganesan S, Bhanot G, Rathmell WK. Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma. JCI Insight. 2018 Aug 23;3(16). PMID:30135306.

Perekatt AO, Shah PP, Cheung S, Jariwala N, Wu A, Gandhi V, Kumar N, Feng Q, Patel N, Chen L, Joshi S, Zhou A, Taketo MM, Xing J, White E, Gao N, Gatza ML, Verzi MP. SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium. Cancer Res. 2018 Sep 1;78(17):4878-4890. PMID:29986996.

Severson EA, Riedlinger GM, Connelly CF, Vergilio JA, Goldfinger M, Ramkissoon S, Frampton GM, Ross JS, Fratella-Calabrese A, Gay L, Ali S, Miller V, Elvin J, Hadigol M, Hirshfield KM, Rodriguez-Rodriguez L, Ganesan S, Khiabanian H. Detection of clonal hematopoiesis of indeterminate potential in clinical sequencing of solid tumor specimens. Blood. 2018 May 31;131(22):2501-2505. PMID:29678827.

Sharma A, Jiang C, De S. Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations. Nucleic Acids Res. 2018 May 18;46(9):4370-4381. PMID:29672706.

Thomas A, Routh ED, Pullikuth A, Jin G, Su J, Chou JW, Hoadley KA, Print C, Knowlton N, Black MA, Demaria S, Wang E, Bedognetti D, Jones WD, Mehta GA, Gatza ML, Perou CM, Page DB, Triozzi P, Miller LD. Tumor mutational burden is a determinant of immune-mediated survival in breast cancer. Oncoimmunology. 2018 Jul 30;7(10):e1490854. PMID:30386679.

Banerjee KK, Saxena M, Kumar N, Chen L, Cavazza A, Toke NH, O'Neill NK, Madha S, Jadhav U, Verzi MP, Shivdasani RA. Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development. Genes Dev. 2018 Nov 1;32(21-22):1430-1442. PMID:30366903.

Nobel YR, Snider EJ, Compres G, Freedberg DE, Khiabanian H, Lightdale CJ, Toussaint NC, Abrams JA. Increasing Dietary Fiber Intake Is Associated with a Distinct Esophageal Microbiome. Clin Transl Gastroenterol. 2018 Oct 25;9(10):199. PMID:30356041.

Larochelle M, Robert MA, Hébert JN, Liu X, Matteau D, Rodrigue S, Tian B, Jacques PÉ, Bachand F. Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nat Commun. 2018 Oct 19;9(1):4364. PMID:30341288.

Simhadri S, Vincelli G, Huo Y, Misenko S, Foo TK, Ahlskog J, Sørensen CS, Oakley GG, Ganesan S, Bunting SF, Xia B. PALB2 connects BRCA1 and BRCA2 in the G2/M checkpoint response. Oncogene. 2018 Oct 18. PMID:30337689.

Coleman N, De S. Mutation Signatures Depend on Epigenomic Contexts. Trends Cancer. 2018 Oct;4(10):659-661. PMID:30292349.

Khiabanian H, Hirshfield KM, Goldfinger M, Bird S, Stein M, Aisner J, Toppmeyer D, Wong S, Chan N, Dhar K, Gheeya J, Vig H, Hadigol M, Pavlick D, Ansari S, Ali S, Xia B, Rodriguez-Rodriguez L, Ganesan S. Inference of Germline Mutational Status and Evaluation of Loss of Heterozygosity in High-Depth, Tumor-Only Sequencing Data. JCO Precis Oncol. 2018;2018. PMID:30246169.

Fomin V, Richard P, Hoque M, Li C, Gu Z, Fissore-O'Leary M, Tian B, Prives C, Manley JL. The C9ORF72 Gene, Implicated in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia, Encodes a Protein That Functions in Control of Endothelin and Glutamate Signaling. Mol Cell Biol. 2018 Oct 29;38(22). PMID:30150298.

Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res. 2018 Oct;28(10):1427-1441. PMID:30143597.

Smith CC, Beckermann KE, Bortone DS, De Cubas AA, Bixby LM, Lee SJ, Panda A, Ganesan S, Bhanot G, Wallen EM, Milowsky MI, Kim WY, Rathmell WK, Swanstrom R, Parker JS, Serody JS, Selitsky SR, Vincent BG. Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma. J Clin Invest. 2018 Nov 1;128(11):4804-4820. PMID:30137025.

Vagner T, Spinelli C, Minciacchi VR, Balaj L, Zandian M, Conley A, Zijlstra A, Freeman MR, Demichelis F, De S, Posadas EM, Tanaka H, Di Vizio D. Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma. J Extracell Vesicles. 2018 Aug 7;7(1):1505403. PMID:30108686.

Kang JS, Zhang AL, Faheem M, Zhang CJ, Ai N, Buynak JD, Welsh WJ, Oelschlaeger P. Virtual Screening and Experimental Testing of B1 Metallo-β-lactamase Inhibitors. J Chem Inf Model. 2018 Sep 24;58(9):1902-1914. PMID:30107123.

Ryan WK, Fernandez J, Peterson MK, Sheneman DW, Podell BK, De S, Torchia EC. Activation of S6 signaling is associated with cell survival and multinucleation in hyperplastic skin after epidermal loss of AURORA-A Kinase. Cell Death Differ. 2018 Jul 26. PMID:30050055.

Hadigol M, Khiabanian H. MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications. BMC Bioinformatics. 2018 Jun 8;19(1):219. PMID:29884116.

Rabadan R, Bhanot G, Marsilio S, Chiorazzi N, Pasqualucci L, Khiabanian H. On statistical modeling of sequencing noise in high depth data to assess tumor evolution. J Stat Phys. 2018 Jul;172(1):143-155. PMID:30034030.

Costa-Machado LF, Martín-Hernández R, Sanchez-Luengo MÁ, Hess K, Vales-Villamarin C, Barradas M, Lynch C, de la Nava D, Diaz-Ruiz A, de Cabo R, Cañamero M, Martinez L, Sanchez-Carbayo M, Herranz D, Serrano M, Fernandez-Marcos PJ. Sirt1 protects from K-Ras-driven lung carcinogenesis. EMBO Rep. 2018 Sep;19(9). PMID:30021836.

Lu C, Romo-Bucheli D, Wang X, Janowczyk A, Ganesan S, Gilmore H, Rimm D, Madabhushi A. Nuclear shape and orientation features from H&E images predict survival in early-stage estrogen receptor-positive breast cancers. Lab Invest. 2018 Nov;98(11):1438-1448. PMID:29959421.

Zheng D, Wang R, Ding Q, Wang T, Xie B, Wei L, Zhong Z, Tian B. Cellular stress alters 3'UTR landscape through alternative polyadenylation and isoform-specific degradation. Nat Commun. 2018 Jun 11;9(1):2268. PMID:29891946.

Yu S, Tong K, Zhao Y, Balasubramanian I, Yap GS, Ferraris RP, Bonder EM, Verzi MP, Gao N. Paneth Cell Multipotency Induced by Notch Activation following Injury. Cell Stem Cell. 2018 Jul 5;23(1):46-59. PMID:29887318.

Whitney J, Corredor G, Janowczyk A, Ganesan S, Doyle S, Tomaszewski J, Feldman M, Gilmore H, Madabhushi A. Quantitative nuclear histomorphometry predicts oncotype DX risk categories for early stage ER+ breast cancer. BMC Cancer. 2018 May 30;18(1):610. PMID:29848291.

Cruz-Roa A, Gilmore H, Basavanhally A, Feldman M, Ganesan S, Shih N, Tomaszewski J, Madabhushi A, González F. High-throughput adaptive sampling for whole-slide histopathology image analysis (HASHI) via convolutional neural networks: Application to invasive breast cancer detection. PLoS One. 2018 May 24;13(5):e0196828. PMID:29795581.

Serrao A, Jenkins LM, Chumanevich AA, Horst B, Liang J, Gatza ML, Lee NY, Roninson IB, Broude EV, Mythreye K. Mediator kinase CDK8/CDK19 drives YAP1-dependent BMP4-induced EMT in cancer. Oncogene. 2018 Aug;37(35):4792-4808. PMID:29780169.

Mahdi AH, Huo Y, Tan Y, Simhadri S, Vincelli G, Gao J, Ganesan S, Xia B. Evidence of Intertissue Differences in the DNA Damage Response and the Pro-oncogenic Role of NF-κB in Mice with Disengaged BRCA1-PALB2 Interaction. Cancer Res. 2018 Jul 15;78(14):3969-3981. PMID:29739757.

Srivillibhuthur M, Warder BN, Toke NH, Shah PP, Feng Q, Gao N, Bonder EM, Verzi MP. TFAM is required for maturation of the fetal and adult intestinal epithelium. Dev Biol. 2018 Jul 15;439(2):92-101. PMID:29684311.

Dhami J, Hirshfield KM, Ganesan S, Hellmann M, Rojas V, Amorosa JK, Riedlinger GM, Zhong H, Ali SM, Pavlick D, Elvin JA, Rodriguez-Rodriguez L. Comprehensive genomic profiling aids in treatment of a metastatic endometrial cancer. Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). PMID:29588307.

Guo Y, Wu R, Gaspar JM, Sargsyan D, Su ZY, Zhang C, Gao L, Cheng D, Li W, Wang C, Yin R, Fang M, Verzi MP, Hart RP, Kong AN. DNA methylome and transcriptome alterations and cancer prevention by curcumin in colitis-accelerated colon cancer in mice. Carcinogenesis. 2018 May 3;39(5):669-680. PMID:29547900.

Snider EJ, Compres G, Freedberg DE, Giddins MJ, Khiabanian H, Lightdale CJ, Nobel YR, Toussaint NC, Uhlemann AC, Abrams JA. Barrett's esophagus is associated with a distinct oral microbiome. Clin Transl Gastroenterol. 2018 Feb 20;9(3):135. PMID:29491399.

Tzoneva G, Dieck CL, Oshima K, Ambesi-Impiombato A, Sánchez-Martín M, Madubata CJ, Khiabanian H, Yu J, Waanders E, Iacobucci I, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Kirschner-Schwabe R, Mullighan CG, Rabadan R, Ferrando AA. Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia. Nature. 2018 Jan 25;553(7689):511-514. PMID:29342136.

Tong K, Pellón-Cárdenas O, Sirihorachai VR, Warder BN, Kothari OA, Perekatt AO, Fokas EE, Fullem RL, Zhou A, Thackray JK, Tran H, Zhang L, Xing J, Verzi MP. Degree of Tissue Differentiation Dictates Susceptibility to BRAF-Driven Colorectal Cancer. Cell Rep. 2017 Dec 26;21(13):3833-3845. PMID:29281831.

Fontes MM, Guvenek A, Kawaguchi R, Zheng D, Huang A, Ho VM, Chen PB, Liu X, O'Dell TJ, Coppola G, Tian B, Martin KC. Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation. Sci Rep. 2017 Dec 12;7(1):17377. PMID:29234016.

Yurko N, Liu X, Yamazaki T, Hoque M, Tian B, Manley JL. MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD. Mol Cell. 2017 Dec 7;68(5):913-925. PMID:29220656.

Ginjala V, Rodriguez-Colon L, Ganguly B, Gangidi P, Gallina P, Al-Hraishawi H, Kulkarni A, Tang J, Gheeya J, Simhadri S, Yao M, Xia B, Ganesan S. Protein-lysine methyltransferases G9a and GLP1 promote responses to DNA damage. Sci Rep. 2017 Nov 30;7(1):16613. PMID:29192276.

Liu J, Zhang C, Zhao Y, Yue X, Wu H, Huang S, Chen J, Tomsky K, Xie H, Khella CA, Gatza ML, Xia D, Gao J, White E, Haffty BG, Hu W, Feng Z. Parkin targets HIF-1α for ubiquitination and degradation to inhibit breast tumor progression. Nat Commun. 2017 Nov 28;8(1):1823. PMID:29180628.

Brighton HE, Angus SP, Bo T, Roques J, Tagliatela AC, Darr DB, Karagoz K, Sciaky N, Gatza ML, Sharpless NE, Johnson GL, Bear JE. New Mechanisms of Resistance to MEK Inhibitors in Melanoma Revealed by Intravital Imaging. Cancer Res. 2018 Jan 15;78(2):542-557. PMID:29180473.

Panda A, Mehnert JM, Hirshfield KM, Riedlinger G, Damare S, Saunders T, Kane M, Sokol L, Stein MN, Poplin E, Rodriguez-Rodriguez L, Silk AW, Aisner J, Chan N, Malhotra J, Frankel M, Kaufman HL, Ali S, Ross JS, White EP, Bhanot G, Ganesan S. Immune Activation and Benefit From Avelumab in EBV-Positive Gastric Cancer. J Natl Cancer Inst. 2018 Mar 1;110(3):316-320. PMID:29155997.

Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI. DNA polymerase η mutational signatures are found in a variety of different types of cancer. Cell Cycle. 2018;17(3):348-355. PMID:29139326.

Baugh EH, Ke H, Levine AJ, Bonneau RA, Chan CS. Why are there hotspot mutations in the TP53 gene in human cancers? Cell Death Differ. 2018 Jan;25(1):154-160. doi: 10. PMID:29099487.

Wang R, Nambiar R, Zheng D, Tian B. PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes. Nucleic Acids Res. 2018 Jan 4;46(D1):D315-D319. PMID:29069441.

Droz-Rosario R, Lu H, Liu J, Liu NA, Ganesan S, Xia B, Haffty BG, Shen Z. Roles of BCCIP deficiency in mammary tumorigenesis. Breast Cancer Res. 2017 Oct 18;19(1):115. PMID:29047390.

Hoque M, Park JY, Chang YJ, Luchessi AD, Cambiaghi TD, Shamanna R, Hanauske-Abel HM, Holland B, Pe'ery T, Tian B, Mathews MB. Regulation of gene expression by translation factor eIF5A: Hypusine-modified eIF5A enhances nonsense-mediated mRNA decay in human cells. Translation (Austin). 2017 Aug 14;5(2):e1366294. PMID:29034140.

Morgan KM, Fischer BS, Lee FY, Shah JJ, Bertino JR, Rosenfeld J, Singh A, Khiabanian H, Pine SR. Gamma Secretase Inhibition by BMS-906024 Enhances Efficacy of Paclitaxel in Lung Adenocarcinoma. Mol Cancer Ther. 2017 Dec;16(12):2759-2769. PMID:28978720.

Smith KS, Liu LL, Ganesan S, Michor F, De S. Nuclear topology modulates the mutational landscapes of cancer genomes. Nat Struct Mol Biol. 2017 Nov;24(11):1000-1006. PMID:28967881.

Shi M, Zhang H, Wu X, He Z, Wang L, Yin S, Tian B, Li G, Cheng H. ALYREF mainly binds to the 5' and the 3' regions of the mRNA in vivo. Nucleic Acids Res. 2017 Sep 19;45(16):9640-9653. PMID:28934468.

Kim Y, Wu AG, Jaja-Chimedza A, Graf BL, Waterman C, Verzi MP, Raskin I. Isothiocyanate-enriched moringa seed extract alleviates ulcerative colitis symptoms in mice. PLoS One. 2017 Sep 18;12(9):e0184709. PMID:28922365.

Liu X, Hoque M, Larochelle M, Lemay JF, Yurko N, Manley JL, Bachand F, Tian B. Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe. PMID:28916539.

Li W, Li W, Laishram RS, Hoque M, Ji Z, Tian B, Anderson RA. Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases. Nucleic Acids Res. 2017 Sep 6;45(15):8930-8942. PMID:28911096.

Liu X, Freitas J, Zheng D, Oliveira MS, Hoque M, Martins T, Henriques T, Tian B, Moreira A. Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster. RNA. 2017 Dec;23(12):1807-1816. PMID:28851752.

Russell LB, Bhanot G, Kim SY, Sinha A. Using Cluster Analysis to Group Countries for Cost-effectiveness Analysis: An Application to Sub-Saharan Africa. Med Decis Making. 2018 Feb;38(2):139-149. PMID:28823186.

Zheng D, Tian B. Polyadenylation Site-Based Analysis of Transcript Expression by 3'READS. Methods Mol Biol. 2017;1648:65-77. PMID:28766290.

Ogami K, Richard P, Chen Y, Hoque M, Li W, Moresco JJ, Yates JR 3rd, Tian B, Manley JL. An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression. Genes Dev. 2017 Jun 15;31(12):1257-1271. PMID:28733371.

Bjørklund SS, Panda A, Kumar S, Seiler M, Robinson D, Gheeya J, Yao M, Alnæs GIG, Toppmeyer D, Riis M, Naume B, Børresen-Dale AL, Kristensen VN, Ganesan S, Bhanot G. Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma. Sci Rep. 2017 Jul 17;7(1):5568. PMID:28717182.

Dolfi SC, Medina DJ, Kareddula A, Paratala B, Rose A, Dhami J, Chen S, Ganesan S, Mackay G, Vazquez A, Hirshfield KM. Riluzole exerts distinct antitumor effects from a metabotropic glutamate receptor 1-specific inhibitor on breast cancer cells. Oncotarget. 2017 Jul 4;8(27):44639-44653. PMID:28591718.

Vest KE, Phillips BL, Banerjee A, Apponi LH, Dammer EB, Xu W, Zheng D, Yu J, Tian B, Pavlath GK, Corbett AH. Novel mouse models of oculopharyngeal muscular dystrophy (OPMD) reveal early onset mitochondrial defects and suggest loss of PABPN1 may contribute to pathology. Hum Mol Genet. 2017 Sep 1;26(17):3235-3252. PMID:28575395.

Elbarbary RA, Miyoshi K, Myers JR, Du P, Ashton JM, Tian B, Maquat LE. Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G(1)/S phase transition. Science. 2017 May 26;356(6340):859-862. PMID:28546213.

Kulkarni A, Al-Hraishawi H, Simhadri S, Hirshfield KM, Chen S, Pine S, Jeyamohan C, Sokol L, Ali S, Teo ML, White E, Rodriguez-Rodriguez L, Mehnert JM, Ganesan S. BRAF Fusion as a Novel Mechanism of Acquired Resistance to Vemurafenib in BRAF(V600E) Mutant Melanoma. Clin Cancer Res. 2017 Sep 15;23(18):5631-5638. PMID:28539463.

Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Brief Bioinform. 2017 May 11. PMID:28498882.

Foran DJ, Chen W, Chu H, Sadimin E, Loh D, Riedlinger G, Goodell LA, Ganesan S, Hirshfield K, Rodriguez L, DiPaola RS. Roadmap to a Comprehensive Clinical Data Warehouse for Precision Medicine Applications in Oncology. Cancer Inform. 2017 Mar 2;16:1176935117694349. PMID:28469389.

Park K, Chen W, Chekmareva MA, Foran DJ, Desai JP. Electromechanical Coupling Factor of Breast Tissue as a Biomarker for Breast Cancer. IEEE Trans Biomed Eng. 2018 Jan;65(1):96-103. PMID:28436838.

Cruz-Roa A, Gilmore H, Basavanhally A, Feldman M, Ganesan S, Shih NNC, Tomaszewski J, González FA, Madabhushi A. Accurate and reproducible invasive breast cancer detection in whole-slide images: A Deep Learning approach for quantifying tumor extent. Sci Rep. 2017 Apr 18;7:46450. PMID:28418027.

Lu K, Alcivar AL, Ma J, Foo TK, Zywea S, Mahdi A, Huo Y, Kensler TW, Gatza ML, Xia B. NRF2 Induction Supporting Breast Cancer Cell Survival Is Enabled by Oxidative Stress-Induced DPP3-KEAP1 Interaction. Cancer Res. 2017 Jun 1;77(11):2881-2892. PMID:28416489.

Anantha RW, Simhadri S, Foo TK, Miao S, Liu J, Shen Z, Ganesan S, Xia B. Functional and mutational landscapes of BRCA1 for homology-directed repair and therapy resistance. Elife. 2017 Apr 11;6. PMID:28398198.

Yamamoto KN, Yachida S, Nakamura A, Niida A, Oshima M, De S, Rosati LM, Herman JM, Iacobuzio-Donahue CA, Haeno H. Personalized Management of Pancreatic Ductal Adenocarcinoma Patients through Computational Modeling. Cancer Res. 2017 Jun 15;77(12):3325-3335. PMID:28381541.

Fabbri G, Holmes AB, Viganotti M, Scuoppo C, Belver L, Herranz D, Yan XJ, Kieso Y, Rossi D, Gaidano G, Chiorazzi N, Ferrando AA, Dalla-Favera R. Common nonmutational NOTCH1 activation in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):E2911-E2919. PMID:28314854.

Kimani SG, Kumar S, Bansal N, Singh K, Kholodovych V, Comollo T, Peng Y, Kotenko SV, Sarafianos SG, Bertino JR, Welsh WJ, Birge RB. Small molecule inhibitors block Gas6-inducible TAM activation and tumorigenicity. Sci Rep. 2017 Mar 8;7:43908. PMID:28272423.

Guo Y, Su ZY, Zhang C, Gaspar JM, Wang R, Hart RP, Verzi MP, Kong AN. Mechanisms of colitis-accelerated colon carcinogenesis and its prevention with the combination of aspirin and curcumin: Transcriptomic analysis using RNA-seq. Biochem Pharmacol. 2017 Jul 1;135:22-34. PMID:28267439.

Gorshein E, Wei C, Ambrosy S, Budney S, Vivas J, Shenkerman A, Manago J, McGrath MK, Tyno A, Lin Y, Patel V, Gharibo M, Schaar D, Jenq RR, Khiabanian H, Strair R. Lactobacillus rhamnosus GG probiotic enteric regimen does not appreciably alter the gut microbiome or provide protection against GVHD after allogeneic hematopoietic stem cell transplantation. Clin Transplant. 2017 May;31(5). PMID:28256022.

Nozad S, Sheehan CE, Gay LM, Elvin JA, Vergilio JA, Suh J, Ramkissoon S, Schrock AB, Hirshfield KM, Ali N, Ganesan S, Ali SM, Miller VA, Stephens PJ, Ross JS, Chung JH. Comprehensive genomic profiling of malignant phyllodes tumors of the breast. Breast Cancer Res Treat. 2017 Apr;162(3):597-602. PMID:28210881.

Cheng LC, Tan VM, Ganesan S, Drake JM. Integrating phosphoproteomics into the clinical management of prostate cancer. Clin Transl Med. 2017 Dec;6(1):9. PMID:28197968.

Mehta GA, Parker JS, Silva GO, Hoadley KA, Perou CM, Gatza ML. Amplification of SOX4 promotes PI3K/Akt signaling in human breast cancer. Breast Cancer Res Treat. 2017 Apr;162(3):439-450. PMID:28176176.

Sanchez-Martin M, Ambesi-Impiombato A, Qin Y, Herranz D, Bansal M, Girardi T, Paietta E, Tallman MS, Rowe JM, De Keersmaecker K, Califano A, Ferrando AA. Synergistic antileukemic therapies in NOTCH1-induced T-ALL. Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):2006-2011. PMID:28174276.

Morgan KM, Riedlinger GM, Rosenfeld J, Ganesan S, Pine SR. Patient-Derived Xenograft Models of Non-Small Cell Lung Cancer and Their Potential Utility in Personalized Medicine. Front Oncol. 2017 Jan 19;7:2. PMID:28154808.

Ramdzan ZM, Ginjala V, Pinder JB, Chung D, Donovan CM, Kaur S, Leduy L, Dellaire G, Ganesan S, Nepveu A. The DNA repair function of CUX1 contributes to radioresistance. Oncotarget. 2017 Mar 21;8(12):19021-19038. PMID:28147323.

Blair LP, Liu Z, Labitigan RL, Wu L, Zheng D, Xia Z, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh SG, Moore CL, Li W, Tian B, Tackett AJ, Yan Q. KDM5 lysine demethylases are involved in maintenance of 3'UTR length. Sci Adv. 2016 Nov 18;2(11):e1501662. PMID:28138513.

Uhlemann AC, McAdam PR, Sullivan SB, Knox JR, Khiabanian H, Rabadan R, Davies PR, Fitzgerald JR, Lowy FD. Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration. MBio. 2017 Jan 17;8(1). PMID:28096484.

Oza J, Ganguly B, Kulkarni A, Ginjala V, Yao M, Ganesan S. A novel role of chromodomain protein CBX8 in DNA damage response. J Biol Chem. 2017 Jan 13;292(2):761. PMID:28087730.

Tsai YH, Hill DR, Kumar N, Huang S, Chin AM, Dye BR, Nagy MS, Verzi MP, Spence JR. LGR4 and LGR5 Function Redundantly During Human Endoderm Differentiation. Cell Mol Gastroenterol Hepatol. 2016 Jun 23;2(5):648-662. PMID:28078320.

Abate F, da Silva-Almeida AC, Zairis S, Robles-Valero J, Couronne L, Khiabanian H, Quinn SA, Kim MY, Laginestra MA, Kim C, Fiore D, Bhagat G, Piris MA, Campo E, Lossos IS, Bernard OA, Inghirami G, Pileri S, Bustelo XR, Rabadan R, Ferrando AA, Palomero T. Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas. Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):764-769. PMID:28062691.

Herranz D. Glutaminolysis gets the spotlight in cancer. Oncotarget. 2017 Feb 14;8(7):10761-10762. PMID:28053289.

Kim JJ, Bennett NK, Devita MS, Chahar S, Viswanath S, Lee EA, Jung G, Shao PP, Childers EP, Liu S, Kulesa A, Garcia BA, Becker ML, Hwang NS, Madabhushi A, Verzi MP, Moghe PV. Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells. Sci Rep. 2017 Jan 4;7:39406. PMID:28051095.

Panda A, Betigeri A, Subramanian K, Ross JS, Pavlick DC, Ali S, Markowski P, Silk A, Kaufman HL, Lattime E, Mehnert JM, Sullivan R, Lovly CM, Sosman J, Johnson DB, Bhanot G, Ganesan S. Identifying a Clinically Applicable Mutational Burden Threshold as a Potential Biomarker of Response to Immune Checkpoint Therapy in Solid Tumors. JCO Precis Oncol. 2017;2017. PMID:29951597.

Kantamneni H, Zevon M, Donzanti MJ, Zhao X, Sheng Y, Barkund SR, McCabe LH, Banach-Petrosky W, Higgins LM, Ganesan S, Riman RE, Roth CM, Tan MC, Pierce MC, Ganapathy V, Moghe PV. Surveillance nanotechnology for multi-organ cancer metastases. Nat Biomed Eng. 2017;1:993-1003. PMID:29531851.

Hu W, Li S, Park JY, Boppana S, Ni T, Li M, Zhu J, Tian B, Xie Z, Xiang M. Dynamic landscape of alternative polyadenylation during retinal development. Cell Mol Life Sci. 2017 May;74(9):1721-1739. PMID:27990575.

Rojas V, Hirshfield KM, Ganesan S, Rodriguez-Rodriguez L. Molecular Characterization of Epithelial Ovarian Cancer: Implications for Diagnosis and Treatment. Int J Mol Sci. 2016 Dec 15;17(12). PMID:27983698.

Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI. Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Sci Rep. 2016 Dec 7;6:38133. PMID:27924834.

Pei S, Minhajuddin M, D'Alessandro A, Nemkov T, Stevens BM, Adane B, Khan N, Hagen FK, Yadav VK, De S, Ashton JM, Hansen KC, Gutman JA, Pollyea DA, Crooks PA, Smith C, Jordan CT. Rational design of a parthenolide-based drug regimen that selectively eradicates acute myelogenous leukemia stem cells. J Biol Chem. 2016 Nov 25;291(48):25280. PMID:27888238.

Yadav A, Radhakrishnan A, Panda A, Singh A, Sinha H, Bhanot G. The Modular Adaptive Ribosome. PLoS One. 2016 Nov 3;11(11):e0166021. PMID:27812193.

Tian B, Manley JL. Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol. 2017 Jan;18(1):18-30. PMID:27677860.

Ai N, Wood RD, Yang E, Welsh WJ. Niclosamide is a Negative Allosteric Modulator of Group I Metabotropic Glutamate Receptors: Implications for Neuropathic Pain. Pharm Res. 2016 Dec;33(12):3044-3056. PMID:27631130.

Tahmasebi S, Jafarnejad SM, Tam IS, Gonatopoulos-Pournatzis T, Matta-Camacho E, Tsukumo Y, Yanagiya A, Li W, Atlasi Y, Caron M, Braunschweig U, Pearl D, Khoutorsky A, Gkogkas CG, Nadon R, Bourque G, Yang XJ, Tian B, Stunnenberg HG, Yamanaka Y, Blencowe BJ, Giguère V, Sonenberg N. Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2. Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12360-12367. PMID:27791185.

Kumar N, Srivillibhuthur M, Joshi S, Walton KD, Zhou A, Faller WJ, Perekatt AO, Sansom OJ, Gumucio DL, Xing J, Bonder EM, Gao N, White E, Verzi MP. A YY1-dependent increase in aerobic metabolism is indispensable for intestinal organogenesis. Development. 2016 Oct 15;143(20):3711-3722. PMID:27802136.

Oza J, Ganguly B, Kulkarni A, Ginjala V, Yao M, Ganesan S. A Novel Role of Chromodomain Protein CBX8 in DNA Damage Response. J Biol Chem. 2016 Oct 28;291(44):22881-22893. PMID:27555324.

Miles WO, Lembo A, Volorio A, Brachtel E, Tian B, Sgroi D, Provero P, Dyson N. Alternative Polyadenylation in Triple-Negative Breast Tumors Allows NRAS and c-JUN to Bypass PUMILIO Posttranscriptional Regulation. Cancer Res. 2016 Dec 15;76(24):7231-7241. PMID:27758885.

Oshima K, Khiabanian H, da Silva-Almeida AC, Tzoneva G, Abate F, Ambesi-Impiombato A, Sanchez-Martin M, Carpenter Z, Penson A, Perez-Garcia A, Eckert C, Nicolas C, Balbin M, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Gastier-Foster JM, Devidas M, Loh ML, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando AA. Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia. Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11306-11311. PMID:27655895.

Pei S, Minhajuddin M, D'Alessandro A, Nemkov T, Stevens BM, Adane B, Khan N, Hagen FK, Yadav VK, De S, Ashton JM, Hansen KC, Gutman JA, Pollyea DA, Crooks PA, Smith C, Jordan CT. Rational Design of a Parthenolide-based Drug Regimen That Selectively Eradicates Acute Myelogenous Leukemia Stem Cells. J Biol Chem. 2016 Oct 14;291(42):21984-22000. PMID:27573247.

 

 

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