CSCB - Selected Publications

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. 2017 Nov 15. PMID:29155997.

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. 2017 Nov 3. doi: 10. PMID:29099487.

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.

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.

Rogozin IB, Goncearenco A, Lada AG, De S, 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. 2017 Nov 15:1-31. PMID:29139326.

Lue HW, Podolak J, Kolahi K, Cheng L, Rao S, Garg D, Xue CH, Rantala JK, Tyner JW, Thornburg KL, Martinez-Acevedo A, Liu JJ, Amling CL, Truillet C, Louie SM, Anderson KE, Evans MJ, O'Donnell VB, Nomura DK, Drake JM, Ritz A, Thomas GV. Metabolic reprogramming ensures cancer cell survival despite oncogenic signaling blockade. Genes Dev. 2017 Oct 15;31(20):2067-2084. PMID:29138276.

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. 2017 Oct 23. 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 Oct 4. PMID:28978720.

Yue X, Zhang C, Zhao Y, Liu J, Lin AW, Tan VM, Drake JM, Liu L, Boateng MN, Li J, Feng Z, Hu W. Gain-of-function mutant p53 activates small GTPase Rac1 through SUMOylation to promote tumor progression. Genes Dev. 2017 Aug 15;31(16):1641-1654. PMID:28947497.

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. 2017 Aug 1:272989X17724773. 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 Jul 21. 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.

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.

Tan VM, Cheng LC, Drake JM. Complementing genomics and transcriptomics: Phosphoproteomics illuminates systems biology in prostate cancer. Mol Cell Oncol. 2016 Oct 14;3(6):e1246075. PMID:28090583.

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.

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.

Stoyanova T, Riedinger M, Lin S, Faltermeier CM, Smith BA, Zhang KX, Going CC, Goldstein AS, Lee JK, Drake JM, Rice MA, Hsu EC, Nowroozizadeh B, Castor B, Orellana SY, Blum SM, Cheng D, Pienta KJ, Reiter RE, Pitteri SJ, Huang J, Witte ON. Activation of Notch1 synergizes with multiple pathways in promoting castration-resistant prostate cancer. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6457-E6466. PMID:27694579.

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.

Hirshfield KM, Tolkunov D, Zhong H, Ali SM, Stein MN, Murphy S, Vig H, Vazquez A, Glod J, Moss RA, Belyi V, Chan CS, Chen S, Goodell L, Foran D, Yelensky R, Palma NA, Sun JX, Miller VA, Stephens PJ, Ross JS, Kaufman H, Poplin E, Mehnert J, Tan AR, Bertino JR, Aisner J, DiPaola RS, Rodriguez-Rodriguez L, Ganesan S. Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers. Oncologist. 2016 Aug 26. PMID:27566247.

Guo JY, Teng X, Laddha SV, Ma S, Van Nostrand SC, Yang Y, Khor S, Chan CS, Rabinowitz JD, White E. Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells. Genes Dev. 2016 Aug 1;30(15):1704-17. PMID:27516533.

Zheng D, Liu X, Tian B. 3'READS+, a sensitive and accurate method for 3' end sequencing of polyadenylated RNA. RNA. 2016 Oct;22(10):1631-9. PMID:27512124.

Yang Q, Lin J, Liu M, Li R, Tian B, Zhang X, Xu B, Liu M, Zhang X, Li Y, Shi H, Wu L. Highly sensitive sequencing reveals dynamic modifications and activities of small RNAs in mouse oocytes and early embryos. Sci Adv. 2016 Jun 10;2(6):e1501482. PMID:27500274.

Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin DE, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, Huang J, Wohlschlegel JA, Graeber TG, Witte ON, Stuart JM. Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Cell. 2016 Aug 11;166(4):1041-1054. PMID:27499020.

Devany E, Park JY, Murphy MR, Zakusilo G, Baquero J, Zhang X, Hoque M, Tian B, Kleiman FE. Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. Cell Discov. 2016 Jun 14;2:16013. PMID:27462460.

Matsuda T, Zhai P, Sciarretta S, Zhang Y, Jeong JI, Ikeda S, Park J, Hsu CP, Tian B, Pan D, Sadoshima J, Del Re DP. NF2 Activates Hippo Signaling and Promotes Ischemia/Reperfusion Injury in the Heart. Circ Res. 2016 Aug 19;119(5):596-606. PMID:27402866.

Lemay JF, Marguerat S, Larochelle M, Liu X, van Nues R, Hunyadkürti J, Hoque M, Tian B, Granneman S, Bähler J, Bachand F. The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection. Genes Dev. 2016 Jul 1;30(13):1558-72. PMID:27401558.

Lund PK, Verzi MP. Singling Out Intestinal Epithelial Stem Cells. Gastroenterology. 2016 Aug;151(2):228-31. PMID:27374365.

Levine AJ, Puzio-Kuter AM, Chan CS, Hainaut P. The Role of the p53 Protein in Stem-Cell Biology and Epigenetic Regulation. Cold Spring Harb Perspect Med. 2016 Sep 1;6(9). PMID:27352800.

Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362-73. PMID:27335277.

Yildirim E, Foran DJ. Parallel Versus Distributed Data Access for Gigapixel-Resolution Histology Images: Challenges and Opportunities. IEEE J Biomed Health Inform. 2017 Jul;21(4):1049-1057. PMID:27323383.

Ganesan S, Rodriguez-Rodriguez L, DiPaola RS. Precision Medicine: Implications for Science and Practice. J Am Coll Surg. 2016 Sep;223(3):433-439. PMID:27321387.

Yadav VK, Smith KS, Flinders C, Mumenthaler SM, De S. Significance of duon mutations in cancer genomes. Sci Rep. 2016 Jun 8;6:27437. PMID:27272679.

Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016 Jun 2;534(7605):55-62. PMID:27251275.

Spencer KR, Wang J, Silk AW, Ganesan S, Kaufman HL, Mehnert JM. Biomarkers for Immunotherapy: Current Developments and Challenges. Am Soc Clin Oncol Educ Book. 2016;35:e493-503. PMID:27249758.

Ali SM, Hensing T, Schrock AB, Allen J, Sanford E, Gowen K, Kulkarni A, He J, Suh JH, Lipson D, Elvin JA, Yelensky R, Chalmers Z, Chmielecki J, Peled N, Klempner SJ, Firozvi K, Frampton GM, Molina JR, Menon S, Brahmer JR, MacMahon H, Nowak J, Ou SH, Zauderer M, Ladanyi M, Zakowski M, Fischbach N, Ross JS, Stephens PJ, Miller VA, Wakelee H, Ganesan S, Salgia R. Comprehensive Genomic Profiling Identifies a Subset of Crizotinib-Responsive ALK-Rearranged Non-Small Cell Lung Cancer Not Detected by Fluorescence In Situ Hybridization. Oncologist. 2016 Jun;21(6):762-70. PMID:27245569.

Hrdlickova R, Toloue M, Tian B. RNA-Seq methods for transcriptome analysis. Wiley Interdiscip Rev RNA. 2017 Jan;8(1). PMID:27198714.

Mehnert JM, Panda A, Zhong H, Hirshfield K, Damare S, Lane K, Sokol L, Stein MN, Rodriguez-Rodriquez L, Kaufman HL, Ali S, Ross JS, Pavlick DC, Bhanot G, White EP, DiPaola RS, Lovell A, Cheng J, Ganesan S. Immune activation and response to pembrolizumab in POLE-mutant endometrial cancer. J Clin Invest. 2016 Jun 1;126(6):2334-40. PMID:27159395.

Paganin M, Buldini B, Germano G, Seganfreddo E, Meglio Ad, Magrin E, Grillo F, Pigazzi M, Rizzari C, Cazzaniga G, Khiabanian H, Palomero T, Rabadan R, Ferrando AA, Basso G. A Case of T-cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia. Pediatr Blood Cancer. 2016 Sep;63(9):1660-3. PMID:27149388.

Choe KN, Nicolae CM, Constantin D, Imamura Kawasawa Y, Delgado-Diaz MR, De S, Freire R, Smits VA, Moldovan GL. HUWE1 interacts with PCNA to alleviate replication stress. EMBO Rep. 2016 Jun;17(6):874-86. PMID:27146073.

Boregowda RK, Medina DJ, Markert E, Bryan MA, Chen W, Chen S, Rabkin A, Vido MJ, Gunderson SI, Chekmareva M, Foran DJ, Lasfar A, Goydos JS, Cohen-Solal KA. The transcription factor RUNX2 regulates receptor tyrosine kinase expression in melanoma. Oncotarget. 2016 May 17;7(20):29689-707. PMID:27102439.

Wang R, Ganesan S, Zheng XF. Yin and yang of 4E-BP1 in cancer. Cell Cycle. 2016 Jun 2;15(11):1401-2. PMID:27096536.

Wu S, Marie Lutz B, Miao X, Liang L, Mo K, Chang YJ, Du P, Soteropoulos P, Tian B, Kaufman AG, Bekker A, Hu Y, Tao YX. Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice. Mol Pain. 2016 Mar 11;12. PMID:27030721.

Hintzsche J, Kim J, Yadav V, Amato C, Robinson SE, Seelenfreund E, Shellman Y, Wisell J, Applegate A, McCarter M, Box N, Tentler J, De S, Robinson WA, Tan AC. IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. J Am Med Inform Assoc. 2016 Jul;23(4):721-30. PMID:27026619.

Gatza ML, Carey LA. Another Breast Cancer Entity Confirmed: Genomics of Invasive Lobular Breast Cancer. J Clin Oncol. 2016 Jun 1;34(16):1838-9. PMID:27022119.

Rodriguez-Rodriguez L, Hirshfield KM, Rojas V, DiPaola RS, Gibbon D, Hellmann M, Isani S, Leiser A, Riedlinger GM, Wagreich A, Ali SM, Elvin JA, Miller VA, Ganesan S. Use of comprehensive genomic profiling to direct point-of-care management of patients with gynecologic cancers. Gynecol Oncol. 2016 Apr;141(1):2-9. PMID:27016222.

Ganguly B, Dolfi SC, Rodriguez-Rodriguez L, Ganesan S, Hirshfield KM. Role of Biomarkers in the Development of PARP Inhibitors. Biomark Cancer. 2016 Mar 9;8(Suppl 1):15-25. PMID:26997874.

Pandya HJ, Park K, Chen W, Goodell LA, Foran DJ, Desai JP. Toward a Portable Cancer Diagnostic Tool Using a Disposable MEMS-Based Biochip. IEEE Trans Biomed Eng. 2016 Jul;63(7):1347-53. PMID:26930673.

Paratala BS, Dolfi SC, Khiabanian H, Rodriguez-Rodriguez L, Ganesan S, Hirshfield KM. Emerging Role of Genomic Rearrangements in Breast Cancer: Applying Knowledge from Other Cancers. Biomark Cancer. 2016 Feb 11;8(Supple 1):1-14. PMID:26917980.

Yadav VK, DeGregori J, De S. The landscape of somatic mutations in protein coding genes in apparently benign human tissues carries signatures of relaxed purifying selection. Nucleic Acids Res. 2016 Mar 18;44(5):2075-84. PMID:26883632.

Groen N, Guvendiren M, Rabitz H, Welsh WJ, Kohn J, de Boer J. Stepping into the omics era: Opportunities and challenges for biomaterials science and engineering. Acta Biomater. 2016 Apr 1;34:133-142. PMID:26876875.

Poczobutt JM, De S, Yadav VK, Nguyen TT, Li H, Sippel TR, Weiser-Evans MC, Nemenoff RA. Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer. J Immunol. 2016 Mar 15;196(6):2847-59. PMID:26873985.

Herranz D, Ferrando AA. Targeting NOTCH1 in T-ALL: Starving the dragon. Cell Cycle. 2016;15(4):483-4. PMID:26864725.

Zhang C, Liu J, Tan C, Yue X, Zhao Y, Peng J, Wang X, Laddha SV, Chan CS, Zheng S, Hu W, Feng Z. microRNA-1827 represses MDM2 to positively regulate tumor suppressor p53 and suppress tumorigenesis. Oncotarget. 2016 Feb 23;7(8):8783-96. PMID:26840028.

Zhang Y, Li Q, Welsh WJ, Moghe PV, Uhrich KE. Micellar and structural stability of nanoscale amphiphilic polymers: Implications for anti-atherosclerotic bioactivity. Biomaterials. 2016 Apr;84:230-40. PMID:26828687.

Rasi S, Khiabanian H, Ciardullo C, Terzi-di-Bergamo L, Monti S, Spina V, Bruscaggin A, Cerri M, Deambrogi C, Martuscelli L, Biasi A, Spaccarotella E, De Paoli L, Gattei V, Foà R, Rabadan R, Gaidano G, Rossi D. Clinical impact of small subclones harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia. Haematologica. 2016 Apr;101(4):e135-8. PMID:26819056.

Li W, Park JY, Zheng D, Hoque M, Yehia G, Tian B. Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control. BMC Biol. 2016 Jan 22;14:6. PMID:26801249.

Yang Y, Li W, Hoque M, Hou L, Shen S, Tian B, Dynlacht BD. PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation. PLoS Genet. 2016 Jan 14;12(1):e1005794. PMID:26765774.

Zhang C, Liu J, Zhao Y, Yue X, Zhu Y, Wang X, Wu H, Blanco F, Li S, Bhanot G, Haffty BG, Hu W, Feng Z. Glutaminase 2 is a novel negative regulator of small GTPase Rac1 and mediates p53 function in suppressing metastasis. Elife. 2016 Jan 11;5:e10727. PMID:26751560.

Su H, Shen Y, Xing F, Qi X, Hirshfield KM, Yang L, Foran DJ. Robust automatic breast cancer staging using a combination of functional genomics and image-omics. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:7226-9. PMID:26737959.

Ren J, Sadimin ET, Wang D, Epstein JI, Foran DJ, Qi X. Computer aided analysis of prostate histopathology images Gleason grading especially for Gleason score 7. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:3013-6. PMID:26736926.

Wang D, Foran DJ, Ren J, Zhong H, Kim IY, Qi X. Exploring automatic prostate histopathology image Gleason grading via local structure modeling. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:2649-52. PMID:26736836.

Joshi S, Tolkunov D, Aviv H, Hakimi AA, Yao M, Hsieh JJ, Ganesan S, Chan CS, White E. The Genomic Landscape of Renal Oncocytoma Identifies a Metabolic Barrier to Tumorigenesis. Cell Rep. 2015 Dec 1;13(9):1895-908. PMID:26655904.

Lee AK, Kulcsar KA, Elliott O, Khiabanian H, Nagle ER, Jones ME, Amman BR, Sanchez-Lockhart M, Towner JS, Palacios G, Rabadan R. De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. BMC Genomics. 2015 Dec 7;16:1033. PMID:26643810.

Levine AJ, Chan CS, Dudgeon C, Puzio-Kuter A, Hainaut P. The Evolution of Tumors in Mice and Humans with Germline p53 Mutations. Cold Spring Harb Symp Quant Biol. 2015;80:139-45. PMID:26642854.

Kurc T, Qi X, Wang D, Wang F, Teodoro G, Cooper L, Nalisnik M, Yang L, Saltz J, Foran DJ. Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies. BMC Bioinformatics. 2015 Dec 1;16:399. PMID:26627175.

Faltermeier CM, Drake JM, Clark PM, Smith BA, Zong Y, Volpe C, Mathis C, Morrissey C, Castor B, Huang J, Witte ON. Functional screen identifies kinases driving prostate cancer visceral and bone metastasis. Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):E172-81. PMID:26621741.

Wu Y, Kwon YS, Labib M, Foran DJ, Singer EA. Magnetic Resonance Imaging as a Biomarker for Renal Cell Carcinoma. Dis Markers. 2015;2015:648495. PMID:26609190.

Smith KS, Yadav VK, Pei S, Pollyea DA, Jordan CT, De S. SomVarIUS: somatic variant identification from unpaired tissue samples. Bioinformatics. 2016 Mar 15;32(6):808-13. PMID:26589277.

White E, Mehnert JM, Chan CS. Autophagy, Metabolism, and Cancer. Clin Cancer Res. 2015 Nov 15;21(22):5037-46. PMID:26567363.

da Silva Almeida AC, Abate F, Khiabanian H, Martinez-Escala E, Guitart J, Tensen CP, Vermeer MH, Rabadan R, Ferrando A, Palomero T. The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome. Nat Genet. 2015 Dec;47(12):1465-70. PMID:26551667.

Neve J, Burger K, Li W, Hoque M, Patel R, Tian B, Gullerova M, Furger A. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Genome Res. 2016 Jan;26(1):24-35. PMID:26546131.

Diller DJ, Connell ND, Welsh WJ. Avalanche for shape and feature-based virtual screening with 3D alignment. J Comput Aided Mol Des. 2015 Nov;29(11):1015-24. PMID:26458937.

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA; TCGA Research Network, Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 8;163(2):506-19. PMID:26451490.

Herranz D, Ambesi-Impiombato A, Sudderth J, Sánchez-Martín M, Belver L, Tosello V, Xu L, Wendorff AA, Castillo M, Haydu JE, Márquez J, Matés JM, Kung AL, Rayport S, Cordon-Cardo C, DeBerardinis RJ, Ferrando AA. Metabolic reprogramming induces resistance to anti-NOTCH1 therapies in T cell acute lymphoblastic leukemia. Nat Med. 2015 Oct;21(10):1182-9. PMID:26390244.

LaCuran AE, Pegg KM, Liu EM, Bethel CR, Ai N, Welsh WJ, Bonomo RA, Oelschlaeger P. Elucidating the Role of Residue 67 in IMP-Type Metallo-β-Lactamase Evolution. Antimicrob Agents Chemother. 2015 Dec;59(12):7299-307. PMID:26369960.

Chen W, Brandes Z, Roy R, Chekmareva M, Pandya HJ, Desai JP, Foran DJ. Robot-Guided Atomic Force Microscopy for Mechano-Visual Phenotyping of Cancer Specimens. Microsc Microanal. 2015 Oct;21(5):1224-35. PMID:26343283.

Yang Y, Del Re DP, Nakano N, Sciarretta S, Zhai P, Park J, Sayed D, Shirakabe A, Matsushima S, Park Y, Tian B, Abdellatif M, Sadoshima J. miR-206 Mediates YAP-Induced Cardiac Hypertrophy and Survival. Circ Res. 2015 Oct 23;117(10):891-904. PMID:26333362.

Pandya HJ, Park K, Chen W, Chekmareva MA, Foran DJ, Desai JP. Simultaneous MEMS-based electro-mechanical phenotyping of breast cancer. Lab Chip. 2015;15(18):3695-706. PMID:26224116.

Bjørklund SS, Kristensen VN, Seiler M, Kumar S, Alnæs GI, Ming Y, Kerrigan J, Naume B, Sachidanandam R, Bhanot G, Børresen-Dale AL, Ganesan S. Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas. BMC Cancer. 2015 Jul 17;15:524. PMID:26183823.

Goodwin JF, Kothari V, Drake JM, Zhao S, Dylgjeri E, Dean JL, Schiewer MJ, McNair C, Jones JK, Aytes A, Magee MS, Snook AE, Zhu Z, Den RB, Birbe RC, Gomella LG, Graham NA, Vashisht AA, Wohlschlegel JA, Graeber TG, Karnes RJ, Takhar M, Davicioni E, Tomlins SA, Abate-Shen C, Sharifi N, Witte ON, Feng FY, Knudsen KE. DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis. Cancer Cell. 2015 Jul 13;28(1):97-113. PMID:26175416.

Garcia CA, Baron JM, Beckwith BA, Brodsky V, Dighe AS, Gudewicz TM, Kim JY, Klepeis VE, Lane WJ, Lee RE, Levy BP, Mahowald MA, Mandelker D, McClintock DS, Quinn AM, Rao LK, Riedlinger GM, Rudolf J, Gilbertson JR. Environmental components and methods for engaging pathology residents in informatics training. J Pathol Inform. 2015 Jun 29;6:42. PMID:26167386.

Hu J, Verzi MP, Robinson AS, Tang PL, Hua LL, Xu SM, Kwok PY, Black BL. Endothelin signaling activates Mef2c expression in the neural crest through a MEF2C-dependent positive-feedback transcriptional pathway. Development. 2015 Aug 15;142(16):2775-80. PMID:26160899.

Dai W, Li W, Hoque M, Li Z, Tian B, Makeyev EV. A post-transcriptional mechanism pacing expression of neural genes with precursor cell differentiation status. Nat Commun. 2015 Jul 6;6:7576. PMID:26144867.

Silva GO, He X, Parker JS, Gatza ML, Carey LA, Hou JP, Moulder SL, Marcom PK, Ma J, Rosen JM, Perou CM. Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. Breast Cancer Res Treat. 2015 Jul;152(2):347-56. PMID:26109346.

Pfister NT, Fomin V, Regunath K, Zhou JY, Zhou W, Silwal-Pandit L, Freed-Pastor WA, Laptenko O, Neo SP, Bargonetti J, Hoque M, Tian B, Gunaratne J, Engebraaten O, Manley JL, Børresen-Dale AL, Neilsen PM, Prives C. Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells. Genes Dev. 2015 Jun 15;29(12):1298-315. PMID:26080815.

Das S, Yu S, Sakamori R, Vedula P, Feng Q, Flores J, Hoffman A, Fu J, Stypulkowski E, Rodriguez A, Dobrowolski R, Harada A, Hsu W, Bonder EM, Verzi MP, Gao N. Rab8a vesicles regulate Wnt ligand delivery and Paneth cell maturation at the intestinal stem cell niche. Development. 2015 Jun 15;142(12):2147-62. PMID:26015543.

Xu J, Xiang L, Wang G, Ganesan S, Feldman M, Shih NN, Gilmore H, Madabhushi A. Sparse Non-negative Matrix Factorization (SNMF) based color unmixing for breast histopathological image analysis. Comput Med Imaging Graph. 2015 Dec;46 Pt 1:20-29. PMID:25958195.

Young CD, Zimmerman LJ, Hoshino D, Formisano L, Hanker AB, Gatza ML, Morrison MM, Moore PD, Whitwell CA, Dave B, Stricker T, Bhola NE, Silva GO, Patel P, Brantley-Sieders DM, Levin M, Horiates M, Palma NA, Wang K, Stephens PJ, Perou CM, Weaver AM, O'Shaughnessy JA, Chang JC, Park BH, Liebler DC, Cook RS, Arteaga CL. Activating PIK3CA Mutations Induce an Epidermal Growth Factor Receptor (EGFR)/Extracellular Signal-regulated Kinase (ERK) Paracrine Signaling Axis in Basal-like Breast Cancer. Mol Cell Proteomics. 2015 Jul;14(7):1959-76. PMID:25953087.

Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res. 2015 Jun 23;43(11):5307-17. PMID:25934800.

Li W, You B, Hoque M, Zheng D, Luo W, Ji Z, Park JY, Gunderson SI, Kalsotra A, Manley JL, Tian B. Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet. 2015 Apr 23;11(4):e1005166. PMID:25906188.

Abdelhamid DS, Zhang Y, Lewis DR, Moghe PV, Welsh WJ, Uhrich KE. Tartaric acid-based amphiphilic macromolecules with ether linkages exhibit enhanced repression of oxidized low density lipoprotein uptake. Biomaterials. 2015 Jun;53:32-9. PMID:25890704.

Teh JL, Shah R, La Cava S, Dolfi SC, Mehta MS, Kongara S, Price S, Ganesan S, Reuhl KR, Hirshfield KM, Karantza V, Chen S. Metabotropic glutamate receptor 1 disrupts mammary acinar architecture and initiates malignant transformation of mammary epithelial cells. Breast Cancer Res Treat. 2015 May;151(1):57-73. PMID:25859923.

Martin AA, Tomasini M, Kholodovych V, Gu L, Sommerfeld SD, Uhrich KE, Murthy NS, Welsh WJ, Moghe PV. Carbohydrate-derived amphiphilic macromolecules: a biophysical structural characterization and analysis of binding behaviors to model membranes. J Funct Biomater. 2015 Apr 8;6(2):171-91. PMID:25855953.

Ai N, Wood RD, Welsh WJ. Identification of Nitazoxanide as a Group I Metabotropic Glutamate Receptor Negative Modulator for the Treatment of Neuropathic Pain: An In Silico Drug Repositioning Study. Pharm Res. 2015 Aug;32(8):2798-807. PMID:25762088.

Emmett KJ, Lee A, Khiabanian H, Rabadan R. High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants. PLoS Curr. 2015 Feb 9;7. PMID:25737802.

Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, De S, Kishony R, Michor F, Dowell R, Pellman D. Polyploidy can drive rapid adaptation in yeast. Nature. 2015 Mar 19;519(7543):349-52. PMID:25731168.

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Herranz D, Ferrando AA. An oncogenic enhancer enemy (N-Me) in T-ALL. Cell Cycle. 2015;14(2):167-8. PMID:25584678.

Pimenta EM, De S, Weiss R, Feng D, Hall K, Kilic S, Bhanot G, Ganesan S, Ran S, Barnes BJ. IRF5 is a novel regulator of CXCL13 expression in breast cancer that regulates CXCR5(+) B- and T-cell trafficking to tumor-conditioned media. Immunol Cell Biol. 2015 May-Jun;93(5):486-99. PMID:25533286.

San Roman AK, Aronson BE, Krasinski SD, Shivdasani RA, Verzi MP. Transcription factors GATA4 and HNF4A control distinct aspects of intestinal homeostasis in conjunction with transcription factor CDX2. J Biol Chem. 2015 Jan 16;290(3):1850-60. PMID:25488664.

Stein MN, Hirshfield KM, Zhong H, Singer EA, Ali SM, Ganesan S. Response to crizotinib in a patient with MET-mutant papillary renal cell cancer after progression on tivantinib. Eur Urol. 2015 Feb;67(2):353-4. PMID:25457019.

Osimitz TG, Welsh WJ, Ai N, Toole C. Polyester monomers lack ability to bind and activate both androgenic and estrogenic receptors as determined by in vitro and in silico methods. Food Chem Toxicol. 2015 Jan;75:128-38. PMID:25455886.

Hormoz S, Bhanot G, Biehl M, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Dayarian A. Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets. Bioinformatics. 2015 Feb 15;31(4):492-500. PMID:25152231.

Pandya HJ, Roy R, Chen W, Chekmareva MA, Foran DJ, Desai JP. Accurate characterization of benign and cancerous breast tissues: aspecific patient studies using piezoresistive microcantilevers. Biosens Bioelectron. 2015 Jan 15;63:414-24. PMID:25128621.

Dayarian A, Romero R, Wang Z, Biehl M, Bilal E, Hormoz S, Meyer P, Norel R, Rhrissorrakrai K, Bhanot G, Luo F, Tarca AL. Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge. Bioinformatics. 2015 Feb 15;31(4):462-70. PMID:25061067.

Biehl M, Sadowski P, Bhanot G, Bilal E, Dayarian A, Meyer P, Norel R, Rhrissorrakrai K, Zeller MD, Hormoz S. Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge. Bioinformatics. 2015 Feb 15;31(4):453-61. PMID:24994890.

Yadav VK, De S. An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. Brief Bioinform. 2015 Mar;16(2):232-41. PMID:24562872.

 

 

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