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Coding-Complete Genome Sequence of a Pollen-Associated Virus Belonging to the Secoviridae Family Recovered from a Japanese Apricot (Prunus mume) Metagenome Data Set.

Fetters AM, Cantalupo PG, Ashman TL, Pipas JM.

Microbiol Resour Announc. 2019 Oct 3;8(40). pii: e00881-19. doi: 10.1128/MRA.00881-19.


Detecting viral sequences in NGS data.

Cantalupo PG, Pipas JM.

Curr Opin Virol. 2019 Aug 26;39:41-48. doi: 10.1016/j.coviro.2019.07.010. [Epub ahead of print] Review.


Randomized Phase II Trial of Seribantumab in Combination with Erlotinib in Patients with EGFR Wild-Type Non-Small Cell Lung Cancer.

Sequist LV, Gray JE, Harb WA, Lopez-Chavez A, Doebele RC, Modiano MR, Jackman DM, Baggstrom MQ, Atmaca A, Felip E, Provencio M, Cobo M, Adiwijaya B, Kuesters G, Kamoun WS, Andreas K, Pipas JM, Santillana S, Cho BC, Park K, Shepherd FA.

Oncologist. 2019 Aug;24(8):1095-1102. doi: 10.1634/theoncologist.2018-0695. Epub 2019 Apr 11.


DNA Tumor Viruses and Their Contributions to Molecular Biology.

Pipas JM.

J Virol. 2019 Apr 17;93(9). pii: e01524-18. doi: 10.1128/JVI.01524-18. Print 2019 May 1. Review.


Human polyomavirus BKV infection of endothelial cells results in interferon pathway induction and persistence.

An P, Sáenz Robles MT, Duray AM, Cantalupo PG, Pipas JM.

PLoS Pathog. 2019 Jan 8;15(1):e1007505. doi: 10.1371/journal.ppat.1007505. eCollection 2019 Jan.


Evolution on the Biophysical Fitness Landscape of an RNA Virus.

Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Lloyd Ung W, Choi JM, Rodrigues JV, Kolawole AO, Koehler SA, Wu S, Thielen PM, Cui N, Demirev PA, Giacobbi NS, Julian TR, Schwab K, Lin JS, Smith TJ, Pipas JM, Wobus CE, Feldman AB, Weitz DA, Shakhnovich EI.

Mol Biol Evol. 2018 Oct 1;35(10):2390-2400. doi: 10.1093/molbev/msy131.


Draft Genome Sequence of a Novel Rhabdovirus Isolated from Deinocerites Mosquitoes.

Xu CL, Cantalupo PG, Sáenz-Robles MT, Baldwin A, Fitzpatrick D, Norris DE, Jackson E, Pipas JM.

Genome Announc. 2018 May 10;6(19). pii: e01438-17. doi: 10.1128/genomeA.01438-17.


Dual Inhibition of IGF-1R and ErbB3 Enhances the Activity of Gemcitabine and Nab-Paclitaxel in Preclinical Models of Pancreatic Cancer.

Camblin AJ, Pace EA, Adams S, Curley MD, Rimkunas V, Nie L, Tan G, Bloom T, Iadevaia S, Baum J, Minx C, Czibere A, Louis CU, Drummond DC, Nielsen UB, Schoeberl B, Pipas JM, Straubinger RM, Askoxylakis V, Lugovskoy AA.

Clin Cancer Res. 2018 Jun 15;24(12):2873-2885. doi: 10.1158/1078-0432.CCR-17-2262. Epub 2018 Mar 16.


Complete Genome Sequence of Pittsburgh Sewage-Associated Virus 1.

Cantalupo PG, Pipas JM.

Genome Announc. 2018 Mar 15;6(11). pii: e01460-17. doi: 10.1128/genomeA.01460-17.


Identification of Head and Neck Cancer Subtypes Based on Human Papillomavirus Presence and E2F-Regulated Gene Expression.

Johnson ME, Cantalupo PG, Pipas JM.

mSphere. 2018 Jan 10;3(1). pii: e00580-17. doi: 10.1128/mSphere.00580-17. eCollection 2018 Jan-Feb.


Viral sequences in human cancer.

Cantalupo PG, Katz JP, Pipas JM.

Virology. 2018 Jan 1;513:208-216. doi: 10.1016/j.virol.2017.10.017. Epub 2017 Nov 5.


Dosage-dependent copy number gains in E2f1 and E2f3 drive hepatocellular carcinoma.

Kent LN, Bae S, Tsai SY, Tang X, Srivastava A, Koivisto C, Martin CK, Ridolfi E, Miller GC, Zorko SM, Plevris E, Hadjiyannis Y, Perez M, Nolan E, Kladney R, Westendorp B, de Bruin A, Fernandez S, Rosol TJ, Pohar KS, Pipas JM, Leone G.

J Clin Invest. 2017 Mar 1;127(3):830-842. doi: 10.1172/JCI87583. Epub 2017 Jan 30.


Complete Genome Sequence of a Polyomavirus Recovered from a Pomona Leaf-Nosed Bat (Hipposideros pomona) Metagenome Data Set.

Cantalupo PG, Buck CB, Pipas JM.

Genome Announc. 2017 Jan 19;5(3). pii: e01053-16. doi: 10.1128/genomeA.01053-16.


Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma.

Starrett GJ, Marcelus C, Cantalupo PG, Katz JP, Cheng J, Akagi K, Thakuria M, Rabinowits G, Wang LC, Symer DE, Pipas JM, Harris RS, DeCaprio JA.

MBio. 2017 Jan 3;8(1). pii: e02079-16. doi: 10.1128/mBio.02079-16.


Nanoliposomal Irinotecan in the Clinical Practice Guideline for Metastatic Pancreatic Cancer: Applicability to Clinical Situations.

Wang-Gillam A, Von Hoff D, Siveke J, Hubner R, Belanger B, Pipas JM, Chen LT.

J Clin Oncol. 2017 Feb 20;35(6):689-690. doi: 10.1200/JCO.2016.70.1607. Epub 2016 Dec 5. No abstract available.


E2f8 mediates tumor suppression in postnatal liver development.

Kent LN, Rakijas JB, Pandit SK, Westendorp B, Chen HZ, Huntington JT, Tang X, Bae S, Srivastava A, Senapati S, Koivisto C, Martin CK, Cuitino MC, Perez M, Clouse JM, Chokshi V, Shinde N, Kladney R, Sun D, Perez-Castro A, Matondo RB, Nantasanti S, Mokry M, Huang K, Machiraju R, Fernandez S, Rosol TJ, Coppola V, Pohar KS, Pipas JM, Schmidt CR, de Bruin A, Leone G.

J Clin Invest. 2016 Aug 1;126(8):2955-69. doi: 10.1172/JCI85506. Epub 2016 Jul 25.


The Ancient Evolutionary History of Polyomaviruses.

Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A.

PLoS Pathog. 2016 Apr 19;12(4):e1005574. doi: 10.1371/journal.ppat.1005574. eCollection 2016 Apr.


Drug eluting biliary stents to decrease stent failure rates: A review of the literature.

Shatzel J, Kim J, Sampath K, Syed S, Saad J, Hussain ZH, Mody K, Pipas JM, Gordon S, Gardner T, Rothstein RI.

World J Gastrointest Endosc. 2016 Jan 25;8(2):77-85. doi: 10.4253/wjge.v8.i2.77. Review.


Expression of the small T antigen of Lymphotropic Papovavirus is sufficient to transform primary mouse embryo fibroblasts.

Gupta T, Robles MT, Schowalter RM, Buck CB, Pipas JM.

Virology. 2016 Jan;487:112-20. doi: 10.1016/j.virol.2015.10.003. Epub 2015 Oct 27.


Randomized, Double-Blind, Phase II Study of Ruxolitinib or Placebo in Combination With Capecitabine in Patients With Metastatic Pancreatic Cancer for Whom Therapy With Gemcitabine Has Failed.

Hurwitz HI, Uppal N, Wagner SA, Bendell JC, Beck JT, Wade SM 3rd, Nemunaitis JJ, Stella PJ, Pipas JM, Wainberg ZA, Manges R, Garrett WM, Hunter DS, Clark J, Leopold L, Sandor V, Levy RS.

J Clin Oncol. 2015 Dec 1;33(34):4039-47. doi: 10.1200/JCO.2015.61.4578. Epub 2015 Sep 8.


Whole-Genome Sequencing of a Single Viral Species from a Highly Heterogeneous Sample.

Han HS, Cantalupo PG, Rotem A, Cockrell SK, Carbonnaux M, Pipas JM, Weitz DA.

Angew Chem Int Ed Engl. 2015 Nov 16;54(47):13985-8. doi: 10.1002/anie.201507047. Epub 2015 Aug 28.


Rapid, targeted and culture-free viral infectivity assay in drop-based microfluidics.

Tao Y, Rotem A, Zhang H, Chang CB, Basu A, Kolawole AO, Koehler SA, Ren Y, Lin JS, Pipas JM, Feldman AB, Wobus CE, Weitz DA.

Lab Chip. 2015 Oct 7;15(19):3934-40. doi: 10.1039/c5lc00556f.


Artifact-Free Quantification and Sequencing of Rare Recombinant Viruses by Using Drop-Based Microfluidics.

Tao Y, Rotem A, Zhang H, Cockrell SK, Koehler SA, Chang CB, Ung LW, Cantalupo PG, Ren Y, Lin JS, Feldman AB, Wobus CE, Pipas JM, Weitz DA.

Chembiochem. 2015 Oct 12;16(15):2167-71. doi: 10.1002/cbic.201500384. Epub 2015 Sep 7.


Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles.

Liu H, Tang X, Srivastava A, Pécot T, Daniel P, Hemmelgarn B, Reyes S, Fackler N, Bajwa A, Kladney R, Koivisto C, Chen Z, Wang Q, Huang K, Machiraju R, Sáenz-Robles MT, Cantalupo P, Pipas JM, Leone G.

Nat Cell Biol. 2015 Aug;17(8):1036-48. doi: 10.1038/ncb3210. Epub 2015 Jul 20.


Molecular profiling of intrahepatic and extrahepatic cholangiocarcinoma using next generation sequencing.

Putra J, de Abreu FB, Peterson JD, Pipas JM, Mody K, Amos CI, Tsongalis GJ, Suriawinata AA.

Exp Mol Pathol. 2015 Oct;99(2):240-4. doi: 10.1016/j.yexmp.2015.07.005. Epub 2015 Jul 17.


Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics.

Zhang H, Cockrell SK, Kolawole AO, Rotem A, Serohijos AW, Chang CB, Tao Y, Mehoke TS, Han Y, Lin JS, Giacobbi NS, Feldman AB, Shakhnovich E, Weitz DA, Wobus CE, Pipas JM.

J Virol. 2015 Aug;89(15):7722-34. doi: 10.1128/JVI.01137-15. Epub 2015 May 13.


The conserved core enzymatic activities and the distinct dynamics of polyomavirus large T antigens.

An P, Brodsky JL, Pipas JM.

Arch Biochem Biophys. 2015 May 1;573:23-31. doi: 10.1016/ Epub 2015 Mar 6.


Cellular transformation of mouse embryo fibroblasts in the absence of activator E2Fs.

Gupta T, Sáenz Robles MT, Pipas JM.

J Virol. 2015 May;89(9):5124-33. doi: 10.1128/JVI.03578-14. Epub 2015 Feb 25.


HeLa nucleic acid contamination in the cancer genome atlas leads to the misidentification of human papillomavirus 18.

Cantalupo PG, Katz JP, Pipas JM.

J Virol. 2015 Apr;89(8):4051-7. doi: 10.1128/JVI.03365-14. Epub 2015 Jan 28.


Polyomavirus T antigens activate an antiviral state.

Giacobbi NS, Gupta T, Coxon AT, Pipas JM.

Virology. 2015 Feb;476:377-385. doi: 10.1016/j.virol.2014.12.032. Epub 2015 Jan 10.


Synthesis and structure–activity relationships of small molecule inhibitors of the simian virus 40 T antigen oncoprotein, an anti-polyomaviral target.

Ireland AW, Gobillot TA, Gupta T, Seguin SP, Liang M, Resnick L, Goldberg MT, Manos-Turvey A, Pipas JM, Wipf P, Brodsky JL.

Bioorg Med Chem. 2014 Nov 15;22(22):6490-6502. doi: 10.1016/j.bmc.2014.09.019.


SummonChimera infers integrated viral genomes with nucleotide precision from NGS data.

Katz JP, Pipas JM.

BMC Bioinformatics. 2014 Oct 22;15:348. doi: 10.1186/s12859-014-0348-4.


Multiorgan Streptococcus milleri Abscesses During FOLFIRINOX Chemotherapy in a Patient With Metastatic Pancreatic Cancer.

Brosnan E, Mody K, Zuckerman RA, Ruoff KL, Pipas JM.

Gastrointest Cancer Res. 2014 May;7(3-4):126-8. No abstract available.


Removal of a small C-terminal region of JCV and SV40 large T antigens has differential effects on transformation.

Seneca NTM, Sáenz Robles MT, Pipas JM.

Virology. 2014 Nov;468-470:47-56. doi: 10.1016/j.virol.2014.07.038. Epub 2014 Aug 16.


The effect of neoadjuvant chemoradiation on pancreatic cancer-associated diabetes mellitus.

Gardner TB, Hessami N, Smith KD, Ripple GH, Barth RJ, Klibansky DA, Colacchio TA, Zaki B, Tsapakos MJ, Suriawinata AA, Putra J, Tsongalis GJ, Mody K, Gordon SR, Pipas JM.

Pancreas. 2014 Oct;43(7):1018-21. doi: 10.1097/MPA.0000000000000162.


Viral oncogene expression in the stem/progenitor cell compartment of the mouse intestine induces adenomatous polyps.

Sáenz Robles MT, Chong JL, Koivisto C, Trimboli A, Liu H, Leone G, Pipas JM.

Mol Cancer Res. 2014 Oct;12(10):1355-64. doi: 10.1158/1541-7786.MCR-14-0166. Epub 2014 Jul 3.


Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions.

Yu X, Bian X, Throop A, Song L, Moral LD, Park J, Seiler C, Fiacco M, Steel J, Hunter P, Saul J, Wang J, Qiu J, Pipas JM, LaBaer J.

Theranostics. 2014 Jun 6;4(8):808-22. doi: 10.7150/thno.8255. eCollection 2014.


Molecular testing for lymph node metastases as a determinant of colon cancer recurrence: results from a retrospective multicenter study.

Sargent DJ, Shi Q, Gill S, Louvet C, Everson RB, Kellner U, Clancy TE, Pipas JM, Resnick MB, Meyers MO, Wu TT, Huntsman D, Validire P, Farooq U, Pavey ES, Beaudry G, Haince JF, Fradet Y.

Clin Cancer Res. 2014 Aug 15;20(16):4361-9. doi: 10.1158/1078-0432.CCR-13-2659. Epub 2014 Jun 11.


Molecular profiling of appendiceal epithelial tumors using massively parallel sequencing to identify somatic mutations.

Liu X, Mody K, de Abreu FB, Pipas JM, Peterson JD, Gallagher TL, Suriawinata AA, Ripple GH, Hourdequin KC, Smith KD, Barth RJ Jr, Colacchio TA, Tsapakos MJ, Zaki BI, Gardner TB, Gordon SR, Amos CI, Wells WA, Tsongalis GJ.

Clin Chem. 2014 Jul;60(7):1004-11. doi: 10.1373/clinchem.2014.225565. Epub 2014 May 12.


Simian virus 40 large T antigen induces IFN-stimulated genes through ATR kinase.

Forero A, Giacobbi NS, McCormick KD, Gjoerup OV, Bakkenist CJ, Pipas JM, Sarkar SN.

J Immunol. 2014 Jun 15;192(12):5933-42. doi: 10.4049/jimmunol.1303470. Epub 2014 May 5.


Identification of a novel polyomavirus in a pancreatic transplant recipient with retinal blindness and vasculitic myopathy.

Mishra N, Pereira M, Rhodes RH, An P, Pipas JM, Jain K, Kapoor A, Briese T, Faust PL, Lipkin WI.

J Infect Dis. 2014 Nov 15;210(10):1595-9. doi: 10.1093/infdis/jiu250. Epub 2014 May 1.


A retinoblastoma allele that is mutated at its common E2F interaction site inhibits cell proliferation in gene-targeted mice.

Cecchini MJ, Thwaites MJ, Talluri S, MacDonald JI, Passos DT, Chong JL, Cantalupo P, Stafford PM, Sáenz-Robles MT, Francis SM, Pipas JM, Leone G, Welch I, Dick FA.

Mol Cell Biol. 2014 Jun;34(11):2029-45. doi: 10.1128/MCB.01589-13. Epub 2014 Mar 24.


Flexibility in surface-exposed loops in a virus capsid mediates escape from antibody neutralization.

Kolawole AO, Li M, Xia C, Fischer AE, Giacobbi NS, Rippinger CM, Proescher JB, Wu SK, Bessling SL, Gamez M, Yu C, Zhang R, Mehoke TS, Pipas JM, Wolfe JT, Lin JS, Feldman AB, Smith TJ, Wobus CE.

J Virol. 2014 Apr;88(8):4543-57. doi: 10.1128/JVI.03685-13. Epub 2014 Feb 5.


Successful retreatment with chemoradiotherapy for local recurrence of pancreatic adenocarcinoma after neoadjuvant therapy and pancreaticoduodenectomy.

Gowarty MA, Zaki BI, Tsapakos MJ, Gordon SR, Suriawinata AA, Tsongalis GJ, Sutton JE, Pipas JM.

Gastrointest Cancer Res. 2013 Jul;6(4):118-9. No abstract available.


Merkel cell polyomavirus and extrapulmonary small cell carcinoma.

Hourdequin KC, Lefferts JA, Brennick JB, Ernstoff MS, Tsongalis GJ, Pipas JM.

Oncol Lett. 2013 Oct;6(4):1049-1052. Epub 2013 Jul 23.


Pancreatic cyst prevalence and the risk of mucin-producing adenocarcinoma in US adults.

Gardner TB, Glass LM, Smith KD, Ripple GH, Barth RJ, Klibansky DA, Colacchio TA, Tsapakos MJ, Suriawinata AA, Tsongalis GJ, Pipas JM, Gordon SR.

Am J Gastroenterol. 2013 Oct;108(10):1546-50. doi: 10.1038/ajg.2013.103.


Two independent regions of simian virus 40 T antigen increase CBP/p300 levels, alter patterns of cellular histone acetylation, and immortalize primary cells.

Sáenz Robles MT, Shivalila C, Wano J, Sorrells S, Roos A, Pipas JM.

J Virol. 2013 Dec;87(24):13499-509. doi: 10.1128/JVI.02658-13. Epub 2013 Oct 2.


MicroRNAs as diagnostic markers for pancreatic ductal adenocarcinoma and its precursor, pancreatic intraepithelial neoplasm.

Xue Y, Abou Tayoun AN, Abo KM, Pipas JM, Gordon SR, Gardner TB, Barth RJ Jr, Suriawinata AA, Tsongalis GJ.

Cancer Genet. 2013 Jun;206(6):217-21. doi: 10.1016/j.cancergen.2013.05.020. Epub 2013 Aug 9.


Gastrointestinal stromal tumor--background, pathology, treatment.

Eisenberg BL, Pipas JM.

Hematol Oncol Clin North Am. 2012 Dec;26(6):1239-59. doi: 10.1016/j.hoc.2012.08.003. Review.


Large T antigens of polyomaviruses: amazing molecular machines.

An P, Sáenz Robles MT, Pipas JM.

Annu Rev Microbiol. 2012;66:213-36. doi: 10.1146/annurev-micro-092611-150154. Review.


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