Publications

James Pipas

Pipas JM. DNA Tumor Viruses and Their Contributions to Molecular Biology. J Virol. 2019 May 1;93(9): doi: 10.1128/JVI.01524-18. PubMed PMID: 30814278; PMCID: PMC6475781.
An P, Sáenz Robles MT, Duray AM, Cantalupo PG, Pipas JM. Human polyomavirus BKV infection of endothelial cells results in interferon pathway induction and persistence. PLoS Pathog. 2019 Jan;15(1):e1007505. doi: 10.1371/journal.ppat.1007505. PubMed PMID: 30620752; PMCID: PMC6338385.
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. Evolution on the Biophysical Fitness Landscape of an RNA Virus. Mol Biol Evol. 2018 Oct 1;35(10):2390-2400. doi: 10.1093/molbev/msy131. PubMed PMID: 29955873; PMCID: PMC6188569.
Xu CL, Cantalupo PG, Sáenz-Robles MT, Baldwin A, Fitzpatrick D, Norris DE, Jackson E, Pipas JM. Draft Genome Sequence of a Novel Rhabdovirus Isolated from Deinocerites Mosquitoes. Genome Announc. 2018 May 10;6(19): doi: 10.1128/genomeA.01438-17. PubMed PMID: 29748415; PMCID: PMC5946037.
Cantalupo PG, Pipas JM. Complete Genome Sequence of Pittsburgh Sewage-Associated Virus 1. Genome Announc. 2018 Mar 15;6(11): doi: 10.1128/genomeA.01460-17. PubMed PMID: 29545305; PMCID: PMC5854781.
Johnson ME, Cantalupo PG, Pipas JM. Identification of Head and Neck Cancer Subtypes Based on Human Papillomavirus Presence and E2F-Regulated Gene Expression. mSphere. 2018 Jan-Feb;3(1): doi: 10.1128/mSphere.00580-17. PubMed PMID: 29359188; PMCID: PMC5760753.
Cantalupo PG, Katz JP, Pipas JM. Viral sequences in human cancer. Virology. 2018 Jan 1;513208-216. doi: 10.1016/j.virol.2017.10.017. PubMed PMID: 29107929; PMCID: PMC5828528.
Cantalupo PG, Buck CB, Pipas JM. Complete Genome Sequence of a Polyomavirus Recovered from a Pomona Leaf-Nosed Bat (Hipposideros pomona) Metagenome Data Set. Genome Announc. 2017 Jan 19;5(3): doi: 10.1128/genomeA.01053-16. PubMed PMID: 28104645; PMCID: PMC5255915.
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. Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma. mBio. 2017 Jan 3;8(1): doi: 10.1128/mBio.02079-16. PubMed PMID: 28049147; PMCID: PMC5210499.
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. The Ancient Evolutionary History of Polyomaviruses. PLoS Pathog. 2016 Apr;12(4):e1005574. doi: 10.1371/journal.ppat.1005574. PubMed PMID: 27093155; PMCID: PMC4836724.
Tang X, Liu H, Srivastava A, Pécot T, Chen Z, Wang Q, Huang K, Sáenz-Robles MT, Cantalupo P, Pipas J, Leone G. Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Sci Data. 2016 Feb 16;3160008. doi: 10.1038/sdata.2016.8. PubMed PMID: 26881867; PMCID: PMC4755127.
Gupta T, Robles MT, Schowalter RM, Buck CB, Pipas JM. Expression of the small T antigen of Lymphotropic Papovavirus is sufficient to transform primary mouse embryo fibroblasts. Virology. 2016 Jan;487112-20. doi: 10.1016/j.virol.2015.10.003. PubMed PMID: 26517398; PMCID: PMC4679568.
Han HS, Cantalupo PG, Rotem A, Cockrell SK, Carbonnaux M, Pipas JM, Weitz DA. Whole-Genome Sequencing of a Single Viral Species from a Highly Heterogeneous Sample. Angew Chem Int Ed Engl. 2015 Nov 16;54(47):13985-8. doi: 10.1002/anie.201507047. PubMed PMID: 26316088; PMCID: PMC4715630.
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. Artifact-Free Quantification and Sequencing of Rare Recombinant Viruses by Using Drop-Based Microfluidics. Chembiochem. 2015 Oct 12;16(15):2167-71. doi: 10.1002/cbic.201500384. PubMed PMID: 26247541.
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. Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles. Nat Cell Biol. 2015 Aug;17(8):1036-48. doi: 10.1038/ncb3210. PubMed PMID: 26192440; PMCID: PMC4526313.
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. Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics. J Virol. 2015 Aug;89(15):7722-34. doi: 10.1128/JVI.01137-15. PubMed PMID: 25972549; PMCID: PMC4505660.
An P, Brodsky JL, Pipas JM. The conserved core enzymatic activities and the distinct dynamics of polyomavirus large T antigens. Arch Biochem Biophys. 2015 May 1;57323-31. doi: 10.1016/j.abb.2015.02.033. PubMed PMID: 25752954; PMCID: PMC4865250.
Gupta T, Sáenz Robles MT, Pipas JM. Cellular transformation of mouse embryo fibroblasts in the absence of activator E2Fs. J Virol. 2015 May;89(9):5124-33. doi: 10.1128/JVI.03578-14. PubMed PMID: 25717106; PMCID: PMC4403490.
Cantalupo PG, Katz JP, Pipas JM. HeLa nucleic acid contamination in the cancer genome atlas leads to the misidentification of human papillomavirus 18. J Virol. 2015 Apr;89(8):4051-7. doi: 10.1128/JVI.03365-14. PubMed PMID: 25631090; PMCID: PMC4442357.
Giacobbi NS, Gupta T, Coxon AT, Pipas JM. Polyomavirus T antigens activate an antiviral state. Virology. 2015 Feb;476377-385. doi: 10.1016/j.virol.2014.12.032. PubMed PMID: 25589241; PMCID: PMC4323618.
Ireland AW, Gobillot TA, Gupta T, Seguin SP, Liang M, Resnick L, Goldberg MT, Manos-Turvey A, Pipas JM, Wipf P, Brodsky JL. Synthesis and structure–activity relationships of small molecule inhibitors of the simian virus 40 T antigen oncoprotein, an anti-polyomaviral target. Bioorg Med Chem. 2014 Nov 15;22(22):6490-6502. doi: 10.1016/j.bmc.2014.09.019. PubMed PMID: 25440730; PMCID: PMC4293281.
Katz JP, Pipas JM. SummonChimera infers integrated viral genomes with nucleotide precision from NGS data. BMC Bioinformatics. 2014 Oct 22;15348. doi: 10.1186/s12859-014-0348-4. PubMed PMID: 25331652; PMCID: PMC4210586.
Seneca NTM, Sáenz Robles MT, Pipas JM. Removal of a small C-terminal region of JCV and SV40 large T antigens has differential effects on transformation. Virology. 2014 Nov;468-47047-56. doi: 10.1016/j.virol.2014.07.038. PubMed PMID: 25129438; PMCID: PMC4253650.
Sáenz Robles MT, Chong JL, Koivisto C, Trimboli A, Liu H, Leone G, Pipas JM. Viral oncogene expression in the stem/progenitor cell compartment of the mouse intestine induces adenomatous polyps. Mol Cancer Res. 2014 Oct;12(10):1355-64. doi: 10.1158/1541-7786.MCR-14-0166. PubMed PMID: 24994749; PMCID: PMC4201981.
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. Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions. Theranostics. 2014;4(8):808-22. doi: 10.7150/thno.8255. PubMed PMID: 24955142; PMCID: PMC4063979.
Forero A, Giacobbi NS, McCormick KD, Gjoerup OV, Bakkenist CJ, Pipas JM, Sarkar SN. Simian virus 40 large T antigen induces IFN-stimulated genes through ATR kinase. J Immunol. 2014 Jun 15;192(12):5933-42. doi: 10.4049/jimmunol.1303470. PubMed PMID: 24799566; PMCID: PMC4078001.
Mishra N, Pereira M, Rhodes RH, An P, Pipas JM, Jain K, Kapoor A, Briese T, Faust PL, Lipkin WI. Identification of a novel polyomavirus in a pancreatic transplant recipient with retinal blindness and vasculitic myopathy. J Infect Dis. 2014 Nov 15;210(10):1595-9. doi: 10.1093/infdis/jiu250. PubMed PMID: 24795478; PMCID: PMC4334791.

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