Select Publications


  • Bruce JW, Bracken M, Evans E, Sherer N, Ahlquist P.  (2021). ZBTB2 represses HIV-1 transcription and is regulated by HIV-1 Vpr and cellular DNA damage responses.  PLoS Pathog. 17:e1009364.
  • Nishikiori, M and Ahlquist P.  (2021). Transmembrane redox regulation of genome replication functions in positive-strand RNA viruses.  Current Opinion in Virology 47:25-31.


  • Unchwaniwala N & Ahlquist P.  (2020). Coronavirus dons a new crown.  Science 369:1306-1307.
  • Unchwaniwala N, Zhan H, Pennington J, Horswill M, den Boon JA, & Ahlquist P. (2020). Subdomain cryo-EM structure of nodaviral replication protein A crown complex provides mechanistic insights into RNA genome replication. Proc Natl Acad Sci U S A. 117:18680-18691.


  • Nishikiori M & Ahlquist P. (2018). Organelle Luminal Dependence of (+)strand RNA Virus Replication Reveals a Hidden Druggable Target.  Science Advances  4:eaap8258.2017
  • Ali S Köksal, Kirsten Beck, Dylan R Cronin, Aaron McKenna, Nathan D Camp, Saurabh Srivastava, Matthew E MacGilvray, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter (2018). Synthesizing signaling pathways from temporal phosphoproteomic data. Cell Rep, 24(13), 3607-3618.


  • Ertel KJ, Benefield D, Castaño-Diez D, Pennington J, Horswill M, den Boon JA, Otegui MS, & Ahlquist P.  (2017). Cryo-Electron Tomography Reveals Novel Features of a Viral RNA Replication Compartment.  eLife 6:e25940.
  • Spurgeon M, den Boon J, Horswill M, Barthakur S, Forouzan O, Rader J, Beebe J, Roopra A, Ahlquist P, & Lambert PF. (2017). Human Papillomavirus Oncogenes Reprogram the Cervical Cancer Micro-environment Independently of and Synergistically with Estrogen. Proc Natl Acad Sci USA 114:E9076-E9085.


  • Pocock, G. M., Becker, J. T., Swanson, C. M., Ahlquist, P., & Sherer, N. M. (2016). HIV-1 and M-PMV RNA nuclear export elements program viral genomes for distinct cytoplasmic trafficking behaviors. PLoS Pathog, 12(4), e1005565. PMCID: PMC4829213.
  • Tuncbag, N., Gosline, S. J., Kedaigle, A., Soltis, A. R., Gitter, A., & Fraenkel, E. (2016). Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PLoS Comput Biol, 12(4), e1004879. PMCID: PMC4838263.


  • den Boon, J. A., Pyeon, D., Wang, S. S., Horswill, M., Schiffman, M., Sherman, M., Zuna, R. E., Wang, Z., Hewitt, S. M., Pearson, R., Schott, M., Chung, L., He, Q., Lambert, P., Walker, J., Newton, M.A., Wentzensen, N., & Ahlquist, P. (2015). Molecular transitions from papillomavirus infection to cervical precancer and cancer: Role of stromal estrogen receptor signaling. Proc Natl Acad Sci USA, 112(25), E3255-E3264. PMCID: PMC4485108.
  • Diaz, A., Zhang, J., Ollwerther, A., Wang, X., & Ahlquist, P. (2015). Host ESCRT proteins are required for bromovirus RNA replication compartment assembly and function. PLoS Pathog, 11(3), e1004742. PMCID: PMC4351987.


  • Chasman, D., Gancarz, B., Hao, L., Ferris, M., Ahlquist, P., & Craven, M. (2014). Inferring host gene subnetworks involved in viral replication. PLoS Comput Biol, 10(5), e1003626. PMCID: PMC4038467.
  • Gitter, A., Braunstein, A., Pagnani, A., Baldassi, C., Borgs, C., Chayes, J., Zecchina, R., & Fraenkel, E. (2014). Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. Pac Symp Biocomput (p. 39). NIH Public Access. PMCID: PMC3910098.
  • Shen, Q. T., Schuh, A. L., Zheng, Y., Quinney, K., Wang, L., Hanna, M., Mitchell, J. C., Otegui, M. S., Ahlquist, P., Cui, Q., & Audhya, A. (2014). Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly. J Cell Biol, 206(6), 763-777. PMCID: PMC4164947.
  • Wang, L., Zhao, Z., Meyer, M. B., Saha, S., Yu, M., Guo, A., Wisinski, K. B., Huang, W., Cai, W., Pike, J. W., Yuan, M., Ahlquist, P., & Xu, W. (2014). CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis. Cancer Cell, 25(1), 21-36. PMCID: PMC4004525.


  • Bruce, J. W., Reddington, R., Mathieu, E., Bracken, M., Young, J. A., & Ahlquist, P. (2013). ZASC1 stimulates HIV-1 transcription elongation by recruiting P-TEFb and TAT to the LTR promoter. PLoS Pathog, 9(10), e1003712. PMCID: PMC3812036.
  • Giménez-Barcons, M., Alves-Rodrigues, I., Jungfleisch, J., Van Wynsberghe, P. M., Ahlquist, P., & Díez, J. (2013). The cellular decapping activators LSm1, Pat1, and Dhh1 control the ratio of subgenomic to genomic Flock House virus RNAs. J Virol, 87(11), 6192-6200. PMCID: PMC3648113.
  • Gitter, A., & Bar-Joseph, Z. (2013). Identifying proteins controlling key disease signaling pathways. Bioinformatics, 29(13), i227-i236. PMCID: PMC3694658.
  • Gitter, A., Carmi, M., Barkai, N., & Bar-Joseph, Z. (2013). Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res, 23(2), 365-376. PMCID: PMC3561877.
  • Hao, L., He, Q., Wang, Z., Craven, M., Newton, M. A., & Ahlquist, P. (2013). Limited agreement of independent RNAi screens for virus-required host genes owes more to false-negative than false-positive factors. PLoS Comput Biol, 9(9), e1003235. PMCID: PMC3777922.