Publications

trainee
corresponding author*

  1. Fishurn AT, Florio CJ, Lopez NJ, Link NL, Shah PS*. Molecular functions of ANKLE2 and its implications in human disease. Disease Models and Mechanisms 2024 Apr 1. doi: 10.1242/dmm.050554
  2. Skawinski CLS, Shah PS*. I’m walking into spiderwebs: making sense of protein-protein interaction data. Journal of Proteome Research 2024 Mar 31. doi: 10.1021/acs.jproteome.3c00892
  3. Minami SA, Garimell SS, Shah PS*. Computational evaluation of light propagation in cylindrical bioreactors for optogenetic mammalian cell cultures. Biotechnology Journal 2023 Oct 25. doi: 10.1002/biot.202300071
  4. Lee EJ, Archasappawat S, Ji K, Pena J, Fernandez-Vega V, Gangaraju R, Beesabathuni NS, Kim MJ, Tian Q, Shah PS, Scampavia L, Spicer T, Hwang CI. A new vulnerability to BET inhibition due to enhanced autophagy in BRCA2 deficient pancreatic cancer. Cell Death and Disease. 2023 Sept 21; doi: 10.1038/s41419-023-06145-9
  5. Gonzales MM, Ledesma L, Costa Navarro G, Pallares HM, Paletta A, De Maio FA, Iglesias NG, Gebhard L, Oviedo Rouco S, Ojeda DS, de Borba L, Giraldo M, Rajsbaum R, Ceballos A, Krogan NJ, Shah PS, Gamarnik AV. Dengue virus NS5 degrades ERC1 during infection to antagonize NF-kB activation. PNAS. 2023 Jun 6, doi: 10.1073/pnas.2220005120.
  6. Kenaston MW, Shah PS*. The Archer and the Prey: The Duality of PAF1C in Antiviral Immunity. Viruses. 2023 Apr 22. doi: 10.3390/v15051032
  7. Beesabathuni NS, Thilakaratne E, Shah PS*. Image-based temporal profiling of autophagy-related phenotypes. [bioRxiv preprint] 2023 Apr 20. doi: 10.1101/2023.03.27.534404
  8. Leon K, Khalid MM, Flynn R, Fontaine KA, Nguyen T, Kumar GR, Simoneau CR, Tomar S, Jimenez-Morales D, Dunlap M, Kaye J, Shah PS, Finkbeiner S, Krogan NJ, Bertozzi C, Carette JE, Ott MNuclear accumulation of host transcripts during Zika Virus Infection. PLoS Pathogens 2023 Jan 5. doi:10.1371/journal.ppat.1011070
  9. Kenaston MW, Pham OH, Petit MJ, Shah PS*. Transcriptomic profiling implicates PAF1 in both active and repressive immune regulatory networks. BMC Genomics 2022 Nov 30. doi:10.1101/2022.03.28.485548
  10. Beesabathuni NS, Park S, Shah PS*. Quantitative and temporal measurement of dynamic autophagy rates. Autophagy 2022 Sept 24. doi:10.1080/15548627.2022.2117515
  11. Shah PS*, Beesabathuni NS, Fishburn AT, Kenaston MW, Minami SA, Pham OH, Tucker I, Systems Biology of Virus-Host Protein Interactions: From Hypothesis Generation to Mechanisms of Replication and Pathogenesis. Annual Review in Virology 2022 Sept doi: 10.1146/annurev-virology-100520-011851
  12. Minami SA, Jung S, Huang Y, Harris BS, Faller R, Nandi S, McDonald K, Shah PS*. Production of novel Spike truncations in Chinese hamster ovary cells. Biotechnology Journal 2022 Jun 3. doi: 10.1002/biot.202100678
  13. Fishburn AT, Hoang V, Lopez NJ, Shiu TN, Haggard-Arcé S, Shah PS*Zika virus NS4A hijacks ANKLE2 to promote viral replication. [bioRxiv preprint] 2022 Mar 16. doi: 10.1101/2022.03.15.484510
  14. Fishburn AT, Pham OH, Kenaston MW, Beesabathuni NS, Shah PS*Let’s get physical: flavivirus-host protein-protein interactions in replication and pathogenesis. Frontiers in Microbiology. 2022 Mar 3. doi: 10.3389/fmicb.2022.847588
  15. Huang Y, Harris BS, Minami SA, Jung S, Shah PS, Nandi S, McDonald K, Faller R. SARS-Cov-2 Spike binding to ACE2 is stronger and longer ranged with glycans. Biophys J. 2021 Dec 7:S0006-3495(21)03893-5. doi: 10.1016/j.bpj.2021.12.002 PMID 34883069
  16. Petit MJ, Kenaston MK, Pham OH, Nagainis AN, Fishburn AT, Shah PS*. Nuclear dengue virus NS5 antagonized expression of PAF1-dependent immune response genes. PLoS Pathog. 2021 Nov 19;17(11):e1010100. doi: 10.1371/journal.ppat.1010100 PMID 34797876
  17. Minami SA, Shah PS*. Transient light-activated gene expression in Chinese hamster ovary cells. BMC Biotechnology. 2021 Feb 4. doi:10.1186/s12896-021-00670-1 PMID 33541329
  18. Link N, Chung H, Jolly A, Withers M, Tepe B, Arenkiel BR, Shah PS, Krogan NJ, Aydin H, Geckinli BB, Tos T, Isikay S, Tuysuz B, Mochida GH, Thomas AX, Clark RD, Mirzaa GM, Lupski JR, Bellen HJ. Mutations in ANKLE2, a ZIKA Virus Target, Disrupt an Asymmetric Cell Division Pathway in Drosophila Neuroblasts to Cause Microcephaly. Developmental Cell. 2019 Dec 16. doi.org/10.1016/j.devcel.2019.10.009. PMID 31735666
  19. Li M, Johnson JR, Truong B, Kim G, Weinbren N, Dittmar M, Shah PS, Von Dollen J, Newton BW, Jang GM, Krogan NJ, Cherry S, Ramage H. Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection. Nature Microbiology. 2019 Jun 4. doi.org/10.1038/s41564-019-0375-z. PMID 30833725
  20. Petit MJ, Shah PS*. Mapping Arbovirus-Vector Interactions Using Systems Biology Approaches. Frontiers in Cellular and Infection Microbiology. 2019 Jan 7. doi.org/10.3389/fcimb.2018.00440 PMID 30666300
  21. Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell. 2018 Dec 13. doi: 10.1016/j.cell.2018.11.028 PMID 30550790.
  22. Fontaine KA, Leon KE, Khalid MM, Tomar S, Jimenez-Morales D, Dunlap M, Kaye JA, Shah PS, Finkbeiner S, Krogan NJ, Ott M.The Cellular NMD Pathway Restricts Zika Virus Infection and Is Targeted by the Viral Capsid Protein. MBio. 2018 Nov 6. doi: 10.1128/mBio.02126-18. PMID 29191913.
  23. Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ. Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov. 2018 Sep 12. doi: 10.1158/2159-8290.CD-17-1018. PMID 30209081.
  24. De Maio FA, Risso G, Iglesias NG, Shah P, Pozzi B, Gebhard LG, Mammi P, Mancini E, Yanovsky MJ, Andino R, Krogan N, Srebrow A,Gamarnik AV. The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing. PLoS Pathogens. 2016 Aug 30;12(8):e1005841 PMID 27575636.
  25. Heaton NS, Moshinka N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist J, Noel J, Sachs D, Hamilton J, Leon PE, Chawdury A, Tripathy S, Melegari C, Campisi L, Hai R, Metreveli G, Gamarnik AV, Garcia-Sastre A, Greenbaum B, Simo V, Fernandez-Sesma A, Krogan NJ, Mulder LCF, van Bakel H, Tortorella D, Taunton J, Palese P, Marazzi I. Limiting influenza virus, HIV and dengue virus infection by targeting viral proteostasis. Immunity. 2016 Feb 16;44(2):438 PMID 26789921.
  26. Shah PSWojcechowskyj JA, Eckhardt M, Krogan NJ. Comparative mapping of host-pathogen protein-protein interactions. Current Opinion in Microbiology. 2015 Oct;27:62-8. PMID 26275922
  27. Ramage HR, Kumar GR, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M. A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Molecular Cell . 2015 Jan 22;57(2):329-40. PMID 25616068.
  28. Miller-Jensen K, Skupsky R, Shah PS, Arkin AP, Schaffer DV. Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression. PLoS Computational Biology. 2013 July (7) e1003135; PMID 23874178.
  29. Ashton RS, Conway A, Pangarkar C, Bergen J, Lim KI, Shah P, Bissell M, Schaffer DV. Astrocytes regulate adult hippocampal neurogenesis through ephrin-B signaling. Nature Neuroscience. 2012 Oct;15(10):1399-406. PMID 22983209.
  30. Shah PS, Pham NP, Schaffer DV. HIV Develops Indirect Cross-resistance to Combinatorial RNAi Targeting Two Distinct and Spatially Distant Sites. Molecular Therapy. 2012 Apr;20(4):840-8. PMID 22294151.
  31. Shah PSSchaffer DV. Antiviral RNAi: Translating Science Towards Therapeutic Success. Pharmaceutical Research. 2011 Dec;28(12):2966-82. PMID 21826573.
  32. Aviran S, Shah PSSchaffer DV, Arkin AP. Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles. PLoS Computational Biology. 2010 Aug 12;6(8) e1000883. PMID 20711350.
  33. Shah PSSchaffer DV. Gene therapy takes a cue from HAART: Combinatorial antiviral therapeutics reach the clinic. Science Translational Medicine.2010 Jun:2(36). PMID 20555021
  34. Burnett JC, Miller-Jensen K, Shah PS, Arkin AP, Schaffer DV. Control of stochastic gene expression by host factors at the HIV promoter. PLoS Pathogens. 2009 Jan;5(1) e1000260. PMID 19132086.
  35. Leonard JN (co-first author), Shah PS (co-first author), Burnett JC, Schaffer DV. HIV evades RNA interference directed at TAR by an indirect compensatory mechanism. Cell Host and Microbe. 2008 Nov 13;4(5):484-94.*   *Featured open-access article. PMID 18996348.
  36. Liu, S, Pereira NA, Teo JJ, Miller P, Shah P, Song Z.  Mitochondrially targeted Bcl-2 and Bcl-X(L) chimeras elicit different apoptotic responses.  Molecules and Cells, 2007 Dec 31;24(3):378-87. PMID 18182854
  37. Vahedi-Faridi A, Brault PA, Shah P, Kim YW, Dunham WR, Funk MO Jr.  Interaction between non-heme iron of lipoxygenases and cumene hydroperoxide: basis for enzyme activation, inactivation, and inhibition.  Journal of the American Chemical Society. 2004 Feb 25;126(7):2006-15. PMID 14971933
  38. Brault PA, Kariapper MS, Pham CV, Flowers RA 2nd, Gunning WT, Shah P, Funk MO Jr.  Protein micelles from lipoxygenase 3.  Biomacromolecules. 2002 Jul-Aug;3(4):649-54. PMID 12099806.