Harvard Catalyst Profiles

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Jonathan Zirin


The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. F32GM082174 (ZIRIN, JONATHAN D) Apr 1, 2008 - Mar 31, 2010
    High-throughput screen for autophagy induction in cultured Drosophila myocytes
    Role: Principal Investigator

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Kim AR, Xu J, Cheloha R, Mohr SE, Zirin J, Ploegh HL, Perrimon N. NanoTag Nanobody Tools for Drosophila In Vitro and In Vivo Studies. Curr Protoc. 2022 Dec; 2(12):e628. PMID: 36571722; PMCID: PMC9811555.
    Citations:    Fields:    Translation:AnimalsCells
  2. Kanca O, Zirin J, Hu Y, Tepe B, Dutta D, Lin WW, Ma L, Ge M, Zuo Z, Liu LP, Levis RW, Perrimon N, Bellen HJ. An expanded toolkit for Drosophila gene tagging using synthesized homology donor constructs for CRISPR-mediated homologous recombination. Elife. 2022 06 20; 11. PMID: 35723254; PMCID: PMC9239680.
    Citations:    Fields:    Translation:AnimalsCells
  3. Xu J, Kim AR, Cheloha RW, Fischer FA, Li JSS, Feng Y, Stoneburner E, Binari R, Mohr SE, Zirin J, Ploegh HL, Perrimon N. Protein visualization and manipulation in Drosophila through the use of epitope tags recognized by nanobodies. Elife. 2022 01 25; 11. PMID: 35076390; PMCID: PMC8853664.
    Citations:    Fields:    Translation:Animals
  4. Zirin J, Bosch J, Viswanatha R, Mohr SE, Perrimon N. State-of-the-art CRISPR for in vivo and cell-based studies in Drosophila. Trends Genet. 2022 05; 38(5):437-453. PMID: 34933779; PMCID: PMC9007876.
    Citations: 3     Fields:    Translation:AnimalsCells
  5. Ravenscroft TA, Phillips JB, Fieg E, Bajikar SS, Peirce J, Wegner J, Luna AA, Fox EJ, Yan YL, Rosenfeld JA, Zirin J, Kanca O, Benke PJ, Cameron ES, Strehlow V, Platzer K, Jamra RA, Klöckner C, Osmond M, Licata T, Rojas S, Dyment D, Chong JSC, Lincoln S, Stoler JM, Postlethwait JH, Wangler MF, Yamamoto S, Krier J, Westerfield M, Bellen HJ. Heterozygous loss-of-function variants significantly expand the phenotypes associated with loss of GDF11. Genet Med. 2021 10; 23(10):1889-1900. PMID: 34113007; PMCID: PMC8487929.
    Citations: 4     Fields:    Translation:HumansAnimals
  6. Mohr SE, Tattikota SG, Xu J, Zirin J, Hu Y, Perrimon N. Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila. Genetics. 2021 04 15; 217(4). PMID: 33713129; PMCID: PMC8049553.
    Citations: 1     Fields:    Translation:Animals
  7. Hu Y, Comjean A, Rodiger J, Liu Y, Gao Y, Chung V, Zirin J, Perrimon N, Mohr SE. FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update. Nucleic Acids Res. 2021 01 08; 49(D1):D908-D915. PMID: 33104800.
    Citations: 7     Fields:    Translation:Animals
  8. Xia B, Amador G, Viswanatha R, Zirin J, Mohr SE, Perrimon N. CRISPR-based engineering of gene knockout cells by homology-directed insertion in polyploid Drosophila S2R+ cells. Nat Protoc. 2020 10; 15(10):3478-3498. PMID: 32958931.
    Citations: 4     Fields:    Translation:AnimalsCells
  9. Bosch JA, Knight S, Kanca O, Zirin J, Yang-Zhou D, Hu Y, Rodiger J, Amador G, Bellen HJ, Perrimon N, Mohr SE. Use of the CRISPR-Cas9 System in Drosophila Cultured Cells to Introduce Fluorescent Tags into Endogenous Genes. Curr Protoc Mol Biol. 2020 03; 130(1):e112. PMID: 31869524; PMCID: PMC7213786.
    Citations: 4     Fields:    Translation:AnimalsCells
  10. Zirin J, Hu Y, Liu L, Yang-Zhou D, Colbeth R, Yan D, Ewen-Campen B, Tao R, Vogt E, VanNest S, Cavers C, Villalta C, Comjean A, Sun J, Wang X, Jia Y, Zhu R, Peng P, Yu J, Shen D, Qiu Y, Ayisi L, Ragoowansi H, Fenton E, Efrem S, Parks A, Saito K, Kondo S, Perkins L, Mohr SE, Ni J, Perrimon N. Large-Scale Transgenic Drosophila Resource Collections for Loss- and Gain-of-Function Studies. Genetics. 2020 04; 214(4):755-767. PMID: 32071193.
    Citations: 20     Fields:    Translation:Animals
  11. Bosch JA, Colbeth R, Zirin J, Perrimon N. Gene Knock-Ins in Drosophila Using Homology-Independent Insertion of Universal Donor Plasmids. Genetics. 2020 01; 214(1):75-89. PMID: 31685521; PMCID: PMC6944404.
    Citations: 8     Fields:    Translation:AnimalsCells
  12. Kanca O, Zirin J, Garcia-Marques J, Knight SM, Yang-Zhou D, Amador G, Chung H, Zuo Z, Ma L, He Y, Lin WW, Fang Y, Ge M, Yamamoto S, Schulze KL, Hu Y, Spradling AC, Mohr SE, Perrimon N, Bellen HJ. An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms. Elife. 2019 11 01; 8. PMID: 31674908; PMCID: PMC6855806.
    Citations: 34     Fields:    Translation:AnimalsCells
  13. Zirin J, Ni X, Sack LM, Yang-Zhou D, Hu Y, Brathwaite R, Bulyk ML, Elledge SJ, Perrimon N. Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells. Proc Natl Acad Sci U S A. 2019 07 16; 116(29):14614-14619. PMID: 31262815; PMCID: PMC6642371.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  14. Escobedo S, Zirin J, Weake V. TRiP stocks contain a previously uncharacterized loss-of-function sevenless allele. MicroPubl Biol. 2019 Apr 04; 2019. PMID: 32550423; PMCID: PMC7252292.
  15. Jia Y, Xu RG, Ren X, Ewen-Campen B, Rajakumar R, Zirin J, Yang-Zhou D, Zhu R, Wang F, Mao D, Peng P, Qiao HH, Wang X, Liu LP, Xu B, Ji JY, Liu Q, Sun J, Perrimon N, Ni JQ. Next-generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM. Proc Natl Acad Sci U S A. 2018 05 01; 115(18):4719-4724. PMID: 29666231; PMCID: PMC5939105.
    Citations: 23     Fields:    Translation:Animals
  16. Tang HW, Hu Y, Chen CL, Xia B, Zirin J, Yuan M, Asara JM, Rabinow L, Perrimon N. The TORC1-Regulated CPA Complex Rewires an RNA Processing Network to Drive Autophagy and Metabolic Reprogramming. Cell Metab. 2018 May 01; 27(5):1040-1054.e8. PMID: 29606597; PMCID: PMC6100782.
    Citations: 17     Fields:    Translation:HumansAnimalsCells
  17. Lee PT, Zirin J, Kanca O, Lin WW, Schulze KL, Li-Kroeger D, Tao R, Devereaux C, Hu Y, Chung V, Fang Y, He Y, Pan H, Ge M, Zuo Z, Housden BE, Mohr SE, Yamamoto S, Levis RW, Spradling AC, Perrimon N, Bellen HJ. A gene-specific T2A-GAL4 library for Drosophila. Elife. 2018 03 22; 7. PMID: 29565247.
    Citations: 71     Fields:    Translation:Animals
  18. Mohr SE, Rudd K, Hu Y, Song WR, Gilly Q, Buckner M, Housden BE, Kelley C, Zirin J, Tao R, Amador G, Sierzputowska K, Comjean A, Perrimon N. Zinc Detoxification: A Functional Genomics and Transcriptomics Analysis in Drosophila melanogaster Cultured Cells. G3 (Bethesda). 2018 02 02; 8(2):631-641. PMID: 29223976; PMCID: PMC5919732.
    Citations: 7     Fields:    Translation:AnimalsCells
  19. Ewen-Campen B, Yang-Zhou D, Fernandes VR, González DP, Liu LP, Tao R, Ren X, Sun J, Hu Y, Zirin J, Mohr SE, Ni JQ, Perrimon N. Optimized strategy for in vivo Cas9-activation in Drosophila. Proc Natl Acad Sci U S A. 2017 08 29; 114(35):9409-9414. PMID: 28808002; PMCID: PMC5584449.
    Citations: 28     Fields:    Translation:Animals
  20. Song W, Owusu-Ansah E, Hu Y, Cheng D, Ni X, Zirin J, Perrimon N. Activin signaling mediates muscle-to-adipose communication in a mitochondria dysfunction-associated obesity model. Proc Natl Acad Sci U S A. 2017 Aug 08; 114(32):8596-8601. PMID: 28739899; PMCID: PMC5559048.
    Citations: 23     Fields:    
  21. Hu Y, Comjean A, Roesel C, Vinayagam A, Flockhart I, Zirin J, Perkins L, Perrimon N, Mohr SE. FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update. Nucleic Acids Res. 2017 01 04; 45(D1):D672-D678. PMID: 27924039; PMCID: PMC5210654.
    Citations: 21     Fields:    Translation:Animals
  22. Zirin J, Nieuwenhuis J, Samsonova A, Tao R, Perrimon N. Regulators of autophagosome formation in Drosophila muscles. PLoS Genet. 2015 Feb; 11(2):e1005006. PMID: 25692684.
    Citations: 9     Fields:    Translation:AnimalsCells
  23. Vinayagam A, Zirin J, Roesel C, Hu Y, Yilmazel B, Samsonova AA, Neumüller RA, Mohr SE, Perrimon N. Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods. 2014 Jan; 11(1):94-9. PMID: 24240319; PMCID: PMC3877743.
    Citations: 53     Fields:    Translation:AnimalsCells
  24. Zirin J, Nieuwenhuis J, Perrimon N. Role of autophagy in glycogen breakdown and its relevance to chloroquine myopathy. PLoS Biol. 2013 Nov; 11(11):e1001708. PMID: 24265594.
    Citations: 47     Fields:    Translation:AnimalsCells
  25. Zirin J, Cheng D, Dhanyasi N, Cho J, Dura JM, Vijayraghavan K, Perrimon N. Ecdysone signaling at metamorphosis triggers apoptosis of Drosophila abdominal muscles. Dev Biol. 2013 Nov 15; 383(2):275-84. PMID: 24051228; PMCID: PMC3991436.
    Citations: 16     Fields:    Translation:AnimalsCells
  26. Perrimon N, Zirin J, Bai J. Primary cell cultures from Drosophila gastrula embryos. J Vis Exp. 2011 Feb 28; (48). PMID: 21403631.
    Citations: 5     Fields:    Translation:AnimalsCells
  27. Zirin J, Perrimon N. Drosophila as a model system to study autophagy. Semin Immunopathol. 2010 Dec; 32(4):363-72. PMID: 20798940; PMCID: PMC3562086.
    Citations: 27     Fields:    Translation:HumansAnimals
  28. Zirin JD, Mann RS. Nubbin and Teashirt mark barriers to clonal growth along the proximal-distal axis of the Drosophila wing. Dev Biol. 2007 Apr 15; 304(2):745-58. PMID: 17313943; PMCID: PMC1945053.
    Citations: 20     Fields:    Translation:Animals
  29. Zirin JD, Mann RS. Differing strategies for the establishment and maintenance of teashirt and homothorax repression in the Drosophila wing. Development. 2004 Nov; 131(22):5683-93. PMID: 15509768.
    Citations: 14     Fields:    Translation:AnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.