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PUBLICATIONS

Recent Publications

  • Bentley-DeSousa A, Holinier C, Moteshareie H, Tseng YC, Kajjo S, Nwosu C, Amodeo GF, Bondy-Chorney E, Sai Y, Rudner A, Golshani A, Davey NE, Downey M. A Screen for Candidate Targets of Lysine Polyphosphorylation Uncovers a Conserved Network Implicated in Ribosome Biogenesis. Cell Rep. 2018 Mar 27;22(13):3427-3439. PMID:29590613

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  • Galván Márquez I, Ghiyasvand M, Massarsky A, Babu M, Samanfar B, Omidi K, Moon TW, Smith ML, Golshani A. Zinc oxide and silver nanoparticles toxicity in the baker's yeast, Saccharomyces cerevisiae. PLoS One. 2018 Mar 19;13(3):e0193111. doi: 10.1371/journal.pone.0193111. eCollection 2018. PMID:29554091

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  • Omidi K, Jessulat M, Hooshyar M, Burnside D, Schoenrock A, Kazmirchuk T, Hajikarimlou M, Daniel M, Moteshareie H, Bhojoo U, Sanders M, Ramotar D, Dehne F, Samanfar B, Babu M, Golshani A. Uncharacterized ORF HUR1 influences the efficiency of non-homologous end-joining repair in Saccharomyces cerevisiae. Gene. 2018 Jan 10;639:128-136. doi: 10.1016/j.gene.2017.10.003. Epub 2017 Oct 5 PMID:2898734

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  • Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A. Global landscape of cell envelope protein complexes in Escherichia coli. Nat Biotechnol. 2018 Jan;36(1):103-112. doi: 10.1038/nbt.4024. Epub 2017 Nov 27. PMID:29176613

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  • Samanfar B, Shostak K, Moteshareie H, Hajikarimlou M, Shaikho S, Omidi K, Hooshyar M, Burnside D, Márquez IG, Kazmirchuk T, Naing T, Ludovico P, York-Lyon A, Szereszewski K, Leung C, Jin JY, Megarbane R, Smith ML, Babu M, Holcik M, Golshani A. The sensitivity of the yeast, Saccharomyces cerevisiae, to acetic acid is influenced by DOM34 and RPL36A. PeerJ. 2017 Nov 14;5:e4037. doi: 10.7717/peerj.4037. eCollection 2017. PMID: 29158977

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  • Kazmirchuk T, Dick K, Burnside D, Barnes B, Moteshareie H, Hajikarimlou M, Omidi K, Ahmed D, Low A, Lettl C, Hooshyar M, Schoenrock A, Pitre S, Babu M, Cassol E, Samanfar B, Wong A, Dehne F, Green JR, Golshani A. Designing anti-Zika virus peptides derived from predicted human-Zika virus protein-protein interactions. Comput Biol Chem. 2017 Dec;71:180-187. doi: 10.1016/j.compbiolchem.2017.10.011. Epub 2017 Nov 2.PMID:29112936

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  • Mehranfar A, Ghadiri N, Kouhsar M, Golshani A. A Type-2 fuzzy data fusion approach for building reliable weighted protein interaction networks with application in protein complex detection. Comput Biol Med. 2017 Sep 1;88:18-31. doi: 10.1016/j.compbiomed.2017.06.019. Epub 2017 Jun 23. PMID:28672176

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  • Schoenrock A, Burnside D, Moteshareie H, Pitre S, Hooshyar M, Green JR, Golshani A, Dehne F, Wong A. Evolution of protein-protein interaction networks in yeast. PLoS One. 2017 Mar 1;12(3):e0171920. doi: 10.1371/journal.pone.0171920. eCollection 2017.
    PMID:28248977

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  • Shaikho S, Dobson CC, Naing T, Samanfar B, Moteshareie H, Hajikarimloo M, Golshani A, Holcik M. Elevated levels of ribosomal proteins eL36 and eL42 control expression of Hsp90 in rhabdomyosarcoma. Translation. 2016 Oct 4;4(2):e1244395.PMID:28090422

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  • Samanfar B, Molnar SJ, Charette M, Schoenrock A, Dehne F, Golshani A, Belzile F, Cober ER. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. Theor Appl Genet. 2017 Feb;130(2):377-390. Epub 2016 Nov 10.PMID:27832313

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  • Gagarinova A, Stewart G, Samanfar B, Phanse S, White CA, Aoki H, Deineko V, Beloglazova N, Yakunin AF, Golshani A, Brown ED, Babu M, Emili A. Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery. Cell Rep. 2016 Oct 11;17(3):904-916. PMID: 27732863
     

  • Pelin A, Moteshareie H, Sak B, Selman M, Naor A, et al. The genome of an Encephalitozoon cuniculi type III strain reveals insights into the genetic diversity and mode of reproduction of a ubiquitous vertebrate pathogen. Heredity (Edinb). 2016 Feb 3;PubMed PMID: 26837273.

 

  • Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, et al. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli. Cell Rep. 2016 Jan 26;14(3):648-61. PubMed PMID: 26774489.

 

  • Jessulat M, Malty RH, Nguyen-Tran DH, Deineko V, Aoki H, et al. Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining. Mol Cell Biol. 2015 Jul;35(14):2448-63. PubMed PMID: 25963654; PubMed Central PMCID: PMC4475915.

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  • Burnside, D., Moteshareie, M., Galvan-Marquez, I., Hooshyar, M., Samanfar, B., Shostak, K., Omidi, K., Peery, H., Smith, M.L., and Golshani, A. 2015. Use of chemical genomics to investigate the mechanism of action for inhibitory bioactive natural compounds In G. Brahmachari (Ed.), Bioactive Natural Compounds: Biology and Chemistry. Wiley-VCH, Weinheim, Germany.

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  • Newsted D, Fallahi F, Golshani A, Azizi A. Advances and challenges in mucosal adjuvant technology. Vaccine. 2015 May 15;33(21):2399-405. PubMed PMID: 25865473.

 

  • Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, et al. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinformatics. 2015 Feb 1;31(3):306-10. PubMed PMID: 25316676; PubMed Central PMCID: PMC4308668.

 

  • Schoenrock A, Samanfar B, Pitre S, Hooshyar M, Jin K, et al. Efficient prediction of human protein-protein interactions at a global scale. BMC Bioinformatics. 2014 Dec 10;15:383. PubMed PMID: 25492630; PubMed Central PMCID: PMC4272565.

 

  • AbouHaidar MG, Venkataraman S, Golshani A, Liu B, Ahmad T. Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt. Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14542-7. PubMed PMID: 25253891; PubMed Central PMCID: PMC4209996.

 

  • Samanfar B, Tan le H, Shostak K, Chalabian F, Wu Z, et al. A global investigation of gene deletion strains that affect premature stop codon bypass in yeast, Saccharomyces cerevisiae. Mol Biosyst. 2014 Apr;10(4):916-24. PubMed PMID: 24535059.

 

  • Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, et al. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet. 2014 Feb;10(2):e1004120. PubMed PMID: 24586182; PubMed Central PMCID: PMC3930520.

 

  • Omidi K, Hooshyar M, Jessulat M, Samanfar B, Sanders M, et al. Phosphatase complex Pph3/Psy2 is involved in regulation of efficient non-homologous end-joining pathway in the yeast Saccharomyces cerevisiae. PLoS One. 2014;9(1):e87248. PubMed PMID: 24498054; PubMed Central PMCID: PMC3909046.

 

  • Darvishi E, Omidi M, Bushehri AA, Golshani A, Smith ML. Thymol antifungal mode of action involves telomerase inhibition. Med Mycol. 2013 Nov;51(8):826-34. PubMed PMID: 23718894.

 

  • Galván Márquez I, Akuaku J, Cruz I, Cheetham J, Golshani A, et al. Disruption of protein synthesis as antifungal mode of action by chitosan. Int J Food Microbiol. 2013 Jun 3;164(1):108-12. PubMed PMID: 23624539.

 

  • Samanfar B, Omidi K, Hooshyar M, Laliberte B, Alamgir M, et al. Large-scale investigation of oxygen response mutants in Saccharomyces cerevisiae. Mol Biosyst. 2013 Jun;9(6):1351-9. PubMed PMID: 23467670.

 

  • Darvishi E, Omidi M, Bushehri AA, Golshani A, Smith ML. The antifungal eugenol perturbs dual aromatic and branched-chain amino acid permeases in the cytoplasmic membrane of yeast. PLoS One. 2013;8(10):e76028. PubMed PMID: 24204588; PubMed Central PMCID: PMC3799837.

 

  • Pitre S, Hooshyar M, Schoenrock A, Samanfar B, Jessulat M, et al. Short Co-occurring Polypeptide Regions Can Predict Global Protein Interaction Maps. Sci Rep. 2012;2:239. PubMed PMID: 22355752; PubMed Central PMCID: PMC3269044.

 

  • Babu M, Díaz-Mejía JJ, Vlasblom J, Gagarinova A, Phanse S, et al. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 2011 Nov;7(11):e1002377. PubMed PMID: 22125496; PubMed Central PMCID: PMC3219608.

 

  • Jessulat M, Pitre S, Gui Y, Hooshyar M, Omidi K, et al. Recent advances in protein-protein interaction prediction: experimental and computational methods. Expert Opin Drug Discov. 2011 Sep;6(9):921-35. PubMed PMID: 22646215.

 

  • Amos-Binks A, Patulea C, Pitre S, Schoenrock A, Gui Y, et al. Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences. BMC Bioinformatics. 2011 Jun 2;12:225. PubMed PMID: 21635751; PubMed Central PMCID: PMC3120708.

 

  • Babu M, Aoki H, Chowdhury WQ, Gagarinova A, Graham C, et al. Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation. PLoS One. 2011 Apr 27;6(4):e18510. PubMed PMID: 21556145; PubMed Central PMCID: PMC3083400.

 

  • Sirskyj D, Diaz-Mitoma F, Golshani A, Kumar A, Azizi A. Innovative bioinformatic approaches for developing peptide-based vaccines against hypervariable viruses. Immunol Cell Biol. 2011 Jan;89(1):81-9. PubMed PMID: 20458336.

 

  • Mir-Rashed N, Cruz I, Jessulat M, Dumontier M, Chesnais C, et al. Disruption of fungal cell wall by antifungal Echinacea extracts. Med Mycol. 2010 Nov;48(7):949-58. PubMed PMID: 20429770.

 

  • Luo X, McKeague M, Pitre S, Dumontier M, Green J, et al. Computational approaches toward the design of pools for the in vitro selection of complex aptamers. RNA. 2010 Nov;16(11):2252-62. PubMed PMID: 20870801; PubMed Central PMCID: PMC2957063.

 

  • Alamgir M, Erukova V, Jessulat M, Azizi A, Golshani A. Chemical-genetic profile analysis of five inhibitory compounds in yeast. BMC Chem Biol. 2010 Aug 6;10:6. PubMed PMID: 20691087; PubMed Central PMCID: PMC2925817.

 

  • Jessulat M, Buist T, Alamgir M, Hooshyar M, Xu J, et al. In vivo investigation of protein-protein interactions for helicases using tandem affinity purification. Methods Mol Biol. 2010;587:99-111. PubMed PMID: 20225144.

 

  • Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, et al. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 2009 Apr 28;7(4):e96. PubMed PMID: 19402753; PubMed Central PMCID: PMC2672614.

 

  • Alamgir M, Eroukova V, Jessulat M, Xu J, Golshani A. Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis. BMC Genomics. 2008 Dec 3;9:583. PubMed PMID: 19055778; PubMed Central PMCID: PMC2613417.

 

  • Pitre S, North C, Alamgir M, Jessulat M, Chan A, et al. Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. Nucleic Acids Res. 2008 Aug;36(13):4286-94. PubMed PMID: 18586826; PubMed Central PMCID: PMC2490765.

 

  • Galván IJ, Mir-Rashed N, Jessulat M, Atanya M, Golshani A, et al. Antifungal and antioxidant activities of the phytomedicine pipsissewa, Chimaphila umbellata. Phytochemistry. 2008 Feb;69(3):738-46. PubMed PMID: 17950387.

 

  • Aoki H, Xu J, Emili A, Chosay JG, Golshani A, et al. Interactions of elongation factor EF-P with the Escherichia coli ribosome. FEBS J. 2008 Feb;275(4):671-81. PubMed PMID: 18201202.

 

  • Jessulat M, Alamgir M, Salsali H, Greenblatt J, Xu J, et al. Interacting proteins Rtt109 and Vps75 affect the efficiency of non-homologous end-joining in Saccharomyces cerevisiae. Arch Biochem Biophys. 2008 Jan 15;469(2):157-64. PubMed PMID: 18036332.

 

  • Pitre S, Alamgir M, Green JR, Dumontier M, Dehne F, et al. Computational methods for predicting protein-protein interactions. Adv Biochem Eng Biotechnol. 2008;110:247-67. PubMed PMID: 18202838.

 

  • Memarian N, Jessulat M, Alirezaie J, Mir-Rashed N, Xu J, et al. Colony size measurement of the yeast gene deletion strains for functional genomics. BMC Bioinformatics. 2007 Apr 4;8:117. PubMed PMID: 17408490; PubMed Central PMCID: PMC1854909.

 

  • Butland G, Krogan NJ, Xu J, Yang WH, Aoki H, et al. Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs. J Cell Biochem. 2007 Feb 15;100(3):642-52. PubMed PMID: 16983699.

 

  • Pitre S, Dehne F, Chan A, Cheetham J, Duong A, et al. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics. 2006 Jul 27;7:365. PubMed PMID: 16872538; PubMed Central PMCID: PMC1557541.

 

  • Xu J, Kiel MC, Golshani A, Chosay JG, Aoki H, et al. Molecular localization of a ribosome-dependent ATPase on Escherichia coli ribosomes. Nucleic Acids Res. 2006;34(4):1158-65. PubMed PMID: 16495476; PubMed Central PMCID: PMC1383619.

 

  • Xu J, Golshani A, Aoki H, Remme J, Chosay J, et al. Protected nucleotide G2608 in 23S rRNA confers resistance to oxazolidinones in E coli. Biochem Biophys Res Commun. 2005 Mar 11;328(2):471-6. PubMed PMID: 15694371.

 

  • Golshani A, Krogan NJ, Xu J, Pacal M, Yang XC, et al. Escherichia coli mRNAs with strong Shine/Dalgarno sequences also contain 5' end sequences complementary to domain # 17 on the 16S ribosomal RNA. Biochem Biophys Res Commun. 2004 Apr 16;316(4):978-83. PubMed PMID: 15044080

 

  • Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003 Jun;23(12):4207-18. PubMed PMID: 12773564; PubMed Central PMCID: PMC427527.

  • Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, et al. The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell. 2003 Mar;11(3):721-9. PubMed PMID: 12667454.

 

  • Wood A, Krogan NJ, Dover J, Schneider J, Heidt J, et al. Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol Cell. 2003 Jan;11(1):267-74. PubMed PMID: 12535539.

 

  • Golshani A, Xu J, Kolev V, Abouhaidar MG, Ivanov IG. Inability of Agrobacterium tumefaciens ribosomes to translate in vivo mRNAs containing non-Shine-Dalgarno translational initiators. Z Naturforsch C. 2002 Mar-Apr;57(3-4):307-12. PubMed PMID: 12064732.

 

  • Golshani A, Kolev V, AbouHaidar MG, Ivanov IG. Epsilon as an initiator of translation of CAT mRNA in Escherichia coli. Biochem Biophys Res Commun. 2000 Jul 5;273(2):528-31. PubMed PMID: 10873639.

  • Golshani A, Kolev V, Mironova R, AbouHaidar MG, Ivanov IG. Enhancing activity of epsilon in Escherichia coli and Agrobacterium tumefaciens cells. Biochem Biophys Res Commun. 2000 Mar 16;269(2):508-12. PubMed PMID: 10708584.

 

  • Odjakova M, Golshani A, Ivanov G, Abou Haidar M, Ivanov I. The low level expression of chloramphenicol acetyltransferase (CAT) mRNA in Escherichia coli is not dependent on either Shine-Dalgarno or the downstream boxes in the CAT gene. Microbiol Res. 1998 Aug;153(2):173-8. PubMed PMID: 9760750.

 

  • Golshani A, Golomehova V, Mironova R, Ivanov IG, AbouHaidar MG. Does the epsilon sequence of phage T7 function as an initiator for the translation of CAT mRNA in Escherichia coli?. Biochem Biophys Res Commun. 1997 Jul 18;236(2):253-6. PubMed PMID: 9240419.

 

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