Publications

Publications 

Zimmer SL. (2018) Revisiting Trypanosome Mitochondrial Genome Mysteries: Broader and Deeper. Trends Parasitol. Available online ahead of print. Article Link

Zimmer SL, Simpson RM, Read LK. (2018) High Throughput Sequencing Revolution Reveals Conserved Fundamentals of U-indel Editing. WIREs RNA. 2018: e1487. Article Link

Kalem MC, Gerasimov ES, Vu PK, Zimmer SL. (2018) Gene expression to mitochondrial metabolism: Variability among cultured Trypanosoma cruzi strains PLOS ONE. 13: e0197983. Article Link

Gerasimov ES, Gasparyan AA, Kaurov I, Tichý B, Logacheva MD, Kolesnikov AA, Lukeš J, Yurchenko V, Zimmer SL*, Flegontov P*. (2018) Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool. Nucleic Acids Res. 6: 765-781. *Co-corresponding authors. Article Link

Gazestani VH, Hampton M, Shaw AK, Liggett C, Salavati R, and Zimmer SL. (2018) Tail characteristics of Trypanosoma brucei mitochondrial transcripts are developmentally altered in a transcript-specific manner. Int. J. Parasitol. 48: 179-189 Article Link

Ishemgulova A*, Kraeva N*, Hlavacova J, Zimmer SL, Butenko A, Podesvova L, Lestinova T, Lukes J, Kostygov A, Votypka J, Volf P, Yurchenko V. (2017) A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts. PLOS Negl. Trop. Dis. 11:  e0005782. *Authors contributed equally.

Kala S*, Mehta V*, Yip CW, Moshiri H, Najafabadi HS, Zimmer SL, and Salavati R. (2017) The interaction of a Trypanosoma brucei KH-domain protein with a ribonuclease is implicated in ribosome processing. Mol. Biochem. Parasitol. 211: 94-103. *Authors contributed equally.

Shaw AK, Kalem MC, and Zimmer SL. (2016) Mitochondrial gene expression is responsive to starvation stress and developmental transition in Trypanosoma cruzi. mSphere. 1: e00051-16.

Gazestani VH, Hampton M, Abrahante JE, Salavati R, and Zimmer SL. (2016) circTAIL-seq: a targeted method for deep analysis of RNA 3’ tails reveals transcript-specific differences by multiple metrics. RNA. 22: 477-486.

Sakyiama J*, Zimmer SL*, Ciganda M, Williams N, and Read LK. (2013) 5’ processing of rRNA precursors and ribosome biogenesis in Trypanosoma brucei utilizes a highly-divergent XRN2-like enzyme. RNA. 19: 1419-31.  *Authors contributed equally

Hashimi H, Zimmer SL, Ammerman ML, Read LK, Lukeš J. (2013) Dual core processing: MRB1 is an emerging kinetoplast RNA editing complex. Trends Parasitol. 29: 91-99.

Kafková L, Ammerman ML, Faktorová D, Fisk JC, Zimmer SL, Sobotka R, Read LK, Lukes J, Hashimi H. (2012) Functional characterization of two paralogs that are novel RNA binding proteins influencing mitochondrial transcripts of Trypanosoma brucei. RNA. 18: 1846-1861.

Zimmer SL, McEvoy SM, Menon S, Read LK. (2012) Additive and Transcript-Specific Effects of KPAP1 and TbRND Activities on 3' Non-Encoded Tail Characteristics and mRNA Stability in Trypanosoma brucei. PLoS ONE. 7(5):e37639.

Read LK, Zimmer SL, ML Ammerman. (2011) Marked for Translation: Long A/U Tails as an Interface between Completion of  RNA Editing and Ribosome Recruitment. Mol. Cell. 42: 6-8.

Zimmer SL, McEvoy SM, Li J, Qu J, Read LK. (2011) A Novel Member of the RNase D Exoribonuclease Family Functions in Mitochondrial Guide RNA Metabolism in Trypanosoma brucei. J. Biol. Chem. 286: 10329-10340.

Zimmer SL*, Schein A*, Zipor G, Stern DB, Schuster G. (2009) Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase. Plant J. 59: 88-99. *Authors contributed equally.

Zimmer SL, Fei Z, Stern DB. (2008) Genome-Based Analysis of Chlamydomonas reinhardtii Exoribonucleases and Poly(A) Polymerases Predicts Unexpected Organellar and Exosomal Features. Genetics 179: 125-36.

Merchant SS, Prochnik SE, Vallon O et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 318: 245-250.

Yehudai-Resheff S, Zimmer SL, Komine Y, Stern DB. (2007) Integration of chloroplast nucleic acid metabolism into the phosphate deprivation response in Chlamydomonas reinhardtii. Plant Cell 19: 1023-38.

Nishimura Y, Kikis EA, Zimmer SL, Komine Y, Stern DB. (2004) Antisense transcript and RNA processing alterations suppress instability of polyadenylated mRNA in Chlamydomonas chloroplasts. Plant Cell 16: 2849-2869.

Mascher T, Zimmer SL*, Smith TA*, Helmann JD. (2004) Antibiotic-inducible promoter regulated by the cell envelope stress-sensing two-component system LiaRS of Bacillus subtilis. Antimicrob Agents Chemother 48: 2888-2896. *Authors contributed equally.

Akbulut S, Byersdorfer CA, Larsen CP, Zimmer SL, Humphreys TD, Clarke BL. (2001) Expression of the Melanocortin 5 Receptor on rat lymphocytes. Biochem. Biophys. Res. Commun 281: 1086-1092.