Sara L Zimmer

2024

Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment

Afonin, D. A., Gerasimov, E. S., Škodová-Sveráková, I., Záhonová, K., Gahura, O., Albanaz, A. T. S., Myšková, E., Bykova, A., Paris, Z., Lukeš, J., Opperdoes, F. R., Horváth, A., Zimmer, S. L. & Yurchenko, V., Apr 24 2024, In: Nucleic acids research. 52, 7, p. 3870-3885 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Role of PIP39 in oxidative stress response appears conserved in kinetoplastids

Durrani, H., Bjork, J. A. & Zimmer, S. L., Sep 2024, In: Molecular and Biochemical Parasitology. 259, 111620.

Research output: Contribution to journal › Article › peer-review

2023

Circular mitochondrial-encoded mRNAs are a distinct subpopulation of mitochondrial mRNA in Trypanosoma brucei

Smoniewski, C. M., Mirzavand Borujeni, P., Petersen, A., Hampton, M., Salavati, R. & Zimmer, S. L., Dec 2023, In: Scientific reports. 13, 1, 7825.

Research output: Contribution to journal › Article › peer-review

Open Access

Kinetoplast Genome of Leishmania spp. Is under Strong Purifying Selection

Gerasimov, E. S., Novozhilova, T. S., Zimmer, S. L. & Yurchenko, V., Aug 2023, In: Tropical Medicine and Infectious Disease. 8, 8, 384.

Research output: Contribution to journal › Article › peer-review

Open Access

Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae

Albanaz, A. T. S., Carrington, M., Frolov, A. O., Ganyukova, A. I., Gerasimov, E. S., Kostygov, A. Y., Lukeš, J., Malysheva, M. N., Votýpka, J., Zakharova, A., Záhonová, K., Zimmer, S. L., Yurchenko, V. & Butenko, A., Dec 2023, In: BMC Genomics. 24, 1, 471.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

2022

Mitochondrial RNA editing in Trypanoplasma borreli: New tools, new revelations

Gerasimov, E. S., Afonin, D. A., Korzhavina, O. A., Lukeš, J., Low, R., Hall, N., Tyler, K., Yurchenko, V. & Zimmer, S. L., Jan 2022, In: Computational and Structural Biotechnology Journal. 20, p. 6388-6402 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Trypanosoma cruzi strain and starvation-driven mitochondrial RNA editing and transcriptome variability

Gerasimov, E. S., Ramirez-Barrios, R., Yurchenko, V. & Zimmer, S. L., Jul 2022, In: RNA. 28, 7, p. 993-1012 20 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Using a Community-Based Participatory Approach to Address Gender Equity in Academic Medicine: The Center for Women in Medicine and Science at the University of Minnesota

Berge, J. M., Macheledt, K., Watson, S., Dorr, H., Pusalavidyasagar, S., Kunin-Batson, A., Pratt, R., Zimmer, S. L., Tolar, J. & Termuhlen, A., Mar 1 2022, In: Academic medicine : journal of the Association of American Medical Colleges. 97, 3, p. 370-377 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

2021

Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events

Gerasimov, E. S., Gasparyan, A. A., Afonin, D. A., Zimmer, S. L., Kraeva, N., Lukeš, J., Yurchenko, V. & Kolesnikov, A., Apr 6 2021, In: Nucleic acids research. 49, 6, p. 3354-3370 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

Probabilistic models of biological enzymatic polymerization

Hampton, M., Galey, M., Smoniewski, C. & Zimmer, S. L., Jan 2021, In: PloS one. 16, 1 January, e0244858.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Reintegrating Biology Through the Nexus of Energy, Information, and Matter

Hoke, K. L., Zimmer, S. L., Roddy, A. B., Ondrechen, M. J., Williamson, C. E. & Buan, N. R., Dec 1 2021, In: Integrative and comparative biology. 61, 6, p. 2082-2094 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

The remarkable metabolism of vickermania ingenoplastis: Genomic predictions

Opperdoes, F. R., Butenko, A., Zakharova, A., Gerasimov, E. S., Zimmer, S. L., Lukeš, J. & Yurchenko, V., Jan 2021, In: Pathogens. 10, 1, p. 1-12 12 p., 68.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

2020

A global analysis of enzyme compartmentalization to glycosomes

Durrani, H., Hampton, M., Rumbley, J. N. & Zimmer, S. L., 2020, In: Pathogens. 9, 4, 281.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

A link between mitochondrial gene expression and life stage morphologies in Trypanosoma cruzi

Ramirez-Barrios, R., Susa, E. K., Smoniewski, C. M., Faacks, S. P., Liggett, C. K. & Zimmer, S. L., May 1 2020, In: Molecular Microbiology. 113, 5, p. 1003-1021 19 p.

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes

Aphasizheva, I., Alfonzo, J., Carnes, J., Cestari, I., Cruz-Reyes, J., Göringer, H. U., Hajduk, S., Lukeš, J., Madison-Antenucci, S., Maslov, D. A., McDermott, S. M., Ochsenreiter, T., Read, L. K., Salavati, R., Schnaufer, A., Schneider, A., Simpson, L., Stuart, K., Yurchenko, V. & Zhou, Z. H. & 4 others, Zíková, A., Zhang, L., Zimmer, S. & Aphasizhev, R., Apr 1 2020, In: Trends in Parasitology. 36, 4, p. 337-355 19 p.

Research output: Contribution to journal › Article › peer-review

66 Scopus citations

2019

Revisiting Trypanosome Mitochondrial Genome Mysteries: Broader and Deeper

Zimmer, S. L., Feb 2019, In: Trends in Parasitology. 35, 2, p. 102-104 3 p.

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

2018

Advances in emerging and neglected infectious diseases 2018

Spencer, C. T., Vasconcelos, J. R., Thornburg, N. J. & Zimmer, S. L., 2018, In: BioMed Research International. 2018, 4619282.

Research output: Contribution to journal › Editorial › peer-review

Open Access

2 Scopus citations

Gene expression to mitochondrial metabolism: Variability among cultured Trypanosoma cruzi strains

Kalem, M. C., Gerasimov, E. S., Vu, P. K. & Zimmer, S. L., May 2018, In: PloS one. 13, 5, e0197983.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

High throughput sequencing revolution reveals conserved fundamentals of U-indel editing

Zimmer, S. L., Simpson, R. M. & Read, L. K., Sep 1 2018, In: Wiley Interdisciplinary Reviews: RNA. 9, 5, e1487.

Research output: Contribution to journal › Article › peer-review

Open Access

24 Scopus citations

Tail characteristics of Trypanosoma brucei mitochondrial transcripts are developmentally altered in a transcript-specific manner

Gazestani, V. H., Hampton, M., Shaw, A. K., Salavati, R. & Zimmer, S. L., Feb 2018, In: International Journal for Parasitology. 48, 2, p. 179-189 11 p.

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Trypanosomatid mitochondrial RNA editing: Dramatically complex transcript repertoires revealed with a dedicated mapping tool

Gerasimov, E. S., Gasparyan, A. A., Kaurov, I., Tichý, B., Logacheva, M. D., Kolesnikov, A. A., Lukeš, J., Yurchenko, V., Zimmer, S. L. & Flegontov, P., Jan 25 2018, In: Nucleic acids research. 46, 2, p. 765-781 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

24 Scopus citations

2017

A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts

Ishemgulova, A., Kraeva, N., Hlaváčová, J., Zimmer, S. L., Butenko, A., Podešvová, L., Leštinová, T., Lukeš, J., Kostygov, A., Votýpka, J., Volf, P. & Yurchenko, V., Jul 24 2017, In: PLoS neglected tropical diseases. 11, 7, e0005782.

Research output: Contribution to journal › Article › peer-review

Open Access

18 Scopus citations

The interaction of a Trypanosoma brucei KH-domain protein with a ribonuclease is implicated in ribosome processing

Kala, S., Mehta, V., Yip, C. W., Moshiri, H., Najafabadi, H. S., Ma, R., Nikpour, N., Zimmer, S. L. & Salavati, R., Jan 1 2017, In: Molecular and Biochemical Parasitology. 211, p. 94-103 10 p.

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

2016

CircTAIL-seq, a targeted method for deep analysis of RNA 3' tails, reveals transcript-specific differences by multiple metrics

Gazestani, V. H., Hampton, M., Abrahante, J. E., Salavati, R. & Zimmer, S. L., Mar 2016, In: RNA. 22, 3, p. 477-486 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

Mitochondrial Gene Expression Is Responsive to Starvation Stress and Developmental Transition in Trypanosoma cruzi

Shaw, A. K., Kalem, M. C. & Zimmer, S. L., Apr 2016, In: mSphere. 1, 2, p. e00051-16 e00051-16.

Research output: Contribution to journal › Article › peer-review

Open Access

19 Scopus citations

2013

Dual core processing: MRB1 is an emerging kinetoplast RNA editing complex

Hashimi, H., Zimmer, S. L., Ammerman, M. L., Read, L. K. & Lukeš, J., Feb 2013, In: Trends in Parasitology. 29, 2, p. 91-99 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

50 Scopus citations

Ribosome biogenesis requires a highly diverged XRN family 5′→3′ exoribonuclease for rRNA processing in Trypanosoma brucei

Sakyiama, J., Zimmer, S. L., Ciganda, M., Williams, N. & Read, L. K., Oct 2013, In: RNA. 19, 10, p. 1419-1431 13 p.

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

2012

Additive and transcript-specific effects of KPAP1 and TbRND activities on 3′ non-encoded tail characteristics and mRNA stability in Trypanosoma brucei

Zimmer, S. L., McEvoy, S. M., Menon, S. & Read, L. K., May 21 2012, In: PloS one. 7, 5, e37639.

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Functional characterization of two paralogs that are novel RNA binding proteins influencing mitochondrial transcripts of Trypanosoma brucei

Kafková, L., Ammerman, M. L., Faktorová, D., Fisk, J. C., Zimmer, S. L., Sobotka, R., Read, L. K., Lukeš, J. & Hashimi, H., Oct 2012, In: RNA. 18, 10, p. 1846-1861 16 p.

Research output: Contribution to journal › Article › peer-review

38 Scopus citations

Functional characterization of two paralogs that are novel RNA binding proteins influencing mitochondrial transcripts of Trypanosoma brucei (RNA (2012) 18, (1846-1861))

Kafková, L., Ammerman, M. L., Faktorová, D., Fisk, J. C., Zimmer, S. L., Sobotka, R., Read, L. K., Lukeš, J. & Hashimi, H., Dec 1 2012, In: RNA. 18, 12, 1 p.

Research output: Contribution to journal › Comment/debate › peer-review

2011

A novel member of the RNase D exoribonuclease family functions in mitochondrial guide RNA metabolism in Trypanosoma brucei

Zimmer, S. L., McEvoy, S. M., Li, J., Qu, J. & Read, L. K., Mar 25 2011, In: Journal of Biological Chemistry. 286, 12, p. 10329-10340 12 p.

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Marked for Translation: Long A/U Tails as an Interface between Completion of RNA Editing and Ribosome Recruitment

Read, L. K., Zimmer, S. L. & Ammerman, M. L., Apr 8 2011, In: Molecular Cell. 42, 1, p. 6-8 3 p.

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

2009

Polyadenylation in Arabidopsis and Chlamydomonas organelles: The input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase

Zimmer, S. L., Schein, A., Zipor, G., Stern, D. B. & Schuster, G., Jul 2009, In: Plant Journal. 59, 1, p. 88-99 12 p.

Research output: Contribution to journal › Article › peer-review

43 Scopus citations

2008

Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features

Zimmer, S. L., Fei, Z. & Stern, D. B., May 2008, In: Genetics. 179, 1, p. 125-136 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

25 Scopus citations

2007

Integration of chloroplast nucleic acid metabolism into the phosphate deprivation response in Chlamydomonas reinhardtii

Yehudai-Resheff, S., Zimmer, S. L., Komine, Y. & Stern, D. B., Mar 2007, In: Plant Cell. 19, 3, p. 1023-1038 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

73 Scopus citations

The Chlamydomonas genome reveals the evolution of key animal and plant functions

Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E. H., Karpowicz, S. J., Witman, G. B., Terry, A., Salamov, A., Fritz-Laylin, L. K., Maréchal-Drouard, L., Marshall, W. F., Qu, L. H., Nelson, D. R., Sanderfoot, A. A., Spalding, M. H., Kapitonov, V. V., Ren, Q., Ferris, P., Lindquist, E. & Shapiro, H. & 97 others, Lucas, S. M., Grimwood, J., Schmutz, J., Grigoriev, I. V., Rokhsar, D. S., Grossman, A. R., Cardol, P., Cerutti, H., Chanfreau, G., Chen, C. L., Cognat, V., Croft, M. T., Dent, R., Dutcher, S., Fernández, E., Fukuzawa, H., González-Ballester, D., González-Halphen, D., Hallmann, A., Hanikenne, M., Hippler, M., Inwood, W., Jabbari, K., Kalanon, M., Kuras, R., Lefebvre, P. A., Lemaire, S. D., Lobanov, A. V., Lohr, M., Manuell, A., Meier, I., Mets, L., Mittag, M., Mittelmeier, T., Moroney, J. V., Moseley, J., Napoli, C., Nedelcu, A. M., Niyogi, K., Novoselov, S. V., Paulsen, I. T., Pazour, G., Purton, S., Ral, J. P., Riaño-Pachón, D. M., Riekhof, W., Rymarquis, L., Schroda, M., Stern, D., Umen, J., Willows, R., Wilson, N., Zimmer, S. L., Allmer, J., Balk, J., Bisova, K., Chen, C. J., Elias, M., Gendler, K., Hauser, C., Lamb, M. R., Ledford, H., Long, J. C., Minagawa, J., Page, M. D., Pan, J., Pootakham, W., Roje, S., Rose, A., Stahlberg, E., Terauchi, A. M., Yang, P., Ball, S., Bowler, C., Dieckmann, C. L., Gladyshev, V. N., Green, P., Jorgensen, R., Mayfield, S., Mueller-Roeber, B., Rajamani, S., Sayre, R. T., Brokstein, P., Dubchak, I., Goodstein, D., Hornick, L., Huang, Y. W., Jhaveri, J., Luo, Y., Martínez, D., Ngau, W. C. A., Otillar, B., Poliakov, A., Porter, A., Szajkowski, L., Werner, G. & Zhou, K., Oct 12 2007, In: Science. 318, 5848, p. 245-251 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access