Postdoc Alumni
Emily (Clowdus) Masser, Ph.D. (2019-2021)
Postdoctoral Alum
Education: Ph.D., University of Oklahoma Health Sciences Center College of Medicine
Research: Emily studies how bacteria regulate the DNA damage checkpoint to cell division.
Current Position: Assistant Professor of Biochemistry and Molecular Biology Marian University College of Osteopathic Medicine
Masser, E.A., Burby P.E., Hawkins, W.D., Gustafson, B.R., Lenhart, J.S. and L.A. Simmons‡(2021) DNA damage checkpoint activation affects peptidoglycan synthesis and late divisome components. In press Molecular Microbiology doi: 10.1111/mmi.14765
Lindsay Matthews, Ph.D. (2014-2020)
Postdoctoral alum
Education: Ph.D. McMaster University
Research: Lindsay studies the pathway that allows for replication forks to maintain integrity when blocked.
Current Position: Research Associate McGill University
Matthews, L.A. and L.A. Simmons‡ (2020) Regulation of DNA Binding and High Order Oligomerization of the DnaB Helicase Loader. Journal of BacteriologyOct 8;202(21):e00286-20. doi: 10.1128/JB.00286-20.
Li,Y., Chen, Z., Matthews, L.A., Simmons, L.A.‡and J.S. Biteen‡ (2019)Two essential replicative DNA polymerases exchange dynamically during DNA replication and after replication fork arrest. (‡co-corresponding authors) Biophysical Journal. In press
Matthews, L.A., and L.A Simmons‡ (2019) Cryptic protein interactions regulate DNA replication initiation. Molecular Microbiology Jan;111(1):118-130. doi: 10.1111/mmi.14142
Lieke van Gijtenbeek, Ph.D. (2018-2019)
Postdoctoral alum
Education: Ph.D. University of Groningen, Netherlands
Research: Lieke studies the effects of DNA methylation on gene expression in bacteria.
Current Position: Research Scientist Chr. Hansen Biotechnology company Denmark
Andy Klocko, PhD (2010-2011)
Postdoctoral alum
Education: Ph.D., University of Wisconsin-Madison
Current position: Assistant Professor University of Colorado, Colorado Springs
Publications: Andy published 4 papers during his postdoc including:
Klocko A.D., Schroeder J.W., Walsh B.W., Lenhart J.S., Evans M.L., Simmons LA. (2011) Mismatch repair causes the dynamic release of an essential DNA polymerase from the replication fork. Mol Microbiol. Nov;82(3):648-63
Ph.D. Alumni
Katie Wozniak (2017-2022)
PhD graduate
Education: B.S. Microbiology Michigan State University
NSF Predoctoral Fellow
Research: Katie studies the connection between the bacterial cell wall and the DNA damage checkpoint.
Publications: Randall, J.R., Nye, T.M., Wozniak, K.J. and L.A. Simmons (2019) Okazaki fragment maturation in Bacillus subtilis. Journal of Bacteriology. pii: JB.00686-18. doi: 10.1128/JB.00686-18
Current position: Postdoc at Baylor College of Medicine
Taylor Nye (2016-2020)
PhD graduate
Education: Taylor completed her B.S. in Microbiology at the University of Michigan. Awarded the Psujek Memorial award for best honors thesis among all the biology majors.
NSF Predoctoral Fellow
Research: Taylor studies the role of DNA methylation on bacterial gene expression.
Current Position: Postdoc Scott Hultgren's lab Washington University, St. Louis School of Medicine
Publications
- Nye, T.M., McLean E.K., Burrage, A.M, Dennison, D.D., Kearns, D.B., L.A. Simmons‡ (2021) RnhP is a plasmid-borne RNase HI that contributes to genome maintenance in Bacillus subtilis ancestral strain NCIB 3610. Molecular MicrobiologyJan;115(1):99-115.
- Nye, T.M. Fernandez, N. L. and L.A. Simmons‡ (2020) A Positive Perspective on DNA Methylation: Regulatory Functions of DNA Methylation Outside of Host Defense in Gram-Positive Bacteria.Critical Reviews in Biochemistry and Molecular Biology.55: (6) 575-591. Oct 15:1-16. doi: 10.1080/10409238.2020.1828257.
- Nye, T.M., van Gijtenbeek, L.A.,Stevens, A.G., Schroeder, J.W., Matthews, L.A. Randall, J.R., and L.A. Simmons‡ (2020) Methyltransferase DnmA is responsible for genome-wide N6-methyladenosine modifications at non-palindromic recognition sites in Bacillus subtilis. Nucleic Acids Research48(10):5332-5348 doi: 10.1093/nar/gkaa266
- Nye, T. M., K. M. Jacob, S. R. Dawid, L. A. Simmons, and M. E. Watson, Jr. (2019) DNA methylation from a type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes. PLoS Pathogens 17;15(6):e1007841. doi: 10.1371/journal.ppat.1007841.
Peter Burby (2014-2019)
PhD graduate
Education: B.S. University of Michigan
Research: Discovery of uncharacterized genes that function in the bacterial cell cycle and DNA repair.
Current Position upon graduation: Scientist Cayman Chemical
Publications: Peter published 7 papers with three examples shown below.
- Burby, P.E. and L.A. Simmons (2019) A bacterial DNA repair pathway specific to a natural antibiotic. Molecular Microbiology doi: 10.1111/mmi.14158
- Burby, P.E., Simmons, Z.W., and L.A. Simmons (2019) DdcA antagonizes a bacterial DNA damage checkpoint. Molecular Microbiology .doi: 10.1111/mmi.14151
- Burby, P.E.Simmons, Z.W., Schroeder J.W.,and L.A. Simmons (2018) Discovery of a dual protease mechanism that promotes DNA damage checkpoint recovery PLoS GeneticsJul 6;14(7):e1007512. doi: 10.1371/journal.pgen.1007512
Justin Randall (2013-2018)
PhD graduate
Education: B.S. University of Arizona
Research: RNase H enzymes and their activity on different RNA-DNA hybrids.
Current position: Postdoctoral Fellow University of Texas at Austin with Dr. Bryan Davies.
Publications: Justin published 6 papers with three examples shown below.
- Randall, J.R., Nye, T.M., Wozniak, K.J. and L.A. Simmons(2019) Okazaki fragment maturation in Bacillus subtilis. Journal of Bacteriology. in press
- Randall, J.R.,Hirst, W.G. and L.A. Simmons (2018) Substrate specificity for bacterial RNase HII and HIII is influenced by metal availability. Journal of Bacteriology 00401-17. doi:
- Schroeder,J.W.,Randall, J.R.,Hirst, W.G.O’Donnell, M.E‡. and L.A. Simmons(2017) Mutagenic cost of ribonucleotides in bacterial DNA. Natl. Acad. Sci. USA. Oct 31;114(44):11733-11738. doi: 10.1073/pnas.1710995114
Brian Walsh (2011-2016)
PhD graduate
Education: B.S. (2006) Michigan State University
Proud to be the longest standing member of the Simmons Lab.
Research: Exploration of the B. subtilis RecD2 helicase.
Publications: Brian published 7 papers during his thesis research. Two examples are below.
- Dupes, N.M.*,Walsh, B.W.*, Klocko, A.D., Lenhart, J.S., Peterson, H.L., Gessert, D.A., Pavlick, C.E., Simmons L.A. (2010). Mutations in Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair. Journal of Bacteriology. 192(13):3452-63. *These authors equally contributed.
- Walsh*,B.W., Bolz*, S.A.,Wessell, S.R., Schroeder, J.W., Keck, J.L. and L.A. Simmons. (2014) RecD2 helicase limits replication fork stress in Bacillus subtilis. (‡corresponding author) (*equally contributed) Journal of Bacteriology 196:1359-1368. PMID: 24443534
Current position: Scientist Rubicon Genomics
Jeremy Schroeder (2010-2016)
PhD graduate
Education: B.S. in Biology, 2009, Ohio Northern University
Research: Studies mismatch repair and ribonucleotide excision repair.
Publications: Jeremy published 17 papers during his thesis with two examples listed below.
- Liao, Y*., Schroeder, J.W*., Burke G., Simmons, L.A., and J.S. Biteen (2015) Single-molecule motions and interactions in live cells reveal target-search dynamics in mismatch repair. Natl. Acad. Sci. USA. PNAS Plus; pp. E68978-E6906. PMID: 26343983. *co-first
- Schroeder J.W., Hirst W.G., Szewczyk G.A. and L.A. Simmons (2016) The effect of local sequence context on mutational bias of genes encoded on the leading and lagging strands. Current Biology 26:692-697. PMID: 26923786.
Current Position: Postdoc in Jade Wang's lab University of Wisconsin-Madison
Justin Lenhart (2008-2014)
PhD graduate
Research: Mismatch repair
Publications: Justin published 10 papers including three examples shown below:
- Lenhart, J.S., Brandes, E.R.,Schroeder, J.W., Sorenson, R. J.,Showalter, H.D. and L.A. Simmons. (2014) RecO and RecR provide distinct roles that couple RecA to DNA replication forks in Bacillus subtilis (‡corresponding author) Journal of Bacteriology196:2851-2860.
- Lenhart, J.S.Pillon, M.C., Guarné, A., and L.A. Simmons. (2013)Trapping and visualizing intermediate steps in the mismatch repair pathway in vivoMolecular Microbiology 90(4):680-98.
- Lenhart, J.S., Anushi, A., Hingorani, M.M. and L.A. Simmons. (2013)DnaN provides a platform for spatiotemporal coupling of mismatch detection to DNA replicationMolecular Microbiology87(3):553-68. (‡corresponding author)
Current Position: Swift Biosciences
M.S. Student Alumni
Emma McLean (2019-2021)
Education: B.S. Movement Science University of Michigan
Research: Emma studies RNase H genes and their contribution to genome integrity.
Avani Kamath M.S. (2009-2010)
Research: I study DNA damage inducible helicases
Education: BE from BMS College of Engineering Bangalore
Interests: When not in lab I like whiling away time reading, dancing, cooking and hanging out with friends!
Will Hirst M.S. (2012-2014)
Education: B.A. Vassar College
Research: Will studied RNase HIII and the contribution of this riboendonuclease to genome stability.
Publication:Schroeder J.W., Hirst W.G., Szewczyk G.A. and L.A. Simmons (2016) The effect of local sequence context on mutational bias of genes encoded on the leading and lagging strands. Current Biology 26:692-697. PMID: 26923786.
Amelia McKitterick M.S. (2013-2014)
Education: B.A. Vassar College, M.S. University of Michigan
Current Position: Amelia finished her Ph.D. at the University of California Berkeley. She is now a postdoc at Harvard Medical School.
Undergraduate Alumni
Lina Jeffery (2020-2023)
Major: MCDB
Research: Okazaki fragment maturation
Amy Stevens (2015-2018)
Amy studied DNA methylation and graduated with Honors in Biochemistry.
Heather Martin (2015-2017)
Heather studied DNA mismatch repair and graduated with a BS in Biomolecular Science. She is currently a medical student at the MSU College of Human Medicine.
Publication: Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarné A (2019) Binding of the regulatory domain of MutL to the sliding beta-clamp is species specific. Nucleic Acids Research 47(9):4831-4842
Taylor Timko (2016-2018)
Taylor studied RNA-DNA hybrids and graduated with a BS in Biology. She is currently a professional soccer player in Australia.
Lane Andrews (2014-2016)
Lane studied DNA helicases. She graduated with a BS in Neurobiology.
Samantha Bolz (2012-2014)
She was co-first author on a research article published in the April 2014 issue of the Journal of Bacteriology. Walsh et al., “RecD2 helicase limits replication fork stress in Bacillus subtilis” J. Bacteriology 196:1359-68 and Sam graduated with High Honors in Microbiology
Current Position: Samantha is in medical school at Rosalind Franklin University.
Brooke Gustafson (2012-2013)
[email protected]
Current Position: Brooke finished medical school, Wayne State University. She is now a resident in pediatrics at the University of Louisville.
Brooke graduated with Honors in Biology
Gabriella Szewczyk (2011-2013)
Current Position: Dual DDS/Ph.D. program at UIC
Gabriella graduated with Honors in Microbiology
Publication:
Schroeder J.W., Hirst W.G., Szewczyk G.A. and L.A. Simmons‡ (2016) The effect of local sequence context on mutational bias of genes encoded on the leading and lagging strands. Current Biology 26:692-697. PMID: 26923786.
Steve Weindorf (2011)
Current position: Medical School, Wayne State University.
Publication: Bolz NJ, Lenhart JS, Weindorf SC, Simmons LA. (2012). “Residues in the N-terminal domain of MutL required for mismatch repair in Bacillus subtilis.” Journal of Bacteriology 194(19)5361-5367.
Eileen Brandes (2010-2011)
Eileen graduated with Highest Honors in Biology and received the 2012 inaugural Marshal Nirenberg award in Life Sciences, a Goldstein prize for Honors seniors given by the Honors College, and the 2012 Christine Psujek Memorial Award, an award given to the graduating senior who submits the best honors thesis in any of the biology concentrations.
Current Position: Eileen finished medical school at Harvard. She is now a resident at Dartmouth.
Publications:
Lenhart JS, Brandes ER, Schroeder JW, Sorenson RJ, Showalter HD, Simmons LA. RecO and RecR are necessary for RecA loading in response to DNA damage and replication fork stress. J Bacteriol. 2014 196:2851-2860.
Tuson, H.H., Aliaj, A., Brandes, E.R., Simmons L.A., and J.S. Biteen (2016) Addressing the requirements of high sensitivity single-molecule imaging of low-copy number proteins in bacteria. ChemPhysChem 18;17(10):1435-40.
Nick Bolz (2009-2012)
Nick graduated with honors in Microbiology and is currently a medical student at New York Medical College. He published his thesis as a first author paper in the Journal of Bacteriology .
Publication: Bolz NJ, Lenhart JS, Weindorf SC, Simmons LA. (2012). “Residues in the N-terminal domain of MutL required for mismatch repair in Bacillus subtilis.” Journal of Bacteriology 194(19)5361-5367. Read abstract.
Current Position: M.D. Resident Physician Detroit Medical Center.
Kaleena Crafton (2008-2009)
B.A. Harvard University
Publication: Klocko A.D., Crafton K.M., Walsh B.W., Lenhart J.S., Simmons L.A. (2010) Imaging of mismatch repair complexes and cellular responses to DNA damage in Bacillus subtilis. J. Vis. Exp. (36) 1-4
Nicole Dupes (2008-2009)
B.S. University of Michigan
Davies BW, Bogard RW, Dupes NM, Gerstenfeld TA, Simmons LA, Mekalanos JJ. DNA damage and reactive Nitrogen species are barriers to Vibrio cholerae colonization of the infant mouse intestine PLoS Pathog. 2011 Feb;7(2):e1001295.
Current position: Nicole finished medical school at Michigan State University (2014). She is a resident in Neurology in Farmington Hills Michigan.
Adam Hafeez (2008-2009)
Cassie Pavlick (2008-2010)
Current position: Research Technician in Synthetic Biology, Draths Corporation, Okemos, Michigan
Publication: Dupes, N.M.*, Walsh, B.W.*, Klocko, A.D., Lenhart, J.S., Peterson, H.L., Gessert, D.A., Pavlick, C.E., Simmons L.A. (2010). Mutations in Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair. 192(13):3452-63.
David Gessert (2008-2009)
Current position: Medical School, Rush University, Chicago, IL
Publication: Dupes, N.M.*, Walsh, B.W.*, Klocko, A.D., Lenhart, J.S., Peterson, H.L., Gessert, D.A., Pavlick, C.E., Simmons L.A. (2010). Mutations in Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair. 192(13):3452-63.
Paul Williams (2008-2009)
Heather (Frodyma) Peterson (2008-2009)
Current position: Research Technician, University of Washington, Seattle
Publication: Publication: Dupes, N.M.*, Walsh, B.W.*, Klocko, A.D., Lenhart, J.S., Peterson, H.L., Gessert, D.A., Pavlick, C.E., Simmons L.A. (2010). Mutations in Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair. 192(13):3452-63.
