Lab Alumni

Ph.D. Alumni

 

IMG_1618Peter Burby Ph.D. (2014-2019)

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(in press) Molecular Microbiology  doi: 10.1111/mmi.14158 (‡corresponding author

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 (‡corresponding author)

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 Genetics Jul 6;14(7):e1007512. doi: 10.1371/journal.pgen.1007512 (‡corresponding author)

Justin Randall-sizedJustin Randall Ph.D. (2013-2018)

justrand@umich.edu
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 subtilisJournal 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 JB.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. Proc. Natl. Acad. Sci. USA. Oct 31;114(44):11733-11738. doi: 10.1073/pnas.1710995114

 

jeremy schroederJeremy Schroeder Ph.D. Student (2010-2016)

schroedj@umich.edu

Research: Studies mismatch repair and ribonucleotide excision repair.

Education: B.S. in Biology, 2009, Ohio Northern University

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. Proc. Natl. Acad. Sci. USA. PNAS Plus; pp. E68978-E6906. PMID: 26343983. *co-first; ‡co-corresponding

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

Brian Walsh (2011-2016)

bwwalsh@umich.edu

Research: Exploration of the B. subtilis RecD2 helicase.

Current position: Scientist Rubicon Genomics

Education: B.S. from Michigan State University in 2006, recently admitted to the MCDB Ph.D. program at the University of Michigan and proud to be the longest standing member of the Simmons Lab.

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

Interests: Outside of the lab Brian can likely be found at any number of city, state or metro parks honing his running, cycling, and swimming skills. He is an avid triathlete and is intent upon finishing his first half-Ironman in September 2010.

 

Justin Lenhart Ph.D. (2008-2014)


Research: Mismatch repair

Current Position: Swift Biosciences

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 MicrobiologyNov. 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)

Postdoctoral Alumni

Lieke van Gijtenbeek, Ph.D. (2018-2019) lavg@umich.edu

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 klockoAndy Klocko Postdoctoral Fellow (2010-2011)

Education: Ph.D., University of Wisconsin-Madison
adklocko@umich.edu

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

 

M.S. Student Alumni

avani kamathAvani Kamath M.S. (2009-2010)

avanii@umich.edu

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)

Amelia-McKitterick-sized2

 

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

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 AndrewsLane Andrews (2014-2016)

andrelan@umich.edu

Lane studied DNA helicases. She graduated with a BS in Neurobiology.

samantha BolzSamantha Bolz (2012-2014)

sbolz@umich.edu

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.

brook gustafsonBrooke Gustafson (2012-2013)

brookerg@umich.edu
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 szewczykGabriella Szewczyk (2011-2013)

gszewczy@umich.edu

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 weindorfSteve Weindorf (2011)

stevecw@umich.edu

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 brandesEileen Brandes (2010-2011)

ebrandes@umich.edu

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 bolzNick Bolz (2009-2012)

nbolz@umich.edu

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 craftonKaleena Crafton (2008-2009)

B.A. Harvard University

kaleena@umich.edu

 

 

 

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 dupesNicole Dupes (2008-2009)

B.S. University of Michigan

nicolemd@umich.edu

Publications: 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.*These authors equally contributed.

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 hafeezAdam Hafeez (2008-2009)

hafeeza@umich.edu

cassie pavlickCassie Pavlick (2008-2010)

cepavli@umich.edu

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 gessertDavid Gessert (2008-2009)

dagesse@umich.edu

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 williamsPaul Williams (2008-2009)

pauchris@umich.edu

 

 

 

 

heather frodyma petersonHeather (Frodyma) Peterson (2008-2009)

pheonix@umich.edu

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.