Daniel M. Stoebel

Associate Professor of BiologydanPortrait

F.W. Olin Science Center, Room 2364
1250 N. Dartmouth Ave.
Claremont, CA 91711
909.607.1141
stoebel@g.hmc.edu

Education and Professional Experience

  • B.A., Biology, Pomona College
  • PhD, Ecology and Evolution, Stony Brook University
  • Postdoctoral Research Fellow, Trinity College, University of Dublin
  • Postdoctoral Research Fellow, University of Houston

Teaching Interests

My teaching interests span molecular and evolutionary genetics, from first years to seniors, in lab, seminar, and lecture settings. I also take great pleasure teaching statistics and courses at the interface of biology and the humanities. In 2017-18, I anticipate teaching Molecular/Cellular Biology lab (Bio 111), Introductory Biology Lab (Bio 54), and two sections of our new lab course for all HMC frosh (Bio 23).

In past years, I have taught:

  • Bio 52: Introduction to Biology
  • Bio 54: Introductory Biology Lab
  • Bio 113: Molecular Genetics
  • Bio 154: Biostatistics
  • Bio 164: Genetics
  • Bio/Chem 189: Current Topics in Molecular Biology and Biochemistry
  • Writing 1: Introduction to Academic Writing

Research Interests

Work in my lab focuses on the molecular biology and evolution of bacterial regulatory networks. The E. coli global transcription regulator RpoS is the focus of work, because it allows for the integration of molecular biology, physiology and evolution. Projects include studying how RpoS levels vary across strains and environments, measuring the affect of this variation in RpoS level on the transcriptome, studying how RpoS interacts with other transcription factors to influence patterns of transcription, and exploring how the regulation of RpoS levels varies in pathogenic relatives of laboratory E. coli.

I encourage students at HMC or any of the other Claremont Colleges for whom this sounds interesting to contact me. I regularly invite students of all backgrounds into my lab.

Selected Publications

(* indicates work done as an undergraduate)

Bush, E. C., A. E. Clark*, C. A. DeRanek*, A. Eng*, J. Forman*, K. Heath*, A. B. Lee*, D. M. Stoebel, Z. Wang*, M. Wilber*, and H. Wu*. “xenoGI: Reconstructing the history of genomic island insertions in clades of closely related bacteria.” [bioRxiv preprint]

G. T. Wong*, R. P. Bonocora, A. N. Schep*, S. M. Beeler*, A. J. Lee Fong, L. M. Shull*, L. E. Batachari*, M. Dillon*, C. J. Becker*, C. Evans*, E. C. Bush, J. Hardin, J. T. Wade, and D. M. Stoebel. 2017. The genome-wide transcriptional response to varying RpoS levels in Escherichia coli K-12. Journal of Bacteriology, 199: e00755-16. doi:  [article] [bioRxiv preprint]

C. Evans*, J. Hardin, and D. M. Stoebel. 2017. Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions. Briefings in Bioinformatics. doi: 10.1093/bib/bbx008 [article]

Wünsche, D. M. Dinh, R. S. Satterwhite, C. Diaz Arenas, D. M. Stoebel, and T. F. Cooper. 2017. Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory.” Nature Ecology & Evolution 1: 61. [article]

Y. Wang, C. D. Arenas, D. M. Stoebel, K. Flynn, E. Knapp, M. M. Dillon, A. Wünsche, P. J. Hatcher, F. B.-G. Moore, V. S. Cooper, and T. F. Cooper. 2016. Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness. PNAS, 113:5047-5052. [article]

Y. Wang, C. D. Arenas, D. M. Stoebel, and T. F. Cooper. 2013. Genetic background affects epistatic interactions between two beneficial mutations. Biology Letters doi:10.1098/rsbl.2012.0328. [article]

E. Snyder*, D. M. Gordon, and D. M. Stoebel. 2012. Escherichia coli lacking RpoS are rare in natural populations of non-pathogens. G3: Genes | Genomes | Genetics2:1341-4 [article]

Cameron, A. D. S., D. M. Stoebel, and C. J. Dorman. 2011. DNA supercoiling is deferentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica. Molecular Microbiology, 80:85-101 [article]

Stoebel, D. M. & C. J. Dorman. 2010. The effect of mobile element IS10 on experimental regulatory evolution in Escherichia coliMolecular Biology and Evolution27: 2105-2112. [article]

Stoebel, D. M. & D. E. Dykhuizen. 2010. Waste and yet want not. Molecular Cell38:625-626. [article]

Stoebel, D. M., K. Hokamp, M. S. Last & C. J. Dorman. 2009. Compensatory evolution of gene regulation in response to stress by E. coli lacking RpoS. PLoS Genetics, 5: e1000671  [article]

Stoebel, D. M., A. Free & C. J. Dorman. 2008. Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology154: 2533-2545. [article]

Stoebel, D. M., A. M. Dean & D. E. Dykhuizen. 2008. The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics178:1653-1660. [article]

Stoebel, D. M. 2005. Lack of evidence for horizontal transfer of the lac operon into Escherichia coliMolecular Biology and Evolution22:683-690. [article]

Feldgarden, M., D. M. Stoebel, D. Brisson & D.E. Dykhuizen. 2003. Size doesn’t matter: microbial selection experiments address ecological questions. Ecology84:1679-1687. [article]