Daniel M. Stoebel

Associate Professor of BiologydanPortrait

F.W. Olin Science Center, Room 2364
1250 N. Dartmouth Ave.
Claremont, CA 91711

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


  • 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 the Stoebel Lab focuses on the molecular biology and evolution of bacterial regulatory networks. The E. coli global transcriptional regulator RpoS is the focus of work, because it allows for the integration of molecular biology, physiology and evolution. Projects include documenting naturally occurring variation in RpoS levels, exploring the physiological consequences of this variation, measuring the effect of variation on the transcriptome, and determining molecular mechanisms of evolution of the RpoS regulon.

Selected Publications

(* indicates work done as an undergraduate)

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]