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1.

Redefining the H-NS protein family: a diversity of specialized core and accessory forms exhibit hierarchical transcriptional network integration.

Fitzgerald, Stephen; Kary, Stefani C; Alshabib, Ebtihal Y; MacKenzie, Keith D; Stoebel, Daniel M; Chao, Tzu-Chiao; Cameron, Andrew D S.

Nucleic Acids Res ; 48(18): 10184-10198, 2020 10 09.

Article in English | MEDLINE | ID: mdl-32894292

2.

Cra and cAMP Receptor Protein Have Opposing Roles in the Regulation of fruB in Vibrio cholerae.

Beck, Christina; Perry, Sayde; Stoebel, Daniel M; Liu, Jane M.

J Bacteriol ; 203(10)2021 04 21.

Article in English | MEDLINE | ID: mdl-33649152

3.

Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions.

Evans, Ciaran; Hardin, Johanna; Stoebel, Daniel M.

Brief Bioinform ; 19(5): 776-792, 2018 09 28.

Article in English | MEDLINE | ID: mdl-28334202

4.

Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness.

Wang, Yinhua; Diaz Arenas, Carolina; Stoebel, Daniel M; Flynn, Kenneth; Knapp, Ethan; Dillon, Marcus M; Wünsche, Andrea; Hatcher, Philip J; Moore, Francisco B-G; Cooper, Vaughn S; Cooper, Tim F.

Proc Natl Acad Sci U S A ; 113(18): 5047-52, 2016 May 03.

Article in English | MEDLINE | ID: mdl-27091964

5.

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria.

Bush, Eliot C; Clark, Anne E; DeRanek, Carissa A; Eng, Alexander; Forman, Juliet; Heath, Kevin; Lee, Alexander B; Stoebel, Daniel M; Wang, Zunyan; Wilber, Matthew; Wu, Helen.

BMC Bioinformatics ; 19(1): 32, 2018 02 05.

Article in English | MEDLINE | ID: mdl-29402213

6.

Waste and yet want not.

Stoebel, Daniel M; Dykhuizen, Daniel E.

Mol Cell ; 38(5): 625-6, 2010 Jun 11.

Article in English | MEDLINE | ID: mdl-20541995

7.

Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12.

Wong, Garrett T; Bonocora, Richard P; Schep, Alicia N; Beeler, Suzannah M; Lee Fong, Anna J; Shull, Lauren M; Batachari, Lakshmi E; Dillon, Moira; Evans, Ciaran; Becker, Carla J; Bush, Eliot C; Hardin, Johanna; Wade, Joseph T; Stoebel, Daniel M.

J Bacteriol ; 199(7)2017 04 01.

Article in English | MEDLINE | ID: mdl-28115545

8.

Erratum for Beck et al., "Cra and cAMP Receptor Protein Have Opposing Roles in the Regulation of fruB in Vibrio cholerae".

Beck, Christina; Perry, Sayde; Stoebel, Daniel M; Liu, Jane M.

J Bacteriol ; 203(18): e0024121, 2021 Aug 20.

Article in English | MEDLINE | ID: mdl-34415193

9.

Genetic background affects epistatic interactions between two beneficial mutations.

Wang, Yinhua; Arenas, Carolina Díaz; Stoebel, Daniel M; Cooper, Tim F.

Biol Lett ; 9(1): 20120328, 2013 Feb 23.

Article in English | MEDLINE | ID: mdl-22896270

10.

The timing of transcription of RpoS-dependent genes varies across multiple stresses in Escherichia coli K-12.

Adams, Josephine; Hoang, Johnson; Petroni, Emily; Ashby, Ethan; Hardin, Johanna; Stoebel, Daniel M.

mSystems ; 8(5): e0066323, 2023 Oct 26.

Article in English | MEDLINE | ID: mdl-37623321

11.

DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica.

Cameron, Andrew D S; Stoebel, Daniel M; Dorman, Charles J.

Mol Microbiol ; 80(1): 85-101, 2011 Apr.

Article in English | MEDLINE | ID: mdl-21276095

12.

Compensatory evolution of gene regulation in response to stress by Escherichia coli lacking RpoS.

Stoebel, Daniel M; Hokamp, Karsten; Last, Michael S; Dorman, Charles J.

PLoS Genet ; 5(10): e1000671, 2009 Oct.

Article in English | MEDLINE | ID: mdl-19798444

13.

The effect of mobile element IS10 on experimental regulatory evolution in Escherichia coli.

Stoebel, Daniel M; Dorman, Charles J.

Mol Biol Evol ; 27(9): 2105-12, 2010 Sep.

Article in English | MEDLINE | ID: mdl-20400481

14.

The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products.

Stoebel, Daniel M; Dean, Antony M; Dykhuizen, Daniel E.

Genetics ; 178(3): 1653-60, 2008 Mar.

Article in English | MEDLINE | ID: mdl-18245823

15.

Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory.

Wünsche, Andrea; Dinh, Duy M; Satterwhite, Rebecca S; Arenas, Carolina Diaz; Stoebel, Daniel M; Cooper, Tim F.

Nat Ecol Evol ; 1(4): 61, 2017 Mar 01.

Article in English | MEDLINE | ID: mdl-28812657

16.

SIZE DOESN'T MATTER: MICROBIAL SELECTION EXPERIMENTS ADDRESS ECOLOGICAL PHENOMENA.

Feldgarden, Michael; Stoebel, Daniel M; Brisson, Dustin; Dykhuizen, Daniel E.

Ecology ; 84(7): 1679-1687, 2003 Jul.

Article in English | MEDLINE | ID: mdl-21423836

17.

Escherichia coli lacking RpoS are rare in natural populations of non-pathogens.

Snyder, Emily; Gordon, David M; Stoebel, Daniel M.

G3 (Bethesda) ; 2(11): 1341-4, 2012 Nov.

Article in English | MEDLINE | ID: mdl-23173085

18.

Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria.

Stoebel, Daniel M; Free, Andrew; Dorman, Charles J.

Microbiology (Reading) ; 154(Pt 9): 2533-2545, 2008 Sep.

Article in English | MEDLINE | ID: mdl-18757787

19.

Lack of evidence for horizontal transfer of the lac operon into Escherichia coli.

Stoebel, Daniel M.

Mol Biol Evol ; 22(3): 683-90, 2005 Mar.

Article in English | MEDLINE | ID: mdl-15563718

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