Publications
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2019. Pseudogene repair driven by selection pressure applied in experimental evolution.. Nat Microbiol.
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2018. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes.. Metab Eng.
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2018. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.. Metab Eng.
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2018. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.. PLoS One. 13(5):e0197272.
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2018. Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.. Nat Commun. 9(1):3796.
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2018. Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiology Resource Announcements. 7
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2018. Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance.. Sci Rep. 8(1):2215.
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2018. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Frontiers in Microbiology.
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2018. Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Frontiers in Microbiology.
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2018. Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions.. Appl Environ Microbiol.
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2016. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. bioRxiv.
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2016. Multi-omic data integration enables discovery of hidden biological regularities.. Nat Commun. 7:13091.
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2015. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.. Nat Commun. 6:7970.
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2015. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.. Cell Rep.
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2015. A streamlined ribosome profiling protocol for the characterization of microorganisms.. Biotechniques. 58(6):329-32.
