About

Yousif Shamoo is the Ralph and Dorothy Looney Professor of BioSciences at Rice University and a member of the Ken Kennedy Institute. He received his doctorate in Molecular Biophysics and Biochemistry from Yale University in 1988 and earned his Bachelor of Science in Biology from Carnegie-Mellon University in 1983. Shamoo has served as Vice Provost for Research from 2014 to 2022, overseeing strategic planning for the university’s research enterprise and engagement with industry through research and technology transfer. He was appointed Professor of BioSciences in 2012 and previously served as Rice’s Director of the Institute of BioSciences and Bioengineering from 2008-2014, leading interdisciplinary research coordination among Rice faculty. His research lab studies the rise of multi-drug resistant bacteria, focusing on antibiotic resistance which threatens to undermine modern medicine. His work aims to elucidate the biophysical principles of adaptation within bacterial populations during protein evolution, employing experimental evolution and biophysical approaches such as X-ray crystallography, enzyme kinetics, protein folding, calorimetry, and genomics. His group seeks to link changes in protein structure and function to phenotypes within evolving populations, extending these principles to predict the success or failure of adaptive alleles. Shamoo’s research is supported by the NIH and the Department of Defense, and he serves on the NIH Genetic Variation and Evolution Study Section, as well as reviewing for NSF and DOD. He has received multiple awards, including the American Society for Microbiology Distinguished Lecturer award (2011-2013), the George R. Brown Award for Excellence in Teaching (2015), and the George R. Brown Award for Superior Teaching four times since 2009. In 2020, he was named the Ralph and Dorothy Looney Professor.

Research topics

• Biology
• Genetics
• Machine Learning
• Ecology
• Computer Science
• Microbiology
• Computational biology
• Biochemistry
• Cell biology
• Zoology
• Biological system

Selected publications

• Identification of Evolutionary Trajectories Associated with Antimicrobial Resistance Using Microfluidics

  ACS Infectious Diseases · 2021 · 15 citations

  Senior authorCorresponding
  • Computer Science
  • Machine Learning
  • Biology

  adaptation to doxycycline, we examined how changes in environmental conditions such as droplet size, starting lambda value, selection strength, and incubation method affected evolutionary outcomes. We also examined the extent to which emulsions could reveal potentially new evolutionary trajectories and dynamics associated with antimicrobial resistance. Interestingly, we identified both expected and unexpected evolutionary trajectories including large-scale chromosomal rearrangements and amplification that were not observed in suspension culture methods. As microdroplet emulsions are well-suited for automation and provide exceptional control of conditions, they can provide a high-throughput approach for biomarker identification as well as preclinical evaluation of lead compounds.

  DOI

• EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde

  PLoS Biology · 2021 · 33 citations

  • Biology
  • Cell biology
  • Biochemistry

  Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here, we identify a member of the DUF336 domain family, named efgA for enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response in M. extorquens PA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that rapidly arrests growth in response to elevated levels of formaldehyde. Heterologous expression of EfgA in Escherichia coli increases formaldehyde resistance, indicating that its interaction partners are widespread and conserved. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and safeguards cells from potential damage.

  DOI

• Pathogenic Nocardia: A diverse genus of emerging pathogens or just poorly recognized?

  PLoS Pathogens · 2020 · 103 citations

  Senior authorCorresponding
  • Microbiology
  • Biology
  • Zoology

  The clear and present danger posed by the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter species) and their ability to evade antimicrobials is generally well appreciated There are, however, a multitude of pathogens, some more rare than others, that can be clinically challenging to diagnose and treat. Nocardia, a genus of aerobic actinomycetes found ubiquitously in soil and water, harbors one such group of pathogens with unique attributes and often complicated properties.

  DOI

Recent grants

• Defining Evolutionary Trajectories: Molecular adaptation to antibiotic resistance

  NIH · $360k · 2013–2014

• NIH Grant R03HD039658

  NIH · $149k · 2004

• Defining Evolutionary Trajectories: Molecular adaptation to antibiotic resistance

  NIH · $4.3M · 2009–2025

Frequent coauthors

• César A. Arias

  Universidad El Bosque

  82 shared

• Truc T. Tran

  Methodist Hospital

  37 shared

• William R. Miller

  Methodist Hospital

  25 shared

• Diana Panesso

  Universidad El Bosque

  24 shared

• M.G. Davlieva

  Rice University

  21 shared

• Kenneth R. Williams

  W. M. Keck Foundation

  20 shared

• Lorena Díaz

  Millennium Initiative for Collaborative Research on Bacterial Resistance

  18 shared

• Ayesha Khan

  Vanderbilt University

  16 shared

Labs

• Shamoo LaboratoryPI

Education

• Ph.D., Molecular Biophysics and Biochemistry

  Yale University

  1988

• B.S.

  Carnegie Mellon University

  1983

Awards & honors

• American Society for Microbiology Distinguished Lecturer awa…
• George R. Brown Award for Excellence in Teaching (2015)
• George R. Brown Award for Superior Teaching (2009, plus thre…
• Ralph and Dorothy Looney Professor (2020)

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