Rice
FIS

FIS image header
  •  
  •  
  •  
  •  
  •  
Download 
Scholarly Interest Report
         
Yousif Shamoo
Professor
Professor of Biochemistry and Cell Biology
 
e-mail:shamoo@rice.edu
 
  • B.S. Biology (1983) Carnegie-Mellon University
  • Ph.D. Molecular Biophysics and Biochemistry (1988) Yale University
 
Primary Department
   Department of BioSciences
Picture
 
Department Affiliations
 
  • Institute of Biosciences and Bioengineering
  • Keck Center for Quantitative Biomedical Sciences
  • Ken Kennedy Institute for Information Technology
  •  
    Websites
     Shamoo Lab
     
    Research Areas
     Structural biology, molecular evolution, X-ray crystallography, microbial evolution, antibiotic resistance
     

    Research Statement 2015

     

    Our interest in molecular evolution is stimulated by the rise in drug resistant pathogens and how understanding the physical basis for adaptation can be used for prediction of resistance and the identification of new targets and strategies for antimicrobial therapies. By combining approaches from biophysics and experimental evolution we are able to identify and characterize intermediates along the mutational pathways of adaptation and then link those intermediates to the overall evolutionary trajectory of the bacterial populations. Adaptive changes in protein sequence and expression impact organismal fitness and, consequently, dictate population dynamics. By combining experimental evolution with molecular biophysics we take a systems level view of adaptation and link it to the molecular mechanism responsible for the resulting evolutionary dynamics.


     
    Selected Publications
     Abstracts
     

    Davlieva M., Doneske J., Michnicka M., Nikonowicz E. and Shamoo Y. "Structural studies of an RNA aptamer with high affinity for the B. anthracis ribosomal protein S8."  (2010)

     
     

    Miller C. and Shamoo Y. "Experimental Evolution of Daptomycin Resistance in Enterococcus Faecalis."  (2010)

     
     

    Pea M., Davlieva M., Bennett M.R., Olson J.S. and Shamoo Y. "Protein folding dynamics and function determine evolutionary fates in a microbial population."  (2010)

     
     

    Walkiewicz K., Lau K. and Shamoo Y. "Biophysical basis for TetX mediated antibiotic resistance."  (2010)

     
     Refereed articles
     

    Beabout, K.R., Saxer, G., Hammerstom, T., and Shamoo, Y. "Evolutionary dynamics of a transposon mediated adaptation to tigecycline by vancomycin-resistant Enterococci." In Progress

     
     

    Davlieva, M., Johnson, T., Leonard, P., Ladbury, J., Arias, C.A and Shamoo, Y. "LiaR oligomerization mediates daptomycin resistance in multidrug-resistant Enterococcus faecalis." In Progress

     
     

    Beabout K, Hammerstrom TG, Perez A, Magalhães B, Prater A, Clements T, Arias C, Saxer G, Shamoo Y. The ribosomal S10 protein is a general target for decreased tigecycline susceptibility. Antimicrob Agents Chemother. 2015.  59(9):5561-5566 PMCID: PMC4538488 

     
     

    Beabout K, Hammerstrom TG, Wang TT, Bhatty M, Christie PJ, Saxer G, Shamoo Y. Rampant parasexuality evolves in a hospital pathogen during antibiotic selection. Molecular biology and evolution. 2015 32(10):2585-97  PMCID: PMC4683365 

     
     
    Davlieva M, Shi Y, Leonard PG, Johnson TA, Zianni MR, Arias CA, Ladbury JE, Shamoo, Y. A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin. Nucleic acids research. 2015; 43(9):4758-73. PMCID: PMC4482077 
     
     

    Hammerstrom TG, Beabout K, Clements TP, Saxer G, Shamoo Y. Acinetobacter baumannii repeatedly evolves a hypermutator phenotype in response to tigecycline that effectively surveys evolutionary trajectories to resistance. PLoS One 2015. 10(10):e0140489. PMCID: PMC4619398  

     
     

    Panesso D, Reyes J, Gaston EP, Deal M, Londoño A, Nigo M, Munita JM, Miller WR, Shamoo Y, Tran TT, Arias CA. Deletion of liaR reverses eaptomycin resistance in Enterococcus faecium independent of the genetic background. Antimicrob Agents Chemother. 2015. 59(12):7327-34. PMCID: PMC4649183 [Available on 2016-06-01]

     
     

    Reyes J, Panesso D, Tran TT, Mishra NN, Cruz MR, Munita JM, Singh KV, Yeaman MR, Murray BE, Shamoo Y, Garsin D, Bayer AS, Arias CA.  A liaR deletion restores susceptibility to daptomycin and antimicrobial peptides in multidrug-resistant Enterococcus faecalis. The Journal of infectious diseases. 2015; 211(8):1317-25. PMCID: PMC4402337

     
     

    Davlieva M, Donarski J, Wang J, Shamoo Y, Nikonowicz EP. "Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis." Nucleic Acids Res., 42(16) (2014) : 10795-808.


    doi: 10.1093/nar/gku743
     
     

    Diaz L, Tran TT, Munita JM, Miller WR, Rincon S, Carvajal LP, Wollam A, Reyes J, Panesso D, Rojas NL, Shamoo Y, Murray BE, Weinstock GM, Arias CA " Whole-genome analyses of Enterococcus faecium isolates with diverse daptomycin MICs." Antimicrob Agents Chemother., 58(8 (2014) : 4527-34.


    doi: 10.1128/AAC.02686-14
     
     

    Miller C, Kong J, Tran TT, Arias CA, Saxer G, Shamoo Y. "Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance." Antimicrob Agents Chemother, 57(11) (2013) : 5373-83 .


    doi: 10.1128/AAC.01473-13
     
     

    Nicolaou KC, Hale CR, Nilewski C, Ioannidou HA, ElMarrouni A, Nilewski LG, Beabout K, Wang TT, Shamoo Y. "Total synthesis of viridicatumtoxin B and analogues thereof: strategy evolution, structural revision, and biological evaluation ."  J Am Chem Soc., 136(34) (2014) : 12137-60.


    doi: 10.1021/ja506472u
     
     

    Saxer G, Krepps MD, Merkley ED, Ansong C, Deatherage Kaiser BL, Valovska MT, Ristic N, Yeh PT, Prakash VP, Leiser OP, Nakhleh L, Gibbons HS, Kreuzer HW, Shamoo Y. "Mutations in global regulators lead to metabolic selection during adaptation to complex environments.." PLoS Genet., 10(12) (2014) : :e1004872.


    doi: 10.1371/journal.pgen.1004872
     
     

    Agrawal A, Chipara AC, Shamoo Y, Patra PK, Carey BJ, Ajayan PM, Chapman WG, Verduzco R. "Dynamic self-stiffening in liquid crystal elastomers." Nat Commun, 4 (2013) : 1739.

     
     

    Davlieva M, Zhang W, Arias CA, Shamoo Y. "Biochemical characterization of cardiolipin synthase mutations associated with daptomycin resistance in enterococci." Antimicrob Agents Chemother, 57(1) (2013) : 289-96.

     
     

    Tran TT, Panesso D, Gao H, Roh JH, Munita JM, Reyes J, Diaz L, Lobos EA, Shamoo Y, Mishra NN, Bayer AS, Murray BE, Weinstock GM, Arias CA. "Whole-Genome Analysis of a Daptomycin-Susceptible Enterococcus faecium Strain and Its Daptomycin-Resistant Variant Arising during Therapy." Antimicrob Agents Chemother, 57(1) (2013) : 261-8.

     
     

    Tran TT, Panesso D, Mishra NN, Mileykovskaya E, Guan Z, Munita JM, Reyes J, Diaz L, Weinstock GM, Murray BE, Shamoo Y, Dowhan W, Bayer AS, Arias CA. "Daptomycin-resistant Enterococcus faecalis diverts the antibiotic molecule from the division septum and remodels cell membrane phospholipids." MBio, 4(4) (2013) : e00281-13.

     
     

    Mishra NN, Bayer AS, Tran TT, Shamoo Y, Mileykovskaya E, Dowhan W, Guan Z, Arias CA. "Daptomycin resistance in enterococci is associated with distinct alterations of cell membrane phospholipid content." PLoS One, 7(8) (2012) : e43958.

     
     

    Walkiewicz K, Benitez Cardenas AS, Sun C, Bacorn C, Saxer G, Shamoo Y. "Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance." Proc Natl Acad Sci U S A., 109(52) ( 2012 Dec 26) : 21408-13.

     
     

    Arias, C.A., McGrath, D., Qin, X.,Mojica M.F., Miller C., Diaz S. L., Tran, T.T., Rincon, S., Barbu, E.M., Reyes, J.C., Panesso, D., Lobos, E., Sodergren, E., Pasqualini, R., Arap, W., Quinn, J.P., Shamoo, Y., Murray, B.E., and Weinstock, G. "Whole-Genome and Cell Envelope Analysis of Daptomycin- Susceptible Enterococcus faecalis and Its Resistant Derivative that Arose During Therapy." New Engl. J. Med., 362 (2011) : 892-900. PMID 21899450.

     
     

    Walkiewicz, K., Davlieva, M., Wu, G. and Shamoo, Y. "Crystal structure of Bacteroides thetaiotaomicron TetX2, a tetracycline degrading monooxygenase at 2.8 resolution." Proteins: Struc. Func. Bioinform, 79: 2335-2340. PMID 21590745.

     
     

    Davilieva, M. and Shamoo, Y. "Crystal structure of a trimeric archaeal adenylate kinase from the mesophile Methanococcus maripaludis with an unusually broad functional range and thermal stability." Proteins, 78 (2010) : 357-364.

     
     

    Miller, C., Davilieva, M., Wilson, C., White, K., Counago, R., Wu, G., Myers, J.C., Wittung-Stafshede, P., and Shamoo, Y. "Experimental evolution of adenylate kinase reveals contrasting strategies towards protein thermostability." Biophys. J, 99 (2010) : 887-896 PMID: 20682267.

     
     

    Peña, M., Davlieva, M. Bennett, M.R., Olson, J.S. and Shamoo, Y. "Evolutionary fates within a microbial population highlight an essential role for reversible and irreversible protein folding during natural selection." Molecular Systems Biology 6:387 (2010). PMID 20631681

     
     

    Peña, M., Van Italie, E., Bennett, M.R., and Shamoo, Y. "Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness." CHAOS 20:026107 (2010). PMID:20590336

     
     

    Davlieva, M. and Shamoo, Y. "Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinus ." Acta Cryst F Struc Biol Cryst Commun, 65 (2009) : 751-756.

     
     

    Guelker, M., Stagg, L., Wittung-Stafshede, P., and Shamoo, Y. "Pseudo symmetry, high copy number and twinning complicate the structure determination of flavodoxin from Desulfovibrio desulfuricans (ATCC 29577)." Acta Cryst D Biol Crystallogr, D65 (2009) : 513-522.

     
     

    Couñago, R., Wilson, C.J., Peña, M.I., Wittung-Stafshede, P., and Shamoo, Y. "An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability-activity trade-offs." Prot. Eng. Des. Sel., 21 (2008) : 19-27.

     
     

    Woodward, A.W., Ratzel, S.E., Woodward, E.E., Shamoo, Y., and Bartel, B. "Mutation of E1-CONJUGATING ENZYME-RELATED1 decreases RELATED TO UBIQUITIN conjugation and alters auxin response and development." Plant Physiology, 144 (2007) : 976-987.

     
     

    Brock, D.A., van Egmond, W.N., Shamoo. Y., Hatton, R.D., and Gomer, R.H. "A 60-kilodalton protein component of the counting factor regulates group size in Dictyostelium discoideum." Eularyotic Cell, 5 (2006) : 1532-1538.

     
     

    Counago, R., Chen, S. and Shamoo, Y. "In vivo evolution reveals biophysical origins of organismal fitness." Molecular Cell, 22 (2006) : 441-446.

     
     

    Maximciuc, A., Putkey, J.A., Shamoo, Y., and Mackenzie, K.R. "Complex of calmodulin with a ryanodine receptor target reveals a novel, flexible binding mode." Structure, 14 (2006) : 1547-1556.

     
     

    Morozova, N., Aller, J.A., Myers, J., and Shamoo, Y. "Protein-RNA interactions: Exploring binding patterns with a three-dimensional superposition analysis of high resolution structures." Bioinformatics, 22 (2006) : 2746-2752.

     
     

    Sun, S., Geng, L., and Shamoo, Y. "Fusion of bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein leads to increased processivity." Prot. Struc. Func. and Bioinform., 65 (2006) : 231-238.

     
     

    Bruning, J.B., and Shamoo, Y. "Structural and thermodynamic analysis of human PCNA bound to peptides derived from DNA polymerase-delta p66-subunit and flap endonuclease-1 (FEN1) proteins." Structure (2004) In Press

     
     

    Counago, R., and Shamoo, Y. "Gene replacement of adenylate kinase in the gram-positive thermophile Geobacillus stearothermophilus disrupts adenine nucleotide homeostasis and reduces cell viability." Extremophiles, 9 (2005) : 135-144.

     
     

    Myers, J., and Shamoo, Y. "Human UP1 as a model for understanding purine recognition in the family of proteins containing the RNA Recognition Motif (RRM)." J. Mol. Biol., 342 (2004) : 743-756.

     
     

    Myers, J.G., Moore, S.A., and Shamoo, Y. "Structure-based incorporation of 6-MI into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures." J. Biol. Chem., 278 (2003) : 42300-42306.

     
     

    Shamoo, Y. "Structural insights into BRCA2 function." Curr. Op. Struc. Biol., 13 (2003) : 206-211.

     
     

    Sun, S., and Shamoo, Y. "Biochemical characterization of interactions between DNA polymerase and single-stranded DNA binding protein in bacteriophage RB69." J. Biol. Chem., 278 (2003) : 3876-3881.

     
     

    Allers, J., and Shamoo, Y. "Structure-based analysis of protein-RNA interactions using the program ENTANGLE." J. Mol. Biol., 311 (2001) : 76-86.

     
     

    Shamoo, Y., and Steitz, T.A. "Building a Replisome Structure from Interacting Pieces: Structures of a Sliding Clamp Complexed with an Interaction Peptide from DNA Polymerase, and a DNA Polymerase Editing Complex." Cell, 99 (1999) : 155-169.

     
     

    Rice, L.M., Shamoo, Y., and Brunger, A.T "Phase Improvement by Multi-start Simulated Annealing Refinement and Structure Factor Averaging." J. Appl. Cryst., 31 (1998) : 798-805.

     
     Book chapters
     

    Shamoo, Y. "Single-stranded DNA Binding Proteins." in Encyclopedia of Life Sciences (2000)

     
    Presentations
     Invited Talks
     

    "Defense Threat Reduction Agency Scientific and Basic Sciences Meeting." Washington D.C. (August 29, 2012)

     
     

    "Experimental evolution of a model organism and a clinical pathogen: What can they tell us about predicting drug resistance?." U. Maryland School of Medicine , Baltimore, MD. ( Dec12)

     
     

    "Experimental evolution of a model organism and a clinical pathogen: What can they tell us about predicting drug resistance?." Rocky Mountain ASM Regional Meeting Keynote Speaker, (April 21, 2012)

     
     

    "Quantitative Evolutionary Dynamics: Experimental evolution of a clinical pathogen." United States Military Academy, West Point, NY. (November 19, 2012)

     
     

    "Use of adaptive genetic networks as predictors for bacterial domestication.." Defense Threat Reduction Agency Biomarkers Meeting, Washington D.C.. (March 8, 2012)

     
     

    "Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection." Protein Society National Meeting, Boston, MA. (August 24, 2011)

     
     

    "Evolutionary fates within a microbial population: The essential role for protein folding during natural selection." Gordon Research Conference - Microbial Populations 2011, (August 23, 2011)

     
     

    "Experimental adaptation and biophysics: building the links between molecules and fitness." Gordon Research Conference on Microbial Populations, Proctor Academy, Andover, NH. (July 17, 2011)

     
     

    "Experimental evolution of a model organism and a clinical pathogen: What can they tell us about predicting drug resistance?." Department of Biochemistry, Baylor College of Medicine, Houston, TX. (December 12, 2011)

     
     

    "Nothing in evolution makes sense except in the light of biophysics." Steitz Symposium, Dept of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT. (June 25, 2011)

     
     

    "Signatures of Laboratory Grown Bio Agents." 2011 DTRA Basic Research Technical Review Meeting, Defense Threat Reduction Agency, Springfield, VA. (July 26, 2011)

     
     

    "Adaptation and atoms: Can we determine a molecular basis for fitness?." U. North Carolina, (02/02/2010)

     
     

    "Evolutionary fates within a microbial population: The essential role for protein folding during natural selection." Georgia Institute of Technology, (10/22/2010)

     
     

    "Molecular evolution within bacterial populations: Can we from fitness to molecules?  ." UT Health Sciences Center Houston, (12/10/2010)

     
     

    "Adaptation and Atoms: Biophysical Origins of Molecular Evolution." Sealy Structural Biology Symposium, University of Texas Medical Branch, Galveston, TX. (May 16-17, 2008)

     
     

    "Adaptation and Atoms: Biophysical Origins of Molecular Evolution." CARB, University of Maryland. (November 17, 2008)

     
     

    Speaker.  "Experimental evolution within a microbial population highlights strategies towards protein adaptation.." Workshops Current Trends in Biomedicine, Baeza, Spain. (October 22, 2007) With R. Counago

     
     

    "Molecular evolution within bacterial populations reveals biophysical origins for fitness." 15th Annual Texas Protein Folders Meeting, Navasota, Texas. (March 31, 2007) With R. Couñago, C. Wilson, P. Wittung-Stafshede

     
     

    "Thinking small: Evolution in a world the size of a coffee pot." Alabama Lectures on Life's Evolution (Allele), (February 22, 2007) With R. Couñago

     
     

    "Using structural superposition for the analysis of protein-RNA interactions." American Chemical Society, Boston. (August 21, 2007) With N. Morozova, J. Myers and J. Allers

     
     

    "Going Beyond the Human Genome Project." Society of Rice University Women, Houston, Texas. (2002)

     
     Keynote Speaker
     

    "Evolution writ small: Molecular evolution within bacterial populations reveals biophysical origins for fitness." Baylor College of Medicine Retreat: Program in Cell and Molecular Biology, With R. Counago, M. Pena, C. Wilson, P. Wittung-Stafshede

     
     Other
     

    "Structural Biology in the 21st Century: Going Beyond the Human Genome Project." Rice University Alumni College, Houston, Texas. (2001)

     
     Posters
     

    "Structural Studies of RB69 DNA Polymerase Bound to an Autoregulatory RNA Element." American Crystallographic Association Meeting, San Antonio, Texas. (2002) With Sun, S.

     
     

    "Structural Studies of the Yeast La Protein Pre-tRNA Complex." American Crystallographic Association Meeting, San Antonio, Texas. (2002) With Bruning, J.

     
     

    "Understanding the Rules of Protein:RNA Interactions." American Crystallographic Association Meeting, San Antonio, Texas. (2002) With Myers, J.

     
     Seminar Speaker
     

    "Evolution writ small: Molecular evolution within bacterial populations reveals biophysical origins for fitness." Department of Human & Molecular Genetics, Baylor College of Medicine, Houston, Texas. (March 15, 2007)

     
     

    "Evolution writ small: Molecular evolution within bacterial populations reveals biophysical origins for fitness." Department of Chemistry, Univeresity of Alabama. (February 22, 2007)

     
     Workshops
     

    "Army Research Office Workshop on Microbial Adaptation." (9/29/08-10/1/08)

     
    Editorial Positions
     Associate Editor, Protein, Structure, Function and Bioinformatics. Wiley. (2008 - 2016)

     Associate Editor, Proteins: Structure, Function and Bioinformatics. Wiley. (2011 - 2011)

     Associate Editor, Proteins: Structure, Function and Bioinformatics. Wiley. (2010 - 2010)

     Associate Editor, Protein Structure, Function and Bioinformatics. (2008 - 2008)

    Supervised Theses & Dissertations
     Lucian Smith, Ph.D. The Effects of Amino Acid Substitution on Apomyoglobin Stability, Folding Intermediates, and Holoprotein Expression. (2002) (Thesis Committee Member)

     Jie Xiao, Ph.D. Structural Characterization and Kinetic Evaluation of RecA-Mediated Strand Exchange. (2002) (Thesis Committee Member)

     Wei Zhang, Ph.D. X-ray Structural Determination and Biophysical Characterization of HemAT, a Chemotaxis Receptor from B. subtilis. (2003) (Thesis Committee Member)

     Rachel Leininger Schweers, Ph.D. Electrostatic Regulation of O2 and CO Binding in the alpha and beta Subunits of Recombinant Human Hemoglobin. (2003) (Thesis Committee Member)

     John Bruning, Ph.D. Structural and Thermodynamic Analysis of Human PCNA Bound to Peptides Derived from DNA Polymerase-delta p66-Subunit and Flap Endonuclease-1 (FEN1) Proteins. (2004) (Thesis Director)

     Rebekah A. Rampey, Ph.D. Genetic Analysis of IAA-Conjugate Sensitivity in Arabidopsis thaliana: Hydrolysis, Transcriptional Regulation, and Metal Homeostasis. (2004) (Thesis Committee Member)

     Jeffrey C. Myers, Ph.D. Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM). (2004) (Thesis Director)

     Siyang Sun, Ph.D. Biochemical and Crystallographic Studies of Bacteriophage RB69 DNA Polymerase and Single-stranded DNA Binding Protein Interactions. (2005) (Thesis Director)

     Jamie Catanese, Ph.D. Biophysical and Biochemical Characterization of the Disconnected Interacting Protein 1, DIP1, from Drosophila melanogaster. (2005) (Thesis Committee Member)

     Renee LeClair, Ph.D. Elucidating the Mechanism of Triterpene Cyclization Using DNA Synthesis and Phylogenetic Approaches. (2005) (Thesis Committee Member)

     Rafael Counago, Ph.D. Single Gene Evolution: A Punctuated History of Chance. (2005) (Thesis Director)

     Corey Wilson, Ph.D. Experimental and Theoretical Approaches to Protein Folding, Stability, and Assembly: A Thorough Assessment of Complex Behavior. (2005) (Thesis Committee Member)

     Hongli Zhan, Ph.D. Biophysical Characterization of the Allosteric Transition in Lactose Repressor Protein (LacI). (2005) (Thesis Committee Member)

     Kathryn Luke, Ph.D. Exploring the Envelope of Life: Folding and Assembly Reactions of the Hyper-Thermostable Co-Chaperonin Protein 10 from Aquifex aeolicus. (2007) (Thesis Committee Member)

     Angela Noel Hvitved, p NO Dioxygenation in Mammalian Hemoglobins and Microbial Flavohemoglobins. (2007) (Thesis Committee Member)

     Liping Dong, M.A. Functional and Structural Studies of the Influenza A Virus Polymerase Subunit PB1 and its Subcomplex with the Subunit PA. (2007) (Thesis Committee Member)

     Endah Sulistijo, Ph.D. Specificity of Membrane Helix-Helix Interactions by Mutagenesis and Structural Analysis. (2007) (Thesis Committee Member)

     Megan Guelker, Ph.D. Overcoming the Challenges of Twinning and Pseudo Symmetry in Solving the Structure of Flavodoxin from Desulfovibrio desulfuricans 29577 by X-ray Crystallography. (2008) (Thesis Director)

     Ian Dews, Ph.D. The Four Syndecans: A Fugue in GxxxG Minor. (2008) (Thesis Committee Member)

     Augustina Rodriguez Granillo, PhD Copper as a Biological Yin-Yang Element: Structural Dynamics, Protein-Protein Interactions and Transfer Mechanisms of Copper Transport Proteins. (2009) (Thesis Committee Member)

     Pietro Morlacchi, PhD Triterpene biosynthesis in plants: Oxidosqualene cyclization in Arabidopsis. (2009) (Thesis Committee Member)

     Y. Nissanka Wickremasinghe, PhD Probing biophysical interactions at the nanoscale. (2009) (Thesis Committee Member)

     Andres Salvador Benitez Cardenas, Ph.D. The Biophysical Basis for Adaptation: Predicting Evolutionary Outcomes from Physicochemical Properties. (2012) (Thesis Director)

     Katarzyna Walkiewicz, Ph.D. Experimental evolution of TetX2: correlating changes in fitness to their structural and functional origins. (2012) (Thesis Director)

     Corwin Miller, Ph.D. Evolutionary Trajectories to Daptomycin Resistance in Enterococcus faecalis. (2013) (Thesis Director)

     Kathryn R Beaubout, PhD Evolutionary dynamics leading to tigecycline resistance in a hospital strain of Enterococcus faecalis. (Thesis Director)

     Xu Wang, PhD Structure-function studies of E. faecalis YybT and GshF associated with daptomycin resistance. (Thesis Director)

     Lu Han, PhD Method development for natural products structure determination. (Thesis Committee Member)

     Yasmin Chebaro, PhD Sulfur metabolism of Candida albicans: Adaptation to sulfite and biofilm formation. (Thesis Committee Member)

     Juan Diaz, PhD Analyses of independent evolution on alleles that confer resistance to anticoagulants in US population rodents. (Thesis Committee Member)

    Awards, Prizes, & Fellowships
     George R. Brown Prize for Excellence in Teaching , Rice University

     Brown Superior Teaching Award, Rice University (2013)

     George R. Brown Superior Teaching Award,

     Wiess Career Development Chair, (2008-present)

     Distinguished Faculty Associate, Brown College, Brown College (2002)

     Member, The RNA Society,

     Member, American Chemical Society,

     Member, American Association for the Advancement of Science,

     Member, American Crystallographic Association,

     Member, American Crystallographic Association

     Member, American Association for the Advancement of Science

     Member, The RNA Society

     Member, The RNA Society

     Member, American Crystallographic Association

    Positions Held
     Member, Gulf Coast Consortia (GCC). (2001 - 2015)

     Member, Computer and Information Technology Institute (CITI-Rice) . (2005 - 2015)