Tran TT, Miller WR, Shamoo Y, Arias CA. Targeting cell membrane adaptation as a novel antimicrobial strategy. Curr Opin Microbiol. 2016 July 23.

Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Christopher Fromme J, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nat Commun. 2016 Mar 7.



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 Daptomycin Resistance in Enterococcus faecium Independent of the Genetic Background. Antimicrob Agents Chemother. 2015 Sep 14.

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 Oct 10.

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 Jun 29.

Beabout K, Hammerstrom TG, Wang TT, Bhatty M, Christie PJ, Saxer G, Shamoo Y. Rampant parasexuality evolves in a hospital pathogen during antibiotic selection. Mol Biol Evol. 2015 Jun 9.

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 Res. 2015 April 19.


Saxer G, Krepps MD, Merkley ED, Ansong C, Deatherage Kasier BL, Valovska M-T, Ristic N, Yeh PT, Prakash VP, Leiser OP, Nahleh L, Gibbons HS, Kreuzr HW, Shamoo Y. Mutations in global regulators lead to metabolic selection during adaptation to complex environments. PLoS Genetics. 2014 June 24;10(12)

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. J Infect Dis. 2014 Oct 31.

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. 2014 Aug;58(8):4527-34. doi: 10.1128/AAC.02686-14.

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. 2014;42(16):10795-808. doi: 10.1093/nar/gku743.

Nicolaou, K.C., Hale, C.R.H., Nilewski, C., Ioannidou, H.A., ElMarrouni, A., Nilewski, L.G., Beabout, K., Wang, T.T., and Shamoo, Y. Total synthesis of viridicatumtoxin B and analogues thereof: strategy evolution, structural revision, and biological evaluation. J Am Chem Soc. 2014 Aug 27;136(34):12137-60. doi: 10.1021/ja506472u.


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. 2013 Jul 23;4(4). pii: e00281-13. doi: 10.1128/mBio.00281-13.

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. 2014 Jan;58(1):631.

Davlieva M, Zhang W, Arias CA, Shamoo Y. Biochemical characterization of cardiolipin synthase mutations associated with daptomycin resistance in enterococci. Antimicrob Agents Chemother. 2013 Jan;57(1):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. 2013 Jan;57(1):261-8. doi: 10.1128/AAC.01454-12.


Walkiewicz, K., Cardenas, A. S. B., 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. 2012 Dec 26;109(52):21408-13.

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. 2012;7(8):e43958. doi: 10.1371/journal.pone.0043958.

Davlieva M, Zhang W, Arias CA, Shamoo Y. Biochemical Characterization of Cardiolipin Synthase Mutations Associated with Daptomycin Resistance in Enterococci. Antimicrob Agents Chemother. 2013 Jan;57(1):289-96. doi: 10.1128/AAC.01743-12.


Arias CA, Panesso D, McGrath DM, Qin X, Mojica MF, Miller C, Diaz L, Tran TT, Rincon S, Barbu EM, Reyes J, Roh JH, Lobos E, Sodergren E, Pasqualini R, Arap W, Quinn JP, Shamoo Y, Murray BE, Weinstock GM. Genetic basis for in vivo daptomycin resistance in enterococci. N Engl J Med. 2011 Sep 8;365(10):892-900. PMID: 21899450

Walkiewicz K, Davlieva M, Wu G, Shamoo Y. Crystal structure of Bacteroides thetaiotaomicron TetX2: a tetracycline degrading monooxygenase at 2.8 Å resolution. Proteins. 2011 Jul;79(7):2335-40. doi: 10.1002/prot.23052. Epub 2011 May 16. PMID: 21590745


Miller C, Davlieva M, Wilson C, White KI, Couñago R, Wu G, Myers JC, Wittung-Stafshede P, Shamoo Y. Experimental evolution of adenylate kinase reveals contrasting strategies toward protein thermostability. Biophys J. 2010 Aug 4;99(3):887-96. PMID: 20682267

Peña MI, Davlieva M, Bennett MR, Olson JS, Shamoo Y. Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection. Mol Syst Biol. 2010 Jul 13;6:387. PMID: 20631681

Peña MI, Van Itallie E, Bennett MR, Shamoo Y. Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness. Chaos. 2010 Jun;20(2):026107. PMID: 20590336

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. FASEB J. 2010 Apr. 24;499.1

Walkiewicz K., Lau K. and Shamoo Y. Biophysical basis for TetX mediated antibiotic resistance. FASEB J.  2010 Apr. 24;909.2

Davlieva M, 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. 2010 Feb 1;78(2):357-64. PMID: 19731371


Davlieva M, Shamoo Y. Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Aug 1;65(Pt 8):751-6. Epub 2009 Jul 21. PMID: 19652331

Guelker M, Stagg L, Wittung-Stafshede P, Shamoo Y. Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin. Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):523-34. Epub 2009 May 15. PMID: 19465766


Couñago R, Wilson CJ, Peña MI, Wittung-Stafshede P, Shamoo Y. An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability-activity trade-offs. Protein Eng Des Sel. 2008 Jan;21(1):19-27. Epub 2007 Dec 19. PMID: 18093993


Woodward AW, Ratzel SE, Woodward EE, Shamoo Y, Bartel B. Mutation of E1-CONJUGATING ENZYME-RELATED1 decreases RELATED TO UBIQUITIN conjugation and alters auxin response and development. Plant Physiol. 2007 Jun;144(2):976-87. Epub 2007 Apr 20. PMID: 17449645


Morozova N, Allers J, Myers J, Shamoo Y. Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures. Bioinformatics. 2006 Nov 15;22(22):2746-52. Epub 2006 Sep 11. PMID: 16966360

Maximciuc AA, Putkey JA, Shamoo Y, Mackenzie KR.  Complex of calmodulin with a ryanodine receptor target reveals a novel, flexible binding mode. Structure. 2006 Oct;14(10):1547-56. PMID: 17027503

Sun S, Geng L, Shamoo Y. Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity. Proteins. 2006 Oct 1;65(1):231-8. PMID: 16881051

Brock DA, van Egmond WN, Shamoo Y, Hatton RD, Gomer RH. A 60-kilodalton protein component of the counting factor complex regulates group size in Dictyostelium discoideum. Eukaryot Cell. 2006 Sep;5(9):1532-8. PMID: 16963635

Couñago R, Chen S, Shamoo Y. In vivo molecular evolution reveals biophysical origins of organismal fitness. Mol Cell. 2006 May 19;22(4):441-9. PMID: 16713575


Couñago R, Shamoo Y. Gene replacement of adenylate kinase in the gram-positive thermophile Geobacillus stearothermophilus disrupts adenine nucleotide homeostasis and reduces cell viability. Extremophiles. 2005 Apr;9(2):135-44. Epub 2005 Jan 13. PMID: 15647886


Bruning JB, Shamoo Y. Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-delta p66 subunit and flap endonuclease-1.

Structure. 2004 Dec;12(12):2209-19. PMID: 15576034

Myers JC, 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. 2004 Sep 17;342(3):743-56. PMID: 15342234


Myers JC, Moore SA, Shamoo Y. Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures. J Biol Chem. 2003 Oct 24;278(43):42300-6. Epub 2003 Aug 6. PMID: 12904298

Shamoo Y. Structural insights into BRCA2 function. Curr Opin Struct Biol. 2003 Apr;13(2):206-11. Review. PMID: 12727514


Sun S, Shamoo Y. Biochemical characterization of interactions between DNA polymerase and single-stranded DNA-binding protein in bacteriophage RB69. J Biol Chem. 2003 Feb 7;278(6):3876-81. Epub 2002 Nov 27. PMID: 12458197


Allers J, Shamoo Y. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J Mol Biol. 2001 Aug 3;311(1):75-86. PMID: 11469858
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