Publications

* = equal contribution; ** = corresponding author(s); Bold Names = Dantas Lab Authors 

[51]
Draft Genome Sequence of the blaOXA-436- and blaNDM-1-Harboring Shewanella putrefaciens SA70 Isolate.
Potter RF*, D’Souza AW*, Wallace MA, Shupe A, Patel S, Gul D, Kwon JH, Andleeb S, Burnham CD**, Dantas G**.
Genome Announcements 2017; doi:10.1128/genomeA.00644-17 | [PDF]

[50]
Plasticity, dynamics, and inhibition of emerging tetracycline-resistance enzymes.
Park J*, Gasparrini AJ*, Reck M, Symister C, Elliott J, Vogel J,  Wencewicz T**, Dantas G**, Tolia N**.
Nature Chemical Biology 2017; doi: 10.1038/nchembio.2376 | [PDF] [supplementary material]

[49]
Next-generation approaches to understand and combat the antibiotic resistome.
Crofts T*, Gasparrini AJ*, and Dantas G**.
Nature Reviews Microbiology 2017; doi: 10.1038/nrmicro.2017.28 | [PDF]

[48]
Evaluation of Machine Learning and Rules-Based Approaches for Predicting Antimicrobial Resistance Profiles in Gram-negative Bacilli from Whole Genome Sequence Data.
Pesesky MW, Hussain TWallace MPatel S, Andleeb S, Burnham CD**, and Dantas G**.
Frontiers in Microbiology. 2016; 10.3389/fmicb.2016.01887 | [PDF]

[47]
Functional Metagenomics to Study Antibiotic Resistance.
Boolchandani M*, Patel S*, Dantas G**.
Chapter in “Antibiotics: Methods and Protocols”, Methods in Molecular Biology. Ed.
Peter Sass. New York: Springer, 2016: 1520:307-329. 10.1007/978-1-4939-6634-9_19 | [PDF]

[46]
Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes.
Adu-Oppong B*, Gasparrini AJ*, Dantas G**.
Annals of the New York Academy of Sciences. 2016; 10.1111/nyas.13257 | [PDF]

[45]
Contextual organismality: beyond pattern to process in the emergence of organisms.
Díaz-Muñoz SL**Boddy ADantas GWaters CM, Bronstein JL.
Evolution 2016; 10.1111/evo.13078 | [PDF]

[44]
The rapid spread of carbapenem-resistant Enterobacteriaceae.
Potter RF*, D'Souza AW*, Dantas G**.
Drug Resistance Updates 2016; 10.1016/j.drup.2016.09.002 | [PDF]

[43]
Antibiotic perturbation of the preterm infant gut microbiome and resistome.
Gasparrini AJ*, Crofts TS*, Gibson MK, Tarr PI, Warner BB, Dantas G**.
Gut Microbes 2016; 10.1080/19490976.2016.1218584 | [PDF]

[42]
Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410. 
Yoneda A, Wittmann BJ, King JD, Blankenship RE, Dantas G**.
Photosynthesis Research 2016; 10.1007/s11120-016-0279-1 | [PDF] [supplementary material 1] [supplementary material 2]

[41]
Interconnected microbiomes and resistomes in low-income human habitats.
Pehrsson EC*, Tsukayama P*, Patel S, Mejía-Bautista M, Sosa-Soto G, Navarrete KM, Calderon M, Cabrera L, Hoyos-Arango W, Teresita Bertoli M, Berg DE, Gilman RH, Dantas G**.
Nature. 2016; 10.1038/nature17672 | [PDF] [supplementary material 1] [ supplementary material 2]

[40]
The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation.
Langdon A*, Crook N*, Dantas G**.
Genome Medicine. 2016; 10.1186/s13073-016-0294-z | [PDF]

[39]
Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. 
Gibson MKWang B, Ahmadi S, Burnham CD, Tarr P, Warner B, Dantas G**.  
Nature Microbiology. 2016 |  [PDF] [supplementary material 1] [supplementary material 2] [supplementary material 3] [supplementary material 4]

[38]
Comparative transcriptomics elucidates adaptive phenol tolerance in lipid-accumulating Rhodococcus opacus PD630. 
Yoneda A*, Henson WR*, Goldner NK, Park KJ, Forsberg KJ, Kim SJ, Pesesky MW, Foston M, Dantas G**, Moon TS**.
Nucleic Acids Research. 2016; 10.1093/nar/gkw055| [PDF] [supplementary material 1] [supplementary material 2]

[37]
Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis.
Krueger A,* Munck C,* Dantas G, Church G, Galagan J, Lehár J,** Sommer MOA.**
PLOS ONE. 2016; 11(1): e0147651  | [PDF] 

[36]
Identification of genes conferring tolerance to lignocellulose-derived inhibitors by functional selections in soil metagenomes.
Forsberg KJ, Patel S, Witt E, Wang B, Ellison TD, Dantas G**.
Applied and Environmental Microbiology. 2015; 82(2):528-3 | [PDF] [supplementary material]

[35]
High-specificity targeted functional profiling in microbial communities with ShortBRED.
Kaminski J*, Gibson MK*, Franzosa EA, Segata N, Dantas G,** Huttenhower C.**
PLOS Computational Biology. 2015; 82(2):528-3 | [PDF] [supplementary material]

[34]
Synergistic, collaterally sensitive β-lactam combinations suppress resistance in MRSA
Gonzales PR, Pesesky MW, Bouley R, Ballard A, Biddy B, Suckow M, Wolter WR, Schroeder VA, Burnham CD, Mobashery S, Chang M, Dantas G.**
Nature Chemical Biology. 2015; 11(11):855-61 [PDF] [supplementary material]

[33]
Antibiotics and the developing infant gut microbiota and resistome
Gibson MK,* Crofts T,* Dantas G.**
Current Opinion in Microbiology. 2015; 27:51-  | [PDF] 

[32]
Gut resistome development in healthy twin pairs in the first year of life
Moore AAhmadi S, Patel S, Gibson MKWang B, Ndao M, Deych E, Shannon W, Tarr P, Warner B, Dantas G.**
Microbiome. 2015; 3:29 [PDF] [supplementary materials]

[31]
The Tetracycline Destructases: A Novel Family of Tetracycline-Inactivating Enzymes
Forsberg K, Patel S, Wencewicz T,** Dantas G.**
Chemistry & Biology. 2015; 22:1-10 | [PDF] [supplementary materials]

[30]
The microbiome of uncontacted Amerindians
Clemente J,* Pehrsson E,* Blaser M, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón O, Lander O, Donald J, Cox M, Water J, Oh P, Ruiz J, Rodriguez S, Shen N, Song S, Metcalf J, Knight R, Dantas G, Dominguez-Bello M.**
Science Advances. 2015; 1(3):e1500183 | [PDF] [supplementary materials]

[29]
Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics
Perron GG, Lyle Whyte, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, Desai M.**
PLOS ONE 2015; 10 (3): e0069533 | [PDF] [supplemental material]

[28]
KPC and NDM-1 Genes in Related Enterobacteriaceae Strains and Plasmids from Pakistan and the United States
Pesesky MW,* Hussain T,* Wallace M, Wang B, Andleeb S, Burnham CD, Dantas G.**
Emerging Infectious Diseases. 2015; 21 (6) [PDF] [supplementary materials]

[27]
Improved Annotation of Antibiotic Resistance Reveals Microbial Communities Cluster by Ecology
Gibson MKForsberg KJDantas G.**
The ISME Journal. 2015; 9:207 | [PDF[supplementary materials]

[26]
Longitudinal Analysis of Microbial Interaction Between Humans and the Indoor Environment
Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbson SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vazquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA.**
Science. 2014; 345(6200):1048 | [PDF] [supplementary materials] 

[25]
The Yin and Yang of Bacterial Resilience in the Human Gut Microbiota
Gibson MK*Pesesky MW*Dantas G.**
J Mol Biol. 2014; 426: 3866 | [PDF] 

[24]
Bacterial Phylogeny Structures Soil Resistomes Across Habitats
Forsberg KJ*Patel S*Gibson MK, Lauber CL, Knight R, Fierer N, Dantas G.**
Nature. 2014 ; 509 (7502): 612| [PDF] [supplementary materials]

[23]
How to Fight Back Against Antibiotic Resistance
Dantas G,** Sommer MOA.
American Scientist. 2014; Volume 103 | [PDF]

[22]
Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes
Moore AMPatel SForsberg KJWang BBentley G, Razia Y, Qin X, Tarr PI, Dantas G.**
PLOS ONE. 2013; 8 (11): e78822 | [PDF] [supplementary materials]

[21]
Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut
Dantas G, Sommer MOA, Degnan PH, Goodman AL.**
Annu Rev Microbiol. 2013; 67: 459 | [PDF] 

[20]
Novel Resistance Functions Uncovered Using Functional Metagenomic Investigations of Resistance Reservoirs
Pehrsson EC, Forsberg KJ, Gibson MK, Ahmadi S and Dantas G.**
Front Microbiol. 2013; 4: 145 | [PDF] 

[19]
Ecological and Clinical Consequences of Antibiotic Subsistence by Environmental Microbes
Dantas G,** Sommer MOA.**
Chapter in Antimicrobial Resistance in the Environment, Eds. Montforts M. & Keen P. 2012
John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118156247.ch4

[18]
The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens
Forsberg KJ*, Reyes A*, Wang B, Selleck EM, Sommer MOA,** Dantas G.**
Science. 2012; 337 (6097): 1107 | [PDF] [supplementary materials]

[17]
Context Matters - The Complex Interplay Between Resistome Genotypes and Resistance Phenotypes
Dantas G,** Sommer MOA.**
Curr Op Microbiol. 2012; 15: 577 | [PDF] 

[16]
Tackling Antibiotic Resistance
Bush K, Courvalin P, Dantas G, Davies J,** Eisenstein B, Huovinen P, Jacoby GA, Kishony R, Kreiswirth BN, Kutter E, Lerner SA, Levy S, Lewis K, Lomovskaya O, Miller JH, Mobashery S, Piddock LJV, Projan S, Thomas CM, Tomasz A, Tulkens PM, Walsh TR, Watson JD, Witkowski J, Witte W, Wright G, Yeh P, Zgurskaya HI.
Nat Rev Microbiol. 2011; 9 (12): 894 | [PDF]

[15]
Functional Metagenomic Investigations of the Human Intestinal Microbiota
Moore AM,* Munck C*, Sommer MOA,** Dantas G.**
Front Microbiol. 2011; 2: 1 | [PDF]

[14]
Antibiotics and the Resistant Microbiome
Sommer MOA, Dantas G.
Curr Op Microbiol. 2011; 14 (5): 556 | [PDF]

[13]
Extensive Personal Human Gut Microbiota Culture Collections Characterized and Manipulated in Gnotobiotic Mice
Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore ADantas G, Gordon JI.**
Proc Natl Acad Sci. 2011; 108 (15): 6252 | [PDF] [supplementary materials]

[12]
The Human Microbiome Harbors a Diverse Reservoir of Antibiotic Resistance Genes
Sommer MOA,** Church GM, Dantas G.
Virulence. 2010; 1 (4): 299 | [PDF]

[11]
A Functional Metagenomic Approach for Expanding the Synthetic Biology Toolbox for Biomass Conversion
Sommer MOA,** Church GM & Dantas G.**
Mol Sys Biol. 2010; 6 (360): 1 | [PDF] [supplementary materials]

[10]
Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora
Sommer MOA,** Dantas G,** Church GM.
Science. 2009; 325 (5944): 1128 | [PDF] [supplementary materials]

[09]
Bacteria Subsisting on Antibiotics
Dantas G*, Sommer MOA*, Oluwasegun RD, Church GM.**
Science; 2008. 320 (5872): 100 | [PDF] [supplementary materials]

[08]
High-Resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design
Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D.**
J Mol Biol. 2006; 366 (4): 1209 | [PDF]

[07]
Mistranslation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution
Dantas G., Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D.**
J Mol Biol. 2006; 362: 1004 | [PDF]

[06]
High-Resolution Structural Validation of the Computational Redesign of Human U1A Protein
Dobson N, Dantas G, Baker D, Varani G.**
Structure. 2006; 14 (5): 847 | [PDF]

[05]
1H, 13C and 15N Resonance Assignments of URNDesign, a Computationally Redesigned RRM Protein
Dobson N, Dantas G, Varani G.**
J Biomol NMR. 2005; 33 (2): 135 | [PDF]

[04]
Predicting protein structures accurately
Bradley P, Kuhlman B, Dantas G, Baker D.**
Science. 2004; 304: 1597 | [PDF]

[03]
Design of a novel globular protein fold with atomic level accuracy
Kuhlman B*, Dantas G*, Ireton GC, Varani G, Stoddard BL, Baker D.**
Science. 2003; 302 (5649): 1364 | [PDF] [supplementary materials]

[02]
A Large Scale Test of Computational Protein Design: Folding and Stability of Nine Completely Redesigned Globular Proteins
Dantas G*, Kuhlman B*, Callender D, Wong M, Baker D.**
J Mol Biol. 2003; 332: 449 | [PDF]

[01]
Synthesis of polyazamacrocyclic compounds via modified Richman-Atkins cyclizations of beta-trimethylsilylethanesulfonamides
Hoye RC,** Richman JE, Dantas G, Lightbourne MF, Shinneman LS.
J Org Chem. 2001; 66: 2722 | [PDF]


Patents

 

[03]  Inhibition and Diagnostics of Emerging Tetracycline Resistance Enzymes. 
Tolia, J., Dantas, G., Wencewicz, T., Park, J., Gasparrini, A., Forsberg, K., Vogel, J.
U.S. Patent Application No. 62/354,404, filed 24 June, 2016.

[02]
Compositions and Methods of Use of Antibacterial Drug Combinations.
Dantas, G., Gonzales, P., Forsberg, K., Pesesky, M., Chang, M., Mobashery, S.
U.S. Patent Application No. 62/190,588, filed 9 July, 2015.

[01]
Assays and Other Reactions Involving Droplets.
Agresti, J., Chu, L., Weitz, D.A., Kim, J., Rowat, A., Sommer, M., Dantas, G., Church, G.
US Patent Application No. 12/529,926, filed 7 March, 2008.