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* Authors contributed equally
# Corresponding author  

2019

Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northern T. EcoFAB: Advancing microbiome science through standardized fabricated ecosystems. 2019. Nature Methods. doi.org/10.1038/s41592-019-0465-0

Harris SL, Pelaez CA, Shank EA#. Monitoring bacterial colonization and maintenance on Arabidopsis thaliana roots in a floating hydroponic system. 2019. JoVE (147): e59517. doi:10.3791/59517 (2019). See video

Yannarell SM, Grandchamp GM, Chen S-Y, Daniels KE, Shank EA#. A dual-species biofilm with emergent mechanical and protective properties. 2019. Journal of Bacteriology. pii: JB.00670-18. PMID: 30833350

Farag S, Bleich RM, Shank EA, Isayev O, Bowers AA, Tropsha A. Inter-modular linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides.  2019. Bioinformatics.
pii: btz127. PMID: 30785185


  
2018
      
Paredes SH*, Gao T*, Law TF, Finkel OM, Mucyn T, Teixeira PJPL, González IS, Feltcher ME, Powers
MJ, Shank EA, Jones CD, Jojic V, Dangl JL, Castrillo G. Design of synthetic bacterial communities for
predictable plant phenotypes. 2018. PLoS Biology. doi.org/10.1371/journal.pbio.2003962.
PMID: 29462153.

Shank EA#. Considering the ‘lives of microbes’ in microbial communities. 2018. mSystems. 3(2) e00155-17. PMID: 29657965.

Townsley L, Yannarell SM, Huynh TN, Woodward JJ, Shank EA#. Cyclic-di-AMP acts as an extracellular signal that impacts Bacillus subtilis biofilm formation and plant attachment. 2018. mBio 9:e00341-18. PMID: 29588402.

2017

Grubbs KJ*, Bleich RM*, Santa Maria KC, Allen SE, AgBiome Team, Shank EA#, and Bowers AA#. Large-scale bioinformatics analysis of Bacillus genomes uncovers conserved roles of natural products in bacterial physiology. 2017. mSystems, Nov 14;2(6). pii: e00040-17. doi: 10.1128/mSystems.00040-17. PMID: 29152584.

Grandchamp GM, Caro L, Shank EA#. Pirated siderophores promote sporulation in Bacillus subtilis. 2017. Applied and Environmental Microbiology. 83(10):e03293-16. doi: 10.1128/AEM.03293-16. PMID: 282835214.

2016

Townsley L, Caro L, Kelkar H, Shank EA#. Draft genome sequence of Bacillus luciferensis isolated from soil. 2016. Genome Announcements, 4(5), e01140-16.
doi: 10.1128/genomeA.01140-16. PMID: 27795273.

Stasulli NM, Shank EA#. Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry. 2016. FEMS Microbiology Reviews. 40(6):807-813. doi: 10.1093/femsre/fuw032. PMID: 28204504.

2015


Powers MJ, Sanabria-Valentín E, Bowers AA, Shank EA#. Inhibition of cell-type differentiation in Bacillus subtilis by Pseudomonas protegens. 2015. Journal of Bacteriology,197(13):2129-38, doi:10.1128/JB.02535-14. PMID: 25825426

Bleich R, Watrous J, Dorrestein PC, Bowers AA, Shank EA#. Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis. 2015. PNAS, 112(10):3086-3091. PMID: 25713360 

Harn YC, Powers, MJ, Shank EA, Jojic V. Deconvolving molecular signatures of interactions between microbial colonies. 2015. Bioinformatics, 31(12):i142-i150, doi: 10.1093/bioinformatics/btv251. PMID: 26072476

Nie D, Shank EA, Jojic V. A deep framework for bacterial image segmentation and classification. 2015. Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics pp. 306-314. doi: 10.1145/2808719.2808751

2013

Nguyen DD, Cheng-Hsuan W, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan R, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous J, Phelan VV, van der Wiel C, Kersten RD, Mehnaz S, de Mot R, Shank EA, Charusanti P, Duggan B, Moore BS, Bandeira N, Palsson B, Pogliano K, Gutiérrez M, Dorrestein PC. MS/MS networking guided analysis of molecule and gene cluster families. PNAS 110(28):E2611-20. PMID: 23798442

Shank EA#. Using coculture to detect chemically mediated interspecies interactions. JoVE (80):e50863. PMID: 24300024
(See video)

2011

Shank EA, Klepac-Ceraj V, Collado-Torres L, Powers GE, Losick R, Kolter R. Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. PNAS 108(48):E1236-43. PMID: 22074846

Shank EA, Kolter R. Extracellular signaling and multicellularity in B. subtilis. Current Opinion in Microbiology 14(6):741-7. PMID: 22024380

Cecconi C, Shank EA, Marqusee S, Bustamante C. DNA Molecular Handles for Single-Molecule Protein-Folding Studies by Optical Tweezers. In: Methods in Molecular Biology, Vol. 749, DNA Nanotechnology: Methods and Protocols. Eds. G. Zuccheri and B. Samori. New York: Humana Press/Springer Science+Business Media. Chapter 18, 749:255-71. PMID: 21674378

2010

Shank EA*, Cecconi C*, Dill JW*, Marqusee S, Bustamante C. The folding cooperativity of a protein is controlled by its chain topology. Nature 465(7298):637-40. PMID: 20495548

2009

Shank EA#, Kolter R. New developments in microbial interspecies signaling. Current Opinion in Microbiology 12(2):205-14. PMID: 19251475

2008

Cecconi C*, Shank EA*, Dahlquist FW, Bustamante C, Marqusee S. Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers. European Biophysics Journal 37(6):729-38. PMID: 18183383

2007

Cellitti J, Llinás M, Echols N, Shank EA, Gillespie B, Kwon E, Crowder SM, Dahlquist FW, Alber T, Marqusee S. Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment. Protein Science 16(5):842-51. PMID: 17400926

Cecconi C, Shank EA, Marqusee S, Bustamante C. Studying protein folding with laser tweezers. In: Proceedings of the International School of Physics “Enrico Fermi”, Vol 165, Protein folding and drug design. Eds. R. A. Broglia, L. Serrano, G. Tiana. Amsterdam: IOS Press. 145-60.

2005

Cecconi C*, Shank EA*, Bustamante C, Marqusee S. Direct observation of the three-state folding of a single protein molecule. Science 309(5743):2057-60. PMID: 16179479


                                                                     * Indicates authors contributed equally

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