* Authors contributed equally
# Corresponding author
# Corresponding author
2025
Zhang H, Li X, Tseyang LT, Giese GE, Wang H, Yao B, Zhang J, Neve R, Shank EA, Spinelli JB, Yilmaz S, Walhout AJM#. A systems-level, semi-quantitative landscape of metabolic flux in C. elegans. 2025. Nature. 640, 194–202. 10.1038/s41586-025-08635-6.
2024
Chai L, Shank EA, Zaburdaev V#. Where bacteria and eukaryotes meet. 2024. Journal of Bacteriology. 10.1128.jb.00049-23.
2023
Müller S, DeLeon O, Atkinson S, Saravia F, Kellogg S, Shank EA, Kirby JR#. Thiocillin contributes to the ecological fitness of Bacilus cereus ATCC 14579 during interspecies interactions with Myxococcus xanthus. 2023. Frontiers in Microbiology. 10.3389/fmicb.2023.1295262.
Yannarell SM, Beaudoin ES, Talley HS, Schoenborn AA, Orr G, Anderton CR, Chrisler WB, Shank EA#. Extensive cellular multitasking within Bacillus subtilis biofilms. 2023. bioRxiv. 2022.09.02.506450v1; doi.org/10.1101/2022.09.02.506450. mSystems 10.1128/msystems.00891-22.
Schoenborn AA, Yannarell SM, MacVicar CT, Barriga-Medina NN, Markillie M, Mitchell H, Bonham KS, Leon-Reyes A, Riveros-Iregui D, Klepac-Ceraj V#, Shank EA#. Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago. 2023. bioRxiv. 2022.04.05.487164; doi: https://doi.org/10.1101/2022.04.05.487164. Environmental Microbiology, 1 - 16. https://doi.org/10.1111/1462-2920.16361.
2022
Vandergrift G, Kew W, Lukowski J, Bhattacharjee A, Liyu A, Shank EA, Paša-Tolić L, Prabhakaran V, Anderton CR#. Imaging and direct sampling capabilities of nanospray desorption electrospray ionization with absorption-mode 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry. 2022. Analytical Chemistry. doi: 10.1021/acs.analchem.1c05216.
2021
Lukowski J, Bhattacharjee A, Yannarell S, Schwarz K, Shor L, Shank EA, Anderton CR#. Expanding the molecular coverage in mass spectrometry imaging of microbial systems using metal-assisted laser desorption/ionization. 2021. Microbiology Spectrum. Jul 21;e0052021. doi: 10.1128/Spectrum.00520-21. PMID: 34287059
Yannarell SM, Velickovic D, Anderton CR#, Shank EA#. Direct visualization of chemical cues and cellular phenotypes throughout Bacillus subtilis biofilms. 2021. mSystems. 6(6):e0103821. doi: 10.1128/mSystems.01038-21. PMID: 3481265
Yourstone S, Weinstein I, Ademski E, Shank EA, Stasulli N#. Selective bacterial community enrichment between the pitcher plants Sarracenia minor and Sarracenia flava. 2021. Microbiology Spectrum. 9(3):e0069621. doi: 10.1128/Spectrum.00696-21. PMID: 34817222
Schoenborn AA, Clapper H, Eckshtain-Levi N, Shank EA#. Rhizobacteria impact colonization of Listeria monocytogenes on Arabidopsis thaliana roots. 2021. Applied and Environmental Microbiology. doi: 10.1128/AEM.01411-21. PMID: 34550783
Schoenborn AA, Yannarell SM, Wallace ED, Clapper H, Weinstein I, Shank EA#. Defining the expression, production, and signaling roles of specialized metabolites during Bacillus subtilis differentiation. 2021. Journal of Bacteriology. doi: 10.1128/JB.00337-21. PMID: 34460312.
2020
Sharma K, Palatinszky M, Nikolov G, Berry D & Shank EA#. Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. 2020. eLife. 9:e56275. doi: 10.7554/eLife.56275. PMID: 33140722
Eckshtain-Levi N*, Harris SL*, Roscious RQ, Shank EA#. Bacterial community members increase Bacillus subtilis maintenance on the roots of Arabidopsis thaliana. 2020. Phytobiomes Journal. doi.org/10.1094/PBIOMES-02-20-0019-R
Yannarrell SM, Townsley L, Shank EA#. Cyclic-di-AMP in Bacillus subtilis biofilm formation. 2020. In Microbial Cyclic Di-Nucleotide Signaling. Eds: Chou S-H, Guiliani N, Lee VT, Römling U. Springer Nature Switzerland AG.
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. PMID: 31227812
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
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
Zhang H, Li X, Tseyang LT, Giese GE, Wang H, Yao B, Zhang J, Neve R, Shank EA, Spinelli JB, Yilmaz S, Walhout AJM#. A systems-level, semi-quantitative landscape of metabolic flux in C. elegans. 2025. Nature. 640, 194–202. 10.1038/s41586-025-08635-6.
2024
Chai L, Shank EA, Zaburdaev V#. Where bacteria and eukaryotes meet. 2024. Journal of Bacteriology. 10.1128.jb.00049-23.
2023
Müller S, DeLeon O, Atkinson S, Saravia F, Kellogg S, Shank EA, Kirby JR#. Thiocillin contributes to the ecological fitness of Bacilus cereus ATCC 14579 during interspecies interactions with Myxococcus xanthus. 2023. Frontiers in Microbiology. 10.3389/fmicb.2023.1295262.
Yannarell SM, Beaudoin ES, Talley HS, Schoenborn AA, Orr G, Anderton CR, Chrisler WB, Shank EA#. Extensive cellular multitasking within Bacillus subtilis biofilms. 2023. bioRxiv. 2022.09.02.506450v1; doi.org/10.1101/2022.09.02.506450. mSystems 10.1128/msystems.00891-22.
Schoenborn AA, Yannarell SM, MacVicar CT, Barriga-Medina NN, Markillie M, Mitchell H, Bonham KS, Leon-Reyes A, Riveros-Iregui D, Klepac-Ceraj V#, Shank EA#. Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago. 2023. bioRxiv. 2022.04.05.487164; doi: https://doi.org/10.1101/2022.04.05.487164. Environmental Microbiology, 1 - 16. https://doi.org/10.1111/1462-2920.16361.
2022
Vandergrift G, Kew W, Lukowski J, Bhattacharjee A, Liyu A, Shank EA, Paša-Tolić L, Prabhakaran V, Anderton CR#. Imaging and direct sampling capabilities of nanospray desorption electrospray ionization with absorption-mode 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry. 2022. Analytical Chemistry. doi: 10.1021/acs.analchem.1c05216.
2021
Lukowski J, Bhattacharjee A, Yannarell S, Schwarz K, Shor L, Shank EA, Anderton CR#. Expanding the molecular coverage in mass spectrometry imaging of microbial systems using metal-assisted laser desorption/ionization. 2021. Microbiology Spectrum. Jul 21;e0052021. doi: 10.1128/Spectrum.00520-21. PMID: 34287059
Yannarell SM, Velickovic D, Anderton CR#, Shank EA#. Direct visualization of chemical cues and cellular phenotypes throughout Bacillus subtilis biofilms. 2021. mSystems. 6(6):e0103821. doi: 10.1128/mSystems.01038-21. PMID: 3481265
Yourstone S, Weinstein I, Ademski E, Shank EA, Stasulli N#. Selective bacterial community enrichment between the pitcher plants Sarracenia minor and Sarracenia flava. 2021. Microbiology Spectrum. 9(3):e0069621. doi: 10.1128/Spectrum.00696-21. PMID: 34817222
Schoenborn AA, Clapper H, Eckshtain-Levi N, Shank EA#. Rhizobacteria impact colonization of Listeria monocytogenes on Arabidopsis thaliana roots. 2021. Applied and Environmental Microbiology. doi: 10.1128/AEM.01411-21. PMID: 34550783
Schoenborn AA, Yannarell SM, Wallace ED, Clapper H, Weinstein I, Shank EA#. Defining the expression, production, and signaling roles of specialized metabolites during Bacillus subtilis differentiation. 2021. Journal of Bacteriology. doi: 10.1128/JB.00337-21. PMID: 34460312.
2020
Sharma K, Palatinszky M, Nikolov G, Berry D & Shank EA#. Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. 2020. eLife. 9:e56275. doi: 10.7554/eLife.56275. PMID: 33140722
Eckshtain-Levi N*, Harris SL*, Roscious RQ, Shank EA#. Bacterial community members increase Bacillus subtilis maintenance on the roots of Arabidopsis thaliana. 2020. Phytobiomes Journal. doi.org/10.1094/PBIOMES-02-20-0019-R
Yannarrell SM, Townsley L, Shank EA#. Cyclic-di-AMP in Bacillus subtilis biofilm formation. 2020. In Microbial Cyclic Di-Nucleotide Signaling. Eds: Chou S-H, Guiliani N, Lee VT, Römling U. Springer Nature Switzerland AG.
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. PMID: 31227812
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
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
