Publications

Publications (August)

S Azimi, J Thomas, SE Cleland, JE Curtis, JB Goldberg, SP Diggle. (2021) O-Specific Antigen-Dependent Surface Hydrophobicity Mediates Aggregate Assembly Type in Pseudomonas aeruginosa. Mbio 12 (4), e00860-21

CV Crisan, H Chandrashekar, C Everly, G Steinbach, SE Hill, PJ Yunker,  RR Lieberman, BK Hammer. (2021) A New Contact Killing Toxin Permeabilizes Cells and Belongs to a Broadly Distributed Protein Family. Msphere 6 (4), e00318-21

M Matherne, C Dowell-Esquivel, O Howington, O Lenaghan, G Steinbach, P Yunker, DL Hu. (2021) Biomechanics of pollen pellet removal by the honey bee. Journal of the Royal Society Interface 18 (181), 20210549

BA Lopman, K Shioda, Q Nguyen, SJ Beckett, AJ Siegler, PS Sullivan, JS Weitz. (2021) A framework for monitoring population immunity to SARS-CoV-2. Annals of Epidemiology

C R Lindsey, F Rosenzweig and MD Herron. (2021) Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae. BMC Biology 2021 19:182

Publications (July)

VG Salmon, DJ Brice, S Bridgham, J Childs, J Graham, NA Griffiths, K Hofmockel, CM Iversen, TM Jicha, RK Kolka, JE Kostka, A Malhotra, RJ Norby, JR Phillips, D Ricciuto, CW Schadt, SD Sebestyen, X Shi, AP Walker, JM Warren, DJ Weston, X Yang, PJ Hanson (2021). Nitrogen and phosphorus cycling in an ombrotrophic peatland: a benchmark for assessing change. Plant and Soil, 1-26

E Libby, WC Ratcliff. (2021). Lichens and microbial syntrophies offer models for an interdependent route to multicellularity. The Lichenologist 53 (4), 283-290

C Rose, AJ Medford, CF Goldsmith, T Vegge, JS Weitz, AA Peterson. (2021). Heterogeneity in susceptibility dictates the order of epidemic models. Journal of Theoretical Biology, 110839

 C Eksin, M Ndeffo-Mbah, JS Weitz. (2021). Reacting to outbreaks at neighboring localities. Journal of Theoretical Biology 520, 110632

G Li, S Shivam, ME Hochberg, Y Wardi, JS Weitz. (2021). Disease-dependent interaction policies to support health and economic outcomes during the COVID-19 epidemic. iScience, 102710

Publications (June)

Rachel M Wilson, Malak M Tfaily, Max Kolton, Eric R Johnston, Caitlin Petro, Cassandra A Zalman, Paul J Hanson, Heino M Heyman, Jennifer E Kyle, David W Hoyt, Elizabeth K Eder, Samuel O Purvine, Randall K Kolka, Stephen D Sebestyen, Natalie A Griffiths, Christopher W Schadt, Jason K Keller, Scott D Bridgham, Jeffrey P Chanton, Joel E Kostka. (2021) Soil metabolome response to whole-ecosystem warming at the Spruce and Peatland Responses under Changing Environments experiment. Proceedings of the National Academy of Sciences 118 (25)

P Márquez-Zacarías, PL Conlin, K Tong, JT Pentz, WC Ratcliff. (2021). Why have aggregative multicellular organisms stayed simple? Current Genetics, 1-6

Publications (May)

C Eksin, M Ndeffo-Mbah, JS Weitz. (2021) Reacting to outbreaks at neighboring localities. Journal of Theoretical Biology 520, 110632 

M Mei, J Thomas, SP Diggle (2021). Heterogenous susceptibility to R-pyocins in populations of Pseudomonas aeruginosa sourced from cystic fibrosis lungs. Mbio 12 (3) 

GO Bozdag, E Libby, R Pineau, CT Reinhard, WC Ratcliff (2021). Oxygen suppression of macroscopic multicellularity. Nature Communications 12 (1), 1-10 

H Isaksson, PL Conlin, B Kerr, WC Ratcliff, E Libby (2021). The Consequences of Budding versus Binary Fission on Adaptation and Aging in Primitive Multicellularity. Genes 12 (5), 661 

D Muratore, JS Weitz. (2021) Infect while the iron is scarce: nutrient-explicit phage-bacteria games. Theoretical Ecology, 1-21

Publications (April)

O Prakash, SJ Green, P Singh, P Jasrotia, JE Kostka (2021). Stress-related ecophysiology of members of the genus Rhodanobacter isolated from a mixed waste contaminated subsurface.Frontiers of Environmental Science & Engineering 15 (2), 1-9 

R Sela, BK Hammer, M Halpern. (2021). Quorum‐sensing signaling by chironomid egg masses’ microbiota, affects haemagglutinin/protease (HAP) production by Vibrio cholerae. Molecular Ecology 30 (7), 1736-1746 

LK Medina-Cordoba, AT Chande, L Rishishwar, LW Mayer,  LC Valderrama-Aguirre, A Valderrama-Aguirre, JC Gaby, JE Kostka, IK Jordan (2021). Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields. Scientific reports 11 (1), 1-15 

JP Barraza, M Whiteley (2021). A Pseudomonas aeruginosa Antimicrobial Affects the Biogeography but Not Fitness of Staphylococcus aureus during Coculture. Mbio 12 (2) 

 

Publications (March)

T Živković, AA Carell, G Granath, MB Nilsson, M Helbig, D Warshan, IJ Klarenberg, D Gilbert, AJ Shaw, Joel E Kostka, David J Weston (2021). Microbial community composition is linked to Sphagnum acclimation to warming. EGU21 

T Day, SA Zamani Dahaj, W Ratcliff, P Yunker (2021). Robust heritability of collective traits via the maximum entropy principle. Bulletin of the American Physical Society 

R Copeland, P Yunker (2021). Differences in bacteria killing rates are mitigated by finite size effects. Bulletin of the American Physical Society

AMS Correa, C Howard-Varona, SR Coy, A Buchan, MB Sullivan, JS Weitz (2021). Revisiting the rules of life for viruses of microorganisms.  Nature Reviews Microbiology 

AR Burmeister, E Hansen, JJ Cunningham, EH Rego, PE Turner, Joshua S Weitz, Michael E Hochberg (2021). Fighting microbial pathogens by integrating host ecosystem interactions and evolution. BioEssays 43 (3), 2000272 

Publications (February)

MA Schorn, S Verhoeven, L Ridder, F Huber, DD Acharya, AA Aksenov, N Garg (2021). A community resource for paired genomic and metabolomic data mining. Nature Chemical Biology, 1-6

CV Crisan, HL Nichols, S Wiesenfeld, G Steinbach, PJ Yunker, BK Hammer (2021). Glucose confers protection to Escherichia coli against contact killing by Vibrio cholerae. Scientific reports 11 (1), 1-11

M Kinnersley, K Schwartz, DD Yang, G Sherlock, F Rosenzweig (2021). Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment. BMC biology 19 (1), 1-21

N Mruwat, MCG Carlson, S Goldin, F Ribalet, S Kirzner, Y Hulata, Stephen J Beckett, Dror Shitrit, Joshua S Weitz, E Virginia Armbrust, Debbie Lindell (2021). A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances. The ISME journal 15 (1), 41-54

Publications (January)

Park SW, Sun K, Champredon D, Li M, Bolker BM, Earn DJD, Weitz JS, Grenfell BT, Dushoff J. (2021) Forward-looking serial intervals correctly link epidemic growth to reproduction numbers. Proc Natl Acad Sci U S A. 118(2):e2011548118

P Bravo, S Ng, B Hammer, P Yunker (2021) Growth and roughening of biofilms. Bulletin of the American Physical Society

G Steinbach, S Ng, B Hammer, P Yunker (2021) Cellular reproduction and death induce diffusion of immotile bacteria in growing biofilms. Bulletin of the American Physical Society

O Prakash, SJ Green, P Singh, P Jasrotia, JE Kostka (2021) Stress-related ecophysiology of members of the genus Rhodanobacter isolated from a mixed waste contaminated subsurface. Frontiers of Environmental Science & Engineering 15 (2), 1-9

T Day, SA Zamani Dahaj, W Ratcliff, P Yunker (2021). Robust heritability of collective traits via the maximum entropy principle. Bulletin of the American Physical Society

A Pokhrel, P Yunker (2021). Role of physical interactions in early stages of biofilm formations. Bulletin of the American Physical Society

H Selvakumar, M Dominguez-Mirazo, J Thomas, S Diggle, J Weitz, J Curtis (2021) Phage-bacteria dynamics in spatially structured bacterial communities. Bulletin of the American Physical Society

 

Publications (December)

Park SW, Sun K, Champredon D, Li M, Bolker BM, Earn DJD, Weitz JS, Grenfell BT, Dushoff J. (2021) Forward-looking serial intervals correctly link epidemic growth to reproduction numbers. Proc Natl Acad Sci U S A. 118(2):e2011548118

Joshua S. Weitz, Sang Woo Park, Ceyhun Eksin, Jonathan Dushoff (2020) Awareness-driven behavior changes can shift the shape of epidemics away from peaks and toward plateaus, shoulders, and oscillations. Proceedings of the National Academy of Sciences Dec 2020, 117 (51) 32764-32771

RM Brooker, AL Seyfferth, A Hunter, JM Sneed, DL Dixson, ME Hay. (2020) Human proximity suppresses fish recruitment by altering mangrove-associated odour cues. Scientific reports 10 (1), 1-9

Conan Y Zhao, Yiqi Hao, Yifei Wang, John J Varga, Arlene A Stecenko, Joanna B Goldberg, Sam P Brown. (2020) Microbiome data enhances predictive models of lung function in people with cystic fibrosis. The Journal of Infectious Diseases, jiaa655

Publications (November)

Sheyda Azimi, LM Wheldon, NJ Oldfield, DAA Ala’Aldeen, KG Wooldridge (2020) A role for fibroblast growth factor receptor 1 in the pathogenesis of Neisseria meningitidis. Microbial Pathogenesis, Volume 149, Article 104534

CS Clements, AS Burns, FJ Stewart, ME Hay (2020) Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes. Animal Microbiome 2 (1), 1-13                         

Rachel Wilson, Anya Hopple, Malak M Tfaily, Cassandra Zalman, Eric Johnston, Caitlin Petro, Max Kolton, Tianze Song, Karis J McFarlane, Stephen Sebestyen, Natalie Griffiths, Randall K Kolka, Christopher W Schadt, Paul J Hanson, Jason Keller, Scott D Bridgham, Jeff Chanton, Joel E Kostka (2020) Plant Exudate-Soil Interactions Linked to Delayed Mineralization of Subsurface C Stores After 3 Years of Experimental Warming. AGU Fall Meeting 2020

Samantha J Mascuch, Sara Fakhretaha-Aval, Jessica C Bowman, Minh Thu H Ma, Gwendell Thomas, Bettina Bommarius, Chieri Ito, Liangjun Zhao, Gary P Newnam, Kavita R Matange, Hem R Thapa, Brett Barlow, Rebecca K Donegan, Nguyet A Nguyen, Emily G Saccuzzo, Chiamaka T Obianyor, Suneesh C Karunakaran, Pamela Pollet, Brooke Rothschild-Mancinelli, Santi Mestre-Fos, Rebecca Guth-Metzler, Anton V Bryksin, Anton S Petrov, Mallory Hazell, Carolyn B Ibberson, Petar I Penev, Robert G Mannino, Wilbur A Lam, Andrés J Garcia, Julia Kubanek, Vinayak Agarwal, Nicholas V Hud, Jennifer B Glass, Loren Dean Williams, Raquel L Lieberman (2020) A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits. Journal of Biological Chemistry 295 (46), 15438-15453

JT Pentz, P Márquez-Zacarías, GO Bozdag, A Burnetti, PJ Yunker, E Libby, William C. Ratcliff (2020). Ecological advantages and evolutionary limitations of aggregative multicellular development. Current Biology 30 (21), 4155-4164. e6

Aroon Chande, Seolha Lee, Mallory Harris, Quan Nguyen, Stephen J Beckett, Troy Hilley, Clio Andris, Joshua S Weitz (2020). Real-time, interactive website for US-county-level COVID-19 event risk assessment. Nature Human Behaviour, 1-7

Publications (October)

Sheyda Azimi, LM Wheldon, NJ Oldfield, DAA Ala’Aldeen, KG Wooldridge (2020) A role for fibroblast growth factor receptor 1 in the pathogenesis of Neisseria meningitidis. Microbial Pathogenesis, Volume 149, Article 104534

Vanderwoude Jelly, Fleming Derek, Azimi Sheyda, Trivedi Urvish, Rumbaugh Kendra P. and Diggle Stephen P (2020) The evolution of virulence in Pseudomonas aeruginosa during chronic wound infection. Proc. R. Soc. B.28720202272

C Rose, AJ Medford, CF Goldsmith, T Vegge, J Weitz, AA Peterson (2020) Population Susceptibility Variation and Its Effect on Contagion Dynamics. arXiv preprint arXiv:2009.09150

KY Inagaki, MG Pennino, SR Floeter, ME Hay, GO Longo (2020) Trophic interactions will expand geographically but be less intense as oceans warm. Global Change Biology

AD Klementiev, Z Jin, M Whiteley (2020) Micron Scale Spatial Measurement of the O2 Gradient Surrounding a Bacterial Biofilm in Real Time. mBio 11 (5)

Rotem Sela, Brian K. Hammer, Malka Halpern (2020) Quorum‐sensing signaling by chironomid egg masses’ microbiota, affects haemagglutinin/protease (HAP) production by Vibrio cholerae. Molecular Ecology

Publications (September)

SE Lester, A Rassweiler, S J McCoy, A K Dubel, M K Donovan, MW Miller, SD Miller, BI Ruttenberg, J F Samhouri, Mark E Hay (2020) Caribbean reefs of the Anthropocene: Variance in ecosystem metrics indicates bright spots on coral depauperate reefs. Global Change Biology 26 (9), 4785-4799

Om Prakash, Stefan J Green, Pooja Singh, Puja Jasrotia, Joel E Kostka (2020) Stress-related ecophysiology of members of the genus Rhodanobacter isolated from a mixed waste contaminated subsurface. Frontiers of Environmental Science & Engineering 15 (2), 1-9

Micah Dettweiler, Lewis Marquez, Michelle Lin, Anne M Sweeney-Jones, Bhuwan Khatri Chhetri, Daniel V Zurawski, Julia Kubanek, Cassandra L Quave (2020) Pentagalloyl glucose from Schinus terebinthifolia inhibits growth of carbapenem-resistant Acinetobacter baumannii. Scientific Reports 10 (1), 1-12

David Yanni, Shane Jacobeen, Pedro Márquez-Zacarías, Joshua S Weitz, William C Ratcliff, Peter J Yunker (2020) Topological constraints in early multicellularity favor reproductive division of labor. eLife 9, e54348

Jennifer T Pentz, Pedro Márquez-Zacarías, G Ozan Bozdag, Anthony Burnetti, Peter J Yunker, Eric Libby, William C Ratcliff (2020) Ecological advantages and evolutionary limitations of aggregative multicellular development. Cell Press

Noor Mruwat, Michael CG Carlson, Svetlana Goldin, François Ribalet, Shay Kirzner, Yotam Hulata, Stephen J Beckett, Dror Shitrit, Joshua S Weitz, E Virginia Armbrust, Debbie Lindell (2020) A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances. The ISME Journal, 1-14