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Research Areas

Biocomplexity: Publications

Sun, H., Mei, R., Zhang, X. X., Ren, H., Liu, W. T., & Ye, L. (2020). Bacterial enrichment in highly-selective acetate-fed bioreactors and its application in rapid biofilm formation. Water Research, 170, [115359]. https://doi.org/10.1016/j.watres.2019.115359

Chen, L., Ling, F., Bakker, G., Liu, W. T., Medema, G., van der Meer, W., & Liu, G. (2020). Assessing the transition effects in a drinking water distribution system caused by changing supply water quality: an indirect approach by characterizing suspended solids. Water Research, 168, [115159]. https://doi.org/10.1016/j.watres.2019.115159

Li, J. J., Fan, J. F., Wang, Z., Wu, Y. C., Dahmen, K. A., & Qiao, J. W. (2020). Temperature rises during strain-rate dependent avalanches in bulk metallic glasses. Intermetallics, 116, [106637]. https://doi.org/10.1016/j.intermet.2019.106637

McFaul, L. W., Wright, W. J., Sickle, J., & Dahmen, K. A. (2019). Force oscillations distort avalanche shapes. Materials Research Letters, 7(12), 496-502. https://doi.org/10.1080/21663831.2019.1659437

Liu, K., Pan, C., Kuhn, A., Nievergelt, A. P., Fantner, G. E., Milenkovic, O., & Radenovic, A. (2019). Detecting topological variations of DNA at single-molecule level. Nature communications, 10(1), [3]. https://doi.org/10.1038/s41467-018-07924-1

Yamamoto, K., Hackley, K. C., Kelly, W. R., Panno, S. V., Sekiguchi, Y., Sanford, R. A., ... Tamaki, H. (2019). Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States. Scientific reports, 9(1), [13484]. https://doi.org/10.1038/s41598-019-49996-z

Wang, M., Zhang, J., Xu, H., & Golding, I. (2019). Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality. Nature Microbiology, 4(12), 2118-2127. https://doi.org/10.1038/s41564-019-0553-z

Singh, A., Lee, J. C. T., Avila, K. E., Chen, Y., Montoya, S. A., Fullerton, E. E., ... Roy, S. (2019). Publisher Correction: Scaling of domain cascades in stripe and skyrmion phases (Nature Communications, (2019), 10, 1, (1988), 10.1038/s41467-019-09934-z). Nature communications, 10(1), [2325]. https://doi.org/10.1038/s41467-019-10314-w

Singh, A., Lee, J. C. T., Avila, K. E., Chen, Y., Montoya, S. A., Fullerton, E. E., ... Roy, S. (2019). Scaling of domain cascades in stripe and skyrmion phases. Nature communications, 10(1), [1988]. https://doi.org/10.1038/s41467-019-09934-z

Cheng, H., Cheng, D., Mao, J., Lu, T., & Hong, P. Y. (2019). Identification and characterization of core sludge and biofilm microbiota in anaerobic membrane bioreactors. Environment International, 133, [105165]. https://doi.org/10.1016/j.envint.2019.105165

Xie, K., Jiang, X., Jiang, D., Xiao, Y., Chen, S., Dahmen, K. A., ... Salje, E. K. H. (2019). Change of crackling noise in granite by thermal damage: Monitoring nuclear waste deposits. American Mineralogist, 104(11), 1578-1584. https://doi.org/10.2138/am-2019-7058

Mitrano, M., Lee, S., Husain, A. A., Zhu, M., Munoz, G. D. L. P., Sun, S. X. L., ... Abbamonte, P. (2019). Evidence for photoinduced sliding of the charge-order condensate in La1.875Ba0.125CuO4. Physical Review B, 100(20), [205125]. https://doi.org/10.1103/PhysRevB.100.205125

Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathöfer, U., ... Schulten, K. (2019). Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell, 179(5), 1098-1111.e23. https://doi.org/10.1016/j.cell.2019.10.021

Dahmen, K. A., Uhl, J. T., & Wright, W. J. (2019). Why the Crackling Deformations of Single Crystals, Metallic Glasses, Rock, Granular Materials, and the Earth's Crust Are So Surprisingly Similar. Frontiers in Physics, 7, [176]. https://doi.org/10.3389/fphy.2019.00176

Mei, R., & Liu, W. T. (2019). Quantifying the contribution of microbial immigration in engineered water systems. Microbiome, 7(1), [144]. https://doi.org/10.1186/s40168-019-0760-0

Long, A. A., Denisov, D. V., Schall, P., Hufnagel, T. C., Gu, X., Wright, W. J., & Dahmen, K. A. (2019). From critical behavior to catastrophic runaways: comparing sheared granular materials with bulk metallic glasses. Granular Matter, 21(4), [99]. https://doi.org/10.1007/s10035-019-0946-y

Tsai, C. W., Lee, C., Lin, P. T., Xie, X., Chen, S., Carroll, R., ... Yeh, J. W. (2019). Portevin-Le Chatelier mechanism in face-centered-cubic metallic alloys from low to high entropy. International journal of plasticity, 122, 212-224. https://doi.org/10.1016/j.ijplas.2019.07.003

One Thousand Plant Transcriptomes Initiative (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574(7780), 679-685. https://doi.org/10.1038/s41586-019-1693-2

Chatterjee, P., & Goldenfeld, N. (2019). Three-body interactions drive the transition to polar order in a simple flocking model. Physical Review E, 100(4), [040602]. https://doi.org/10.1103/PhysRevE.100.040602

Mungan, M., Sastry, S., Dahmen, K., & Regev, I. (2019). Networks and hierarchies: How amorphous materials learn to remember. Physical review letters, 123(17), [178002]. https://doi.org/10.1103/PhysRevLett.123.178002

Amato, K. R., Mallott, E. K., McDonald, D., Dominy, N. J., Goldberg, T., Lambert, J. E., ... Knight, R. (2019). Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. Genome biology, 20(1), [201]. https://doi.org/10.1186/s13059-019-1807-z

Silevitch, D. M., Xu, J., Tang, C., Dahmen, K. A., & Rosenbaum, T. F. (2019). Magnetic domain dynamics in an insulating quantum ferromagnet. Physical Review B, 100(13), [134405]. https://doi.org/10.1103/PhysRevB.100.134405

Greening, C., Geier, R., Wang, C., Woods, L. C., Morales, S. E., McDonald, M. J., ... Mackie, R. I. (2019). Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME Journal, 13(10), 2617-2632. https://doi.org/10.1038/s41396-019-0464-2

Donohue, M. E., Asangba, A. E., Ralainirina, J., Weisrock, D. W., Stumpf, R. M., & Wright, P. C. (2019). Extensive variability in the gut microbiome of a highly-specialized and critically endangered lemur species across sites. American journal of primatology, 81(10-11), [e23046]. https://doi.org/10.1002/ajp.23046

Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., ... Dutilh, B. E. (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nature Microbiology, 4(10), 1727-1736. https://doi.org/10.1038/s41564-019-0494-6

Amato, K. R., & Stumpf, R. M. (2019). Moving forward with the primate microbiome: Introduction to a special issue of the American Journal of Primatology. American journal of primatology, 81(10-11), [e23060]. https://doi.org/10.1002/ajp.23060

Asangba, A. E., Donohue, M. E., Lamb, A., Wright, P. C., Halajian, A., Leigh, S. R., & Stumpf, R. M. (2019). Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity. American journal of primatology, 81(10-11), [e23045]. https://doi.org/10.1002/ajp.23045

Bernardi, R. C., Durner, E., Schoeler, C., Malinowska, K. H., Carvalho, B. G., Bayer, E. A., ... Nash, M. A. (2019). Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. Journal of the American Chemical Society, 141(37), 14752-14763. https://doi.org/10.1021/jacs.9b06776

Oosterkamp, M. J., Bauer, S., Ibáñez, A. B., Méndez-García, C., Hong, P. Y., Cann, I., & Mackie, R. I. (2019). Identification of methanogenesis and syntrophy as important microbial metabolic processes for optimal thermophilic anaerobic digestion of energy cane thin stillage. Bioresource Technology Reports, 7, [100254]. https://doi.org/10.1016/j.biteb.2019.100254

Christensen, S., Molloy, E. K., Vachaspati, P., & Warnow, T. (2019). Traction: Fast non-parametric improvement of estimated gene trees. In K. T. Huber, & D. Gusfield (Eds.), 19th International Workshop on Algorithms in Bioinformatics, WABI 2019 [4] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 143). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.WABI.2019.4

Hsiao, H. W., Li, S., Dahmen, K. A., & Zuo, J-M. (2019). Shear banding mechanism in compressed nanocrystalline ceramic nanopillars. Physical Review Materials, 3(8), [083601]. https://doi.org/10.1103/PhysRevMaterials.3.083601

Mitrano, M., Lee, S., Husain, A. A., Delacretaz, L., Zhu, M., De La Peña Munoz, G., ... Abbamonte, P. (2019). Ultrafast time-resolved x-ray scattering reveals diffusive charge order dynamics in La2-xBaxCuO4 Science Advances, 5(8), [eaax3346]. https://doi.org/10.1126/sciadv.aax3346

MacGregor-Chatwin, C., Jackson, P. J., Sener, M., Chidgey, J. W., Hitchcock, A., Qian, P., ... Hunter, C. N. (2019). Membrane organization of photosystem I complexes in the most abundant phototroph on Earth. Nature Plants, 5(8), 879-889. https://doi.org/10.1038/s41477-019-0475-z

Hull, N. M., Ling, F., Pinto, A. J., Albertsen, M., Jang, H. G., Hong, P. Y., ... Liu, W-T. (2019). Drinking Water Microbiome Project: Is it Time? Trends in Microbiology, 27(8), 670-677. https://doi.org/10.1016/j.tim.2019.03.011

Gomez, A., Sharma, A. K., Mallott, E. K., Petrzelkova, K. J., Jost Robinson, C. A., Yeoman, C. J., ... Mcmahon, K. (2019). Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints. mSphere, 4(4). https://doi.org/10.1128/mSphere.00271-19

Molloy, E. K., & Warnow, T. (2019). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms for Molecular Biology, 14(1), [14]. https://doi.org/10.1186/s13015-019-0151-x

Deng, J., Zhou, L., Sanford, R. A., Shechtman, L. A., Dong, Y., Alcalde, R. E., ... Fouke, B. W. (2019). Adaptive evolution of escherichia coli to ciprofloxacin in controlled stress environments: Contrasting patterns of resistance in spatially varying versus uniformly mixed concentration conditions. Environmental Science and Technology, 53(14), 7996-8005. https://doi.org/10.1021/acs.est.9b00881

Molloy, E. K., & Warnow, T. (2019). TreeMerge: A new method for improving the scalability of species tree estimation methods. Bioinformatics, 35(14), i417-i426. [btz344]. https://doi.org/10.1093/bioinformatics/btz344

Ni, X., Zhang, H., Liarte, D. B., McFaul, L. W., Dahmen, K. A., Sethna, J. P., & Greer, J. R. (2019). Yield Precursor Dislocation Avalanches in Small Crystals: The Irreversibility Transition. Physical review letters, 123(3), [035501]. https://doi.org/10.1103/PhysRevLett.123.035501

Zhang, Y., & Liu, W-T. (2019). The application of molecular tools to study the drinking water microbiome–Current understanding and future needs. Critical Reviews in Environmental Science and Technology, 49(13), 1188-1235. https://doi.org/10.1080/10643389.2019.1571351

Zhang, C., Wipfler, R. L., Li, Y., Wang, Z., Hallett, E. N., & Whitaker, R. J. (2019). Cell structure changes in the hyperthermophilic crenarchaeon Sulfolobus islandicus lacking the S-layer. mBio, 10(4), [e01589-19]. https://doi.org/10.1128/mBio.01589-19

Yang, W., Keith Cassidy, C., Ames, P., Diebolder, C. A., Schulten, K., Luthey-Schulten, Z., ... Briegel, A. (2019). In situ conformational changes of the escherichia coli serine chemoreceptor in different signaling states. mBio, 10(4), [e00973-19]. https://doi.org/10.1128/mBio.00973-19

Ozer, E. A., Nnah, E., Didelot, X., Whitaker, R. J., & Hauser, A. R. (2019). The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages. Genome biology and evolution, 11(1), 1780-1796. https://doi.org/10.1093/gbe/evz119

Kostochka, A. V., Liu, X., Machado, R., & Milenkovic, O. (2019). Directed Intersection Representations and the Information Content of Digraphs. In 2019 IEEE International Symposium on Information Theory, ISIT 2019 - Proceedings (pp. 1477-1481). [8849253] (IEEE International Symposium on Information Theory - Proceedings; Vol. 2019-July). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT.2019.8849253

Pafčo, B., Sharma, A. K., Petrželková, K. J., Vlčková, K., Todd, A., Yeoman, C. J., ... Gomez, A. (2019). Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors. American journal of physical anthropology, 169(3), 575-585. https://doi.org/10.1002/ajpa.23842

Gabrys, R., Dau, H., Colbourn, C. J., & Milenkovic, O. (2019). Set-Codes with Small Intersections and Small Discrepancies. In 2019 IEEE International Symposium on Information Theory, ISIT 2019 - Proceedings (pp. 2359-2363). [8849651] (IEEE International Symposium on Information Theory - Proceedings; Vol. 2019-July). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT.2019.8849651

Tang, L., Zhong, L., Xue, K., Wang, S., Xu, Z., Lin, Q., ... Wang, Y. (2019). Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grassland. Soil Biology and Biochemistry, 134, 113-121. https://doi.org/10.1016/j.soilbio.2019.02.018

Mohamed, E. T., Mundhada, H., Landberg, J., Cann, I., MacKie, R. I., Nielsen, A. T., ... Feist, A. M. (2019). Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution. Microbial cell factories, 18(1), [116]. https://doi.org/10.1186/s12934-019-1165-2

Sivaguru, M., Fouke, K. W., Todorov, L., Kingsford, M. J., Fouke, K. E., Trop, J. M., & Fouke, B. W. (2019). Correction Factors for δ18O-Derived Global Sea Surface Temperature Reconstructions From Diagenetically Altered Intervals of Coral Skeletal Density Banding. Frontiers in Marine Science, 6(JUN), [306]. https://doi.org/10.3389/fmars.2019.00306, https://doi.org/10.3389/fmars.2019.00306

Sedlak, S. M., Schendel, L. C., Melo, M. C. R., Pippig, D. A., Luthey-Schulten, Z., Gaub, H. E., & Bernardi, R. C. (2019). Direction Matters: Monovalent Streptavidin/Biotin Complex under Load. Nano letters, 19(6), 3415-3421. https://doi.org/10.1021/acs.nanolett.8b04045

Gao, H., Mao, Y., Zhao, X., Liu, W. T., Zhang, T., & Wells, G. (2019). Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess. Water Research, 155, 275-287. https://doi.org/10.1016/j.watres.2019.02.020

Pauly, M. D., Bautista, M. A., Black, J. A., & Whitaker, R. J. (2019). Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1772), [20180093]. https://doi.org/10.1098/rstb.2018.0093

Westra, E. R., Van Houte, S., Gandon, S., & Whitaker, R. (2019). The ecology and evolution of microbial CRISPR-Cas adaptive immune systems. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1772), [20190101]. https://doi.org/10.1098/rstb.2019.0101

Nute, M., Saleh, E., & Warnow, T. (2019). Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets. Systematic biology, 68(3), 396-411. https://doi.org/10.1093/sysbio/syy068

Shah, N., Nute, M. G., Warnow, T., & Pop, M. (2019). Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinformatics, 35(9), 1613-1614. https://doi.org/10.1093/bioinformatics/bty833

Mei, R., Kim, J., Wilson, F. P., Bocher, B. T. W., & Liu, W-T. (2019). Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process. Microbiome, 7(1), [65]. https://doi.org/10.1186/s40168-019-0682-x

Sivaguru, M., Saw, J. J., Williams, J. C., Lieske, J. C., Krambeck, A. E., Romero, M. F., ... Fouke, B. W. (2019). Re: Geobiology reveals how human kidney stones dissolve in vivo. Journal of Urology, 201(4), 663-664. https://doi.org/10.1097/01.JU.0000553253.71668.e3

Fung, T., O'Dwyer, J. P., & Chisholm, R. A. (2019). Partitioning the effects of deterministic and stochastic processes on species extinction risk. Ecological Complexity, 38, 156-167. https://doi.org/10.1016/j.ecocom.2019.03.004

Alcalde, R. E., Michelson, K., Zhou, L., Schmitz, E. V., Deng, J., Sanford, R. A., ... Werth, C. J. (2019). Motility of Shewanella oneidensis MR-1 Allows for Nitrate Reduction in the Toxic Region of a Ciprofloxacin Concentration Gradient in a Microfluidic Reactor. Environmental Science and Technology, 53(5), 2778-2787. https://doi.org/10.1021/acs.est.8b04838

Amato, K. R., G. Sanders, J., Song, S. J., Nute, M., Metcalf, J. L., Thompson, L. R., ... R. Leigh, S. (2019). Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME Journal, 13(3), 576-587. https://doi.org/10.1038/s41396-018-0175-0

Roch, S., Nute, M., & Warnow, T. (2019). Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods. Systematic biology, 68(2), 281-297. https://doi.org/10.1093/sysbio/syy061

Bibak, K., & Milenkovic, O. (2019). Explicit formulas for the weight enumerators of some classes of deletion correcting codes. IEEE Transactions on Communications, 67(3), 1809-1816. [8573841]. https://doi.org/10.1109/TCOMM.2018.2886354

Xie, X., Lo, Y. C., Tong, Y., Qiao, J., Wang, G., Ogata, S., ... Liaw, P. K. (2019). Origin of serrated flow in bulk metallic glasses. Journal of the Mechanics and Physics of Solids, 124, 634-642. https://doi.org/10.1016/j.jmps.2018.11.015

Zhang, Q., Rao, S., & Warnow, T. (2019). Constrained incremental tree building: New absolute fast converging phylogeny estimation methods with improved scalability and accuracy. Algorithms for Molecular Biology, 14(1), [2]. https://doi.org/10.1186/s13015-019-0136-9

Murphy, K. A., Dahmen, K. A., & Jaeger, H. M. (2019). Transforming Mesoscale Granular Plasticity Through Particle Shape. Physical Review X, 9(1), [011014]. https://doi.org/10.1103/PhysRevX.9.011014

Breuer, M., Earnest, T. M., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., ... Luthey-Schulten, Z. (2019). Essential metabolism for a minimal cell. eLife, 8. https://doi.org/10.7554/eLife.36842

DeVille, L. (2019). Synchronization and Stability for Quantum Kuramoto. Journal of Statistical Physics, 174(1), 160-187. https://doi.org/10.1007/s10955-018-2168-9

Gregg, J. M., Kaczmarek, S. E., Bish, D. L., Machel, H. G., & Fouke, B. W. (2019). A dolomitization event at the oceanic chemocline during the Permian-Triassic transition. Geology, 47(7), e467-e467. https://doi.org/10.1130/G46203C.1

O’Dwyer, J. P. (Accepted/In press). Beyond an ecological ideal gas law. Nature Ecology and Evolution. https://doi.org/10.1038/s41559-019-1066-0

Mann, A. E., Mazel, F., Lemay, M. A., Morien, E., Billy, V., Kowalewski, M., ... Wegener Parfrey, L. (Accepted/In press). Biodiversity of protists and nematodes in the wild nonhuman primate gut. ISME Journal. https://doi.org/10.1038/s41396-019-0551-4

Li, Y., Li, Y., Jin, W., Sharpton, T. J., Mackie, R. I., Cann, I., ... Zhu, W. (2019). Combined genomic, transcriptomic, proteomic, and physiological characterization of the growth of Pecoramyces sp. F1 in Monoculture and Co-culture with a Syntrophic Methanogen. Frontiers in Microbiology, 10(MAR), [435]. https://doi.org/10.3389/fmicb.2019.00435

DeVille, L. X., Riemer, N., & West, M. (2019). Convergence of a generalized weighted flow algorithm for stochastic particle coagulation. Journal of Computational Dynamics, 6(1), 69-94. https://doi.org/10.3934/jcd.2019003

Salje, E. K. H., Xue, D., Ding, X., Dahmen, K. A., & Scott, J. F. (2019). Ferroelectric switching and scale invariant avalanches in BaTi O3. Physical Review Materials, 3(1), [014415]. https://doi.org/10.1103/PhysRevMaterials.3.014415

Sivaguru, M., Lieske, J. C., Krambeck, A. E., & Fouke, B. W. (Accepted/In press). GeoBioMed sheds new light on human kidney stone crystallization and dissolution. Nature Reviews Urology. https://doi.org/10.1038/s41585-019-0256-5

Clifton, S. M., Kim, T., Chandrashekhar, J. H., O'Toole, G. A., Rapti, Z., & Whitaker, R. J. (2019). Lying in wait: Modeling the control of bacterial infections via antibiotic-induced proviruses. mSystems, 4(5), [e00221-19]. https://doi.org/10.1128/mSystems.00221-19

Zealand, A. M., Mei, R., Roskilly, A. P., Liu, W. T., & Graham, D. W. (2019). Molecular microbial ecology of stable versus failing rice straw anaerobic digesters. Microbial Biotechnology, 12(5), 879-891. https://doi.org/10.1111/1751-7915.13438

Warnow, T. (2019). New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation. In M. A. Vega-Rodríguez, I. Holmes, & C. Martín-Vide (Eds.), Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings (pp. 3-21). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11488 LNBI). Springer-Verlag. https://doi.org/10.1007/978-3-030-18174-1_1

Yuan, H., Mei, R., Liao, J., & Liu, W. T. (2019). Nexus of stochastic and deterministic processes on microbial community assembly in biological systems. Frontiers in Microbiology, 10(JULY), [1536]. https://doi.org/10.3389/fmicb.2019.01536

Dau, H., Milenkovic, O., & Puleo, G. J. (Accepted/In press). On the triangle clique cover and Kt clique cover problems. Discrete Mathematics, [111627]. https://doi.org/10.1016/j.disc.2019.111627

Golding, I. (Accepted/In press). Revisiting Replication-Induced Transcription in Escherichia coli. BioEssays, [1900193]. https://doi.org/10.1002/bies.201900193

Doden, H. L., Pollet, R. M., Mythen, S. M., Wawrzak, Z., Devendran, S., Cann, I., ... Ridlon, J. M. (2019). Structural and biochemical characterization of 20-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32. Journal of Biological Chemistry, 294(32), 12040-12053. https://doi.org/10.1074/jbc.RA119.009390

Lu, T., Liu, F., Mao, J., & Hua, Q. (2019). Synthetic, Context-Dependent Microbial Consortium of Predator and Prey. ACS synthetic biology. https://doi.org/10.1021/acssynbio.9b00110

Ridlon, J. M., Devendran, S., Alves, J. M., Doden, H., Wolf, P. G., Pereira, G. V., ... Gaskins, H. R. (2019). The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. Gut Microbes. https://doi.org/10.1080/19490976.2019.1618173

Andris, C., Liu, X., Mitchell, J., O’Dwyer, J., & Van Cleve, J. (Accepted/In press). Threads across the urban fabric: Youth mentorship relationships as neighborhood bridges. Journal of Urban Affairs. https://doi.org/10.1080/07352166.2019.1662726

Le, T., Sy, A., Molloy, E. K., Zhang, Q. R., Rao, S., & Warnow, T. (2019). Using INC Within Divide-and-Conquer Phylogeny Estimation. In M. A. Vega-Rodríguez, I. Holmes, & C. Martín-Vide (Eds.), Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings (pp. 167-178). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11488 LNBI). Springer-Verlag. https://doi.org/10.1007/978-3-030-18174-1_12

Bohn-Wippert, K., Tevonian, E. N., Lu, Y., Huang, M. Y., Megaridis, M. R., & Dar, R. D. (2018). Cell Size-Based Decision-Making of a Viral Gene Circuit. Cell Reports, 25(13), 3844-3857.e5. https://doi.org/10.1016/j.celrep.2018.12.009

Mei, R., Nobu, M. K., Narihiro, T., Yu, J., Sathyagal, A., Willman, E., & Liu, W-T. (2018). Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. Water Research, 147, 403-412. https://doi.org/10.1016/j.watres.2018.10.026

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