Skip to main content

Illinois IGB

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].

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].

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].

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

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].

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].

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.

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].

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].

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].

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.

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].

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.

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].

Mei, R., & Liu, W. T. (2019). Quantifying the contribution of microbial immigration in engineered water systems. Microbiome, 7(1), [144].

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].

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.

One Thousand Plant Transcriptomes Initiative (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574(7780), 679-685.

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].

Mungan, M., Sastry, S., Dahmen, K., & Regev, I. (2019). Networks and hierarchies: How amorphous materials learn to remember. Physical review letters, 123(17), [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].

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].

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.

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].

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.

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].

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].

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.

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].

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.

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].

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].

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.

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.

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).

Molloy, E. K., & Warnow, T. (2019). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms for Molecular Biology, 14(1), [14].

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.

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].

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].

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.

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].

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].

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.

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..

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.

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..

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.

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].

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].,

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.

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.

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].

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].

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.

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.

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].

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.

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.

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.

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.

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.

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].

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.

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].

Murphy, K. A., Dahmen, K. A., & Jaeger, H. M. (2019). Transforming Mesoscale Granular Plasticity Through Particle Shape. Physical Review X, 9(1), [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.

DeVille, L. (2019). Synchronization and Stability for Quantum Kuramoto. Journal of Statistical Physics, 174(1), 160-187.

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.

O’Dwyer, J. P. (Accepted/In press). Beyond an ecological ideal gas law. Nature Ecology and Evolution.

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.

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].

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.

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].

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.

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].

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.

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.

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].

Dau, H., Milenkovic, O., & Puleo, G. J. (Accepted/In press). On the triangle clique cover and Kt clique cover problems. Discrete Mathematics, [111627].

Golding, I. (Accepted/In press). Revisiting Replication-Induced Transcription in Escherichia coli. BioEssays, [1900193].

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.

Lu, T., Liu, F., Mao, J., & Hua, Q. (2019). Synthetic, Context-Dependent Microbial Consortium of Predator and Prey. ACS synthetic biology.

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.

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.

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.

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.

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.

Ravanmehr, V., Puleo, G. J., Bolouki, S., & Milenkovic, O. (2018). Paired threshold graphs. Discrete Applied Mathematics, 250, 291-308.

Lee, G., Sherer, N. A., Kim, N. H., Rajic, E., Kaur, D., Urriola, N., ... Kuhlman, T. E. (2018). Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell. Proceedings of the National Academy of Sciences of the United States of America, 115(49), 12465-12470.

O'Dwyer, J. P., & Cornell, S. J. (2018). Cross-scale neutral ecology and the maintenance of biodiversity. Scientific reports, 8(1), [10200].

Hu, Y., Shu, L., Yang, Q., Guo, W., Liaw, P. K., Dahmen, K. A., & Zuo, J. M. (2018). Dislocation avalanche mechanism in slowly compressed high entropy alloy nanopillars. Communications Physics, 1(1), [61].

Shen, Y., Huang, P. C., Huang, C., Sun, P., Monroy, G. L., Wu, W., ... Nguyen, T. H. (2018). Effect of divalent ions and a polyphosphate on composition, structure, and stiffness of simulated drinking water biofilms. npj Biofilms and Microbiomes, 4(1), [15].

Sivaguru, M., Saw, J. J., Williams, J. C., Lieske, J. C., Krambeck, A. E., Romero, M. F., ... Fouke, B. W. (2018). Geobiology reveals how human kidney stones dissolve in vivo. Scientific reports, 8(1), [13731].

Butler, S., & O'Dwyer, J. P. (2018). Stability criteria for complex microbial communities. Nature communications, 9(1), [2970].

Zhang, C., Phillips, A. P. R., Wipfler, R. L., Olsen, G. J., & Whitaker, R. J. (2018). The essential genome of the crenarchaeal model Sulfolobus islandicus. Nature communications, 9(1), [4908].

Shiraishi, M., Ishino, S., Heffernan, M., Cann, I., & Ishino, Y. (2018). The mesophilic archaeon Methanosarcina acetivorans counteracts uracil in DNA with multiple enzymes: EndoQ, ExoIII, and UDG. Scientific reports, 8(1), [15791].

Neu, L., Bänziger, C., Proctor, C. R., Zhang, Y., Liu, W. T., & Hammes, F. (2018). Ugly ducklings - The dark side of plastic materials in contact with potable water. npj Biofilms and Microbiomes, 4(1), [7].

Narihiro, T., Nobu, M. K., Bocher, B. T. W., Mei, R., & Liu, W-T. (2018). Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors. Environmental Microbiology Reports, 10(6), 673-685.

Hidalgo-Ahumada, C. A. P., Nobu, M. K., Narihiro, T., Tamaki, H., Liu, W. T., Kamagata, Y., ... Sousa, D. Z. (2018). Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environmental Microbiology, 20(12), 4503-4511.

Ozgen, V. C., Kong, W., Blanchard, A. E., Liu, F., & Lu, T. (2018). Spatial interference scale as a determinant of microbial range expansion. Science Advances, 4(11), [eaau0695].

Collins, K., & Warnow, T. (2018). PASTA for proteins. Bioinformatics, 34(22), 3939-3941.

Wright, W. J., Long, A. A., Gu, X., Liu, X., Hufnagel, T. C., & Dahmen, K. A. (2018). Slip statistics for a bulk metallic glass composite reflect its ductility. Journal of Applied Physics, 124(18), [185101].

Harris, S. C., Devendran, S., Méndez- García, C., Mythen, S. M., Wright, C. L., Fields, C. J., ... Ridlon, J. M. (2018). Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243 T Gut Microbes, 9(6), 523-539.

Post, K. W., McLeod, A. S., Hepting, M., Bluschke, M., Wang, Y., Cristiani, G., ... Basov, D. N. (2018). Coexisting first- and second-order electronic phase transitions in a correlated oxide. Nature Physics, 14(10), 1056-1061.

Bronski, J. C., Carty, T., & Deville, L. (2018). Configurational stability for the Kuramoto-Sakaguchi model. Chaos, 28(10), [103109].

Zealand, A. M., Mei, R., Papachristodoulou, P., Roskilly, A. P., Liu, W. T., & Graham, D. W. (2018). Microbial community composition and diversity in rice straw digestion bioreactors with and without dairy manure. Applied Microbiology and Biotechnology, 102(19), 8599-8612.

Dau, H., Duursma, I. M., Kiah, H. M., & Milenkovic, O. (2018). Repairing Reed-Solomon Codes With Multiple Erasures. IEEE Transactions on Information Theory, 64(10), 6567-6582. [8340062].

Khatun, M. A., Hoque, M. A., Zhang, Y., Lu, T., Cui, L., Zhou, N. Y., & Feng, Y. (2018). Bacterial Consortium-Based Sensing System for Detecting Organophosphorus Pesticides. Analytical chemistry, 90(17), 10577-10584.

Sutton, N. M., & O'Dwyer, J. P. (2018). Born to run? Quantifying the balance of prior bias and new information in prey escape decisions. American Naturalist, 192(3), 321-331.

Gaulke, C. A., Arnold, H. K., Humphreys, I. R., Kembel, S. W., O’dwyer, J. P., & Sharpton, T. J. (2018). Ecophylogenetics clarifies the evolutionary association between mammals and their gut microbiota. mBio, 9(5), [e01348-18].

Tabatabaei Yazdi, S. M. H., Kiah, H. M., Gabrys, R., & Milenkovic, O. (2018). Mutually uncorrelated primers for DNA-based data storage. IEEE Transactions on Information Theory, 64(9), 6283-6296. [8255669].

D'Alessandro-Gabazza, C. N., Méndez-García, C., Hataji, O., Westergaard, S., Watanabe, F., Yasuma, T., ... Gabazza, E. C. (2018). Identification of halophilic microbes in lung fibrotic tissue by oligotyping. Frontiers in Microbiology, 9(AUG), [1892].

Pattabiraman, S., & Warnow, T. (2018). Are Profile Hidden Markov Models Identifiable? In ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 448-456). (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery, Inc.

Gabrys, R., & Milenkovic, O. (2018). Unique Reconstruction of Coded Sequences from Multiset Substring Spectra. In 2018 IEEE International Symposium on Information Theory, ISIT 2018 (Vol. 2018-June, pp. 2540-2544). [8437909] Institute of Electrical and Electronics Engineers Inc..

Bibak, K., & Milenkovic, O. (2018). Weight Enumerators of Some Classes of Deletion Correcting Codes. In 2018 IEEE International Symposium on Information Theory, ISIT 2018 (Vol. 2018-June, pp. 431-435). [8437121] Institute of Electrical and Electronics Engineers Inc..

Kong, W., Meldgin, D. R., Collins, J. J., & Lu, T. (2018). Designing microbial consortia with defined social interactions. Nature chemical biology, 14(8), 821-829.

Bianchi, D. M., Peterson, J. R., Earnest, T. M., Hallock, M. J., & Luthey-Schulten, Z. A. (2018). Hybrid CME-ODE method for efficient simulation of the galactose switch in yeast. IET Systems Biology, 12(4), 170-176.

Zhang, Q., Rao, S., & Warnow, T. (2018). New absolute fast converging phylogeny estimation methods with improved scalability and accuracy. In L. Parida, & E. Ukkonen (Eds.), 18th International Workshop on Algorithms in Bioinformatics, WABI 2018 [8] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 113). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing.

Tang, Q., Lu, T., & Liu, S. J. (2018). Developing a Synthetic Biology Toolkit for Comamonas testosteroni, an Emerging Cellular Chassis for Bioremediation. ACS synthetic biology, 7(7), 1753-1762.

Shih, H. Y., Mickalide, H., Fraebel, D. T., Goldenfeld, N., & Kuehn, S. (2018). Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution. Physical Biology, 15(6), [065003].

The Genome Standards Consortium (2018). Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893). Nature Biotechnology, 36(7).

Arkin, A. P., Cottingham, R. W., Henry, C. S., Harris, N. L., Stevens, R. L., Maslov, S., ... Yu, D. (2018). KBase: The United States department of energy systems biology knowledgebase. Nature Biotechnology, 36(7), 566-569.

Chen, S., Li, W., Xie, X., Brechtl, J., Chen, B., Li, P., ... Liaw, P. K. (2018). Nanoscale serration and creep characteristics of Al0.5CoCrCuFeNi high-entropy alloys. Journal of Alloys and Compounds, 752, 464-475.

Liu, G., Zhang, Y., van der Mark, E., Magic-Knezev, A., Pinto, A., van den Bogert, B., ... Medema, G. (2018). Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints. Water Research, 138, 86-96.

Lao, Y., Caravelli, F., Sheikh, M., Sklenar, J., Gardeazabal, D., Watts, J. D., ... Schiffer, P. (2018). Classical topological order in the kinetics of artificial spin ice. Nature Physics, 14(7), 723-727.

Jia, H., Xie, X., Zhao, L., Wang, J., Gao, Y., Dahmen, K. A., ... Ma, C. (2018). Effects of similar-element-substitution on the glass-forming ability and mechanical behaviors of Ti-Cu-Zr-Pd bulk metallic glasses. Journal of Materials Research and Technology, 7(3), 261-269.

Vachaspati, P., & Warnow, T. (2018). SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. Molecular Phylogenetics and Evolution, 124, 122-136.

McFaul, L. W., Wright, W. J., Gu, X., Uhl, J. T., & Dahmen, K. A. (2018). Aftershocks in slowly compressed bulk metallic glasses: Experiments and theory. Physical Review E, 97(6), [063005].

Karig, D., Michael Martini, K., Lu, T., DeLateur, N. A., Goldenfeld, N., & Weiss, R. (2018). Stochastic Turing patterns in a synthetic bacterial population. Proceedings of the National Academy of Sciences of the United States of America, 115(26), 6572-6577.

Vlčková, K., Pafčo, B., Petrželková, K. J., Modrý, D., Todd, A., Yeoman, C. J., ... Gomez, A. (2018). Relationships between gastrointestinal parasite infections and the fecal microbiome in free-ranging western lowland gorillas. Frontiers in Microbiology, 9(JUN), [1202].

Hansen, M. M. K., Wen, W. Y., Ingerman, E., Razooky, B. S., Thompson, C. E., Dar, R. D., ... Weinberger, L. S. (2018). A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization. Cell, 173(7), 1609-1621.e15.

Baró, J., Dahmen, K. A., Davidsen, J., Planes, A., Castillo, P. O., Nataf, G. F., ... Vives, E. (2018). Experimental Evidence of Accelerated Seismic Release without Critical Failure in Acoustic Emissions of Compressed Nanoporous Materials. Physical review letters, 120(24), [245501].

Munson-Mcgee, J. H., Peng, S., Dewerff, S., Stepanauskas, R., Whitaker, R., Weitz, J. S., & Young, M. J. (2018). A virus or more in (nearly) every cell: Ubiquitous networks of virus-host interactions in extreme environments. ISME Journal, 12(7), 1706-1714.

Ling, F., Whitaker, R., LeChevallier, M. W., & Liu, W. T. (2018). Drinking water microbiome assembly induced by water stagnation. ISME Journal, 12(6), 1520-1531.

Puleo, G. J., & Milenkovic, O. (2018). Correlation Clustering and Biclustering with Locally Bounded Errors. IEEE Transactions on Information Theory, 64(6), 4105-4119.

Cassidy, C. K., Himes, B. A., Luthey-Schulten, Z. A., & Zhang, P. (2018). CryoEM-based hybrid modeling approaches for structure determination. Current Opinion in Microbiology, 43, 14-23.

Clayton, J. B., Gomez, A., Amato, K., Knights, D., Travis, D. A., Blekhman, R., ... Johnson, T. J. (2018). The gut microbiome of nonhuman primates: Lessons in ecology and evolution. American journal of primatology, 80(6), [e22867].

D'Andrea, R., Ostling, A., & O'Dwyer, J. P. (2018). Translucent windows: how uncertainty in competitive interactions impacts detection of community pattern. Ecology Letters, 21(6), 826-835.

Tang, Q., Lu, T., & Liu, S. J. (2018). Engineering the bacterium Comamonas testosteroni CNB-1: Plasmid curing and genetic manipulation. Biochemical Engineering Journal, 133, 74-82.

Vachaspati, P., & Warnow, T. (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC genomics, 19, [252].

Nute, M., Chou, J., Molloy, E. K., & Warnow, T. (2018). The performance of coalescent-based species tree estimation methods under models of missing data. BMC genomics, 19, [286].

Chen, S., Xie, X., Li, W., Feng, R., Chen, B., Qiao, J., ... Liaw, P. K. (2018). Temperature effects on the serrated behavior of an Al0.5CoCrCuFeNi high-entropy alloy. Materials Chemistry and Physics, 210, 20-28.

Nishihama, K., Yasuma, T., Yano, Y., D' Alessandro-Gabazza, C. N., Toda, M., Hinneh, J. A., ... Gabazza, E. C. (2018). Anti-apoptotic activity of human matrix metalloproteinase-2 attenuates diabetes mellitus. Metabolism: Clinical and Experimental, 82, 88-99.

Milenkovic, O., Gabrys, R., Kiah, H. M., & Yazdi, S. M. H. T. (2018). Exabytes in a Test Tube: With the right coding, DNA could archive our entire civilization. IEEE Spectrum, 55(5), 40-45.

Cao, P., Dahmen, K. A., Kushima, A., Wright, W. J., Park, H. S., Short, M. P., & Yip, S. (2018). Nanomechanics of slip avalanches in amorphous plasticity. Journal of the Mechanics and Physics of Solids, 114, 158-171.

Fung, T., O'Dwyer, J. P., & Chisholm, R. A. (2018). Quantifying species extinction risk under temporal environmental variance. Ecological Complexity, 34, 139-146.

Coleman, J. P., Dahmen, K. A., & Weaver, R. L. (2018). Avalanches and scaling collapse in the large- N Kuramoto model. Physical Review E, 97(4), [042219].

Melo, M. C. R., Bernardi, R. C., Rudack, T., Scheurer, M., Riplinger, C., Phillips, J. C., ... Luthey-Schulten, Z. A. (2018). NAMD goes quantum: An integrative suite for hybrid simulations. Nature Methods, 15(5), 351-354.

Bronski, J. C., DeVille, L. X., Ferguson, T., & Livesay, M. (2018). Stable configurations in social networks. Nonlinearity, 31(6), 2518-2531.

O'Dwyer, J. P. (Accepted/In press). Whence Lotka-Volterra? Conservation laws and integrable systems in ecology. Theoretical Ecology, 1-12.

Ma, W., Whitley, K. D., Chemla, Y. R., Luthey-Schulten, Z., & Schulten, K. (2018). Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase. eLife, 7, [e34186].

Earnest, T. M., Cole, J. A., & Luthey-Schulten, Z. A. (2018). Simulating biological processes: Stochastic physics from whole cells to colonies. Reports on Progress in Physics, 81(5), [052601].

Mythen, S. M., Devendran, S., Méndez-García, C., Cann, I., & Ridlon, J. M. (2018). Targeted synthesis and characterization of a gene cluster encoding NAD(P)H-dependent 3α-, 3β-, and 12α-hydroxysteroid dehydrogenases from Eggerthella CAG:298, a gut metagenomic sequence. Applied and environmental microbiology, 84(7), [e02475-17].

Gabrys, R., Yaakobi, E., & Milenkovic, O. (2018). Codes in the Damerau Distance for Deletion and Adjacent Transposition Correction. IEEE Transactions on Information Theory, 64(4), 2550-2570.

Antonopoulos, D. A., Assaf, R., Aziz, R. K., Brettin, T., Bun, C., Conrad, N., ... Yoo, H. (2018). PATRIC as a unique resource for studying antimicrobial resistance. Briefings in bioinformatics, 20(4), 1094-1102.

Branscomb, E., Biancalani, T., Goldenfeld, N., & Russell, M. (2018). Escapement mechanisms and the conversion of disequilibria; the engines of creation. Physics Reports, 677, 1-60.

Ravanmehr, V., Kim, M., Wang, Z., & Milenkovic, O. (2018). ChIPWig: A random access-enabling lossless and lossy compression method for ChIP-seq data. Bioinformatics, 34(6), 911-919.

Christensen, S., Molloy, E. K., Vachaspati, P., & Warnow, T. (2018). OCTAL: Optimal Completion of gene trees in polynomial time. Algorithms for Molecular Biology, 13(1), [6].

Molloy, E. K., & Warnow, T. (2018). To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods. Systematic biology, 67(2), 285-303.

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., ... Baker, W. J. (2018). A roadmap for global synthesis of the plant tree of life. American journal of botany, 105(3), 614-622.

Raulo, A., Ruokolainen, L., Lane, A., Amato, K., Knight, R., Leigh, S., ... Tecot, S. R. (2018). Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. Journal of Animal Ecology, 87(2), 388-399.

Gernat, T., Rao, V. D., Middendorf, M., Dankowicz, H., Goldenfeld, N., & Robinson, G. E. (2018). Automated monitoring of behavior reveals bursty interaction patterns and rapid spreading dynamics in honeybee social networks. Proceedings of the National Academy of Sciences of the United States of America, 115(7), 1433-1438.

Blanchard, A. E., Liao, C., & Lu, T. (2018). Circuit-Host Coupling Induces Multifaceted Behavioral Modulations of a Gene Switch. Biophysical journal, 114(3), 737-746.

Fang, T., Cui, Q., Huang, Y., Dong, P., Wang, H., Liu, W-T., & Ye, Q. (2018). Distribution comparison and risk assessment of free-floating and particle-attached bacterial pathogens in urban recreational water: Implications for water quality management. Science of the Total Environment, 613-614, 428-438.

Chen, P. Y., Lee, C., Wang, S. Y., Seifi, M., Lewandowski, J. J., Dahmen, K. A., ... Liaw, P. K. (2018). Fatigue behavior of high-entropy alloys: A review. Science China Technological Sciences, 61(2), 168-178.

Mackie, R. I., & Cann, I. (2018). Let them eat fruit. Nature Microbiology, 3(2), 127-129.

Chen, S. H., Domel, A., Yue, T. M., Tsui, C. P., Chan, K. C., Dahmen, K. A., & Liaw, P. K. (2018). Deformation behavior of bulk metallic glasses under a mixed-mode (I/II) loading condition. Intermetallics, 93, 148-154.

Mulder, N., Schwartz, R., Brazas, M. D., Brooksbank, C., Gaeta, B., Morgan, S. L., ... Welch, L. (2018). The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS computational biology, 14(2), [e1005772].

Bayzid, M. S., & Warnow, T. (2018). Gene tree parsimony for incomplete gene trees: Addressing true biological loss. Algorithms for Molecular Biology, 13(1), [1].

Seo, S. O., Lu, T., Jin, Y-S., & Blaschek, H-P. M. (2018). Development of an oxygen-independent flavin mononucleotide-based fluorescent reporter system in Clostridium beijerinckii and its potential applications. Journal of Biotechnology, 265, 119-126.

Zhang, Z. T., Jiménez-Bonilla, P., Seo, S. O., Lu, T., Jin, Y-S., Blaschek, H-P. M., & Wang, Y. (2018). Bacterial genome editing with CRISPR-Cas9: Taking clostridium beijerinckii as an example. In Methods in Molecular Biology (pp. 297-325). (Methods in Molecular Biology; Vol. 1772). Humana Press Inc..

Naas, A. E., Solden, L. M., Norbeck, A. D., Brewer, H., Hagen, L. H., Heggenes, I. M., ... Pope, P. B. (2018). "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system. Microbiome, 6(1), [44].

Dau, H., & Milenkovic, O. (2018). Maxminsum steiner systems for access balancing in distributed storage. SIAM Journal on Discrete Mathematics, 32(3), 1644-1671.

Oh, S., Hammes, F., & Liu, W-T. (2018). Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant. Water Research, 128, 278-285.

Peng, J., Milenkovic, O., & Ochoa, I. (2018). METHCOMP: A special purpose compression platform for DNA methylation data. Bioinformatics, 34(15), 2654-2656.

Zhang, C., & Whitaker, R. J. (2018). Microhomology-mediated high-throughput gene inactivation strategy for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Applied and environmental microbiology, 84(1), [e02167-17].

Molloy, E. K., & Warnow, T. (2018). NJMerge: A Generic technique for scaling phylogeny estimation methods and its application to species trees. In A. Ouangraoua, & M. Blanchette (Eds.), Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Proceedings (pp. 260-276). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11183 LNBI). Springer-Verlag.

Johnson, K. P., Nguyen, N. P., Sweet, A. D., Boyd, B. M., Warnow, T., & Allen, J. M. (2018). Simultaneous radiation of bird and mammal lice following the K-Pg boundary. Biology Letters, 14(5), [20180141].

Li, P., & Milenkovic, O. (2018). Submodular hypergraphs: P-Laplacians, cheeger inequalities and spectral clustering. In J. Dy, & A. Krause (Eds.), 35th International Conference on Machine Learning, ICML 2018 (pp. 4690-4719). (35th International Conference on Machine Learning, ICML 2018; Vol. 7). International Machine Learning Society (IMLS).

Vlčková, K., Shutt-Phillip, K., Heisterman, M., Pafčo, B., Petrželkov, K. J., Todd, A., ... Gomez, A. (2018). Impact of stress on the gut microbiome of free-ranging western lowland gorillas. Microbiology (United Kingdom), 164(1), 40-44. [000587].

Thomer, A. K., Wickett, K. M., Baker, K. S., Fouke, B. W., & Palmer, C. L. (2018). Documenting provenance in noncomputational workflows: Research process models based on geobiology fieldwork in Yellowstone National Park. Journal of the Association for Information Science and Technology.