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Carl R. Woese Institute for Genomic Biology

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Research Areas

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

DeVille, L. X. (2019). Optimizing Gershgorin for symmetric matrices. Linear Algebra and Its Applications, 577, 360-383. https://doi.org/10.1016/j.laa.2019.04.034

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

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

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

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. https://doi.org/10.3389/fmars.2019.00306

Sedlak, S. M., Schendel, L. C., Melo, M. C. R., Pippig, D. A., Luthey-Schulten, Z. A., 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, 275-287. https://doi.org/10.1016/j.watres.2019.02.020

Pauly, M. D., Bautista, M. A., Black, J. A., & Whitaker, R. (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 (Oxford, England), 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

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

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. A. (2019). Essential metabolism for a minimal cell. eLife, 8. https://doi.org/10.7554/eLife.36842

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

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

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. https://doi.org/10.1016/j.tim.2019.03.011

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

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

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

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

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. https://doi.org/10.1073/pnas.1807709115

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. https://doi.org/10.1111/1758-2229.12689

O'Dwyer, J. P., & Cornell, S. J. (2018). Cross-scale neutral ecology and the maintenance of biodiversity. Scientific Reports, 8(1), [10200]. https://doi.org/10.1038/s41598-018-27712-7

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]. https://doi.org/10.1038/s41522-018-0058-1

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]. https://doi.org/10.1038/s41598-018-31890-9

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. https://doi.org/10.1111/1462-2920.14388

Butler, S., & O'Dwyer, J. P. (2018). Stability criteria for complex microbial communities. Nature Communications, 9(1), [2970]. https://doi.org/10.1038/s41467-018-05308-z

Zhang, C., Phillips, A. P. R., Wipfler, R. L., Olsen, G. J., & Whitaker, R. (2018). The essential genome of the crenarchaeal model Sulfolobus islandicus. Nature communications, 9(1), [4908]. https://doi.org/10.1038/s41467-018-07379-4

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]. https://doi.org/10.1038/s41598-018-34000-x

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]. https://doi.org/10.1038/s41522-018-0050-9

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]. https://doi.org/10.1126/sciadv.aau0695

Collins, K., & Warnow, T. (2018). PASTA for proteins. Bioinformatics, 34(22), 3939-3941. https://doi.org/10.1093/bioinformatics/bty495

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]. https://doi.org/10.1063/1.5051723

Molloy, E. K., & Warnow, T. (2018). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. https://doi.org/10.1101/469130

Bronski, J. C., Carty, T., & DeVille, L. X. (2018). Configurational stability for the Kuramoto-Sakaguchi model. Chaos, 28(10), [103109]. https://doi.org/10.1063/1.5029397

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. https://doi.org/10.1007/s00253-018-9243-7

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. https://doi.org/10.1021/acs.analchem.8b02709

Sutton, N. M., & O'Dwyer, J. P. (Accepted/In press). Born to Run? Quantifying the Balance of Prior Bias and New Information in Prey Escape Decisions. American Naturalist. https://doi.org/10.1086/698692

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]. https://doi.org/10.1128/mBio.01348-18

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]. https://doi.org/10.3389/fmicb.2018.01892

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. https://doi.org/10.1145/3233547.3233563

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. https://doi.org/10.1038/s41589-018-0091-7

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. https://doi.org/10.1049/iet-syb.2017.0070

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. https://doi.org/10.4230/LIPIcs.WABI.2018.8

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. https://doi.org/10.1021/acssynbio.7b00430

Shih, H. Y., Mickalide, H., Fraebel, D. T., Goldenfeld, N. D., & Kuehn, S. (2018). Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution. Physical Biology, 15(6), [065003]. https://doi.org/10.1088/1478-3975/aac4e6

Post, K. W., Mcleod, A. S., Hepting, M., Bluschke, M., Wang, Y., Cristiani, G., ... Basov, D. N. (Accepted/In press). Coexisting first- and second-order electronic phase transitions in a correlated oxide. Nature Physics, 1-6. https://doi.org/10.1038/s41567-018-0201-1

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. https://doi.org/10.1038/nbt.4163

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. https://doi.org/10.1016/j.jallcom.2018.04.137

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. https://doi.org/10.1016/j.watres.2018.03.043

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. https://doi.org/10.1038/s41567-018-0077-0

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. https://doi.org/10.1016/j.jmrt.2017.08.009

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. https://doi.org/10.1016/j.ympev.2018.03.006

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]. https://doi.org/10.1103/PhysRevE.97.063005

Karig, D., Michael Martini, K., Lu, T., DeLateur, N. A., Goldenfeld, N. D., & 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. https://doi.org/10.1073/pnas.1720770115

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]. https://doi.org/10.3389/fmicb.2018.01202

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]. https://doi.org/10.1103/PhysRevLett.120.245501

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. https://doi.org/10.1038/s41396-018-0071-7

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. https://doi.org/10.1016/j.mib.2017.10.002

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. https://doi.org/10.1038/s41396-018-0101-5

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]. https://doi.org/10.1002/ajp.22867

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. https://doi.org/10.1111/ele.12946

Harris, S. C., Devendran, S., Méndez- García, C., Mythen, S. M., Wright, C. L., Fields, C. J., ... Ridlon, J. M. (Accepted/In press). Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243TGut Microbes, 1-17. https://doi.org/10.1080/19490976.2018.1458180

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. https://doi.org/10.1016/j.bej.2018.01.030

Vachaspati, P., & Warnow, T. (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC genomics, 19, [252]. https://doi.org/10.1186/s12864-018-4621-1

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]. https://doi.org/10.1186/s12864-018-4619-8

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. https://doi.org/10.1016/j.metabol.2018.01.016

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. https://doi.org/10.1016/j.jmps.2018.02.012

Fung, T., O'Dwyer, J. P., & Chisholm, R. A. (2018). Quantifying species extinction risk under temporal environmental variance. Ecological Complexity, 34, 139-146. https://doi.org/10.1016/j.ecocom.2017.09.006

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. https://doi.org/10.1016/j.matchemphys.2017.09.004

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]. https://doi.org/10.1103/PhysRevE.97.042219

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. https://doi.org/10.1038/nmeth.4638

Bronski, J. C., DeVille, L. X., Ferguson, T., & Livesay, M. (2018). Stable configurations in social networks. Nonlinearity, 31(6), 2518-2531. https://doi.org/10.1088/1361-6544/aab0b5

O'Dwyer, J. P. (Accepted/In press). Whence Lotka-Volterra? Conservation laws and integrable systems in ecology. Theoretical Ecology, 1-12. https://doi.org/10.1007/s12080-018-0377-0

Ma, W., Whitley, K. D., Chemla, Y. R., Luthey-Schulten, Z. A., & Schulten, K. (2018). Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase. eLife, 7, [e34186]. https://doi.org/10.7554/eLife.34186

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]. https://doi.org/10.1088/1361-6633/aaae2c

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]. https://doi.org/10.1128/AEM.02475-17

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. https://doi.org/10.1016/j.physrep.2017.02.001

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]. https://doi.org/10.1186/s13015-018-0124-5

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. https://doi.org/10.1002/ajb2.1041

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