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Research Areas

Biocomplexity: Publications

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].

DeVille, L. X. (2019). Optimizing Gershgorin for symmetric matrices. Linear Algebra and Its Applications, 577, 360-383.

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.

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.

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.

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.

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.

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.

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].

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 (Oxford, England), 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].

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.

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. A. (2019). Essential metabolism for a minimal cell. eLife, 8.

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

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].

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.

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].

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.

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.

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.

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.

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.

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

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].

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.

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. (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].

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].

Molloy, E. K., & Warnow, T. (2018). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge.

Bronski, J. C., Carty, T., & DeVille, L. X. (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.

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. (Accepted/In press). Born to Run? Quantifying the Balance of Prior Bias and New Information in Prey Escape Decisions. American Naturalist.

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].

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.

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. D., & Kuehn, S. (2018). Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution. Physical Biology, 15(6), [065003].

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.

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. 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.

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].

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.

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.

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.

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.

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.

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].

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.

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.

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.

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. A., & 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].

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.

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].

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.

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.

Gernat, T., Rao, V. D., Middendorf, M., Dankowicz, H., Goldenfeld, N. D., & 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.

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.

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.

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].

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].

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.

Zhang, C., & Whitaker, R. (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].

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.