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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Dong, Y., Sanford, R. A., Boyanov, M. I., Kemner, K. M., Flynn, T. M., O’Loughlin, E. J., ... Fouke, B. W. (2016). Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater. International Journal of Systematic and Evolutionary Microbiology, 66(10), 3964-3971. [001295]. DOI: 10.1099/ijsem.0.001295
 
Xue, C., & Goldenfeld, N. (2016). Stochastic predator-prey dynamics of transposons in the human genome. Physical Review Letters, 117(20), [208101]. DOI: 10.1103/PhysRevLett.117.208101
 
Dong, Y., Sanford, R. A., Boyanov, M. I., Kemner, K. M., Flynn, T. M., O'Loughlin, E. J., ... Fouke, B. W. (2016). Orenia metallireducens sp. nov. strain Z6, a novel metal-reducing member of the phylum firmicutes from the deep subsurface. Applied and Environmental Microbiology, 82(21), 6440-6453. DOI: 10.1128/AEM.02382-16
 
Stone, J. E., Hallock, M. J., Phillips, J. C., Peterson, J. R., Luthey-Schulten, Z., & Schulten, K. (2016). Evaluation of emerging energy-efficient heterogeneous computing platforms for biomolecular and cellular simulation workloads. In Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2016. (Vol. 2016-August, pp. 89-100). [7529854] IEEE Computer Society. DOI: 10.1109/IPDPSW.2016.130
 
Hallock, M. J., & Luthey-Schulten, Z. (2016). Improving reaction kernel performance in lattice microbes: Particle-wise propensities and run-time generated code. In Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2016. (Vol. 2016-August, pp. 428-434). [7529899] IEEE Computer Society. DOI: 10.1109/IPDPSW.2016.118
 
Narihiro, T., Nobu, M. K., Tamaki, H., Kamagata, Y., Sekiguchi, Y., & Liu, W. T. (2016). Comparative genomics of syntrophic branched-chain fatty acid degrading bacteria. Microbes and Environments, 31(3), 288-292. DOI: 10.1264/jsme2.ME16057
 
Mei, R., Narihiro, T., Nobu, M. K., Kuroda, K., & Liu, W. T. (2016). Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity. Scientific Reports, 6, [34090]. DOI: 10.1038/srep34090
 
Wang, K., Pereira, G. V., Cavalcante, J. J. V., Zhang, M., Mackie, R., & Cann, I. (2016). Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan. Scientific Reports, 6, [34360]. DOI: 10.1038/srep34360
 
Ghaemi, Z., Guzman, I., Baek, J. U. J., Gruebele, M., & Luthey-Schulten, Z. (2016). Estimation of Relative Protein-RNA Binding Strengths from Fluctuations in the Bound State. Journal of Chemical Theory and Computation, 12(9), 4593-4599. DOI: 10.1021/acs.jctc.6b00418
 
He, F., Karve, A. A., Maslov, S., & Babst, B. A. (2016). Large-scale public transcriptomic data mining reveals a tight connection between the transport of nitrogen and other transport processes in arabidopsis. Frontiers in Plant Science, 7(AUG2016), [1207]. DOI: 10.3389/fpls.2016.01207
 
Cook, M. D., Allen, J. M., Pence, B. D., Wallig, M. A., Gaskins, H. R., White, B. A., & Woods, J. A. (2016). Exercise and gut immune function: Evidence of alterations in colon immune cell homeostasis and microbiome characteristics with exercise training. Immunology and Cell Biology, 94(2), 158-163. DOI: 10.1038/icb.2015.108
 
Iakiviak, M., Devendran, S., Skorupski, A., Moon, Y. H., Mackie, R. I., & Cann, I. (2016). Functional and modular analyses of diverse endoglucanases from Ruminococcus albus 8, a specialist plant cell wall degrading bacterium. Scientific Reports, 6, [29979]. DOI: 10.1038/srep29979
 
Mirarab, S., Bayzid, M. S., & Warnow, T. (2016). Evaluating summarymethods for multilocus species tree estimation in the presence of incomplete lineage sorting. Systematic Biology, 65(3), 366-380. DOI: 10.1093/sysbio/syu063
 
Bennett, G., Malone, M., Sauther, M. L., Cuozzo, F. P., White, B., Nelson, K. E., ... Amato, K. R. (2016). Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta). American Journal of Primatology, 78(8), 883-892. DOI: 10.1002/ajp.22555
 
He, F., Yoo, S., Wang, D., Kumari, S., Gerstein, M., Ware, D., & Maslov, S. (2016). Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. Plant Journal, 86(6), 472-480. DOI: 10.1111/tpj.13175
 
Despres, J., Forano, E., Lepercq, P., Comtet-Marre, S., Jubelin, G., Chambon, C., ... Mosoni, P. (2016). Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics, 17(1), [326]. DOI: 10.1186/s12864-016-2680-8
 
Kim, N. H., Leea, G., Sherer, N. A., Martini, K. M., Goldenfeld, N., & Kuhlman, T. E. (2016). Real-time transposable element activity in individual live cells. Proceedings of the National Academy of Sciences of the United States of America, 113(26), 7278-7283. DOI: 10.1073/pnas.1601833113
 
Whitaker, R. J., & Vanderpool, C. K. (2016). CRISPR-Cas Gatekeeper: Slow on the Uptake but Gets the Job Done. Cell Host and Microbe, 19(2), 135-137. DOI: 10.1016/j.chom.2016.01.015
 
Oh, S., Yoo, D., & Liu, W. T. (2016). Metagenomics reveals a novel virophage population in a Tibetan mountain lake. Microbes and Environments, 31(2), 173-177. DOI: 10.1264/jsme2.ME16003
 
Welch, L., Brooksbank, C., Schwartz, R., Morgan, S. L., Gaeta, B., Kilpatrick, A. M., ... Warnow, T. (2016). Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee). PLoS Computational Biology, 12(5), [e1004943]. DOI: 10.1371/journal.pcbi.1004943
 
Yasuma, T., Yano, Y., D'Alessandro-Gabazza, C. N., Toda, M., Gil-Bernabe, P., Kobayashi, T., ... Gabazza, E. C. (2016). Amelioration of diabetes by protein S. Diabetes, 65(7), 1940-1951. DOI: 10.2337/db15-1404
 
Jeraldo, P., Hernandez, A., Nielsen, H. B., Chen, X., White, B. A., Goldenfeld, N., ... Chia, N. (2016). Capturing one of the human gut microbiome's most wanted: Reconstructing the genome of a novel butyrate-producing, clostridial scavenger from metagenomic sequence data. Frontiers in Microbiology, 7(MAY), [783]. DOI: 10.3389/fmicb.2016.00783
 
Despres, J., Forano, E., Lepercq, P., Comtet-Marre, S., Jubelin, G., Yeoman, C. J., ... Mosoni, P. (2016). Erratum to Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis [BMC Genomics, (2016), 17] DOI: 10.1186/s12864-016-2472-1. BMC Genomics, 17(1), [426]. DOI: 10.1186/s12864-016-2758-3
 
Hüter, C., Friák, M., Weikamp, M., Neugebauer, J., Goldenfeld, N., Svendsen, B., & Spatschek, R. (2016). Nonlinear elastic effects in phase field crystal and amplitude equations: Comparison to ab initio simulations of bcc metals and graphene. Physical Review B - Condensed Matter and Materials Physics, 93(21), [214105]. DOI: 10.1103/PhysRevB.93.214105
 
Braundmeier-Fleming, A., Russell, N. T., Yang, W., Nas, M. Y., Yaggie, R. E., Berry, M., ... Klumpp, D. J. (2016). Stool-based biomarkers of interstitial cystitis/bladder pain syndrome. Scientific Reports, 6, [26083]. DOI: 10.1038/srep26083
Despres, J., Forano, E., Lepercq, P., Comtet-Marre, S., Jubelin, G., Yeoman, C. J., ... Mosoni, P. (2016). Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics, 17(1), [147]. DOI: 10.1186/s12864-016-2472-1
 
Stumpf, R. M., Gomez, A., Amato, K. R., Yeoman, C. J., Polk, J. D., Wilson, B. A., ... Leigh, S. R. (2016). Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biological Conservation, 199, 56-66. DOI: 10.1016/j.biocon.2016.03.035
 
Zhang, C., She, Q., Bi, H., & Whitaker, R. J. (2016). The apt/6-methylpurine counterselection system and its applications in genetic studies of the hyperthermophilic archaeon Sulfolobus islandicus. Applied and Environmental Microbiology, 82(10), 3070-3081. DOI: 10.1128/AEM.00455-16
 
Shiraishi, M., Ishino, S., Yoshida, K., Yamagami, T., Cann, I., & Ishino, Y. (2016). PCNA is involved in the EndoQ-mediated DNA repair process in Thermococcales. Scientific Reports, 6, [25532]. DOI: 10.1038/srep25532
 
Oh, S., Zhang, R., Wu, Q. L., & Liu, W. T. (2016). Evolution and adaptation of SAR11 and Cyanobium in a saline Tibetan lake. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12408
 
Liu, G., Ling, F. Q., Van Der Mark, E. J., Zhang, X. D., Knezev, A., Verberk, J. Q. J. C., ... Van Dijk, J. C. (2016). Comparison of Particle-Associated Bacteria from a Drinking Water Treatment Plant and Distribution Reservoirs with Different Water Sources. Scientific Reports, 6, [20367]. DOI: 10.1038/srep20367
 
Srivastava, V., Weber, J. R., Malm, E., Fouke, B. W., & Bulone, V. (2016). Proteomic analysis of a poplar cell suspension culture suggests a major role of protein S-acylation in diverse cellular processes. Frontiers in Plant Science, 7(APR2016), [477]. DOI: 10.3389/fpls.2016.00477
 
Goldenfeld, N. (2016). Samuel Frederick Edwards: Founder of modern polymer and softmatter theory. Proceedings of the National Academy of Sciences of the United States of America, 113(1), 10-11. DOI: 10.1073/pnas.1523001113
 
Shih, H. Y., Hsieh, T. L., & Goldenfeld, N. (2016). Ecological collapse and the emergence of travelling waves at the onset of shear turbulence. Nature Physics, 12(3), 245-248. DOI: 10.1038/nphys3548
 
Davis, J. J., Gerdes, S., Olsen, G. J., Olson, R., Pusch, G. D., Shukla, M., ... Yoo, H. (2016). PATtyFams: Protein families for the microbial genomes in the PATRIC database. Frontiers in Microbiology, 7(FEB), [118]. DOI: 10.3389/fmicb.2016.00118
 
Bian, G., Ma, S., Zhu, Z., Su, Y., Zoetendal, E. G., Mackie, R., ... Zhu, W. (2016). Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model. Environmental Microbiology, 18(5), 1566-1577. DOI: 10.1111/1462-2920.13272
 
Haward, S. J., Poole, R. J., Alves, M. A., Oliveira, P. J., Goldenfeld, N., & Shen, A. Q. (2016). Tricritical spiral vortex instability in cross-slot flow. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 93(3), [031101]. DOI: 10.1103/PhysRevE.93.031101
 
Vlčková, K., Gomez, A., Petrželková, K. J., Whittier, C. A., Todd, A. F., Yeoman, C. J., ... Leigh, S. R. (2016). Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla). Microbial Ecology, 72(4), 943-954. DOI: 10.1007/s00248-016-0745-5
 
Gomez, A., Petrzelkova, K. J., Burns, M. B., Yeoman, C. J., Amato, K. R., Vlckova, K., ... Blekhman, R. (2016). Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Reports, 14(9), 2142-2153. DOI: 10.1016/j.celrep.2016.02.013
 
Cann, I., Bernardi, R. C., & Mackie, R. I. (2016). Cellulose degradation in the human gut: Ruminococcus champanellensis expands the cellulosome paradigm. Environmental Microbiology, 18(2), 307-310. DOI: 10.1111/1462-2920.13152
 
Li, Y., Lin, Q., Wang, S., Li, X., Liu, W., Luo, C., ... Li, X. (2016). Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow. FEMS Microbiology Ecology, 92(1), [fiv152]. DOI: 10.1093/femsec/fiv152
 
Nobu, M. K., Narihiro, T., Kuroda, K., Mei, R., & Liu, W. T. (2016). Chasing the elusive Euryarchaeota class WSA2: Genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME Journal, 10(10), 2478-2487. DOI: 10.1038/ismej.2016.33
 
Amato, K. R., Martinez-Mota, R., Righini, N., Raguet-Schofield, M., Corcione, F. P., Marini, E., ... Leigh, S. R. (2016). Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia, 180(3), 717-733. DOI: 10.1007/s00442-015-3507-z
 
Lu, H., Ulanov, A. V., Nobu, M., & Liu, W. T. (2016). Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns. Applied Microbiology and Biotechnology, 100(4), 1843-1852. DOI: 10.1007/s00253-015-7095-y
 
Shen, Y., Huang, C., Monroy, G. L., Janjaroen, D., Derlon, N., Lin, J., ... Nguyen, T. H. (2016). Response of Simulated Drinking Water Biofilm Mechanical and Structural Properties to Long-Term Disinfectant Exposure. Environmental Science and Technology, 50(4), 1779-1787. DOI: 10.1021/acs.est.5b04653
 
Nobu, M. K., Dodsworth, J. A., Murugapiran, S. K., Rinke, C., Gies, E. A., Webster, G., ... Hedlund, B. P. (2016). Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. ISME Journal, 10(2), 273-286. DOI: 10.1038/ismej.2015.97
 
Gomez, A., Rothman, J. M., Petrzelkova, K., Yeoman, C. J., Vlckova, K., Umaña, J. D., ... Leigh, S. R. (2016). Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. ISME Journal, 10(2), 514-526. DOI: 10.1038/ismej.2015.146
 
Liu, Y. Q., Zhang, X., Zhang, R., Liu, W. T., & Tay, J. H. (2016). Effects of hydraulic retention time on aerobic granulation and granule growth kinetics at steady state with a fast start-up strategy. Applied Microbiology and Biotechnology, 100(1), 469-477. DOI: 10.1007/s00253-015-6993-3
 
Kim, N. K., Oh, S., & Liu, W. T. (2016). Enrichment and characterization of microbial consortia degrading soluble microbial products discharged from anaerobic methanogenic bioreactors. Water Research, 90, 395-404. DOI: 10.1016/j.watres.2015.12.021
 
Zhang, M., Sun, Y., Liu, Y., Qiao, F., Chen, L., Liu, W. T., ... Li, E. (2016). Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference. Aquaculture, 454, 72-80. DOI: 10.1016/j.aquaculture.2015.12.014
 
Lu, H., Xue, Z., Saikaly, P., Nunes, S. P., Bluver, T. R., & Liu, W. T. (2016). Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination. Water Research, 88, 337-345. DOI: 10.1016/j.watres.2015.10.013
 
Ling, F., Hwang, C., LeChevallier, M. W., Andersen, G. L., & Liu, W. T. (2016). Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system. ISME Journal, 10(3), 582-595. DOI: 10.1038/ismej.2015.136