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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Seo, S., Chang, T. W., & Liu, G. L. (2018). 3D Plasmon Coupling Assisted Sers on Nanoparticle-Nanocup Array Hybrids. Scientific Reports, 8(1), [3002]. DOI: 10.1038/s41598-018-19256-7

Tabe-Bordbar, S., Emad, A., Zhao, S. D., & Sinha, S. (2018). A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models. Scientific Reports, 8(1), [6620]. DOI: 10.1038/s41598-018-24937-4

Adami, G. R., Tangney, C. C., Tang, J. L., Zhou, Y., Ghaffari, S., Naqib, A., ... Schwartz, J. L. (2018). Effects of green tea on miRNA and microbiome of oral epithelium. Scientific Reports, 8(1), [5873]. DOI: 10.1038/s41598-018-22994-3

Tapsin, S., Sun, M., Shen, Y., Zhang, H., Lim, X. N., Susanto, T. T., ... Wan, Y. (2018). Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes. Nature Communications, 9(1), [1289]. DOI: 10.1038/s41467-018-03675-1

Lane, S., Xu, H., Oh, E. J., Kim, H., Lesmana, A., Jeong, D., ... Kim, S. R. (2018). Glucose repression can be alleviated by reducing glucose phosphorylation rate in Saccharomyces cerevisiae. Scientific Reports, 8(1), [2613]. DOI: 10.1038/s41598-018-20804-4

Głowacka, K., Kromdijk, J., Kucera, K., Xie, J., Cavanagh, A. P., Leonelli, L., ... Long, S. P. (2018). Photosystem II Subunit S overexpression increases the efficiency of water use in a field-grown crop. Nature Communications, 9(1), [868]. DOI: 10.1038/s41467-018-03231-x

Ammar, E. M., Wang, X., & Rao, C. V. (2018). Regulation of metabolism in Escherichia coli during growth on mixtures of the non-glucose sugars: Arabinose, lactose, and xylose. Scientific Reports, 8(1), [609]. DOI: 10.1038/s41598-017-18704-0

Xia, P. F., Li, Q., Tan, L. R., Liu, M. M., Jin, Y. S., & Wang, S. G. (2018). Synthetic Whole-Cell Biodevices for Targeted Degradation of Antibiotics. Scientific Reports, 8(1), [2906]. DOI: 10.1038/s41598-018-21350-9

Bao, Z., HamediRad, M., Xue, P., Xiao, H., Tasan, I., Chao, R., ... Zhao, H. (2018). Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision. Nature biotechnology, 36(6), 505-508. DOI: 10.1038/nbt.4132

Kim, H., Oh, E. J., Lane, S. T., Lee, W. H., Cate, J. H. D., & Jin, Y. S. (2018). Enhanced cellobiose fermentation by engineered Saccharomyces cerevisiae expressing a mutant cellodextrin facilitator and cellobiose phosphorylase. Journal of Biotechnology, 275, 53-59. DOI: 10.1016/j.jbiotec.2018.04.008

Puleo, G. J., & Milenkovic, O. (2018). Correlation Clustering and Biclustering with Locally Bounded Errors. IEEE Transactions on Information Theory, 64(6), 4105-4119. DOI: 10.1109/TIT.2018.2819696

Lian, J., Bao, Z., Hu, S., & Zhao, H. (2018). Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains. Biotechnology and bioengineering, 115(6), 1630-1635. DOI: 10.1002/bit.26569

HamediRad, M., Lian, J., Li, H., & Zhao, H. (2018). RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization. Biotechnology and bioengineering, 115(6), 1552-1560. DOI: 10.1002/bit.26570

Kim, J. S., Daum, M. A., Jin, Y. S., & Miller, M. J. (2018). Yeast derived lysA2 can control bacterial contamination in ethanol fermentation. Viruses, 10(6), [281]. DOI: 10.3390/v10060281

Iritani, K., Ikeda, M., Yang, A., Tahara, K., Anzai, M., Hirose, K., ... Tobe, Y. (2018). Electrostatically Driven Guest Binding in a Self-Assembled Porous Network at the Liquid/Solid Interface. Langmuir, 34(21), 6036-6045. DOI: 10.1021/acs.langmuir.8b00699

Beerling, D. J., Leake, J. R., Long, S. P., Scholes, J. D., Ton, J., Nelson, P. N., ... Hansen, J. (Accepted/In press). Publisher Correction: Farming with crops and rocks to address global climate, food and soil security. Nature Plants. DOI: 10.1038/s41477-018-0162-5

Montoto, E. C., Cao, Y., Hernández-Burgos, K., Sevov, C. S., Braten, M. N., Helms, B. A., ... Rodríguez-López, J. (2018). Effect of the Backbone Tether on the Electrochemical Properties of Soluble Cyclopropenium Redox-Active Polymers. Macromolecules, 51(10), 3539-3546. DOI: 10.1021/acs.macromol.8b00574

Checco, J. W., Zhang, G., Yuan, W. D., Yu, K., Yin, S. Y., Roberts-Galbraith, R. H., ... Sweedler, J. V. (2018). Molecular and Physiological Characterization of a Receptor for d -Amino Acid-Containing Neuropeptides. ACS chemical biology, 13(5), 1343-1352. DOI: 10.1021/acschembio.8b00167

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. DOI: 10.1016/j.bej.2018.01.030

Anapindi, K. D. B., Romanova, E. V., Southey, B. R., & Sweedler, J. V. (2018). Peptide identifications and false discovery rates using different mass spectrometry platforms. Talanta, 182, 456-463. DOI: 10.1016/j.talanta.2018.01.062

Yun, E. J., Oh, E. J., Liu, J. J., Yu, S., Kim, D. H., Kwak, S., ... Jin, Y. S. (2018). Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass. Biotechnology for Biofuels, 11(1), [140]. DOI: 10.1186/s13068-018-1135-7

Robertson, I. D., Yourdkhani, M., Centellas, P. J., Aw, J. E., Ivanoff, D. G., Goli, E., ... White, S. R. (2018). Rapid energy-efficient manufacturing of polymers and composites via frontal polymerization. Nature, 557(7704), 223-227. DOI: 10.1038/s41586-018-0054-x

Moneypenny, T. P., Yang, A., Walter, N. P., Woods, T. J., Gray, D. L., Zhang, Y., & Moore, J. S. (2018). Product Distribution from Precursor Bite Angle Variation in Multitopic Alkyne Metathesis: Evidence for a Putative Kinetic Bottleneck. Journal of the American Chemical Society, 140(17), 5825-5833. DOI: 10.1021/jacs.8b02184

Liu, J. J., Zhang, G. C., Kong, I. I., Yun, E. J., Zheng, J. Q., Kweon, D. H., & Jin, Y. S. (2018). A mutation in PGM2 causing inefficient galactose metabolism in the probiotic yeast Saccharomyces boulardii. Applied and Environmental Microbiology, 84(10), [e02858-17]. DOI: 10.1128/AEM.02858-17

Sweedler, J. V. (2018). A Resource for Our Reagents: ACS Reagent Chemicals. Analytical chemistry, 90(9). DOI: 10.1021/acs.analchem.8b01729

Li, L., Andrén, P. E., & Sweedler, J. V. (2018). Editorial and Review: 29th ASMS Sanibel Conference on Mass Spectrometry—Peptidomics: Bridging the Gap between Proteomics and Metabolomics by MS. Journal of the American Society for Mass Spectrometry, 29(5), 801-806. DOI: 10.1007/s13361-018-1939-5

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. DOI: 10.1109/MSPEC.2018.8352574

Monroe, E. B., Annangudi, S. P., Wadhams, A. A., Richmond, T. A., Yang, N., Southey, B. R., ... Sweedler, J. V. (2018). Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry. Journal of the American Society for Mass Spectrometry, 29(5), 923-934. DOI: 10.1007/s13361-018-1898-x

Cui, H., Qin, Y., Liu, G. L., & Padua, G. W. (Accepted/In press). MDA-MB-231 and HeLa cells attachment to nanostructured zein surfaces. Journal of Bioactive and Compatible Polymers. DOI: 10.1177/0883911518769681

Dunham, S. J. B., Ellis, J. F., Baig, N. F., Morales-Soto, N., Cao, T., Shrout, J. D., ... Sweedler, J. V. (2018). Quantitative SIMS Imaging of Agar-Based Microbial Communities. Analytical chemistry, 90(9), 5654-5663. DOI: 10.1021/acs.analchem.7b05180

Greenwood, M. P., Greenwood, M., Romanova, E. V., Mecawi, A. S., Paterson, A., Sarenac, O., ... Murphy, D. (2018). The effects of aging on biosynthetic processes in the rat hypothalamic osmoregulatory neuroendocrine system. Neurobiology of Aging, 65, 178-191. DOI: 10.1016/j.neurobiolaging.2018.01.008

Goli, E., Robertson, I. D., Geubelle, P. H., & Moore, J. S. (2018). Frontal Polymerization of Dicyclopentadiene: A Numerical Study. Journal of Physical Chemistry B, 122(16), 4583-4591. DOI: 10.1021/acs.jpcb.7b12316

Yun, E. J., Lee, J., Kim, D. H., Kim, J., Kim, S., Jin, Y. S., & Kim, K. H. (2018). Metabolomic elucidation of the effects of media and carbon sources on fatty acid production by Yarrowia lipolytica. Journal of Biotechnology, 272-273, 7-13. DOI: 10.1016/j.jbiotec.2018.02.011

Limsakul, P., Peng, Q., Wu, Y., Allen, M. E., Liang, J., Remacle, A. G., ... Wang, Y. (2018). Directed Evolution to Engineer Monobody for FRET Biosensor Assembly and Imaging at Live-Cell Surface. Cell Chemical Biology, 25(4), 370-379.e4. DOI: 10.1016/j.chembiol.2018.01.002

Sung, J., Robb, M. J., White, S. R., Moore, J. S., & Sottos, N. R. (2018). Interfacial mechanophore activation using laser-induced stress waves. Journal of the American Chemical Society, 140(15), 5000-5003. DOI: 10.1021/jacs.8b01427

Dau, H., Duursma, I., Kiah, H. M., & Milenkovic, O. (Accepted/In press). Repairing Reed-Solomon Codes With Multiple Erasures. IEEE Transactions on Information Theory. DOI: 10.1109/TIT.2018.2827942

Yang, N., Anapindi, K. D. B., Rubakhin, S. S., Wei, P., Yu, Q., Li, L., ... Sweedler, J. V. (2018). Neuropeptidomics of the Rat Habenular Nuclei. Journal of Proteome Research, 17(4), 1463-1473. DOI: 10.1021/acs.jproteome.7b00811

Sun, H., Zhang, H., Ang, E. L., & Zhao, H. (2018). Biocatalysis for the synthesis of pharmaceuticals and pharmaceutical intermediates. Bioorganic and Medicinal Chemistry, 26(7), 1275-1284. DOI: 10.1016/j.bmc.2017.06.043

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. DOI: 10.1109/TIT.2017.2778143

Wei, Y., Ang, E. L., & Zhao, H. (2018). Recent developments in the application of P450 based biocatalysts. Current Opinion in Chemical Biology, 43, 1-7. DOI: 10.1016/j.cbpa.2017.08.006

Sekerak, N. M., Hutchins, K. M., Luo, B., Kang, J. G., Braun, P. V., Chen, Q., & Moore, J. S. (2018). Size control of cross-linked carboxy-functionalized polystyrene particles: Four orders of magnitude of dimensional versatility. European Polymer Journal, 101, 202-210. DOI: 10.1016/j.eurpolymj.2018.01.028

Baran, M. J., Braten, M. N., Montoto, E. C., Gossage, Z. T., Ma, L., Chénard, E., ... Helms, B. A. (Accepted/In press). Designing Redox-Active Oligomers for Crossover-Free, Non-Aqueous Redox-Flow Batteries with High Volumetric Energy Density. Chemistry of Materials. DOI: 10.1021/acs.chemmater.8b01318

Satyavolu, N. S. R., Pishevaresfahani, N., Tan, L. H., & Lu, Y. (Accepted/In press). DNA-encoded morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a high-indexed core. Nano Research, 1-13. DOI: 10.1007/s12274-018-2035-7

Hackett, L. P., Li, W., Ameen, A., Goddard, L. L., & Liu, G. L. (2018). Plasmonic Metal-Insulator-Metal Capped Polymer Nanopillars for SERS Analysis of Protein-Protein Interactions. Journal of Physical Chemistry C, 122(11), 6255-6266. DOI: 10.1021/acs.jpcc.7b08656

Davis, R. G., Park, H. M., Kim, K., Greer, J. B., Fellers, R. T., Leduc, R. D., ... Kelleher, N. L. (2018). Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms between Mouse Strains. Analytical chemistry, 90(6), 3802-3810. DOI: 10.1021/acs.analchem.7b04108

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. DOI: 10.1093/bioinformatics/btx685

Lu, X., Katz, J. S., Schmitt, A. K., & Moore, J. S. (2018). A Robust Oil-in-Oil Emulsion for the Nonaqueous Encapsulation of Hydrophilic Payloads. Journal of the American Chemical Society, 140(10), 3619-3625. DOI: 10.1021/jacs.7b11847

Cepeda-Plaza, M., McGhee, C. E., & Lu, Y. (2018). Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme. Biochemistry, 57(9), 1517-1522. DOI: 10.1021/acs.biochem.7b01096

Sweedler, J. V. (2018). Who Are Your Coauthors? Make Sure to Follow Appropriate Practices. Analytical Chemistry, 90(5), 2977-2978. DOI: 10.1021/acs.analchem.8b00785

Wang, Y., Ren, H., & Zhao, H. (2018). Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production. Critical Reviews in Biochemistry and Molecular Biology, 53(2), 115-129. DOI: 10.1080/10409238.2018.1431201

Beerling, D. J., Leake, J. R., Long, S. P., Scholes, J. D., Ton, J., Nelson, P. N., ... Hansen, J. (2018). Farming with crops and rocks to address global climate, food and soil security /631/449 /706/1143 /704/47 /704/106 perspective. Nature Plants, 4(3), 138-147. DOI: 10.1038/s41477-018-0108-y

Hackett, L. P., Ameen, A., Li, W., Dar, F. K., Goddard, L. L., & Liu, G. L. (2018). Spectrometer-Free Plasmonic Biosensing with Metal-Insulator-Metal Nanocup Arrays. ACS Sensors, 3(2), 290-298. DOI: 10.1021/acssensors.7b00878

Sweedler, J. V. (2018). The ACS Measurement Journals, the Analytical Division, and Pittcon 2018: A Busy Four Days. Analytical Chemistry, 90(4). DOI: 10.1021/acs.analchem.8b00575

Chan, M. P. S., Lohmann, S., Morales, A., Zhai, C., Ungar, L., Holtgrave, D. R., & Albarracín, D. (Accepted/In press). An Online Risk Index for the Cross-Sectional Prediction of New HIV Chlamydia, and Gonorrhea Diagnoses Across U.S. Counties and Across Years. AIDS and Behavior, 1-12. DOI: 10.1007/s10461-018-2046-0

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. DOI: 10.1016/j.bpj.2017.12.010

Li, B., Dunham, S. J. B., Ellis, J. F., Lange, J. D., Smith, J. R., Yang, N., ... Sweedler, J. V. (Accepted/In press). A Versatile Strategy for Characterization and Imaging of Drip Flow Microbial Biofilms. Analytical chemistry. DOI: 10.1021/acs.analchem.8b00560

Chang, Y., & Zhai, C. (2018). Welcome by the general chairs. WSDM 2018 - Proceedings of the 11th ACM International Conference on Web Search and Data Mining, 2018-Febuary, iii.

Kumar, D., Long, S. P., & Singh, V. (2018). Biorefinery for combined production of jet fuel and ethanol from lipid-producing sugarcane: a techno-economic evaluation. GCB Bioenergy, 10(2), 92-107. DOI: 10.1111/gcbb.12478

Walker, B. J., Drewry, D. T., Slattery, R. A., VanLoocke, A., Cho, Y. B., & Ort, D. R. (2018). Chlorophyll can be reduced in crop canopies with little penalty to photosynthesis. Plant physiology, 176(2), 1215-1232. DOI: 10.1104/pp.17.01401

Rao, C. V. (2018). Sparsity of Linear Discrete-Time Optimal Control Problems with $l-1$ Objectives. IEEE Transactions on Automatic Control, 63(2), 513-517. [7993042]. DOI: 10.1109/TAC.2017.2732286

Slattery, R. A., Walker, B. J., Weber, A. P. M., & Ort, D. R. (2018). The impacts of fluctuating light on crop performance. Plant physiology, 176(2), 990-1003. DOI: 10.1104/pp.17.01234

Shi, S., Ang, E. L., & Zhao, H. (Accepted/In press). In vivo biosensors: mechanisms, development, and applications. Journal of Industrial Microbiology and Biotechnology, 1-26. DOI: 10.1007/s10295-018-2004-x

Bae, J. H., Kim, H. J., Kim, M. J., Sung, B. H., Jeon, J. H., Kim, H. S., ... Sohn, J. H. (2018). Direct fermentation of Jerusalem artichoke tuber powder for production of L-lactic acid and D-lactic acid by metabolically engineered Kluyveromyces marxianus. Journal of Biotechnology, 266, 27-33. DOI: 10.1016/j.jbiotec.2017.12.001

Qi, M., Philip, M. C., Yang, N., & Sweedler, J. V. (2018). Single Cell Neurometabolomics. ACS Chemical Neuroscience, 9(1), 40-50. DOI: 10.1021/acschemneuro.7b00304

Zhao, J., Gao, J., Xue, W., Di, Z., Xing, H., Lu, Y., & Li, L. (2018). Upconversion Luminescence-Activated DNA Nanodevice for ATP Sensing in Living Cells. Journal of the American Chemical Society, 140(2), 578-581. DOI: 10.1021/jacs.7b11161

Feinberg, A. M., Hernandez, H. L., Plantz, C. L., Mejia, E. B., Sottos, N. R., White, S. R., & Moore, J. S. (2018). Cyclic Poly(phthalaldehyde): Thermoforming a Bulk Transient Material. ACS Macro Letters, 7(1), 47-52. DOI: 10.1021/acsmacrolett.7b00769

Lourentzou, I., Morales, A., & Zhai, C. (2018). Text-based geolocation prediction of social media users with neural networks. In Proceedings - 2017 IEEE International Conference on Big Data, Big Data 2017 (Vol. 2018-January, pp. 696-705). Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/BigData.2017.8257985

Yazdi, S. M. H. T., Kiah, H. M., Gabrys, R., & Milenkovic, O. (Accepted/In press). Mutually Uncorrelated Primers for DNA-Based Data Storage. IEEE Transactions on Information Theory. DOI: 10.1109/TIT.2018.2792488

Seo, S. O., Lu, T., Jin, Y. S., & Blaschek, H. P. (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. DOI: 10.1016/j.jbiotec.2017.11.003

Tang, S., Tang, L., Lu, X., Liu, H., & Moore, J. S. (2018). Programmable Payload Release from Transient Polymer Microcapsules Triggered by a Specific Ion Coactivation Effect. Journal of the American Chemical Society, 140(1), 94-97. DOI: 10.1021/jacs.7b11022

Lopez Hernandez, H., Lee, O. P., Possanza, C., Kaitz, J. A., Park, C. W., Plantz, C. L., ... White, S. R. (Accepted/In press). Accelerated Thermal Depolymerization of Cyclic Polyphthalaldehyde with a Polymeric Thermoacid Generator. Macromolecular Rapid Communications. DOI: 10.1002/marc.201800046

Lian, J., Hamedirad, M., & Zhao, H. (Accepted/In press). Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System. Biotechnology Journal. DOI: 10.1002/biot.201700601

Welle, T. M., Alanis, K., Colombo, M. L., Sweedler, J. V., & Shen, M. (2018). A high spatiotemporal study of somatic exocytosis with scanning electrochemical microscopy and nanoITIES electrodes. Chemical Science, 9(22), 4937-4941. DOI: 10.1039/c8sc01131a

Guo, T., Lohan, D. J., Allison, J. T., Cang, R., & Ren, Y. (2018). An indirect design representation for topology optimization using variational autoencoder and style transfer. In AIAA/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials (210049 ed.). American Institute of Aeronautics and Astronautics Inc, AIAA. DOI: 10.2514/6.2018-0804

Zhang, Z. T., Jiménez-Bonilla, P., Seo, S. O., Lu, T., Jin, Y. S., Blaschek, H. P., & 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.. DOI: 10.1007/978-1-4939-7795-6_17

LeBauer, D., Kooper, R., Mulrooney, P., Rohde, S., Wang, D., Long, S. P., & Dietze, M. C. (2018). BETYdb: a yield, trait, and ecosystem service database applied to second-generation bioenergy feedstock production. GCB Bioenergy, 10(1), 61-71. DOI: 10.1111/gcbb.12420

Southey, B. R., Romanova, E. V., Rodriguez-Zas, S. L., & Sweedler, J. V. (2018). Bioinformatics for prohormone and neuropeptide discovery. In Methods in Molecular Biology (pp. 71-96). (Methods in Molecular Biology; Vol. 1719). Humana Press Inc.. DOI: 10.1007/978-1-4939-7537-2_5

Ramchandran, D., Hojilla-Evangelista, M. P., Moose, S. P., Rausch, K. D., Tumbleson, M. E., & Singh, V. (Accepted/In press). Changes in Corn Protein Content During Storage and Their Relationship with Dry Grind Ethanol Production. JAOCS, Journal of the American Oil Chemists' Society. DOI: 10.1002/aocs.12070

Hu, Y., Ameen, A., Hsiao, A., & Liu, G. L. (2018). Colorimetric imaging of layer-by-layer molecular deposition on nanoplasmonic lycurgus cup array. Sensors and Actuators, B: Chemical, 254, 827-833. DOI: 10.1016/j.snb.2017.07.039

Turner, T. L., Kim, H., Kong, I. I., Liu, J. J., Zhang, G. C., & Jin, Y. S. (2018). Engineering and evolution of saccharomyces cerevisiae to produce biofuels and chemicals. In Advances in Biochemical Engineering/Biotechnology (pp. 175-215). (Advances in Biochemical Engineering/Biotechnology; Vol. 162). Springer Science and Business Media Deutschland GmbH. DOI: 10.1007/10_2016_22

Rasmussen, B. P., Price, C., Koeln, J., Keating, B., & Alleyne, A. (2018). HVAC system modeling and control: Vapor compression system modeling and control. In Advances in Industrial Control (9783319684611 ed., pp. 73-103). (Advances in Industrial Control; No. 9783319684611). Springer International Publishing. DOI: 10.1007/978-3-319-68462-8_4

Wei, L. J., Kwak, S., Liu, J. J., Lane, S., Hua, Q., Kweon, D. H., & Jin, Y. S. (Accepted/In press). Improved squalene production through increasing lipid contents in Saccharomyces cerevisiae. Biotechnology and bioengineering. DOI: 10.1002/bit.26595

Walukiewicz, H. E., Ordal, G. W., & Rao, C. V. (2018). In vitro assay for measuring receptor-kinase activity in the bacillus subtilis chemotaxis pathway. In Methods in Molecular Biology (pp. 95-105). (Methods in Molecular Biology; Vol. 1729). Humana Press Inc.. DOI: 10.1007/978-1-4939-7577-8_10

Schultz, C., Lian, J., & Zhao, H. (Accepted/In press). Metabolic Engineering of Saccharomyces cerevisiae Using a Trifunctional CRISPR/Cas System for Simultaneous Gene Activation, Interference, and Deletion. Methods in enzymology. DOI: 10.1016/bs.mie.2018.04.010

Koeln, J., Keating, B., Alleyne, A., Price, C., & Rasmussen, B. P. (2018). Multi-zone temperature modeling and control. In Advances in Industrial Control (9783319684611 ed., pp. 139-166). (Advances in Industrial Control; No. 9783319684611). Springer International Publishing. DOI: 10.1007/978-3-319-68462-8_6

Tai, H. C., Checco, J. W., & Sweedler, J. V. (2018). Non-targeted identification of d-amino acid-containing peptides through enzymatic screening, chiral amino acid analysis, and LC-MS. In Methods in Molecular Biology (pp. 107-118). (Methods in Molecular Biology; Vol. 1719). Humana Press Inc.. DOI: 10.1007/978-1-4939-7537-2_7

Do, T. D., Ellis, J. F., Neumann, E. K., Comi, T. J., Tillmaand, E. G., Lenhart, A. E., ... Sweedler, J. V. (Accepted/In press). Optically Guided Single Cell Mass Spectrometry of Rat Dorsal Root Ganglia to Profile Lipids, Peptides and Proteins. ChemPhysChem. DOI: 10.1002/cphc.201701364

Garcia-Ruiz, E., HamediRad, M., & Zhao, H. (2018). Pathway design, engineering, and optimization. In Advances in Biochemical Engineering/Biotechnology (Advances in Biochemical Engineering/Biotechnology; Vol. 162). Springer Science and Business Media Deutschland GmbH. DOI: 10.1007/10_2016_12

Jagtap, S. S., & Rao, C. V. (2018). Production of d-arabitol from d-xylose by the oleaginous yeast Rhodosporidium toruloides IFO0880. Applied Microbiology and Biotechnology, 102(1), 143-151. DOI: 10.1007/s00253-017-8581-1

Lian, J., Mishra, S., & Zhao, H. (Accepted/In press). Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metabolic Engineering. DOI: 10.1016/j.ymben.2018.04.011

Lee, Y. H., Schuh, J. K., Ewoldt, R. H., & Allison, J. T. (2018). Simultaneous design of non-newtonian lubricant and surface texture using surrogate-based optimization. In AIAA/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials (210049 ed.). American Institute of Aeronautics and Astronautics Inc, AIAA. DOI: 10.2514/6.2018-1906

Zhang, J., Xing, H., & Lu, Y. (2018). Translating molecular detections into a simple temperature test using a target-responsive smart thermometer. Chemical Science, 9(16), 3906-3910. DOI: 10.1039/c7sc05325h

Lane, S., Dong, J., & Jin, Y. S. (Accepted/In press). Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. Bioresource Technology. DOI: 10.1016/j.biortech.2018.04.013    

Farnoud (Hassanzadeh), F., Milenkovic, O., Puleo, G. J., & Su, L. (2017). Computing similarity distances between rankings. Discrete Applied Mathematics, 232, 157-175. DOI: 10.1016/j.dam.2017.07.038

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Tian, S., Liu, J., Cowley, R. E., Hosseinzadeh, P., Marshall, N. M., Yu, Y., ... Lu, Y. (2016). Reversible S-nitrosylation in an engineered azurin. Nature Chemistry, 8(7), 670-677. DOI: 10.1038/nchem.2489

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Xing, H., Li, J., Xu, W., Hwang, K., Wu, P., Yin, Q., ... Lu, Y. (2016). The Effects of Spacer Length and Composition on Aptamer-Mediated Cell-Specific Targeting with Nanoscale PEGylated Liposomal Doxorubicin. ChemBioChem, 1111-1117. DOI: 10.1002/cbic.201600092

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Wu, Q., Comi, T. J., Li, B., Rubakhin, S. S., & Sweedler, J. V. (2016). On-Tissue Derivatization via Electrospray Deposition for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Endogenous Fatty Acids in Rat Brain Tissues. Analytical Chemistry, 88(11), 5988-5995. DOI: 10.1021/acs.analchem.6b01021

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Lee, C. Y., Fan, Y., Rubakhin, S. S., Yoon, S., & Sweedler, J. V. (2016). A neuron-in-capillary platform for facile collection and mass spectrometric characterization of a secreted neuropeptide. Scientific Reports, 6, [26940]. DOI: 10.1038/srep26940

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Kiah, H. M., Puleo, G. J., & Milenkovic, O. (2016). Codes for DNA Sequence Profiles. IEEE Transactions on Information Theory, 62(6), 3125-3146. [7454723]. DOI: 10.1109/TIT.2016.2555321

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Yang, K., Cai, Z., Tyagi, M., Feygenson, M., Neuefeind, J. C., Moore, J. S., & Zhang, Y. (2016). Odd-Even Structural Sensitivity on Dynamics in Network-Forming Ionic Liquids. Chemistry of Materials, 28(9), 3227-3233. DOI: 10.1021/acs.chemmater.6b01429

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Lan, T., Zhang, J., & Lu, Y. (2016). Transforming the blood glucose meter into a general healthcare meter for in vitro diagnostics in mobile health. Biotechnology Advances, 34(3), 331-341. DOI: 10.1016/j.biotechadv.2016.03.002

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Chauhan, S., Hosseinzadeh, P., Lu, Y., & Blackburn, N. J. (2016). Stopped-Flow Studies of the Reduction of the Copper Centers Suggest a Bifurcated Electron Transfer Pathway in Peptidylglycine Monooxygenase. Biochemistry, 55(13), 2008-2021. DOI: 10.1021/acs.biochem.6b00061

Matsumura, H., Chakraborty, S., Reed, J., Lu, Y., & Moënne-Loccoz, P. (2016). Effect of Outer-Sphere Side Chain Substitutions on the Fate of the trans Iron-Nitrosyl Dimer in Heme/Nonheme Engineered Myoglobins (FeBMbs): Insights into the Mechanism of Denitrifying NO Reductases. Biochemistry, 55(14), 2091-2099. DOI: 10.1021/acs.biochem.5b01109

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Sweedler, J. V. (2016). Choosing an Important Project: The First Stage to Getting Research Published. Analytical Chemistry, 88(7), 3421. DOI: 10.1021/acs.analchem.6b01036

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Emad, A., & Milenkovic, O. (2016). Code Construction and Decoding Algorithms for Semi-Quantitative Group Testing with Nonuniform Thresholds. IEEE Transactions on Information Theory, 62(4), 1674-1687. [7398035]. DOI: 10.1109/TIT.2016.2524002

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Kim, J. S., Cho, D. H., Heo, P., Jung, S. C., Park, M., Oh, E. J., ... Kweon, D. H. (2016). Fumarate-mediated persistence of Escherichia coli against antibiotics. Antimicrobial Agents and Chemotherapy, 60(4), 2232-2240. DOI: 10.1128/AAC.01794-15

Liu, J. J., Kong, I. I., Zhang, G. C., Jayakody, L. N., Kim, H., Xia, P. F., ... Jin, Y. S. (2016). Metabolic engineering of probiotic Saccharomyces boulardii. Applied and Environmental Microbiology, 82(8), 2280-2287. DOI: 10.1128/AEM.00057-16

Sweedler, J. V. (2016). Please Welcome John Yates, III as Editor of the Journal of Proteome Research. Journal of Proteome Research, 15(4), 1115. DOI: 10.1021/acs.jproteome.6b00195

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Kim, S. Y., Bender, K. W., Walker, B. J., Zielinski, R. E., Spalding, M. H., Ort, D. R., & Huber, S. C. (2016). The plastid casein kinase 2 phosphorylates rubisco activase at the Thr-78 site but is not essential for regulation of rubisco activation state. Frontiers in Plant Science, 7(MAR2016), [404]. DOI: 10.3389/fpls.2016.00404

Xu, Z., Jiang, J., Wang, X., Han, K., Ameen, A., Khan, I., ... Liu, G. L. (2016). Large-area, uniform and low-cost dual-mode plasmonic naked-eye colorimetry and SERS sensor with handheld Raman spectrometer. Nanoscale, 8(11), 6162-6172. DOI: 10.1039/c5nr08357e

Hosseinzadeh, P., Mirts, E. N., Pfister, T. D., Gao, Y. G., Mayne, C., Robinson, H., ... Lu, Y. (2016). Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions. Biochemistry, 55(10), 1494-1502. DOI: 10.1021/acs.biochem.5b01299

Lee, S., Yang, A., Moneypenny, T. P., & Moore, J. S. (2016). Kinetically Trapped Tetrahedral Cages via Alkyne Metathesis. Journal of the American Chemical Society, 138(7), 2182-2185. DOI: 10.1021/jacs.6b00468

Nagamani, C., Liu, H., & Moore, J. S. (2016). Mechanogeneration of Acid from Oxime Sulfonates. Journal of the American Chemical Society, 138(8), 2540-2543. DOI: 10.1021/jacs.6b00097

Kromdijk, J., & Long, S. P. (2016). One crop breeding cycle from starvation? How engineering crop photosynthesis for rising CO2 and temperature could be one important route to alleviation. Proceedings of the Royal Society B: Biological Sciences, 283(1826), [20152578]. DOI: 10.1098/rspb.2015.2578

Glowacka, K., Ahmed, A., Sharma, S., Abbott, T., Comstock, J. C., Long, S. P., & Sacks, E. J. (2016). Can chilling tolerance of C4 photosynthesis in Miscanthus be transferred to sugarcane? GCB Bioenergy, 8(2), 407-418. DOI: 10.1111/gcbb.12283

Sweedler, J. V. (2016). Career Advice for Graduate Students and Postdoctoral Fellows. Analytical Chemistry, 88(5), 2513-2514. DOI: 10.1021/acs.analchem.6b00532

Li, X., Park, A., Estrela, R., Kim, S. R., Jin, Y. S., & Cate, J. H. D. (2016). Comparison of xylose fermentation by two high-performance engineered strains of Saccharomyces cerevisiae. Biotechnology Reports, 9, 53-56. DOI: 10.1016/j.btre.2016.01.003

Wang, M., Yu, C., & Zhao, H. (2016). Directed evolution of xylose specific transporters to facilitate glucose-xylose co-utilization. Biotechnology and Bioengineering, 113(3), 484-491. DOI: 10.1002/bit.25724

Kim, E. P., Choi, J., Shanbhag, N. R., & Rutenbar, R. A. (2016). Error resilient and energy efficient MRF message-passing-based stereo matching. IEEE Transactions on Very Large Scale Integration (VLSI) Systems, 24(3), 897-908. [2437331]. DOI: 10.1109/TVLSI.2015.2437331

Soleh, M. A., Tanaka, Y., Nomoto, Y., Iwahashi, Y., Nakashima, K., Fukuda, Y., ... Shiraiwa, T. (2016). Factors underlying genotypic differences in the induction of photosynthesis in soybean [Glycine max (L.) Merr.]. Plant Cell and Environment, 39(3), 685-693. DOI: 10.1111/pce.12674

Massung, S., & Zhai, C. (2016). Non-native text analysis: A survey. Natural Language Engineering, 22(2), 163-186. DOI: 10.1017/S1351324915000303

Xu, H., Kim, S., Sorek, H., Lee, Y., Jeong, D., Kim, J., ... Jin, Y. S. (2016). PHO13 deletion-induced transcriptional activation prevents sedoheptulose accumulation during xylose metabolism in engineered Saccharomyces cerevisiae. Metabolic Engineering, 34, 88-96. DOI: 10.1016/j.ymben.2015.12.007

Luo, T., Milenkovic, O., & Peleato, B. (2016). Compensating for sneak currents in multi-level crosspoint resistive memories. In Conference Record of the 49th Asilomar Conference on Signals, Systems and Computers, ACSSC 2015 (Vol. 2016-February, pp. 839-843). [7421253] IEEE Computer Society. DOI: 10.1109/ACSSC.2015.7421253

Kim, M., Zhang, X., Ligo, J. G., Farnoud, F., Veeravalli, V. V., & Milenkovic, O. (2016). MetaCRAM: An integrated pipeline for metagenomic taxonomy identification and compression. BMC Bioinformatics, 17(1), [94]. DOI: 10.1186/s12859-016-0932-x

May, P. A., Munaretto, N. F., Hamoy, M. B., Robb, M. J., & Moore, J. S. (2016). Is Molecular Weight or Degree of Polymerization a Better Descriptor of Ultrasound-Induced Mechanochemical Transduction? ACS Macro Letters, 5(2), 177-180. DOI: 10.1021/acsmacrolett.5b00855

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Kim, S. K., Cho, J., Moore, J. S., Park, H. S., & Braun, P. V. (2016). High-Performance Mesostructured Organic Hybrid Pseudocapacitor Electrodes. Advanced Functional Materials, 26(6), 903-910. DOI: 10.1002/adfm.201504307

Petrik, I. D., Davydov, R., Ross, M., Zhao, X., Hoffman, B., & Lu, Y. (2016). Spectroscopic and Crystallographic Evidence for the Role of a Water-Containing H-Bond Network in Oxidase Activity of an Engineered Myoglobin. Journal of the American Chemical Society, 138(4), 1134-1137. DOI: 10.1021/jacs.5b12004

Xing, H., Zhang, C. L., Ruan, G., Zhang, J., Hwang, K., & Lu, Y. (2016). Multimodal Detection of a Small Molecule Target Using Stimuli-Responsive Liposome Triggered by Aptamer-Enzyme Conjugate. Analytical Chemistry, 88(3), 1506-1510. DOI: 10.1021/acs.analchem.5b04031

Govindjee, Prince, R. C., & Ort, D. R. (2016). Colin A. Wraight, 1945-2014. Photosynthesis research, 127(2), 237-256. DOI: 10.1007/s11120-015-0174-1

Freestone, T. S., & Zhao, H. (2016). Combinatorial pathway engineering for optimized production of the anti-malarial FR900098. Biotechnology and Bioengineering, 113(2), 384-392. DOI: 10.1002/bit.25719

Seo, J. H., & Jin, Y. S. (2016). Editorial overview: Food biotechnology: Critical gap filler in the nexus of food, energy, and waste for a prosperous future. Current Opinion in Biotechnology, 37, 4-7. DOI: 10.1016/j.copbio.2016.01.001

Guo, W., Sheng, J., Zhao, H., & Feng, X. (2016). Metabolic engineering of Saccharomyces cerevisiae to produce 1-hexadecanol from xylose. Microbial Cell Factories, 15(1), [24]. DOI: 10.1186/s12934-016-0423-9

Jayakody, L. N., Lane, S., Kim, H., & Jin, Y. S. (2016). Mitigating health risks associated with alcoholic beverages through metabolic engineering. Current Opinion in Biotechnology, 37, 173-181. DOI: 10.1016/j.copbio.2015.12.001

Luo, Y., Enghiad, B., & Zhao, H. (2016). New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters. Natural Product Reports, 33(2), 174-182. DOI: 10.1039/c5np00085h

Park, Y. C., Oh, E. J., Jo, J. H., Jin, Y. S., & Seo, J. H. (2016). Recent advances in biological production of sugar alcohols. Current Opinion in Biotechnology, 37, 105-113. DOI: 10.1016/j.copbio.2015.11.006

Choi, J., & Rutenbar, R. A. (2016). Video-Rate Stereo Matching Using Markov Random Field TRW-S Inference on a Hybrid CPU+FPGA Computing Platform. IEEE Transactions on Circuits and Systems for Video Technology, 26(2), 385-398. [7029069]. DOI: 10.1109/TCSVT.2015.2397198

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Plucinski, L., Ranjan Gartia, M., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., ... Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346. DOI: 10.1016/j.bios.2015.07.041

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