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Recent Publicatons by GST Students

  • Jinchao Lou, Jennifer A. Schuster, Francisco N. Barrera, and Michael D. Best. (2022). Journal of the American Chemical Society 2022 144 (8), 3746-3756 ATP-Responsive Liposomes via Screening of Lipid Switches Designed to Undergo Conformational Changes upon Binding Phosphorylated Metabolites. 10.1021/jacs.2c00191
  • McCord, Xu, Y., Li, H., Das, P., & San Martin, R. (2022). SnapShot: Chromosome organization. Molecular Cell, 82(12), 2350–2350.e1. https://doi.org/10.1016/j.molcel.2022.05.020
  • Daniel DeGennaro, Ricardo Andres Urquidi Camacho, Liang Zhang 1, Elena D Shpak. (2022) Initiation of aboveground organ primordia depends on combined action of auxin, ERECTA family genes, and PINOID. Plant Physiology. 10.1093/plphys/kiac288
  • Manuel I Villalobos Solis, Payal Chirania, Robert L Hettich. (2022) In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors. Biotechnology for Biofuels and Bioproducts. 10.1186/s13068-022-02125-x.
  • Rachel Patton McCord , Yang Xu, Heng Li, Priyojit Das , Rebeca San Martin (2022) SnapShot: Chromosome organization. Mol Cell. 10.1016/j.molcel.2022.05.020
  • Appidi MR, Bible AN, Carper DL, Jawdy SS, Giannone RJ, Hettich RL, Morrell-Falvey J, Abraham. (2022) Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated MetaproteomicsUsing an Agar-Plate System. Mol Plant Microbe Interact. 10.1094/MPMI-01-22-0011-TA
  • Chirania P, Holwerda EK, Giannone RJ, Liang X, Poudel S, Ellis JC, Bomble YJ, Hettich RL. (2022) Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids. Nat Commun .10.1038/s41467-022-31433–x.
  • Sanders JT, Golloshi R, Das P, Xu Y, Terry PH, Nash DG, Dekker J, McCord RP (2022) Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling. Sci Rep. 10.1038/s41598-022-08602-5. Grady SK, Abu-Khzam FN, Hagan RD, Shams H, Langston MA (2022). Domination based classification algorithms for the controllability analysis of biological interaction networks.10.1038/s41598-022-15464-4 .
  • Mucci NC, Jones KA, Cao M, Wyatt MR 2nd, Foye S, Kauffman SJ, Richards GR, Taufer M, Chikaraishi Y, Steffan SA, Campagna SR, GoodrichBlair H (2022). Apex Predator Nematodes and Meso-Predator Bacteria Consume Their Basal Insect Prey through Discrete Stages of Chemical Transformations. mSystems. 10.1128/msystems.00312-22 .
  • Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI (2022) Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep. 10.1038/s41598-022-12376-1 .
  • Barros J, Shrestha HK, Serrani-Yarce JC, Engle N, Abraham PE, Tschaplinski TJ, Hettich RL, Dixon RA. (2022) Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon. Plant Cell 10.1093/plcell/ koac171
  • Lou J, Schuster JA, Barrera FN, Best MD. (2022) ATP-Responsive liposomes via screening of lipid switches designed to undergo conformational changes upon binding phosphorylated metabolites. J Am Chem Soc doi: 10.1021/jacs.2c00191.

  • Wesener DA, Beller ZW, Peters SL, Rajabi A, Dimartino G, Giannone RJ, Hettich RL, Gordon JI. (2021) Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo. Elife. 10:e64478.
  • Teodor AH, Eu-Jee Ooi, Jackeline Medina, Miguel Alarcon, Michael D. Vaughn, Barry D. Bruce, Jesse J. Bergkamp (2021) Aqueous-soluble bipyridine cobalt(ii/iii) complexes act as direct redox mediators in photosystem I-based biophotovoltaic devices. RSC Adv. 2021,11, 10434-10450.
  • Hooker KL, Ganusov VV. (2021) Impact of Oseltamivir Treatment on Influenza A and B Virus Dynamics in Human Volunteers. Front Microbiol.  1;12:631211.
  • Yang Xu, Priyojit Das, Rachel Patton McCord (2021) SMILE: Mutual Information Learning for Integration of Single Cell Omics Data bioRxiv. 10.1101/2021.01.28.428619 .
  • Schlum KA, Lamour K, de Bortoli CP, Banerjee R, Meagher R, Pereira E, Murua MG, Sword GA, Tessnow AE, Viteri Dillon D, Linares Ramirez AM, Akutse KS, Schmidt-Jeffris R, Huang F, Reisig D, Emrich SJ, Jurat-Fuentes JL (2021). Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations. BMC Genomics. 10.1186/s12864-021-07492-7.
  • Pawat Pattarawat, Jessica T. Hunt, Jacob Poloway, Collin J. Archibald & Hwa-Chain Robert Wang (2021). A triple combination gemcitabine + romidepsin + cisplatin to effectively control triple-negative breast cancer tumor development, recurrence, and metastasis. Cancer Chemotherapy and Pharmacology. 10.1007/s00280-021-04298-y.
  • Amber N Bible, Mang Chang, Jennifer L Morrell-Falvey (2021) Identification of a diguanylate cyclase expressed in the presence of plants and its application for discovering candidate gene products involved in plant colonization. 10.1371/journal.pone.0248607
  • Kyla L Hooker, Vitaly V Ganusov (2021) Impact of Oseltamivir Treatment on Influenza A and B Virus Dynamics in Human Volunteers. Front Microbiol. 10.3389/fmicb.2021.631211
  • Jaime Lorenzo N Dinglasan, David T Reeves, Robert L Hettich, Mitchel J Doktycz (2021) Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems. JoVE Journal. 10.3791/62852
  • Gao Chen, Nannan Jiang , Manuel I Villalobos Solis, Fadime Kara Murdoch, Robert Waller Murdoch, Yongchao Xie, Cynthia M Swift , Robert L Hettich, Frank E Löffler. (2021) Anaerobic Microbial Metabolism of Dichloroacetate. 10.1128/mBio.00537-21.
  • Schlum K, Lamour K, Tandy P, Emrich SJ, de Bortoli CP, Rao T, Viteri Dillon DM, Linares-Ramirez AM, Jurat-Fuentes JL. (2021) Genetic Screening to Identify Candidate Resistance Alleles to Cry1F Corn in Fall Armyworm Using Targeted Sequencing. 10.3390/insects12070618
  • Teodor AH, Thal LB, Vijayakumar S, Chan M, Little G, Bruce BD (2021) Cryo-EM structure of a tetrameric photosystem I Photosystem I integrated into mesoporous microspheres has enhanced stability and photoactivity in biohybrid solar cells. Mater Today Bio 10.1016/j.mtbio.2021.100122.

  • Das P, Shen T, McCord RP. (2020) Inferring chromosome radial organization from Hi-C data. BMC Bioinformatics. 10.1186/s12859-020-03841-7.
  • Yu J, Conrad AO, Decroocq V, Zhebentyayeva T, Williams DE, Bennett D, Roch G, Audergon JM, Dardick C, Liu Z, Abbott AG, Staton ME. (2020) Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach. Front Plant Sci. 10.3389/fpls.2020.00180.
  • Ricardo A. Urquidi Camacho, Ansul Lokdarshi, Albrecht G. von Arnim (2020) Translational gene regulation in plants: A green new deal.WIREs RNA . 10.1002/wrna.1597.
  • Stefanski KM, Russell CM, Westerfield JM, Lamichhane R, Barrera FN. (2020) PIP2 promotes conformation-specific dimerization of the EphA2 membrane region. J Biol Chem.  296:100149 .

  • Bourn J, Rathore K, Donnell R, White W, Uddin MJ, Marnett L, Cekanova M. (2019 )Detection of carcinogen-induced bladder cancer by fluorocoxib A. BMC Cancer. 19(1):1152
  • Bourn J, Pandey S, Uddin J, Marnett L, Cekanova M. (2019) Detection of tyrosine kinase inhibitors-induced COX-2 expression in bladder cancer by fluorocoxib A. Oncotarget.  10(50):5168-5180.
  • Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ (2019) Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad.. Angew Chem Int Ed Engl. 58(45):16260-16266.
  • Bafna K, Narayanan C, Chennubhotla SC, Doucet N, Agarwal PK. (2019) Nucleotide substrate binding characterization in human pancreatic-type ribonucleases. PLoS One. 14(8):e0220037.
  • Kumar SV, Taylor G, Hasim S, Collier CP, Farmer AT, Campagna SR, Bible AN, Doktycz MJ, Morrell-Falvey J. (2019) Loss of carotenoids from membranes of Pantoea sp. YR343 results in altered lipid composition and changes in membrane biophysical properties. Biochim Biophys Acta Biomembr. 1861(7):1338-1345.
  • Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA, Ficklin SP. Tripal v3: 2019 an ontology-based toolkit for construction of FAIR biological community databases. Database (Oxford). pii: baz077
  • Wegrzyn JL, Staton MA, Street NR, Main D, Grau E, Herndon N, Buehler S, Falk T, Zaman S, Ramnath R, Richter P, Sun L, Condon B, Almsaeed A, Chen M, Mannapperuma C, Jung S, Ficklin S. (2019) Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. Front Plant Sci. 10:813.
  • Hu X, Smith MD, Humphreys BM, Green AT, Parks JM, Baudry JY, Smith JC. (2019) Ligand-Dependent Sodium Ion Dynamics within the A2A Adenosine Receptor: A Molecular Dynamics Study. J Phys Chem B. 123(38):7947-7954
  • Poudel S, Giannone RJ, Farmer AT, Campagna SR, Bible AN, Morrell-Falvey JL, Elkins JG, Hettich RL. (2019)Integrated Proteomics and Lipidomics Reveal That the Swarming Motility of Paenibacillus polymyxa Is Characterized by Phospholipid Modification, Surfactant Deployment, and Flagellar Specialization Relative to Swimming Motility. Front Microbiol. 10:2594.

  • Kumar P, Selvaraj B, Serpersu EH, Cuneo MJ. (2018) Encoding of Promiscuity in an Aminoglycoside Acetyltransferase. J Med Chem. 61(22):10218-10227.
  • Varanasi SK, Rajasagi NK, Jaggi U, Rouse BT. (2018) Role of IL-18 induced Amphiregulin expression on virus induced ocular lesions. Mucosal Immunol. 11(6):1705-1715.
  • Shukla S, Bafna K, Gullett C, Myles DAA, Agarwal PK, Cuneo MJ. (2018) Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry. 57(40):5864-5876.
  • Narayanan C, Bernard DN, Bafna K, Gagné D, Chennubhotla CS, Doucet N, Agarwal PK. (2018) Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily. Structure. 26(3):426-436.e3.
  • Qian C, Chen H, Johs A, Lu X, An J, Pierce EM, Parks JM, Elias DA, Hettich RL, Gu B. (2018) Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of Its Mercury Methylation Genes.Proteomics. 18(17):e1700479.
  • Estenson K, Hurst GB, Standaert RF, Bible AN, Garcia D, Chourey K, Doktycz MJ, Morrell-Falvey JL. (2018) Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343. J Proteome Res. 17(4):1361-1
  • Poudel S, Giannone RJ, Basen M, Nookaew I, Poole FL 2nd, Kelly RM, Adams MWW, Hettich RL. (2018) The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate. Biotechnol Biofuels. 11:80.374.
  • Wells A, Barrington WT, Dearth S, May A, Threadgill DW, Campagna SR, Voy BH (2018) Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography-Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice.. J Proteome Res.17(3):1077-1090.
  • Bakshi A, Piya S, Fernandez JC, Chervin C, Hewezi T, Binder BM. (2018) Ethylene Receptors Signal via a Noncanonical Pathway to Regulate Abscisic Acid Responses. Plant Physiol. 76(1):910-929.
  • Barrington WT, Wulfridge P, Wells AE, Rojas CM, Howe SYF, Perry A, Hua K, Pellizzon MA, Hansen KD, Voy BH, Bennett BJ, Pomp D, Feinberg AP, Threadgill DW. (2018) Improving Metabolic Health Through Precision Dietetics in Mice. Genetics. 208(1):399-417.
  • Varanasi SK, Jaggi U, Hay N, Rouse BT. (2018) Hexokinase II may be dispensable for CD4 T cell responses against a virus infection. PLoS One. 13(1):e0191533

  • Varanasi SK, Reddy PBJ, Bhela S, Jaggi U, Gimenez F, Rouse BT. (2017) Azacytidine Treatment Inhibits the Progression of Herpes Stromal Keratitis by Enhancing Regulatory T Cell Function. J Virol. 91(7). pii: e02367-16.
  • Chen M, Henry N, Almsaeed A, Zhou X, Wegrzyn J, Ficklin S, Staton M. (2017) New extension software modules to enhance searching and display of transcriptome data in Tripal databases. Database (Oxford). Jan 1;2017.
  • Haynes KM, Abdali N, Jhawar V, Zgurskaya HI, Parks JM, Green AT, Baudry J, Rybenkov VV, Smith JC, Walker JK. (2017) Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli. J Med Chem. 60(14):6205-6219.
  • Dahal, S., Poudel, S., Thompson, R.A.  (2017) Genome-scale modeling of thermophilic microorganisms  Advances in Biochemical Engineering/Biotechnology 160, pp. 103-119
  • Bakshi A, Piya S, Fernandez JC, Chervin C, Hewezi T, Binder B. (2017)  Ethylene receptors signal via a non-canonical pathway to regulate abscisic acid responses. Plant Physiol [Epub ahead of print] PubMed PMID: 29158332.
  • Narayanan C, Bafna K, Roux LD, Agarwal PK, Doucet N. (2017) Applications of NMR and computational methodologies to study protein dynamics. Arch Biochem Biophys 628:71-80.
  • Qian C, Hettich RL. (2017) Optimized Extraction Method To Remove Humic AcidInterferences from Soil Samples Prior to Microbial Proteome Measurements. J Proteome Res 16(7):2537-2546.
  • Li L, Shukla S, Meilleur F, Standaert RF, Pierce J, Myles DAA, Cuneo MJ. (2017) Neutron crystallographic studies of T4 lysozyme at cryogenic temperature. Protein Sci 26(10):2098-2104.
  • Bhela S, Varanasi SK, Jaggi U, Sloan SS, Rajasagi NK, Rouse BT. (2017) The Plasticity and Stability of Regulatory T Cells during Viral-Induced Inflammatory Lesions. J Immunol 199(4):1342-1352.
  • Varanasi SK, Donohoe D, Jaggi U, Rouse BT. (2017) Manipulating Glucose Metabolism during Different Stages of Viral Pathogenesis Can Have either Detrimental or Beneficial Effects. J Immunol 199(5):1748-1761.
  • Luck K, Jia Q, Huber M, Handrick V, Wong GK, Nelson DR, Chen F, Gershenzon J, Köllner TG. (2017) CYP79 P450 monooxygenases in gymnosperms: CYP79A118 is associated with the formation of taxiphyllin in Taxus baccata. Plant Mol Biol 95(1-2):169-180.
  • Zhou J, Smith MD, Cooper SJ, Cheng X, Smith JC, Parks JM. (2017) Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane. Environ Sci Technol 51(18):10595-10604.
  • Banerjee R, Hasler J, Meagher R, Nagoshi R, Hietala L, Huang F, Narva K,
    Jurat-Fuentes JL. (2017) Mechanism and DNA-based detection of field-evolved resistance to transgenic Bt corn in fall armyworm (Spodoptera frugiperda). Sci Rep 7(1):10877.
  • Hauser M, Qian C, King ST, Kauffman S, Naider F, Hettich RL, Becker JM. (2017) Identification of peptide-binding sites within BSA using rapid, laser-induced covalent cross-linking combined with high-performance mass spectrometry. J Mol Recognit [Epub ahead of print] PubMed PMID: 28994207.
  • Varanasi SK, Rouse BT. (2017) How host metabolism impacts on virus pathogenesis. Curr Opin Virol 28:37-42.
  • Bobik K, McCray TN, Ernest B, Fernandez JC, Howell KA, Lane T, Staton M, Burch-Smith TM. (2017) The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana. Plant J 91(1):114-131.
  • Rempe CS, Burris KP, Lenaghan SC, Stewart CN Jr. (2017) The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics. Front Microbiol Review. PubMed PMID: 28360902.
  • Kumar P, Serpersu EH. (2017) Thermodynamics of an aminoglycoside modifying enzyme with low substrate promiscuity: The aminoglycoside N3 acetyltransferase-VIa. Proteins [Epub ahead of print] PubMed PMID: 28316100.
  • Chotewutmontri P, Holbrook K, Bruce BD. (2017) Plastid Protein Targeting: Preprotein  Recognition and Translocation. Int Rev Cell Mol Biol 330:227-294.
  • Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I. (2017) Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep 7:40712.
  • Varanasi SK, Reddy PB, Bhela S, Jaggi U, Gimenez F, Rouse BT. (2017) Azacytidine Treatment Inhibits the Progression of Herpes Stromal Keratitis by Enhancing Regulatory T Cell Function. J Virol 91: Print 2017.
  • Poudel S, Giannone RJ, Rodriguez M Jr, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL. (2017) Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. Biotechnol Biofuels 10:14.

  • Dahal S, Poudel S, Thompson RA. (2016) Genome-Scale Modeling of Thermophilic Microorganisms. Adv Biochem Eng Biotechnol. 160:103-119.
  • Adebali O, Zhulin IB. (2017) Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. Proteins 85:72-77.
  • Kapoor K, Duff MR, Upadhyay A, Bucci JC, Saxton AM, Hinde RJ, Howell EE, Baudry J. (2016) Highly Dynamic Anion-Quadrupole Networks in Proteins. Biochemistry 55:6056-6069.
  • Jia Q, Li G, Köllner TG, Fu J, Chen X, Xiong W, Crandall-Stotler BJ, Bowman JL, Weston DJ, Zhang Y, Chen L, Xie Y, Li FW, Rothfels CJ, Larsson A, Graham SW, Stevenson DW, Wong GK, Gershenzon J, Chen F. (2016) Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants. Proc Natl Acad Sci USA  113:12328-12333.
  • Chen X, Köllner TG, Jia Q, Norris A, Santhanam B, Rabe P, Dickschat JS, Shaulsky G, Gershenzon J, Chen F. (2016) Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae. Proc Natl Acad Sci USA 113:12132-12137.
  • Smolensky D, Rathore K, Cekanova M. (2016) Molecular targets in urothelial cancer: detection, treatment, and animal models of bladder cancer. Drug Des Devel Ther 10:3305-3322. Review.
  • Smolensky D, Rathore K, Bourn J, Cekanova M. (2016) Inhibition of the PI3K/AKT Pathway Sensitizes Oral Squamous Cell Carcinoma Cells to Anthracycline-Based Chemotherapy In Vitro. J Cell Biochem [Epub ahead of print] .
  • Hu X, Hong L, Smith MD, Neusius T, Cheng X, Smith JC (2016) The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time. Nature Physics 12: 171–174.
  • Manga P, Klingeman DM, Lu TY, Mehlhorn TL, Pelletier DA, Hauser LJ, Wilson CM, Brown SD (2016) Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets. Front Microbiol 7:794
  • Qian C, Johs A, Chen H, Mann BF, Lu X, Abraham PE, Hettich RL, Gu B. (2016) Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA. J Proteome Res [Epub ahead of print]
  • Jia Q, Chen F. (2016) Catalytic Functions of the Isoprenyl Diphosphate Synthase Superfamily in Plants: A Growing Repertoire. Mol Plant. 9:189-91.
  • Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, Shen T. (2016) DMSO enhanced conformational switch of an interfacial enzyme. Biopolymers [Epub ahead of print]
  • Utturkar SM, Cude WN, Robeson MS 2nd, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TS, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA. (2016) Enrichment of root endophytic bacteria from Populus deltoides and single-cell genomics analysis. Appl Environ Microbiol [Epub ahead of print].
  • Wurch L, Giannone, RJ, Belisle BS, Swift C, Utturkar S, Hettich RL, Reysenbach AL, Podar M. (2016) Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment. Nat Commun 7:12115.
  • Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB. (2016) Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. PLoS Comput Biol 12:e1004862.
  • Adebali O, Reznik AO, Ory DS, Zhulin IB. (2016) Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations. Genet Med [Epub ahead of print].
  • Johnson QR, Lindsay RJ, Nellas RB, Shen T. (2016) Pressure-induced con-formational switch of an interfacial protein. Proteins 84:820-7.
  • Kapoor K, McGill N, Peterson CB, Meyers HV, Blackburn MN, Baudry J. (2016) Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex. J Chem Inf Model 56:535-47.
  • Smith MD, Mostofian B, Petridis L, Cheng X, Smith JC. (2016) Molecular Driving Forces behind the Tetrahydrofuran-Water Miscibility Gap. J Phys Chem B 120:740-7.
  • Lane TS, Rempe CS, (…),Stewart CN Jr. (2016) Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. BMC Biotechnol 16:47.

  • Missra A, Ernest B, Lohoff T, Jia Q, Satterlee J, Ke K, von Arnim AG.(2015) The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading. Plant Cell 27:2582-99.
  • Bakshi A, Wilson RL, Lacey RF, Kim H, Wuppalapati SK, Binder BM. (2015) Identification of Regions in the Receiver Domain of the ETHYLENE RESPONSE1 Ethylene Receptor of Arabidopsis Important for Functional Divergence. Plant Physiol 169:219-32.
  • Chotewutmontri P, Bruce BD. (2015) Non-native, N-terminal Hsp70 mo-lecular motor recognition elements in transit peptides support plastid protein translocation. J Biol Chem 290:7602-21.
  • Smolensky D, Rathore K, Cekanova M. (2015) Phosphatidylinositol- 3-kinase inhibitor induces chemosensitivity to a novel derivative of doxorubicin, AD198 chemotherapyin human bladder cancer cells in vitro. BMC Cancer 15:927.
  • Ellingson SR, Miao Y, Baudry J, Smith JC. (2015) Multi-conformer ensemble docking to difficult protein targets. J Phys Chem B 119:1026-34.
  • Abraham PE, Wang X, Ranjan P, Nookaew I, Zhang B, Tuskan GA, Hettich RL. (2015) Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa. J Proteome Res 14:5318-26.
  • Xiong W, Abraham PE, Li Z, Pan C, Hettich RL. (2015) Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota. Proteomics 15:3424-38.
  • Johnson QR, Lindsay RJ, Petridis L, Shen T. (2015) Investigation of Carbohydrate Recognition via Computer Simulation. Molecules 20:7700-18.
  • Adebali O, Ortega DR, Zhulin IB (2015) CDvist: a webserver for identification and visualization of conserved domains in protein sequences. Bioinformatics 31: 1475-1477.
  • Berthelier V, Harris JB, Estenson KN, Baudry J (2015) Discovery of an inhibitor of Z-alpha1 antitrypsin polymerization. PLoS One 10: e0126256.
  • Hultman J,Shah MB, Verberkmoes NV, Lee LH, Mavrommatis K, Jansson JK (2015) Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521: 208-212.
  • Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T (2015) Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts. Biochemistry 54: 1534-1541.
  • Pluchino LA, Liu AK, Wang HC (2015) Reactive oxygen species-mediated breast cell carcinogenesis enhanced by multiple carcinogens and intervened by dietary ergosterol and mimosine. Free Radic Biol Med 80: 12-26.
  • Rempe CS, Burris KP, Woo HL, Goodrich B, Gosnell DK, Tschaplinski TJ, Stewart CN (2015) Computational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus. PLoS One 10: e0123925.
  • Utturkar SM, Klingeman DM, Bruno-Barcena JM, Chinn MS, Grunden AM, Kopke M, Brown SD (2015) Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Sci Data 2: 150014.
  • Xiong W, Giannone RJ, Morowitz MJ, Banfield JF, Hettich RL (2015) Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut. J Proteome Res 14: 133-141.
  • SELECTED PUBLICATIONS

  • Iyer S, Doktycz MJ (2014) Thrombin-mediated transcriptional regulation using DNA aptamers in DNA-based cell-free protein synthesis. ACS Synth Biol 3: 340-346.
  • Johnson QR, Lindsay RJ, Raval SR, Shen T, et al (2014) Effects of branched O-glycosylation on a semiflexible peptide linker. J Phys Chem B 118: 2050-2057.
  • Kelemen RK, He GF, Woo HL, Lane T, Rempe C, Ganusov VV, Berry MW (2014) Classification of T cell movement tracks all allows for prediction of cell function. Int J Comput Biol Drug Des 7: 113-129.
  • Li Z, Wang Y, Yao Q, Justice NB, Ahn TH, Xu D, Hettich RL, Banfield JF, Pan C (2014) Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat Commun 5: 4405.
  • Mostofian B, Cheng X, Smith JC (2014) Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride. J Phys Chem B 118: 11037-11049.
  • Pluchino LA, Wang HC (2014) Chronic exposure to combined carcinogens enhances breast cell carcinogenesis with mesenchymal and stem-like cell properties. PLoS One 9: e108698.
  • Zhou J, Riccardi D, Beste A, Smith JC, Parks JM (2014) Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II). Inorg Chem 53: 772-777.

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