CIBC Project Leader Research Publications


Center Members

(Project Leaders shown in bold)

08/2016 – 12/2016 (Total: 18; junior investigators: 6)

*Project leader; **Pilot and/or seed grant recipient   

  1. Aldridge JT, Catlett JL, Smith ML, Buan NR*. Methods for Detecting Microbial Methane Production and Consumption by Gas Chromatography. Bio Protoc. 2016;6(7). Epub 2016/08/26. doi: 10.21769/bioprotoc.1779. PubMed PMID: 27559541; PMCID: PMC4993457.
  2. Arentson BW, Hayes EL, Zhu W, Singh H, Tanner JJ, Becker DF. Engineering a trifunctional proline utilization A chimaera by fusing a DNA-binding domain to a bifunctional PutA. Biosci Rep. 2016;36(6). Epub 2016/10/16. doi: 10.1042/BSR20160435. PubMed PMID: 27742866; PMCID: PMC5293562.
  3. Casey CA, Bhat G, Holzapfel MS, Petrosyan A*. Study of Ethanol-Induced Golgi Disorganization Reveals the Potential Mechanism of Alcohol-Impaired N-Glycosylation. Alcohol Clin Exp Res. 2016;40(12):2573-90. Epub 2016/10/18. doi: 10.1111/acer.13247. PubMed PMID: 27748959; PMCID: PMC5133184.
  4. Clarke BS, Amiri S, Clarke JL. EnsCat: clustering of categorical data via ensembling. BMC Bioinformatics. 2016;17(1):380. Epub 2016/09/17. doi: 10.1186/s12859-016-1245-9. PubMed PMID: 27634377; PMCID: PMC5025633.
  5. Diamond J, McQuillan J, Spiegel AN, Hill PW, Smith R, West J, Wood C. Viruses, Vaccines and the Public. Mus Soc Issues. 2016;11(1):9-16. Epub 2016/08/16. doi: 10.1080/15596893.2016.1131099. PubMed PMID: 27524953; PMCID: PMC4980086.
  6. Ding Y, Li Z, Li Y, Lu C, Wang H, Shen Y, Du L. HSAF-induced antifungal effects in Candida albicans through ROS-mediated apoptosis. RSC Adv. 2016;6(37):30895-904. Epub 2016/09/07. doi: 10.1039/C5RA26092B. PubMed PMID: 27594989; PMCID: PMC5006743.
  7. Kubyshkin A, Chegodar D, Katsev A, Petrosyan A*, Krivorutchenko Y, Postnikova O. Antimicrobial Effects of Silver Nanoparticles Stabilized in Solution by Sodium Alginate. Biochem Mol Biol J. 2016;2(2). Epub 2016/10/18. doi: 10.21767/2471-8084.100022. PubMed PMID: 27747311; PMCID: PMC5061134.
  8. Li Q, Lin H, Wang O, Qiu X, Kidambi S*, Deleyrolle LP, Reynolds BA, Lei Y. Scalable Production of Glioblastoma Tumor-initiating Cells in 3 Dimension Thermoreversible Hydrogels. Sci Rep. 2016;6:31915. Epub 2016/08/24. doi: 10.1038/srep31915. PubMed PMID: 27549983; PMCID: PMC4994035.
  9. Liu W, Xu X, Zhang R, Cheng T, Cao Y, Li X, Liu H, Xian M, Guo J. Engineering Escherichia coli for high-yield geraniol production with biotransformation of geranyl acetate to geraniol under fed-batch culture. Biotechnol Biofuels. 2016;9:58.
  10. Luo M, Gamage TT, Arentson BW, Schlasner KN, Becker DF, Tanner JJ. Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function. J Biol Chem. 2016;291(46):24065-75. Epub 2016/09/30. doi: 10.1074/jbc.M116.756965. PubMed PMID: 27679491; PMCID: PMC5104932.
  11. Petrosyan A*, Casey CA, Cheng PW. The role of Rab6a and phosphorylation of non-muscle myosin IIA tailpiece in alcohol-induced Golgi disorganization. Sci Rep. 2016;6:31962. Epub 2016/08/19. doi: 10.1038/srep31962. PubMed PMID: 27535804; PMCID: PMC4989220.
  12. Pinto JT, Zempleni J. Riboflavin. Adv Nutr. 2016;7(5):973-5. Epub 2016/09/17. doi: 10.3945/an.116.012716. PubMed PMID: 27633112; PMCID: PMC5015041.
  13. Tyler KA, Handema R, Schmitz RM, Phiri F, Wood C, Olson K. Risk Factors for HIV among Zambian Street Youth. J HIV AIDS Soc Serv. 2016;15(3):254-68. Epub 2016/08/30. doi: 10.1080/15381501.2016.1138178. PubMed PMID: 27570499; PMCID: PMC4996545.
  14. Walter ME, Ortiz A, Sondgeroth C, Sindt NM, Duszenko N, Catlett JL, Zhou Y, Valloppilly S, Anderson C, Fernando S, Buan NR*. High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea. J Microbiol Methods. 2016;131:113-21. Epub 2016/10/25. doi: 10.1016/j.mimet.2016.10.010. PubMed PMID: 27771305.
  15. Weh KM, Clarke J, Kresty LA. Cranberries and Cancer: An Update of Preclinical Studies Evaluating the Cancer Inhibitory Potential of Cranberry and Cranberry Derived Constituents. Antioxidants (Basel). 2016;5(3). Epub 2016/08/23. doi: 10.3390/antiox5030027. PubMed PMID: 27548236; PMCID: PMC5039576.
  16. Worley B, Powers R. PCA as a practical indicator of OPLS-DA model reliability. Curr Metabolomics. 2016;4(2):97-103. Epub 2016/08/23. doi: 10.2174/2213235X04666160613122429. PubMed PMID: 27547730; PMCID: PMC4990351.
  17. Ye F, Zeng Y, Sha J, Jones T, Kuhne K, Wood C, Gao SJ. High Glucose Induces Reactivation of Latent Kaposi's Sarcoma-Associated Herpesvirus. J Virol. 2016;90(21):9654-63. Epub 2016/08/19. doi: 10.1128/JVI.01049-16. PubMed PMID: 27535045; PMCID: PMC5068518.
  18. Zawatzky K, Reibarkh M, Canfield N, Wang TC, Li S, Du L, Welch CJ. Visualizing small differences using subtractive chromatographic analysis. J Chromatogr A. 2016;1468:245-9. Epub 2016/09/25. doi: 10.1016/j.chroma.2016.09.025. PubMed PMID: 27663729.


01/2017 – 12/2017 (Total: 71; junior investigators: 11)

*Project leader; **Pilot and/or seed grant recipient


  1. Anandhan A, Jacome MS, Lei S, Hernandez-Franco P, Pappa A, Panayiotidis MI, Powers R, Franco R. Metabolic Dysfunction in Parkinson's Disease: Bioenergetics, Redox Homeostasis and Central Carbon Metabolism. Brain Res Bull. 2017;133:12-30. Epub 2017/03/28. doi: 10.1016/j.brainresbull.2017.03.009. PubMed PMID: 28341600; PMCID: PMC5555796.
  2. Beck JR, Harris EN, Stains CI. Quantification of Cell Signaling Networks Using Kinase Activity Chemosensors. Methods Mol Biol. 2017;1636:61-70. Epub 2017/07/22. doi: 10.1007/978-1-4939-7154-1_4. PubMed PMID: 28730472; PMCID: PMC6623968.
  3. Bernier M, Catazaro J, Singh NS, Wnorowski A, Boguszewska-Czubara A, Jozwiak K, Powers R, Wainer IW. GPR55 receptor antagonist decreases glycolytic activity in PANC-1 pancreatic cancer cell line and tumor xenografts. Int J Cancer. 2017;141(10):2131-42. Epub 2017/07/26. doi: 10.1002/ijc.30904. PubMed PMID: 28741686; PMCID: PMC6028007.
  4. Brahma S, Martinez I, Walter J, Clarke J, Gonzalez T, Menon R, Rose DJ. Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans. Journal of Functional Foods. 2017;29:281-9. doi: 10.1016/j.jff.2016.12.042. PubMed PMID: WOS:000393847800033.
  5. Catazaro J, Lowe AJ, Cerny RL, Powers R. The NMR solution structure and function of RPA3313: a putative ribosomal transport protein from Rhodopseudomonas palustris. Proteins. 2017;85(1):93-102. Epub 2016/11/02. doi: 10.1002/prot.25201. PubMed PMID: 27802574; PMCID: PMC5167650.
  6. Catazaro J, Periago J, Shortridge MD, Worley B, Kirchner A, Powers R, Griep MA. Identification of a Ligand-Binding Site on the Staphylococcus aureus DnaG Primase C-Terminal Domain. Biochemistry. 2017;56(7):932-43. Epub 2017/01/27. doi: 10.1021/acs.biochem.6b01273. PubMed PMID: 28125218; PMCID: PMC6476306.
  7. Chaudhari SS, Kim M, Lei S, Razvi F, Alqarzaee AA, Hutfless EH, Powers R, Zimmerman MC, Fey PD, Thomas VC. Nitrite Derived from Endogenous Bacterial Nitric Oxide Synthase Activity Promotes Aerobic Respiration. mBio. 2017;8(4):e00887/1-e/16. Epub 2017/08/03. doi: 10.1128/mBio.00887-17. PubMed PMID: 28765220; PMCID: PMC5539425.
  8. Child MA, Garland M, Foe I, Madzelan P, Treeck M, van der Linden WA, Oresic Bender K, Weerapana E, Wilson MA, Boothroyd JC, Reese ML, Bogyo M. Toxoplasma DJ-1 Regulates Organelle Secretion by a Direct Interaction with Calcium-Dependent Protein Kinase 1. mBio. 2017;8(1). Epub 2017/03/02. doi: 10.1128/mBio.02189-16. PubMed PMID: 28246362; PMCID: PMC5347346.
  9. Christensen EM, Patel SM, Korasick DA, Campbell AC, Krause KL, Becker DF, Tanner JJ. Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1. J Biol Chem. 2017;292(17):7233-43. Epub 2017/03/05. doi: 10.1074/jbc.M117.780288. PubMed PMID: 28258219; PMCID: PMC5409489.
  10. Christgen SL, Zhu W, Sanyal N, Bibi B, Tanner JJ, Becker DF. Discovery of the Membrane Binding Domain in Trifunctional Proline Utilization A. Biochemistry. 2017;56(47):6292-303. Epub 2017/11/02. doi: 10.1021/acs.biochem.7b01008. PubMed PMID: 29090935; PMCID: PMC6044449.
  11. Crabtree KL, Wojcicki JM, Minhas V, Kankasa C, Mitchell C, Wood C. Association of Household Food- and Drink-Sharing Practices With Human Herpesvirus 8 Seroconversion in a Cohort of Zambian Children. J Infect Dis. 2017;216(7):842-9. Epub 2017/09/30. doi: 10.1093/infdis/jix399. PubMed PMID: 28961804; PMCID: PMC5853242.
  12. Cui J, Zhou B, Ross SA, Zempleni J. Nutrition, microRNAs, and Human Health. Adv Nutr. 2017;8(1):105-12. Epub 2017/01/18. doi: 10.3945/an.116.013839. PubMed PMID: 28096131; PMCID: PMC5227982.
  13. David G, Pedrigi RM**, Humphrey JD. Accommodation of the human lens capsule using a finite element model based on nonlinear regionally anisotropic biomembranes. Comput Methods Biomech Biomed Engin. 2017;20(3):302-7. Epub 2016/09/10. doi: 10.1080/10255842.2016.1228907. PubMed PMID: 27609339.
  14. Duszenko N, Buan NR*. Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea. Appl Environ Microbiol. 2017;83(18):e00950-17/12. Epub 2017/07/16. doi: 10.1128/AEM.00950-17. PubMed PMID: 28710268; PMCID: PMC5583484.
  15. Gebregiworgis T, Purohit V, Shukla SK, Tadros S, Chaika NV, Abrego J, Mulder SE, Gunda V, Singh PK, Powers R. Glucose Limitation Alters Glutamine Metabolism in MUC1-Overexpressing Pancreatic Cancer Cells. J Proteome Res. 2017;16(10):3536-46. Epub 2017/08/16. doi: 10.1021/acs.jproteome.7b00246. PubMed PMID: 28809118; PMCID: PMC5634392.
  16. Gomes-Neto JC, Kittana H, Mantz S, Segura Munoz RR, Schmaltz RJ, Bindels LB, Clarke J, Hostetter JM, Benson AK, Walter J, Ramer-Tait AE. A gut pathobiont synergizes with the microbiota to instigate inflammatory disease marked by immunoreactivity against other symbionts but not itself. Sci Rep. 2017;7(1):17707. Epub 2017/12/20. doi: 10.1038/s41598-017-18014-5. PubMed PMID: 29255158; PMCID: PMC5735134.
  17. Gomes-Neto JC, Kittana H, Mantz S, Segura Munoz RR, Schmaltz RJ, Bindels LB, Clarke J, Hostetter JM, Benson AK, Walter J, Ramer-Tait AE. A gut pathobiont synergizes with the microbiota to instigate inflammatory disease marked by immunoreactivity against other symbionts but not itself. bioRxiv, Immunol. 2017:1-36. doi: 10.1101/178038.
  18. Halsey CR, Lei S, Wax JK, Lehman MK, Nuxoll AS, Steinke L, Sadykov M, Powers R, Fey PD. Amino Acid Catabolism in Staphylococcus aureus and the Function of Carbon Catabolite Repression. mBio. 2017;8(1):e01434-16/1-e-16/19. Epub 2017/02/16. doi: 10.1128/mBio.01434-16. PubMed PMID: 28196956; PMCID: PMC5312079.
  19. Han Y, Wang Y, Yu Y, Chen H, Shen Y, Du L. Indole-Induced Reversion of Intrinsic Multiantibiotic Resistance in Lysobacter enzymogenes. Appl Environ Microbiol. 2017;83(17). Epub 2017/06/20. doi: 10.1128/AEM.00995-17. PubMed PMID: 28625984; PMCID: PMC5561299.
  20. Hoang GL, Takacs JM. Enantioselective gamma-borylation of unsaturated amides and stereoretentive Suzuki-Miyaura cross-coupling. Chem Sci. 2017;8(6):4511-6. Epub 2017/08/02. doi: 10.1039/c7sc01093a. PubMed PMID: 28758006; PMCID: PMC5514528.
  21. Hu D, Bowder D, Wei W, Thompson J, Wilson MA, Xiang SH. Tryptophan 375 stabilizes the outer-domain core of gp120 for HIV vaccine immunogen design. Vaccine. 2017;35(23):3067-75. Epub 2017/05/04. doi: 10.1016/j.vaccine.2017.04.054. PubMed PMID: 28461065; PMCID: PMC5440730.
  22. Kolli V, Schumacher KN, Dodds ED. Ion mobility-resolved collision-induced dissociation and electron transfer dissociation of N-glycopeptides: gathering orthogonal connectivity information from a single mass-selected precursor ion population. Analyst. 2017;142(24):4691-702. Epub 2017/11/10. doi: 10.1039/c7an01196b. PubMed PMID: 29119999; PMCID: PMC7169368.
  23. Korasick DA, Gamage TT, Christgen S, Stiers KM, Beamer LJ, Henzl MT, Becker DF, Tanner JJ. Structure and characterization of a class 3B proline utilization A: Ligand-induced dimerization and importance of the C-terminal domain for catalysis. J Biol Chem. 2017;292(23):9652-65. Epub 2017/04/20. doi: 10.1074/jbc.M117.786855. PubMed PMID: 28420730; PMCID: PMC5465489.
  24. Korasick DA, Pemberton TA, Arentson BW, Becker DF, Tanner JJ. Structural Basis for the Substrate Inhibition of Proline Utilization A by Proline. Molecules. 2017;23(1). Epub 2018/01/04. doi: 10.3390/molecules23010032. PubMed PMID: 29295473; PMCID: PMC5786444.
  25. Levytskyy RM, Bohovych I, Khalimonchuk O. Metalloproteases of the Inner Mitochondrial Membrane. Biochemistry. 2017;56(36):4737-46. Epub 2017/08/15. doi: 10.1021/acs.biochem.7b00663. PubMed PMID: 28806058; PMCID: PMC5792295.
  26. Li S, Wu X, Zhang L*, Shen Y, Du L. Activation of a Cryptic Gene Cluster in Lysobacter enzymogenes Reveals a Module/Domain Portable Mechanism of Nonribosomal Peptide Synthetases in the Biosynthesis of Pyrrolopyrazines. Org Lett. 2017;19(19):5010-3. Epub 2017/09/13. doi: 10.1021/acs.orglett.7b01611. PubMed PMID: 28898095; PMCID: PMC5632221.
  27. Lin J, Pozharski E, Wilson MA. Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons. Biochemistry. 2017;56(2):391-402. Epub 2016/12/19. doi: 10.1021/acs.biochem.6b00906. PubMed PMID: 27989121; PMCID: PMC5805389.
  28. Liu K, Enns B, Evans B, Wang N, Shang X, Sittiwong W, Dussault PH, Guo J. A genetically encoded cyclobutene probe for labelling of live cells. Chem Commun (Camb). 2017;53(76):10604-7. Epub 2017/09/14. doi: 10.1039/c7cc05580c. PubMed PMID: 28902227; PMCID: PMC5648060.
  29. Liu LK, Becker DF, Tanner JJ. Structure, function, and mechanism of proline utilization A (PutA). Arch Biochem Biophys. 2017;632:142-57. Epub 2017/07/18. doi: 10.1016/ PubMed PMID: 28712849; PMCID: PMC5650515.
  30. Liu Z, Fang Q, Zhou S, Minhas V, Wood C, He N, Zhang T. Seroprevalence of Kaposi's sarcoma-associated herpesvirus among HIV-infected Uygurs in Xinjiang, China. J Med Virol. 2017;89(9):1629-35. Epub 2017/03/03. doi: 10.1002/jmv.24804. PubMed PMID: 28252177.
  31. Liu Z, Fang Q, Zuo J, He N, Zhang T, Liu Z, Fang Q, Zuo J, He N, Zhang T, Minhas V, Wood C, Zhang T. Was Kaposi's sarcoma-associated herpesvirus introduced into China via the ancient Silk Road? An evolutionary perspective. Arch Virol. 2017;162(10):3061-8.
  32. Liu Z, Fang Q, Zuo J, Wang J, Chen Y, Minhas V, Wood C, He N, Zhang T. High seroprevalence of human herpesvirus 8 and herpes simplex virus 2 infections in men who have sex with men in Shanghai, China. J Med Virol. 2017;89(5):887-94. Epub 2016/10/22. doi: 10.1002/jmv.24718. PubMed PMID: 27769110.
  33. Markley JL, Bruschweiler R, Edison AS, Eghbalnia HR, Powers R, Raftery D, Wishart DS. The future of NMR-based metabolomics. Curr Opin Biotechnol. 2017;43:34-40. Epub 2016/09/01. doi: 10.1016/j.copbio.2016.08.001. PubMed PMID: 27580257; PMCID: PMC5305426.
  34. Marshall DD, Halouska S, Zinniel DK, Fenton RJ, Kenealy K, Chahal HK, Rathnaiah G, Barletta RG, Powers R. Assessment of Metabolic Changes in Mycobacterium smegmatis Wild-Type and alr Mutant Strains: Evidence of a New Pathway of d-Alanine Biosynthesis. J Proteome Res. 2017;16(3):1270-9. Epub 2017/01/26. doi: 10.1021/acs.jproteome.6b00871. PubMed PMID: 28121156; PMCID: PMC6599645.
  35. Marshall DD, Powers R. Beyond the paradigm: Combining mass spectrometry and nuclear magnetic resonance for metabolomics. Prog Nucl Magn Reson Spectrosc. 2017;100:1-16. Epub 2017/05/30. doi: 10.1016/j.pnmrs.2017.01.001. PubMed PMID: 28552170; PMCID: PMC5448308.
  36. Mohammed A, Biegert G, Adamec J, Helikar T. Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers. Oncotarget. 2017;8(49):85692-715. Epub 2017/11/22. doi: 10.18632/oncotarget.21127. PubMed PMID: 29156751; PMCID: PMC5689641.
  37. Moxley MA, Zhang L*, Christgen S, Tanner JJ, Becker DF. Identification of a Conserved Histidine As Being Critical for the Catalytic Mechanism and Functional Switching of the Multifunctional Proline Utilization A Protein. Biochemistry. 2017;56(24):3078-88. Epub 2017/05/31. doi: 10.1021/acs.biochem.7b00046. PubMed PMID: 28558236; PMCID: PMC5663281.
  38. Natarajan G, Perriotte-Olson C, Bhinderwala F, Powers R, Desouza CV, Talmon GA, Yuhang J, Zimmerman MC, Kabanov AV, Saraswathi V. Nanoformulated copper/zinc superoxide dismutase exerts differential effects on glucose vs lipid homeostasis depending on the diet composition possibly via altered AMPK signaling. Transl Res. 2017;188:10-26. Epub 2017/09/05. doi: 10.1016/j.trsl.2017.08.002. PubMed PMID: 28867395; PMCID: PMC5819896.
  39. Natarajan SK, Muthukrishnan E, Khalimonchuk O, Mott JL, Becker DF. Evidence for Pipecolate Oxidase in Mediating Protection Against Hydrogen Peroxide Stress. J Cell Biochem. 2017;118(7):1678-88. Epub 2016/12/07. doi: 10.1002/jcb.25825. PubMed PMID: 27922192; PMCID: PMC5413420.
  40. Natarajan V, Harris EN, Kidambi S*. SECs (Sinusoidal Endothelial Cells), Liver Microenvironment, and Fibrosis. Biomed Res Int. 2017;2017:4097205. Epub 2017/03/16. doi: 10.1155/2017/4097205. PubMed PMID: 28293634; PMCID: PMC5331310 publication of this paper.
  41. Niu W, Guo J. Novel Fluorescence-Based Biosensors Incorporating Unnatural Amino Acids. Methods Enzymol. 2017;589(Enzymes as Sensors):191-219. Epub 2017/03/25. doi: 10.1016/bs.mie.2017.01.012. PubMed PMID: 28336064.
  42. Pedrigi RM**, Papadimitriou KI, Kondiboyina A, Sidhu S, Chau J, Patel MB, Baeriswyl DC, Drakakis EM, Krams R. Disturbed Cyclical Stretch of Endothelial Cells Promotes Nuclear Expression of the Pro-Atherogenic Transcription Factor NF-kappaB. Ann Biomed Eng. 2017;45(4):898-909. Epub 2016/11/01. doi: 10.1007/s10439-016-1750-z. PubMed PMID: 27796516; PMCID: PMC5362665.
  43. Pierce BG, Boucher EN, Piepenbrink KH*, Ejemel M, Rapp CA, Thomas WD, Jr., Sundberg EJ, Weng Z, Wang Y. Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope. J Virol. 2017;91(20):e01032-17/1-e. Epub 2017/08/11. doi: 10.1128/JVI.01032-17. PubMed PMID: 28794021; PMCID: PMC5625506.
  44. Poppe LK, Chunda-Liyoka C, Kwon EH, Gondwe C, West JT, Kankasa C, Ndongmo CB, Wood C. HIV drug resistance in infants increases with changing prevention of mother-to-child transmission regimens. AIDS. 2017;31(13):1885-9. Epub 2017/07/27. doi: 10.1097/QAD.0000000000001569. PubMed PMID: 28746086; PMCID: PMC5567858.
  45. Powers R, Lei S, Anandhan A, Marshall DD, Worley B, Cerny RL, Dodds ED, Huang Y, Panayiotidis MI, Pappa A, Franco R. Metabolic Investigations of the Molecular Mechanisms Associated with Parkinson's Disease. Metabolites. 2017;7(2):22/1-/6. Epub 2017/05/26. doi: 10.3390/metabo7020022. PubMed PMID: 28538683; PMCID: PMC5487993.
  46. Rakowski R, Golovin G, O'Neal J, Zhang J, Zhang P, Zhao B, Wilson MD, Veale MC, Seller P, Chen S, Banerjee S, Umstadter D, Fuchs M. Single-shot structural analysis by high-energy X-ray diffraction using an ultrashort all-optical source. Sci Rep. 2017;7(1):16603. Epub 2017/12/02. doi: 10.1038/s41598-017-16477-0. PubMed PMID: 29192189; PMCID: PMC5709386.
  47. Riekeberg E, Powers R. New frontiers in metabolomics: from measurement to insight. F1000Res. 2017;6:1148. Epub 2017/08/07. doi: 10.12688/f1000research.11495.1. PubMed PMID: 28781759; PMCID: PMC5521158.
  48. Rose J, Brian C, Woods J, Pappa A, Panayiotidis MI, Powers R, Franco R. Mitochondrial dysfunction in glial cells: Implications for neuronal homeostasis and survival. Toxicology. 2017;391:109-15. Epub 2017/06/29. doi: 10.1016/j.tox.2017.06.011. PubMed PMID: 28655545; PMCID: PMC5681369.
  49. Shang X, Lai R, Song X, Li H**, Niu W, Guo J. Improved Photoinduced Fluorogenic Alkene-Tetrazole Reaction for Protein Labeling. Bioconjug Chem. 2017;28(11):2859-64. Epub 2017/10/13. doi: 10.1021/acs.bioconjchem.7b00562. PubMed PMID: 29022697; PMCID: PMC5688003.
  50. Shang X, Song X, Faller C, Lai R, Li H**, Cerny R, Niu W, Guo J. Fluorogenic protein labeling using a genetically encoded unstrained alkene. Chem Sci. 2017;8(2):1141-5. Epub 2017/04/30. doi: 10.1039/c6sc03635j. PubMed PMID: 28451254; PMCID: PMC5369545.
  51. Shang X, Wang N, Cerny R, Niu W, Guo J. Fluorescent Protein-Based Turn-On Probe through a General Protection-Deprotection Design Strategy. ACS Sens. 2017;2(7):961-6. Epub 2017/07/29. doi: 10.1021/acssensors.7b00223. PubMed PMID: 28750537; PMCID: PMC5648012.
  52. Shoba VM, Takacs JM. Remarkably Facile Borane-Promoted, Rhodium-Catalyzed Asymmetric Hydrogenation of Tri- and Tetrasubstituted Alkenes. J Am Chem Soc. 2017;139(16):5740-3. Epub 2017/04/11. doi: 10.1021/jacs.7b02581. PubMed PMID: 28394591; PMCID: PMC5408738.
  53. Shukla SK, Purohit V, Mehla K, Gunda V, Chaika NV, Vernucci E, King RJ, Abrego J, Goode GD, Dasgupta A, Illies AL, Gebregiworgis T, Dai B, Augustine JJ, Murthy D, Attri KS, Mashadova O, Grandgenett PM, Powers R, Ly QP, Lazenby AJ, Grem JL, Yu F, Mates JM, Asara JM, Kim JW, Hankins JH, Weekes C, Hollingsworth MA, Serkova NJ, Sasson AR, Fleming JB, Oliveto JM, Lyssiotis CA, Cantley LC, Berim L, Singh PK. MUC1 and HIF-1alpha Signaling Crosstalk Induces Anabolic Glucose Metabolism to Impart Gemcitabine Resistance to Pancreatic Cancer. Cancer Cell. 2017;32(1):71-87 e7. Epub 2017/07/12. doi: 10.1016/j.ccell.2017.06.004. PubMed PMID: 28697344; PMCID: PMC5533091.
  54. Smith N, Wilson MA. Structural Biology of the DJ-1 Superfamily. Adv Exp Med Biol. 2017;1037(DJ-1/PARK7 Protein):5-24. Epub 2017/11/18. doi: 10.1007/978-981-10-6583-5_2. PubMed PMID: 29147900.
  55. Su Z, Chen H, Wang P, Tombosa S, Du L, Han Y, Shen Y, Qian G, Liu F. 4-Hydroxybenzoic acid is a diffusible factor that connects metabolic shikimate pathway to the biosynthesis of a unique antifungal metabolite in Lysobacter enzymogenes. Mol Microbiol. 2017;104(1):163-78. Epub 2017/01/21. doi: 10.1111/mmi.13619. PubMed PMID: 28105648.
  56. Taylor NG, Swenson S, Harris NJ, Germany EM, Fox JL, Khalimonchuk O. The Assembly Factor Pet117 Couples Heme a Synthase Activity to Cytochrome Oxidase Assembly. J Biol Chem. 2017;292(5):1815-25. Epub 2016/12/22. doi: 10.1074/jbc.M116.766980. PubMed PMID: 27998984; PMCID: PMC5290955.
  57. Tso FY, Sawyer A, Kwon EH, Mudenda V, Langford D, Zhou Y, West J, Wood C. Kaposi's Sarcoma-Associated Herpesvirus Infection of Neurons in HIV-Positive Patients. J Infect Dis. 2017;215(12):1898-907. Epub 2016/12/10. doi: 10.1093/infdis/jiw545. PubMed PMID: 27932611; PMCID: PMC5853869.
  58. Wang J, Wen S, Zhao R, Qi J, Liu Z, Li W, An J, Wood C, Wang Y. Covalent conjugation of the equine infectious anemia virus Gag with SUMO. Biochem Biophys Res Commun. 2017;486(3):712-9. Epub 2017/03/28. doi: 10.1016/j.bbrc.2017.03.103. PubMed PMID: 28342872.
  59. Wang N, Yuan Z, Niu W, Li Q, Guo J. Synthetic biology approach for the development of conditionally replicating HIV-1 vaccine. J Chem Technol Biotechnol. 2017;92(3):455-62. Epub 2017/10/07. doi: 10.1002/jctb.5174. PubMed PMID: 28983143; PMCID: PMC5624719.
  60. Wang Y, Singh NK, Spear TT, Hellman LM, Piepenbrink KH*, McMahan RH, Rosen HR, Vander Kooi CW, Nishimura MI, Baker BM. How an alloreactive T-cell receptor achieves peptide and MHC specificity. Proc Natl Acad Sci U S A. 2017;114(24):E4792-E801. Epub 2017/06/03. doi: 10.1073/pnas.1700459114. PubMed PMID: 28572406; PMCID: PMC5474831.
  61. Wilson MA. Structural Insight into a Fatty-Acyl Chaperone for Wnt Proteins. Structure. 2017;25(12):1781-2. Epub 2017/12/07. doi: 10.1016/j.str.2017.11.009. PubMed PMID: 29211982.
  62. Xie JL, Bohovych I, Wong EOY, Lambert JP, Gingras AC, Khalimonchuk O, Cowen LE, Leach MD. Ydj1 governs fungal morphogenesis and stress response, and facilitates mitochondrial protein import via Mas1 and Mas2. Microb Cell. 2017;4(10):342-61. Epub 2017/10/31. doi: 10.15698/mic2017.10.594. PubMed PMID: 29082232; PMCID: PMC5657825.
  63. Yuan Z, Wang N, Kang G, Niu W, Li Q, Guo J. Controlling Multicycle Replication of Live-Attenuated HIV-1 Using an Unnatural Genetic Switch. ACS Synth Biol. 2017;6(4):721-31. Epub 2017/01/21. doi: 10.1021/acssynbio.6b00373. PubMed PMID: 28106981; PMCID: PMC5400733.
  64. Zempleni J. Milk exosomes: beyond dietary microRNAs. Genes Nutr. 2017;12(1):12. Epub 2017/07/12. doi: 10.1186/s12263-017-0562-6. PubMed PMID: 28694874; PMCID: PMC5501576.
  65. Zempleni J, Aguilar-Lozano A, Sadri M, Sukreet S, Manca S, Wu D, Zhou F, Mutai E. Biological Activities of Extracellular Vesicles and Their Cargos from Bovine and Human Milk in Humans and Implications for Infants. J Nutr. 2017;147(1):3-10. Epub 2016/11/18. doi: 10.3945/jn.116.238949. PubMed PMID: 27852870; PMCID: PMC5177735.
  66. Zhang T, Liu Z, Wang J, Minhas V, Wood C, Clifford GM, He N, Franceschi S. Seroprevalence of antibodies against Kaposi's sarcoma-associated herpesvirus among HIV-negative people in China. Infect Agent Cancer. 2017;12:32. Epub 2017/06/03. doi: 10.1186/s13027-017-0142-9. PubMed PMID: 28572838; PMCID: PMC5450136.
  67. Zhang W, Huffman J, Li S, Shen Y, Du L. Unusual acylation of chloramphenicol in Lysobacter enzymogenes, a biocontrol agent with intrinsic resistance to multiple antibiotics. BMC Biotechnol. 2017;17(1):59. Epub 2017/07/06. doi: 10.1186/s12896-017-0377-y. PubMed PMID: 28676112; PMCID: PMC5496308.
  68. Zhang W, Zhao B, Du L, Shen Y. Cytotoxic Polyketides with an Oxygen-Bridged Cyclooctadiene Core Skeleton from the Mangrove Endophytic Fungus Phomosis sp. A818. Molecules. 2017;22(9). Epub 2017/09/15. doi: 10.3390/molecules22091547. PubMed PMID: 28906443; PMCID: PMC6151419.
  69. Zhao Y, Qian G, Chen Y, Du L, Liu F. Transcriptional and Antagonistic Responses of Biocontrol Strain Lysobacter enzymogenes OH11 to the Plant Pathogenic Oomycete Pythium aphanidermatum. Front Microbiol. 2017;8:1025. Epub 2017/06/22. doi: 10.3389/fmicb.2017.01025. PubMed PMID: 28634478; PMCID: PMC5459918.
  70. Zheng J, Yang Y, Cui M, Shu ZJ, Han LL, Liu ZQ, Wood C, Zhang T, Zeng Y. Prevalence of Kaposi's sarcoma-associated herpesvirus in Uygur and Han populations from the Urumqi and Kashgar regions of Xinjiang, China. Virol Sin. 2017;32(5):396-403. Epub 2017/11/09. doi: 10.1007/s12250-017-4049-9. PubMed PMID: 29116591; PMCID: PMC6704202.
  71. Zhou X, Lesiak L, Lai R, Beck JR, Zhao J, Elowsky CG, Li H**, Stains CI. Chemoselective Alteration of Fluorophore Scaffolds as a Strategy for the Development of Ratiometric Chemodosimeters. Angew Chem Int Ed Engl. 2017;56(15):4197-200. Epub 2017/03/21. doi: 10.1002/anie.201612628. PubMed PMID: 28319304; PMCID: PMC5453638.


01/2018 – 12/2018 (Total: 84; junior investigators: 22)

*Project leader; **Pilot and/or seed grant recipient


  1. Aboufazeli F, Dodds ED. Precursor ion survival energies of protonated N-glycopeptides and their weak dependencies on high mannose N-glycan composition in collision-induced dissociation. Analyst. 2018;143(18):4459-68. Epub 2018/08/29. doi: 10.1039/c8an00830b. PubMed PMID: 30151520; PMCID: PMC6131044.
  2. Aguilar-Lozano A, Baier S, Grove R, Shu J, Giraud D, Leiferman A, Mercer KE, Cui J, Badger TM, Adamec J, Andres A, Zempleni J. Concentrations of Purine Metabolites Are Elevated in Fluids from Adults and Infants and in Livers from Mice Fed Diets Depleted of Bovine Milk Exosomes and their RNA Cargos. J Nutr. 2018;148(12):1886-94. Epub 2018/12/06. doi: 10.1093/jn/nxy223. PubMed PMID: 30517726; PMCID: PMC6280001.
  3. Bai W, Kuang T, Chitrakar C, Yang R*, Li S, Zhu D, Chang L. Patchable micro/nanodevices interacting with skin. Biosens Bioelectron. 2018;122:189-204. Epub 2018/09/29. doi: 10.1016/j.bios.2018.09.035. PubMed PMID: 30265969.
  4. Bano F, Tammi MI, Kang DW, Harris EN, Richter RP. Single-Molecule Unbinding Forces between the Polysaccharide Hyaluronan and Its Binding Proteins. Biophys J. 2018;114(12):2910-22. Epub 2018/06/21. doi: 10.1016/j.bpj.2018.05.014. PubMed PMID: 29925027; PMCID: PMC6026378.
  5. Barberis M, Helikar T, Verbruggen P. Simulation of Stimulation: Cytokine Dosage and Cell Cycle Crosstalk Driving Timing-Dependent T Cell Differentiation. Front Physiol. 2018;9:879. Epub 2018/08/18. doi: 10.3389/fphys.2018.00879. PubMed PMID: 30116196; PMCID: PMC6083814.
  6. Bhinderwala F, Lonergan S, Woods J, Zhou C, Fey PD, Powers R. Expanding the Coverage of the Metabolome with Nitrogen-Based NMR. Anal Chem. 2018;90(7):4521-8. Epub 2018/03/06. doi: 10.1021/acs.analchem.7b04922. PubMed PMID: 29505241; PMCID: PMC6472702.
  7. Bhinderwala F, Wase N, DiRusso C, Powers R. Combining Mass Spectrometry and NMR Improves Metabolite Detection and Annotation. J Proteome Res. 2018;17(11):4017-22. Epub 2018/10/12. doi: 10.1021/acs.jproteome.8b00567. PubMed PMID: 30303385; PMCID: PMC6668615.
  8. Bisker G, Bakh NA, Lee MA, Ahn J, Park M, O'Connell EB, Iverson NM**, Strano MS. Insulin Detection Using a Corona Phase Molecular Recognition Site on Single-Walled Carbon Nanotubes. ACS Sens. 2018;3(2):367-77. Epub 2018/01/24. doi: 10.1021/acssensors.7b00788. PubMed PMID: 29359558.
  9. Boukhenouna S, Wilson MA, Bahmed K, Kosmider B. Reactive Oxygen Species in Chronic Obstructive Pulmonary Disease. Oxid Med Cell Longev. 2018;2018:5730395. Epub 2018/03/31. doi: 10.1155/2018/5730395. PubMed PMID: 29599897; PMCID: PMC5828402.
  10. Cabral F, Miller CM, Kudrna KM, Hass BE, Daubendiek JG, Kellar BM, Harris EN. Purification of Hepatocytes and Sinusoidal Endothelial Cells from Mouse Liver Perfusion. J Vis Exp. 2018(132):e56993/1-e/11. Epub 2018/03/20. doi: 10.3791/56993. PubMed PMID: 29553556; PMCID: PMC5894826.
  11. Camara Teixeira D, Cordonier EL, Wijeratne SSK, Huebbe P, Jamin A, Jarecke S, Wiebe M, Zempleni J. A cell death assay for assessing the mitochondrial targeting of proteins. J Nutr Biochem. 2018;56:48-54. Epub 2018/02/20. doi: 10.1016/j.jnutbio.2018.01.006. PubMed PMID: 29454998; PMCID: PMC5971163.
  12. Casey CA, Thomes P, Manca S, Petrosyan A*. Giantin Is Required for Post-Alcohol Recovery of Golgi in Liver Cells. Biomolecules. 2018;8(4). Epub 2018/11/21. doi: 10.3390/biom8040150. PubMed PMID: 30453527; PMCID: PMC6316505.
  13. Casey CA, Thomes P, Manca S, Riethoven J-JM, Clarke J, Petrosyan A*. Golgi Renaissance: the pivotal role of the largest Golgi protein giantin. bioRxiv, Cell Biol. 2018:1-40. doi: 10.1101/296517.
  14. Catazaro J, Andrews T, Milkovic NM, Lin J, Lowe AJ, Wilson MA, Powers R. (15)N CEST data and traditional model-free analysis capture fast internal dynamics of DJ-1. Anal Biochem. 2018;542:24-8. Epub 2017/11/25. doi: 10.1016/j.ab.2017.11.012. PubMed PMID: 29169778; PMCID: PMC5817017.
  15. Cerqueira SR, Lee YS, Cornelison RC, Mertz MW, Wachs RA*, Schmidt CE, Bunge MB. Decellularized peripheral nerve supports Schwann cell transplants and axon growth following spinal cord injury. Biomaterials. 2018;177:176-85. Epub 2018/06/22. doi: 10.1016/j.biomaterials.2018.05.049. PubMed PMID: 29929081; PMCID: PMC6034707.
  16. Chakrabarty S, Takacs JM. Phosphonate-Directed Catalytic Asymmetric Hydroboration: Delivery of Boron to the More Substituted Carbon, Leading to Chiral Tertiary Benzylic Boronic Esters. ACS Catal. 2018;8(11):10530-6. Epub 2019/05/28. doi: 10.1021/acscatal.8b03591. PubMed PMID: 31134137; PMCID: PMC6533611.
  17. Chen Y, Wan Y, Wang N, Yuan Z, Niu W, Li Q, Guo J. Controlling the Replication of a Genomically Recoded HIV-1 with a Functional Quadruplet Codon in Mammalian Cells. ACS Synth Biol. 2018;7(6):1612-7. Epub 2018/05/23. doi: 10.1021/acssynbio.8b00096. PubMed PMID: 29787233; PMCID: PMC6003876.
  18. Chen Y, Yu L, Liu F, Du L. Spermidine-Regulated Biosynthesis of Heat-Stable Antifungal Factor (HSAF) in Lysobacter enzymogenes OH11. Front Microbiol. 2018;9:2984. Epub 2018/12/20. doi: 10.3389/fmicb.2018.02984. PubMed PMID: 30564221; PMCID: PMC6288370.
  19. Cornelison RC, Wellman SM, Park JH, Porvasnik SL, Song YH, Wachs RA*, Schmidt CE. Development of an apoptosis-assisted decellularization method for maximal preservation of nerve tissue structure. Acta Biomater. 2018;77:116-26. Epub 2018/07/10. doi: 10.1016/j.actbio.2018.07.009. PubMed PMID: 29981947; PMCID: PMC6126930.
  20. Cui J, Zempleni J. Reply to B Fromm et al. J Nutr. 2018;148(9):1508. Epub 2018/09/06. doi: 10.1093/jn/nxy145. PubMed PMID: 30184225.
  21. Fang Q, Wang X, Liu Z, Zhu M, Ding M, Minhas V, Wood C, Zhang T. Seroprevalence of human herpesvirus 8 and its impact on the hemoglobin level in patients of end stage of renal diseases. J Med Virol. 2018;90(2):338-43. Epub 2017/09/07. doi: 10.1002/jmv.24937. PubMed PMID: 28876458; PMCID: PMC5794214.
  22. Ganesan M, Dagur RS, Makarov E, Poluektova LI, Kidambi S*, Osna NA. Matrix stiffness regulate apoptotic cell death in HIV-HCV co-infected hepatocytes: Importance for liver fibrosis progression. Biochem Biophys Res Commun. 2018;500(3):717-22. Epub 2018/04/22. doi: 10.1016/j.bbrc.2018.04.142. PubMed PMID: 29679566; PMCID: PMC6863049.
  23. Gardner SG, Marshall DD, Daum RS, Powers R, Somerville GA. Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility. Antimicrob Agents Chemother. 2018;62(1):1-13. Epub 2017/11/08. doi: 10.1128/AAC.01608-17. PubMed PMID: 29109158; PMCID: PMC5740343.
  24. Gaus H, Miller CM, Seth PP, Harris EN. Structural Determinants for the Interactions of Chemically Modified Nucleic Acids with the Stabilin-2 Clearance Receptor. Biochemistry. 2018;57(14):2061-4. Epub 2018/03/29. doi: 10.1021/acs.biochem.8b00126. PubMed PMID: 29589907; PMCID: PMC5905987.
  25. Gebregiworgis T, Bhinderwala F, Purohit V, Chaika NV, Singh PK, Powers R. Insights into gemcitabine resistance and the potential for therapeutic monitoring. Metabolomics. 2018;14(12):156. Epub 2019/03/05. doi: 10.1007/s11306-018-1452-7. PubMed PMID: 30830412; PMCID: PMC6620022.
  26. Germany EM, Zahayko N, Huebsch ML, Fox JL, Prahlad V, Khalimonchuk O. The AAA ATPase Afg1 preserves mitochondrial fidelity and cellular health by maintaining mitochondrial matrix proteostasis. J Cell Sci. 2018;131(22):jcs219956/1-jcs/13. Epub 2018/10/12. doi: 10.1242/jcs.219956. PubMed PMID: 30301782; PMCID: PMC6262775.
  27. Hayward SL, Kidambi S*. CD44 Targeted Lipid Nanoparticles for MicroRNA Therapy. Methods Mol Biol. 2018;1831:95-109. Epub 2018/07/28. doi: 10.1007/978-1-4939-8661-3_8. PubMed PMID: 30051427.
  28. Hoang GL, Zhang S, Takacs JM. Rhodium-catalyzed asymmetric hydroboration of gamma,delta-unsaturated amide derivatives: delta-borylated amides. Chem Commun (Camb). 2018;54(38):4838-41. Epub 2018/04/27. doi: 10.1039/c8cc01563e. PubMed PMID: 29696267; PMCID: PMC5975375.
  29. Howell ME, van Dijk K, Booth CS, Helikar T, Couch BA, Roston RL. Visualizing the Invisible: A Guide to Designing, Printing, and Incorporating Dynamic 3D Molecular Models to Teach Structure-Function Relationships. J Microbiol Biol Educ. 2018;19(3). Epub 2018/11/01. doi: 10.1128/jmbe.v19i3.1663. PubMed PMID: 30377475; PMCID: PMC6203631.
  30. Iverson NM**, Hofferber EM, Stapleton JA. Nitric Oxide Sensors for Biological Applications. Chemosensors. 2018;6(1):8/1-8/13. doi: 10.3390/chemosensors6010008. PubMed PMID: WOS:000428506700007.
  31. Jacobs BY, Lakes EH, Reiter AJ, Lake SP, Ham TR, Leipzig ND, Porvasnik SL, Schmidt CE, Wachs RA*, Allen KD. The Open Source GAITOR Suite for Rodent Gait Analysis. Sci Rep. 2018;8(1):9797. Epub 2018/06/30. doi: 10.1038/s41598-018-28134-1. PubMed PMID: 29955094; PMCID: PMC6023937.
  32. Jiang J, Guiza Beltran D, Schacht A, Wright S, Zhang L*, Du L. Functional and Structural Analysis of Phenazine O-Methyltransferase LaPhzM from Lysobacter antibioticus OH13 and One-Pot Enzymatic Synthesis of the Antibiotic Myxin. ACS Chem Biol. 2018;13(4):1003-12. Epub 2018/03/07. doi: 10.1021/acschembio.8b00062. PubMed PMID: 29510028; PMCID: PMC5910208.
  33. Johnson TB, Mechels K, Anderson RH, Cain JT, Sturdevant DA, Braddock S, Pinz H, Wilson MA, Landsverk M, Roux KJ, Weimer JM. Characterization of a recurrent missense mutation in the forkhead DNA-binding domain of FOXP1. Sci Rep. 2018;8(1):16161. Epub 2018/11/06. doi: 10.1038/s41598-018-34437-0. PubMed PMID: 30385778; PMCID: PMC6212433.
  34. Klein C, Gonzalez D, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C, Angeletti PC. The relationship between the cervical microbiome, hiv status, and pre-cancerous lesions. bioRxiv, Cancer Biol. 2018:1-36. doi: 10.1101/375592.
  35. Kopf JC, Suhr MJ, Clarke J, Eyun SI, Riethoven JM, Ramer-Tait AE, Rose DJ. Role of whole grains versus fruits and vegetables in reducing subclinical inflammation and promoting gastrointestinal health in individuals affected by overweight and obesity: a randomized controlled trial. Nutr J. 2018;17(1):72. Epub 2018/08/01. doi: 10.1186/s12937-018-0381-7. PubMed PMID: 30060746; PMCID: PMC6066923.
  36. Korasick DA, Campbell AC, Christgen SL, Chakravarthy S, White TA, Becker DF, Tanner JJ. Redox Modulation of Oligomeric State in Proline Utilization A. Biophys J. 2018;114(12):2833-43. Epub 2018/06/21. doi: 10.1016/j.bpj.2018.04.046. PubMed PMID: 29925020; PMCID: PMC6026346.
  37. Kramer L, Hankore ED, Liu Y, Liu K, Jimenez E, Guo J, Niu W. Characterization of Carboxylic Acid Reductases for Biocatalytic Synthesis of Industrial Chemicals. Chembiochem. 2018;19(13):1452-60. Epub 2018/04/17. doi: 10.1002/cbic.201800157. PubMed PMID: 29659112.
  38. Krumbeck JA, Rasmussen HE, Hutkins RW, Clarke J, Shawron K, Keshavarzian A, Walter J. Probiotic Bifidobacterium strains and galactooligosaccharides improve intestinal barrier function in obese adults but show no synergism when used together as synbiotics. Microbiome. 2018;6(1):121. Epub 2018/06/30. doi: 10.1186/s40168-018-0494-4. PubMed PMID: 29954454; PMCID: PMC6022452.
  39. Kubyshkin AV, Fomochkina, II, Petrosyan A*. The Impact of Alcohol on Pro-Metastatic N-Glycosylation in Prostate Cancer. Krim Z Eksp Klin Med. 2018;8(4):11-20. Epub 2018/01/01. PubMed PMID: 31131224; PMCID: PMC6534161.
  40. Lai R, Dodds ED, Li H**. Molecular dynamics simulation of ion mobility in gases. J Chem Phys. 2018;148(6):064109. Epub 2018/02/17. doi: 10.1063/1.4998955. PubMed PMID: 29448783; PMCID: PMC5812742.
  41. Lai R, Tang WJ, Li H**. Catalytic Mechanism of Amyloid-beta Peptide Degradation by Insulin Degrading Enzyme: Insights from Quantum Mechanics and Molecular Mechanics Style Moller-Plesset Second Order Perturbation Theory Calculation. J Chem Inf Model. 2018;58(9):1926-34. Epub 2018/08/23. doi: 10.1021/acs.jcim.8b00406. PubMed PMID: 30133282; PMCID: PMC6670292.
  42. Lawrie J, Song X, Niu W, Guo J. A high throughput approach for the generation of orthogonally interacting protein pairs. Sci Rep. 2018;8(1):867. Epub 2018/01/19. doi: 10.1038/s41598-018-19281-6. PubMed PMID: 29343761; PMCID: PMC5772552.
  43. Leiferman A, Shu J, Grove R, Cui J, Adamec J, Zempleni J. A diet defined by its content of bovine milk exosomes and their RNA cargos has moderate effects on gene expression, amino acid profiles and grip strength in skeletal muscle in C57BL/6 mice. J Nutr Biochem. 2018;59:123-8. Epub 2018/07/10. doi: 10.1016/j.jnutbio.2018.06.007. PubMed PMID: 29986306; PMCID: PMC6129415.
  44. Li Y, Wang H, Liu Y, Jiao Y, Li S, Shen Y, Du L. Biosynthesis of the Polycyclic System in the Antifungal HSAF and Analogues from Lysobacter enzymogenes. Angew Chem Int Ed Engl. 2018;57(21):6221-5. Epub 2018/03/25. doi: 10.1002/anie.201802488. PubMed PMID: 29573092; PMCID: PMC6017996.
  45. Liu Y, He X, Lim W, Mueller J, Lawrie J, Kramer L, Guo J, Niu W. Deciphering molecular details in the assembly of alpha-type carboxysome. Sci Rep. 2018;8(1):15062. Epub 2018/10/12. doi: 10.1038/s41598-018-33074-x. PubMed PMID: 30305640; PMCID: PMC6180065.
  46. Liu Y, Wang H, Song R, Chen J, Li T, Li Y, Du L, Shen Y. Targeted Discovery and Combinatorial Biosynthesis of Polycyclic Tetramate Macrolactam Combamides A-E. Org Lett. 2018;20(12):3504-8. Epub 2018/05/25. doi: 10.1021/acs.orglett.8b01285. PubMed PMID: 29792712.
  47. Liu Z, Fang Q, Zuo J, Chen Y, Minhas V, Wood C, Zhang T. Global epidemiology of human herpesvirus 8 in men who have sex with men: A systematic review and meta-analysis. J Med Virol. 2018;90(3):582-91. Epub 2017/10/05. doi: 10.1002/jmv.24960. PubMed PMID: 28975631.
  48. Liu Z, Fang Q, Zuo J, Minhas V, Wood C, Zhang T. The world-wide incidence of Kaposi's sarcoma in the HIV/AIDS era. HIV Med. 2018;19(5):355-64. Epub 2018/01/26. doi: 10.1111/hiv.12584. PubMed PMID: 29368388.
  49. Manca S, Upadhyaya B, Mutai E, Desaulniers AT, Cederberg RA, White BR, Zempleni J. Milk exosomes are bioavailable and distinct microRNA cargos have unique tissue distribution patterns. Sci Rep. 2018;8(1):11321. Epub 2018/07/29. doi: 10.1038/s41598-018-29780-1. PubMed PMID: 30054561; PMCID: PMC6063888.
  50. Marcone A, Pierobon M**, Magarini M. Parity-Check Coding Based on Genetic Circuits for Engineered Molecular Communication Between Biological Cells. Ieee Transactions on Communications. 2018;66(12):6221-36. doi: 10.1109/Tcomm.2018.2859308. PubMed PMID: WOS:000454112200029.
  51. Martins DP, Barros MT, Pierobon M**, Kandhavelu M, Lio P, Balasubramaniam S. Computational Models for Trapping Ebola Virus Using Engineered Bacteria. IEEE/ACM Trans Comput Biol Bioinform. 2018;15(6):2017-27. Epub 2018/07/12. doi: 10.1109/TCBB.2018.2836430. PubMed PMID: 29994771.
  52. Mendoza JR, Rodas A, Oliva A, Sabillon L, Colmenares A, Clarke J, Hallen-Adams HE, Campabadal C, Bianchini A. Safety and Quality Assessment of Smallholder Farmers' Maize in the Western Highlands of Guatemala. J Food Prot. 2018;81(5):776-84. Epub 2018/04/07. doi: 10.4315/0362-028X.JFP-17-355. PubMed PMID: 29624105.
  53. Miller CM, Tanowitz M, Donner AJ, Prakash TP, Swayze EE, Harris EN, Seth PP. Receptor-Mediated Uptake of Phosphorothioate Antisense Oligonucleotides in Different Cell Types of the Liver. Nucleic Acid Ther. 2018;28(3):119-27. Epub 2018/02/10. doi: 10.1089/nat.2017.0709. PubMed PMID: 29425080; PMCID: PMC6037193.
  54. Miller CM, Wan WB, Seth PP, Harris EN. Endosomal Escape of Antisense Oligonucleotides Internalized by Stabilin Receptors Is Regulated by Rab5C and EEA1 During Endosomal Maturation. Nucleic Acid Ther. 2018;28(2):86-96. Epub 2018/02/14. doi: 10.1089/nat.2017.0694. PubMed PMID: 29437530; PMCID: PMC5899299.
  55. Miller CM, Xu Y, Kudrna KM, Hass BE, Kellar BM, Egger AW, Liu J, Harris EN. 3-O sulfation of heparin leads to hepatotropism and longer circulatory half-life. Thromb Res. 2018;167:80-7. Epub 2018/05/25. doi: 10.1016/j.thromres.2018.05.018. PubMed PMID: 29793137; PMCID: PMC6242777.
  56. Mohammed A, Biegert G, Adamec J, Helikar T. CancerDiscover: an integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data. Oncotarget. 2018;9(2):2565-73. Epub 2018/02/09. doi: 10.18632/oncotarget.23511. PubMed PMID: 29416792; PMCID: PMC5788660.
  57. Monemian EA, Zhao W, Yang R*, Chen JY, Xi J, Huang C, Xi N. On the Measurement of Energy Dissipation of Adhered Cells with the Quartz Microbalance with Dissipation Monitoring. Anal Chem. 2018;90(17):10340-9.
  58. Mtonga W, Mujajati A, Munkombwe D, Kalungia A, Muungo LT, West J, Wood C, Ngalamika O. Therapeutic Outcomes in AIDS-Associated Kaposi's Sarcoma Patients on Antiretroviral Therapy Treated with Chemotherapy at Two Tertiary Hospitals in Lusaka, Zambia. Curr HIV Res. 2018;16(3):231-6. Epub 2018/07/12. doi: 10.2174/1570162X16666180711103610. PubMed PMID: 29992888.
  59. Naldi A, Hernandez C, Levy N, Stoll G, Monteiro PT, Chaouiya C, Helikar T, Zinovyev A, Calzone L, Cohen-Boulakia S, Thieffry D, Pauleve L. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. Front Physiol. 2018;9:680. Epub 2018/07/05. doi: 10.3389/fphys.2018.00680. PubMed PMID: 29971009; PMCID: PMC6018415.
  60. Pentzien T, Puniya BL, Helikar T, Matache MT. Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes. Front Physiol. 2018;9:1185. Epub 2018/09/21. doi: 10.3389/fphys.2018.01185. PubMed PMID: 30233390; PMCID: PMC6127445.
  61. Petyuk VA, Chang R, Ramirez-Restrepo M, Beckmann ND, Henrion MYR, Piehowski PD, Zhu K, Wang S, Clarke J, Huentelman MJ, Xie F, Andreev V, Engel A, Guettoche T, Navarro L, De Jager P, Schneider JA, Morris CM, McKeith IG, Perry RH, Lovestone S, Woltjer RL, Beach TG, Sue LI, Serrano GE, Lieberman AP, Albin RL, Ferrer I, Mash DC, Hulette CM, Ervin JF, Reiman EM, Hardy JA, Bennett DA, Schadt E, Smith RD, Myers AJ. The human brainome: network analysis identifies HSPA2 as a novel Alzheimer’s disease target. Brain. 2018;141(9):2721-39. Epub 2018/08/24. doi: 10.1093/brain/awy215. PubMed PMID: 30137212; PMCID: PMC6136080.
  62. Pirie E, Ray S, Pan C, Fu W, Powers AF, Polikoff D, Miller CM, Kudrna KM, Harris EN, Lusis AJ, Crooke RM, Lee RG. Mouse genome-wide association studies and systems genetics uncover the genetic architecture associated with hepatic pharmacokinetic and pharmacodynamic properties of a constrained ethyl antisense oligonucleotide targeting Malat1. PLoS Genet. 2018;14(10):e1007732. Epub 2018/10/30. doi: 10.1371/journal.pgen.1007732. PubMed PMID: 30372444; PMCID: PMC6224167 following competing interests: Authors EP, SR, WF, AFP, DP, RMC, and RGL are or were employed by Ionis Pharmaceuticals.
  63. Poulsen CB, Pedrigi RM**, Pareek N, Kilic ID, Holm NR, Bentzon JF, Botker HE, Falk E, Krams R, de Silva R. Plaque burden influences accurate classification of fibrous cap atheroma by in vivo optical coherence tomography in a porcine model of advanced coronary atherosclerosis. EuroIntervention. 2018;14(10):1129-35. Epub 2018/04/05. doi: 10.4244/EIJ-D-17-01028. PubMed PMID: 29616625.
  64. Puniya BL, Todd RG, Mohammed A, Brown DM, Barberis M, Helikar T. A Mechanistic Computational Model Reveals That Plasticity of CD4(+) T Cell Differentiation Is a Function of Cytokine Composition and Dosage. Front Physiol. 2018;9:878. Epub 2018/08/18. doi: 10.3389/fphys.2018.00878. PubMed PMID: 30116195; PMCID: PMC6083813.
  65. Robinson NP, Buan NR*. Methanogens: pushing the boundaries of biology. Emerging Topics in Life Sciences. 2018;2(4):629-46. doi: 10.1042/etls20180031.
  66. Rotzinger FP, Li H**. Quantum Chemical Study of the Redox Potential of the Co(OH2)6(2+/3+) Couple and the Singlet-Quintet Gibbs Energy Difference of the Co(OH2)6(3+) Ion. Inorg Chem. 2018;57(16):10122-7. Epub 2018/08/03. doi: 10.1021/acs.inorgchem.8b01308. PubMed PMID: 30070480.
  67. Schumann C, Chan S, Millar JA, Bortnyak Y, Carey K, Fedchyk A, Wong L, Korzun T, Moses AS, Lorenz A, Shea D, Taratula O, Khalimonchuk O, Taratula O. Intraperitoneal nanotherapy for metastatic ovarian cancer based on siRNA-mediated suppression of DJ-1 protein combined with a low dose of cisplatin. Nanomedicine. 2018;14(4):1395-405. Epub 2018/04/11. doi: 10.1016/j.nano.2018.03.005. PubMed PMID: 29635082; PMCID: PMC6174103.
  68. Shang X, Chen Y, Wang N, Niu W, Guo J. Oxidation-induced generation of a mild electrophile for proximity-enhanced protein-protein crosslinking. Chem Commun (Camb). 2018;54(33):4172-5. Epub 2018/04/10. doi: 10.1039/c8cc01639a. PubMed PMID: 29629441; PMCID: PMC5908726.
  69. Singh V, Ostaszewski M, Kalliolias GD, Chiocchia G, Olaso R, Petit-Teixeira E, Helikar T, Niarakis A. Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model. Genom Comput Biol. 2018;4(1). Epub 2018/06/29. doi: 10.18547/gcb.2018.vol4.iss1.e100050. PubMed PMID: 29951575; PMCID: PMC6016388.
  70. Sinha R, Weissenburger-Moser LA, Clarke JL, Smith LM, Heires AJ, Romberger DJ, LeVan TD. Short term dynamics of the sputum microbiome among COPD patients. PLoS One. 2018;13(3):e0191499. Epub 2018/03/09. doi: 10.1371/journal.pone.0191499. PubMed PMID: 29518088; PMCID: PMC5843169.
  71. Soubeyrand E, Johnson TS, Latimer S, Block A, Kim J, Colquhoun TA, Butelli E, Martin C, Wilson MA, Basset GJ. The Peroxidative Cleavage of Kaempferol Contributes to the Biosynthesis of the Benzenoid Moiety of Ubiquinone in Plants. Plant Cell. 2018;30(12):2910-21. Epub 2018/11/16. doi: 10.1105/tpc.18.00688. PubMed PMID: 30429224; PMCID: PMC6354277.
  72. Srivastava T, Diba P, Dean JM, Banine F, Shaver D, Hagen M, Gong X, Su W, Emery B, Marks DL, Harris EN, Baggenstoss B, Weigel PH, Sherman LS, Back SA. A TLR/AKT/FoxO3 immune tolerance-like pathway disrupts the repair capacity of oligodendrocyte progenitors. J Clin Invest. 2018;128(5):2025-41. Epub 2018/04/18. doi: 10.1172/JCI94158. PubMed PMID: 29664021; PMCID: PMC5919806.
  73. Still GG, Li S, Wilson M, Sammut P. Persistent Pulmonary Hypertension Without Underlying Cardiac Disease as a Presentation of Pulmonary Interstitial Glycogenosis. Fetal Pediatr Pathol. 2018;37(1):22-6. Epub 2018/01/18. doi: 10.1080/15513815.2017.1397071. PubMed PMID: 29336713.
  74. Still GG, Li S, Wilson M, Wong L, Sammut P. Retrotracheal Aberrant Right Subclavian Artery: Congenital Anomaly or Postsurgical Complication? Glob Pediatr Health. 2018;5:2333794X18762689. Epub 2018/03/20. doi: 10.1177/2333794X18762689. PubMed PMID: 29552601; PMCID: PMC5846904 conflicts of interest with respect to the research, authorship, and/or publication of this article.
  75. Tanner JJ, Fendt SM, Becker DF. The Proline Cycle As a Potential Cancer Therapy Target. Biochemistry. 2018;57(25):3433-44. Epub 2018/04/13. doi: 10.1021/acs.biochem.8b00215. PubMed PMID: 29648801; PMCID: PMC6026536.
  76. Tso FY, Kang G, Kwon EH, Julius P, Li Q, West JT, Wood C. Brain is a potential sanctuary for subtype C HIV-1 irrespective of ART treatment outcome. PLoS One. 2018;13(7):e0201325. Epub 2018/07/25. doi: 10.1371/journal.pone.0201325. PubMed PMID: 30040863; PMCID: PMC6057662.
  77. Tso FY, Kossenkov AV, Lidenge SJ, Ngalamika O, Ngowi JR, Mwaiselage J, Wickramasinghe J, Kwon EH, West JT, Lieberman PM, Wood C. RNA-Seq of Kaposi's sarcoma reveals alterations in glucose and lipid metabolism. PLoS Pathog. 2018;14(1):e1006844. Epub 2018/01/21. doi: 10.1371/journal.ppat.1006844. PubMed PMID: 29352292; PMCID: PMC5792027.
  78. Tsushima K, Bugger H, Wende AR, Soto J, Jenson GA, Tor AR, McGlauflin R, Kenny HC, Zhang Y, Souvenir R, Hu XX, Sloan CL, Pereira RO, Lira VA, Spitzer KW, Sharp TL, Shoghi KI, Sparagna GC, Rog-Zielinska EA, Kohl P, Khalimonchuk O, Schaffer JE, Abel ED. Mitochondrial Reactive Oxygen Species in Lipotoxic Hearts Induce Post-Translational Modifications of AKAP121, DRP1, and OPA1 That Promote Mitochondrial Fission. Circ Res. 2018;122(1):58-73. Epub 2017/11/03. doi: 10.1161/CIRCRESAHA.117.311307. PubMed PMID: 29092894; PMCID: PMC5756120.
  79. Vu T, Riekeberg E, Qiu Y, Powers R. Comparing normalization methods and the impact of noise. Metabolomics. 2018;14(8):108. Epub 2019/03/05. doi: 10.1007/s11306-018-1400-6. PubMed PMID: 30830388; PMCID: PMC6638559.
  80. Wang L, Sadri M, Giraud D, Zempleni J. RNase H2-Dependent Polymerase Chain Reaction and Elimination of Confounders in Sample Collection, Storage, and Analysis Strengthen Evidence That microRNAs in Bovine Milk Are Bioavailable in Humans. J Nutr. 2018;148(1):153-9. Epub 2018/01/30. doi: 10.1093/jn/nxx024. PubMed PMID: 29378054; PMCID: PMC6251634.
  81. Wang O, Ismail A, Fabian FM, Lin H, Li Q, Elowsky C, Carlson MA, Burgess W, Velander WH, Kidambi S*, Lei Y. A totally recombinant fibrin matrix for mesenchymal stem cell culture and delivery. J Biomed Mater Res A. 2018;106(12):3135-42. Epub 2018/08/29. doi: 10.1002/jbm.a.36508. PubMed PMID: 30152030.
  82. Xu Z, Duan Q, Cui J, Qiu Y, Jia Q, Wu C, Clarke J. Analysis of genetic and nongenetic factors influencing triglycerides-lowering drug effects based on paired observations. BMC Proc. 2018;12(Suppl 9):46. Epub 2018/10/03. doi: 10.1186/s12919-018-0153-6. PubMed PMID: 30275894; PMCID: PMC6157156 interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
  83. Yang R*, Broussard JA, Green KJ, Espinosa HD. Techniques to stimulate and interrogate cell-cell adhesion mechanics. Extreme Mech Lett. 2018;20:125-39. Epub 2018/10/16. doi: 10.1016/j.eml.2017.12.002. PubMed PMID: 30320194; PMCID: PMC6181239.
  84. Yu L, Su W, Fey PD, Liu F, Du L. Yield Improvement of the Anti-MRSA Antibiotics WAP-8294A by CRISPR/dCas9 Combined with Refactoring Self-Protection Genes in Lysobacter enzymogenes OH11. ACS Synth Biol. 2018;7(1):258-66. Epub 2017/11/11. doi: 10.1021/acssynbio.7b00293. PubMed PMID: 29125739; PMCID: PMC5775038.


01/2019 – 12/2019 (Total: 86; junior investigators: 27)

*Project leader; **Pilot and/or seed grant recipient


  1. Akyildiz IF, Chen J, Ghovanloo M, Guler U, Ozkaya-Ahmadov T, Pierobon M**, Sarioglu AF, Unluturk BD. Microbiome-Gut-Brain Axis as a Biomolecular Communication Network for the Internet of Bio-NanoThings. IEEE Access. 2019;7:136161-75. doi: 10.1109/access.2019.2942312. PubMed PMID: WOS:000498691000002.
  2. Akyildiz IF, Pierobon M**, Balasubramaniam S. An Information Theoretic Framework to Analyze Molecular Communication Systems Based on Statistical Mechanics. Proceedings of the Ieee. 2019;107(7):1230-55. doi: 10.1109/Jproc.2019.2927926. PubMed PMID: WOS:000477720400003.
  3. Akyildiz IF, Pierobon M**, Balasubramaniam S. Moving Forward With Molecular Communication: From Theory to Human Health Applications. Proceedings of the Ieee. 2019;107(5):858-65. doi: 10.1109/Jproc.2019.2913890. PubMed PMID: WOS:000467557300001.
  4. Bahmed K, Boukhenouna S, Karim L, Andrews T, Lin J, Powers R, Wilson MA, Lin CR, Messier E, Reisdorph N, Powell RL, Tang HY, Mason RJ, Criner GJ, Kosmider B. The effect of cysteine oxidation on DJ-1 cytoprotective function in human alveolar type II cells. Cell Death Dis. 2019;10(9):638. Epub 2019/09/03. doi: 10.1038/s41419-019-1833-5. PubMed PMID: 31474749; PMCID: PMC6717737.
  5. Beck JR, Cabral F, Rasineni K, Casey CA, Harris EN, Stains CI. A Panel of Protein Kinase Chemosensors Distinguishes Different Types of Fatty Liver Disease. Biochemistry. 2019;58(37):3911-7. Epub 2019/08/23. doi: 10.1021/acs.biochem.9b00547. PubMed PMID: 31433166; PMCID: PMC6820001.
  6. Bhinderwala F, Lei S, Woods J, Rose J, Marshall DD, Riekeberg E, Leite AL, Morton M, Dodds ED, Franco R, Powers R. Metabolomics Analyses from Tissues in Parkinson's Disease. Methods Mol Biol. 2019;1996:217-57. Epub 2019/05/28. doi: 10.1007/978-1-4939-9488-5_19. PubMed PMID: 31127560; PMCID: PMC6625357.
  7. Bhinderwala F, Powers R. NMR Metabolomics Protocols for Drug Discovery. Methods Mol Biol. 2019;2037:265-311. Epub 2019/08/30. doi: 10.1007/978-1-4939-9690-2_16. PubMed PMID: 31463851; PMCID: PMC7025395.
  8. Bochat AJ, Shoba VM, Takacs JM. Ligand-Controlled Regiodivergent Enantioselective Rhodium-Catalyzed Alkene Hydroboration. Angew Chem Int Ed Engl. 2019;58(28):9434-8. Epub 2019/05/09. doi: 10.1002/anie.201903308. PubMed PMID: 31067341; PMCID: PMC6663592.
  9. Bohovych I, Dietz JV, Swenson S, Zahayko N, Khalimonchuk O. Redox Regulation of the Mitochondrial Quality Control Protease Oma1. Antioxid Redox Signal. 2019;31(6):429-43. Epub 2019/05/03. doi: 10.1089/ars.2018.7642. PubMed PMID: 31044600; PMCID: PMC6653804.
  10. Bouzid T, Kim E, Riehl BD, Esfahani AM, Rosenbohm J, Yang R*, Duan B, Lim JY. The LINC complex, mechanotransduction, and mesenchymal stem cell function and fate. J Biol Eng. 2019;13:68. Epub 2019/08/14. doi: 10.1186/s13036-019-0197-9. PubMed PMID: 31406505; PMCID: PMC6686368.
  11. Cao Y, Zhang R, Liu W, Zhao G, Niu W, Guo J, Xian M, Liu H. Manipulation of the precursor supply for high-level production of longifolene by metabolically engineered Escherichia coli. Sci Rep. 2019;9(1):95. Epub 2019/01/16. doi: 10.1038/s41598-018-36495-w. PubMed PMID: 30643175; PMCID: PMC6331559.
  12. Casavale KO, Ahuja JKC, Wu X, Li Y, Quam J, Olson R, Pehrsson P, Allen L, Balentine D, Hanspal M, Hayward D, Hines EP, McClung JP, Perrine CG, Belfort MB, Dallas D, German B, Kim J, McGuire M, McGuire M, Morrow AL, Neville M, Nommsen-Rivers L, Rasmussen KM, Zempleni J, Lynch CJ. NIH workshop on human milk composition: summary and visions. Am J Clin Nutr. 2019;110(3):769-79. Epub 2019/07/06. doi: 10.1093/ajcn/nqz123. PubMed PMID: 31274142; PMCID: PMC6895543.
  13. Catazaro J, Caprez A, Swanson D, Powers R. Functional Evolution of Proteins. Proteins. 2019;87(6):492-501. Epub 2019/02/05. doi: 10.1002/prot.25670. PubMed PMID: 30714210; PMCID: PMC6462239.
  14. Chakrabarty S, Palencia H, Morton MD, Carr RO, Takacs JM. Facile access to functionalized chiral secondary benzylic boronic esters via catalytic asymmetric hydroboration. Chem Sci. 2019;10(18):4854-61. Epub 2019/06/12. doi: 10.1039/c8sc05613g. PubMed PMID: 31183035; PMCID: PMC6520923.
  15. Chang L, Wang YC, Ershad F, Yang R*, Yu C, Fan Y. Wearable Devices for Single-Cell Sensing and Transfection. Trends Biotechnol. 2019;37(11):1175-88. Epub 2019/05/11. doi: 10.1016/j.tibtech.2019.04.001. PubMed PMID: 31072609.
  16. Chen X, Li S, Yu L, Miller A, Du L. Systematic optimization for production of the anti-MRSA antibiotics WAP-8294A in an engineered strain of Lysobacter enzymogenes. Microb Biotechnol. 2019;12(6):1430-40. Epub 2019/09/15. doi: 10.1111/1751-7915.13484. PubMed PMID: 31520522; PMCID: PMC6801147.
  17. Chen Z, Zou J, Chen B, Du L, Wang M. Protecting books from mould damage by decreasing paper bioreceptivity to fungal attack using decoloured cell-free supernatant of Lysobacter enzymogenes C3. J Appl Microbiol. 2019;126(6):1772-84. Epub 2019/03/29. doi: 10.1111/jam.14265. PubMed PMID: 30920096.
  18. Christgen SL, Becker DF. Role of Proline in Pathogen and Host Interactions. Antioxid Redox Signal. 2019;30(4):683-709. Epub 2017/12/16. doi: 10.1089/ars.2017.7335. PubMed PMID: 29241353; PMCID: PMC6338583.
  19. Christgen SL, Becker SM, Becker DF. Methods for determining the reduction potentials of flavin enzymes. Methods Enzymol. 2019;620(New Approaches for Flavin Catalysis):1-25. Epub 2019/05/11. doi: 10.1016/bs.mie.2019.03.004. PubMed PMID: 31072483.
  20. Cui M, Fang Q, Zheng J, Shu Z, Chen Y, Fan Y, Zhao J, Wood C, Zhang T, Zeng Y. Kaposi's sarcoma-associated herpesvirus seropositivity is associated with type 2 diabetes mellitus: A case-control study in Xinjiang, China. Int J Infect Dis. 2019;80:73-9. Epub 2019/01/15. doi: 10.1016/j.ijid.2019.01.003. PubMed PMID: 30639407.
  21. Dasgupta M, Budday D, de Oliveira SHP, Madzelan P, Marchany-Rivera D, Seravalli J, Hayes B, Sierra RG, Boutet S, Hunter MS, Alonso-Mori R, Batyuk A, Wierman J, Lyubimov A, Brewster AS, Sauter NK, Applegate GA, Tiwari VK, Berkowitz DB, Thompson MC, Cohen AE, Fraser JS, Wall ME, van den Bedem H, Wilson MA. Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis. Proc Natl Acad Sci U S A. 2019;116(51):25634-40. Epub 2019/12/06. doi: 10.1073/pnas.1901864116. PubMed PMID: 31801874; PMCID: PMC6926069.
  22. Daverey A, Levytskyy RM, Stanke KM, Viana MP, Swenson S, Hayward SL, Narasimhan M, Khalimonchuk O, Kidambi S*. Depletion of mitochondrial protease OMA1 alters proliferative properties and promotes metastatic growth of breast cancer cells. Sci Rep. 2019;9(1):14746. Epub 2019/10/16. doi: 10.1038/s41598-019-49327-2. PubMed PMID: 31611601; PMCID: PMC6791882.
  23. Dietz JV, Bohovych I, Viana MP, Khalimonchuk O. Proteolytic regulation of mitochondrial dynamics. Mitochondrion. 2019;49:289-304. Epub 2019/04/29. doi: 10.1016/j.mito.2019.04.008. PubMed PMID: 31029640; PMCID: PMC6814530.
  24. Feng T, Han Y, Li B, Li Z, Yu Y, Sun Q, Li X, Du L, Zhang XH, Wang Y. Interspecies and Intraspecies Signals Synergistically Regulate Lysobacter enzymogenes Twitching Motility. Appl Environ Microbiol. 2019;85(23). Epub 2019/09/22. doi: 10.1128/AEM.01742-19. PubMed PMID: 31540995; PMCID: PMC6856324.
  25. Frisbie CP, Lushnikov AY, Krasnoslobodtsev AV, Riethoven JM, Clarke JL, Stepchenkova EI, Petrosyan A*. Post-ER Stress Biogenesis of Golgi Is Governed by Giantin. Cells. 2019;8(12):1631. Epub 2019/12/19. doi: 10.3390/cells8121631. PubMed PMID: 31847122; PMCID: PMC6953117.
  26. Frisbie CP, Lushnikov AY, Krasnoslobodtsev AV, Riethoven JM, Clarke JL, Stepchenkova EI, Petrosyan A*. Post-ER Stress Biogenesis of Golgi Is Governed by Giantin. Cells. 2019;8(12). Epub 2019/12/19. doi: 10.3390/cells8121631. PubMed PMID: 31847122; PMCID: PMC6953117.
  27. Gallenito MJ, Irvine GW, Zhang L*, Meloni G. Coordination promiscuity guarantees metal substrate selection in transmembrane primary-active Zn(2+) pumps. Chem Commun (Camb). 2019;55(73):10844-7. Epub 2019/08/29. doi: 10.1039/c9cc05936a. PubMed PMID: 31461510; PMCID: PMC6736703.
  28. Ganesan M, New-Aaron M, Dagur RS, Makarov E, Wang W, Kharbanda KK, Kidambi S*, Poluektova LY, Osna NA. Alcohol Metabolism Potentiates HIV-Induced Hepatotoxicity: Contribution to End-Stage Liver Disease. Biomolecules. 2019;9(12). Epub 2019/12/15. doi: 10.3390/biom9120851. PubMed PMID: 31835520; PMCID: PMC6995634.
  29. Gelb AS, Lai R, Li H**, Dodds ED. Composition and charge state influence on the ion-neutral collision cross sections of protonated N-linked glycopeptides: an experimental and theoretical deconstruction of coulombic repulsion vs. charge solvation effects. Analyst. 2019;144(19):5738-47. Epub 2019/08/28. doi: 10.1039/c9an00875f. PubMed PMID: 31453603; PMCID: PMC6756964.
  30. Germany EM, Zahayko N, Khalimonchuk O. Isolation of Specific Neuron Populations from Roundworm Caenorhabditis elegans. J Vis Exp. 2019(150):e60145/1-e/6. Epub 2019/08/27. doi: 10.3791/60145. PubMed PMID: 31449245; PMCID: PMC7227805.
  31. Hankore ED, Zhang L*, Chen Y, Liu K, Niu W, Guo J. Genetic Incorporation of Noncanonical Amino Acids Using Two Mutually Orthogonal Quadruplet Codons. ACS Synth Biol. 2019;8(5):1168-74. Epub 2019/04/19. doi: 10.1021/acssynbio.9b00051. PubMed PMID: 30995842; PMCID: PMC6525065.
  32. Harris EN, Cabral F. Ligand Binding and Signaling of HARE/Stabilin-2. Biomolecules. 2019;9(7):273. Epub 2019/07/25. doi: 10.3390/biom9070273. PubMed PMID: 31336723; PMCID: PMC6681266.
  33. Hofferber EM, Stapleton JA, Adams J, Kuss M, Duan B, Iverson NM**. Implantable Nanotube Sensor Platform for Rapid Analyte Detection. Macromol Biosci. 2019;19(6):e1800469. Epub 2019/04/04. doi: 10.1002/mabi.201800469. PubMed PMID: 30942955; PMCID: PMC6827871.
  34. Howell ME, Booth CS, Sikich SM, Helikar T, Roston RL, Couch BA, van Dijk K. Student Understanding of DNA Structure-Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models. Biochem Mol Biol Educ. 2019;47(3):303-17. Epub 2019/03/22. doi: 10.1002/bmb.21234. PubMed PMID: 30897273.
  35. Hu H, Petrosyan A*, Osna NA, Liu T, Olou AA, Alakhova DY, Singh PK, Kabanov AV, Faber EA, Jr., Bronich TK. Pluronic block copolymers enhance the anti-myeloma activity of proteasome inhibitors. J Control Release. 2019;306:149-64. Epub 2019/05/24. doi: 10.1016/j.jconrel.2019.05.026. PubMed PMID: 31121280; PMCID: PMC6822276.
  36. Johnson T, Payne S, Grove R, McCarthy S, Oeltjen E, Mach C, Adamec J, Wilson MA, Van Cott K, Blum P. Methylation deficiency of chromatin proteins is a non-mutational and epigenetic-like trait in evolved lines of the archaeon Sulfolobus solfataricus. J Biol Chem. 2019;294(19):7821-32. Epub 2019/03/29. doi: 10.1074/jbc.RA118.006469. PubMed PMID: 30918025; PMCID: PMC6514617.
  37. Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C, Angeletti PC. Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions. mBio. 2019;10(1):e02785. Epub 2019/02/21. doi: 10.1128/mBio.02785-18. PubMed PMID: 30782659; PMCID: PMC6381280.
  38. Kochert BA, Fleischhacker AS, Wales TE, Becker DF, Engen JR, Ragsdale SW. Dynamic and structural differences between heme oxygenase-1 and -2 are due to differences in their C-terminal regions. J Biol Chem. 2019;294(20):8259-72. Epub 2019/04/05. doi: 10.1074/jbc.RA119.008592. PubMed PMID: 30944174; PMCID: PMC6527177.
  39. Korasick DA, Koncitikova R, Kopecna M, Hajkova E, Vigouroux A, Morera S, Becker DF, Sebela M, Tanner JJ, Kopecny D. Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants. J Mol Biol. 2019;431(3):576-92. Epub 2018/12/24. doi: 10.1016/j.jmb.2018.12.010. PubMed PMID: 30580036; PMCID: PMC6365017.
  40. Kramer L, Le X, Hankore ED, Wilson MA, Guo J, Niu W. Engineering and characterization of hybrid carboxylic acid reductases. J Biotechnol. 2019;304:52-6. Epub 2019/08/21. doi: 10.1016/j.jbiotec.2019.08.008. PubMed PMID: 31430496.
  41. Lawrie J, Niu W, Guo J. Engineering of a sulfotyrosine-recognizing small protein scaffold for the study of protein tyrosine O-sulfation. Methods Enzymol. 2019;622(Chemical and Synthetic Biology Approaches to Understand Cellular Functions, Part B):67-89. Epub 2019/06/04. doi: 10.1016/bs.mie.2019.02.004. PubMed PMID: 31155066.
  42. Leiferman A, Shu J, Upadhyaya B, Cui J, Zempleni J. Storage of Extracellular Vesicles in Human Milk, and MicroRNA Profiles in Human Milk Exosomes and Infant Formulas. J Pediatr Gastroenterol Nutr. 2019;69(2):235-8. Epub 2019/06/07. doi: 10.1097/MPG.0000000000002363. PubMed PMID: 31169664; PMCID: PMC6658346.
  43. Li X, Li T, Gong W, Wang H, Attri KS, Lewis RE, Singh PK, Kalil AC, Bhinderwala F, Powers R, Yin G, Herring LE, Asara JM, Lei YL, Yang X, Rodriguez DA, Yang M, Green DR, Wen H. O-GlcNAc Transferase Suppresses Inflammation and Necroptosis by Targeting Receptor-Interacting Serine/Threonine-Protein Kinase 3. Immunity. 2019;50(3):576-90.e6.
  44. Li X, Wang H, Li Y, Du L. Construction of a hybrid gene cluster to reveal coupled ring formation-hydroxylation in the biosynthesis of HSAF and analogues from Lysobacter enzymogenes. Medchemcomm. 2019;10(6):907-12. Epub 2019/07/16. doi: 10.1039/c9md00154a. PubMed PMID: 31303988; PMCID: PMC6595964.
  45. Li X, Wang H, Shen Y, Li Y, Du L. OX4 Is an NADPH-Dependent Dehydrogenase Catalyzing an Extended Michael Addition Reaction To Form the Six-Membered Ring in the Antifungal HSAF. Biochemistry. 2019;58(52):5245-8. Epub 2019/05/01. doi: 10.1021/acs.biochem.9b00280. PubMed PMID: 31038929; PMCID: PMC6825872.
  46. Lidenge SJ, Tso FY, Ngalamika O, Ngowi JR, Mortazavi Y, Kwon EH, Shea DM, Minhas V, Mwaiselage J, Wood C, West JT. Similar Immunological Profiles Between African Endemic and Human Immunodeficiency Virus Type 1-Associated Epidemic Kaposi Sarcoma (KS) Patients Reveal the Primary Role of KS-Associated Herpesvirus in KS Pathogenesis. J Infect Dis. 2019;219(8):1318-28. Epub 2018/11/20. doi: 10.1093/infdis/jiy654. PubMed PMID: 30452681; PMCID: PMC6452303.
  47. Lin CR, Bahmed K, Tomar D, Marchetti N, Criner GJ, Bolla S, Wilson MA, Madesh M, Kosmider B. The relationship between DJ-1 and S100A8 in human primary alveolar type II cells in emphysema. Am J Physiol Lung Cell Mol Physiol. 2019;317(6):L791-L804. Epub 2019/07/18. doi: 10.1152/ajplung.00494.2018. PubMed PMID: 31313618; PMCID: PMC6962598.
  48. Manca S, Frisbie CP, LaGrange CA, Casey CA, Riethoven JM, Petrosyan A*. The Role of Alcohol-Induced Golgi Fragmentation for Androgen Receptor Signaling in Prostate Cancer. Mol Cancer Res. 2019;17(1):225-37. Epub 2018/09/19. doi: 10.1158/1541-7786.MCR-18-0577. PubMed PMID: 30224543; PMCID: PMC6318054.
  49. Marzo JL, Jornet JM, Pierobon M**. Nanonetworks in Biomedical Applications. Curr Drug Targets. 2019;20(8):800-7. Epub 2019/01/17. doi: 10.2174/1389450120666190115152613. PubMed PMID: 30648507.
  50. Meier J, Hofferber EM, Stapleton JA, Iverson NM**. Hydrogen Peroxide Sensors for Biomedical Applications. Chemosensors. 2019;7(4):64. doi: 10.3390/chemosensors7040064. PubMed PMID: WOS:000505721400015.
  51. Monemian EA, Rosenbohm J, Reddy K, Jin X, Bouzid T, Riehl B, Kim E, Lim JY, Yang R*, Lim JY, Yang R, Yang R. Tissue Regeneration from Mechanical Stretching of Cell-Cell Adhesion. Tissue Eng Part C Methods. 2019;25(11):631-40.
  52. Natarajan G, Perriotte-Olson C, Casey CA, Donohue TM, Jr., Talmon GA, Harris EN, Kabanov AV, Saraswathi V. Effect of nanoformulated copper/zinc superoxide dismutase on chronic ethanol-induced alterations in liver and adipose tissue. Alcohol. 2019;79:71-9. Epub 2019/01/07. doi: 10.1016/j.alcohol.2018.12.005. PubMed PMID: 30611703; PMCID: PMC6610811.
  53. Niu W, Kramer L, Mueller J, Liu K, Guo J. Metabolic engineering of Escherichia coli for the de novo stereospecific biosynthesis of 1,2-propanediol through lactic acid. Metab Eng Commun. 2019;8:e00082.
  54. Nordgren TM, Heires AJ, Zempleni J, Swanson BJ, Wichman C, Romberger DJ. Bovine milk-derived extracellular vesicles enhance inflammation and promote M1 polarization following agricultural dust exposure in mice. J Nutr Biochem. 2019;64:110-20. Epub 2018/11/27. doi: 10.1016/j.jnutbio.2018.10.017. PubMed PMID: 30476878; PMCID: PMC6363837.
  55. Parry HA, Mobley CB, Mumford PW, Romero MA, Haun CT, Zhang Y, Roberson PA, Zempleni J, Ferrando AA, Vechetti IJ, Jr., McCarthy JJ, Young KC, Roberts MD, Kavazis AN. Bovine Milk Extracellular Vesicles (EVs) Modification Elicits Skeletal Muscle Growth in Rats. Front Physiol. 2019;10:436. Epub 2019/05/02. doi: 10.3389/fphys.2019.00436. PubMed PMID: 31040795; PMCID: PMC6476979.
  56. Penas C, Maloof ME, Stathias V, Long J, Tan SK, Mier J, Fang Y, Valdes C, Rodriguez-Blanco J, Chiang CM, Robbins DJ, Liebl DJ, Lee JK, Hatten ME, Clarke J, Ayad NG. Time series modeling of cell cycle exit identifies Brd4 dependent regulation of cerebellar neurogenesis. Nat Commun. 2019;10(1):3028. Epub 2019/07/12. doi: 10.1038/s41467-019-10799-5. PubMed PMID: 31292434; PMCID: PMC6620341.
  57. Petrosyan A*. Unlocking Golgi: Why Does Morphology Matter? Biochemistry (Mosc). 2019;84(12):1490-501. Epub 2019/12/25. doi: 10.1134/S0006297919120083. PubMed PMID: 31870253; PMCID: PMC7291852.
  58. Piepenbrink KH*. DNA Uptake by Type IV Filaments. Front Mol Biosci. 2019;6:1. Epub 2019/02/26. doi: 10.3389/fmolb.2019.00001. PubMed PMID: 30805346; PMCID: PMC6370729.
  59. Privatt SR, Bullard BL, Weaver EA, Wood C, West JT. Longitudinal quantification of adenovirus neutralizing responses in Zambian mother-infant pairs: Impact of HIV-1 infection and its treatment. Vaccine. 2019;37(36):5177-84. Epub 2019/08/06. doi: 10.1016/j.vaccine.2019.07.074. PubMed PMID: 31378535; PMCID: PMC7182153.
  60. Rasineni K, Thomes PG, Kubik JL, Harris EN, Kharbanda KK, Casey CA. Chronic alcohol exposure alters circulating insulin and ghrelin levels: role of ghrelin in hepatic steatosis. Am J Physiol Gastrointest Liver Physiol. 2019;316(4):G453-G61. Epub 2019/02/01. doi: 10.1152/ajpgi.00334.2018. PubMed PMID: 30702902; PMCID: PMC6483023.
  61. Rezapour M, Quintero MA, Khakoo NS, Sussman DA, Barkin JA, Clarke J, Varma T, Deshpande AR, Kerman DH, Damas O, Abreu MT. Reclassifying Pseudopolyps in Inflammatory Bowel Disease: Histologic and Endoscopic Description in the New Era of Mucosal Healing. Crohns Colitis 360. 2019;1(3):otz033. Epub 2019/11/02. doi: 10.1093/crocol/otz033. PubMed PMID: 31667471; PMCID: PMC6798790.
  62. Rister AL, Bidne KL, Wood JR, Dodds ED. Microscale Serum Extraction Method for the Simultaneous Analysis of Corticosterone and Lipids. Anal Methods. 2019;11(45):5746-9. Epub 2020/03/10. doi: 10.1039/c9ay01757g. PubMed PMID: 32148562; PMCID: PMC7059636.
  63. Rister AL, Dodds ED. Ion Mobility Spectrometry and Tandem Mass Spectrometry Analysis of Estradiol Glucuronide Isomers. J Am Soc Mass Spectrom. 2019;30(10):2037-40. Epub 2019/08/07. doi: 10.1007/s13361-019-02272-w. PubMed PMID: 31385258; PMCID: PMC6812596.
  64. Rister AL, Martin TL, Dodds ED. Formation of multimeric steroid metal adducts and implications for isomer mixture separation by traveling wave ion mobility spectrometry. J Mass Spectrom. 2019;54(5):429-36. Epub 2019/03/13. doi: 10.1002/jms.4350. PubMed PMID: 30860640; PMCID: PMC6556764.
  65. Rister AL, Martin TL, Dodds ED. Application of Group I Metal Adduction to the Separation of Steroids by Traveling Wave Ion Mobility Spectrometry. J Am Soc Mass Spectrom. 2019;30(2):248-55. Epub 2018/11/11. doi: 10.1007/s13361-018-2085-9. PubMed PMID: 30414066; PMCID: PMC6551524.
  66. Rodrigues de Almeida N, Catazaro J, Krishnaiah M, Singh Chhonker Y, Murry DJ, Powers R, Conda-Sheridan M. Understanding interactions of Citropin 1.1 analogues with model membranes and their influence on biological activity. Peptides. 2019;119:170119. Epub 2019/07/25. doi: 10.1016/j.peptides.2019.170119. PubMed PMID: 31336137; PMCID: PMC7161086.
  67. Ronish LA, Lillehoj E, Fields JK, Sundberg EJ, Piepenbrink KH*. The structure of PilA from Acinetobacter baumannii AB5075 suggests a mechanism for functional specialization in Acinetobacter type IV pili. J Biol Chem. 2019;294(1):218-30. Epub 2018/11/11. doi: 10.1074/jbc.RA118.005814. PubMed PMID: 30413536; PMCID: PMC6322890.
  68. Samwel K, Kahesa C, Mwaiselage J, Gonzalez D, West JT, Wood C, Palefsky J, Angeletti PC. Analytical performance of a low-cost multiplex polymerase chain reaction human papillomavirus genotyping assay for use in Sub-Saharan Africa. J Med Virol. 2019;91(2):308-16. Epub 2018/10/04. doi: 10.1002/jmv.25329. PubMed PMID: 30281790; PMCID: PMC6519259.
  69. Sang M, Wang H, Shen Y, Rodrigues de Almeida N, Conda-Sheridan M, Li S, Li Y, Du L. Identification of an Anti-MRSA Cyclic Lipodepsipeptide, WBP-29479A1, by Genome Mining of Lysobacter antibioticus. Org Lett. 2019;21(16):6432-6. Epub 2019/08/07. doi: 10.1021/acs.orglett.9b02333. PubMed PMID: 31386380.
  70. Shanmugam S, Patel D, Wolpert JM, Keshvani C, Liu X, Bergeson SE, Kidambi S*, Mahimainathan L, Henderson GI, Narasimhan M. Ethanol Impairs NRF2/Antioxidant and Growth Signaling in the Intact Placenta In Vivo and in Human Trophoblasts. Biomolecules. 2019;9(11). Epub 2019/11/02. doi: 10.3390/biom9110669. PubMed PMID: 31671572; PMCID: PMC6921053.
  71. Shradhanjali A, Riehl BD, Duan B, Yang R*, Lim JY. Spatiotemporal Characterizations of Spontaneously Beating Cardiomyocytes with Adaptive Reference Digital Image Correlation. Sci Rep. 2019;9(1):18382. Epub 2019/12/06. doi: 10.1038/s41598-019-54768-w. PubMed PMID: 31804542; PMCID: PMC6895104.
  72. Stewart KL, Rathore D, Dodds ED, Cordes MHJ. Increased sequence hydrophobicity reduces conformational specificity: A mutational case study of the Arc repressor protein. Proteins. 2019;87(1):23-33. Epub 2018/10/14. doi: 10.1002/prot.25613. PubMed PMID: 30315592; PMCID: PMC6322834.
  73. Tso FY, West JT, Wood C. Reduction of Kaposi's Sarcoma-Associated Herpesvirus Latency Using CRISPR-Cas9 To Edit the Latency-Associated Nuclear Antigen Gene. J Virol. 2019;93(7):e02183-18/1-e-18/17. Epub 2019/01/18. doi: 10.1128/JVI.02183-18. PubMed PMID: 30651362; PMCID: PMC6430552.
  74. van den Bedem H, Wilson MA. Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. J Synchrotron Radiat. 2019;26(Pt 4):958-66. Epub 2019/07/06. doi: 10.1107/S160057751900568X. PubMed PMID: 31274417; PMCID: PMC6613112.
  75. Vecchio AJ*, Stroud RM. Claudin-9 structures reveal mechanism for toxin-induced gut barrier breakdown. Proc Natl Acad Sci U S A. 2019;116(36):17817-24. Epub 2019/08/23. doi: 10.1073/pnas.1908929116. PubMed PMID: 31434788; PMCID: PMC6731655.
  76. Vecchio AJ*, Stroud RM. High-Throughput Nano-Scale Characterization of Membrane Proteins Using Fluorescence-Detection Size-Exclusion Chromatography. Methods Mol Biol. 2019;2025:361-88.
  77. Vila T, Kong EF, Ibrahim A, Piepenbrink K*, Shetty AC, McCracken C, Bruno V, Jabra-Rizk MA. Candida albicans quorum-sensing molecule farnesol modulates staphyloxanthin production and activates the thiol-based oxidative-stress response in Staphylococcus aureus. Virulence. 2019;10(1):625-42. Epub 2019/07/10. doi: 10.1080/21505594.2019.1635418. PubMed PMID: 31280653; PMCID: PMC6629188.
  78. Vu T, Siemek P, Bhinderwala F, Xu Y, Powers R. Evaluation of Multivariate Classification Models for Analyzing NMR Metabolomics Data. J Proteome Res. 2019;18(9):3282-94. Epub 2019/08/07. doi: 10.1021/acs.jproteome.9b00227. PubMed PMID: 31382745; PMCID: PMC6733656.
  79. Wang Y, Tian T, Zhang J, Jin X, Yue H, Zhang XH, Du L, Bai F. Indole Reverses Intrinsic Antibiotic Resistance by Activating a Novel Dual-Function Importer. mBio. 2019;10(3). Epub 2019/05/30. doi: 10.1128/mBio.00676-19. PubMed PMID: 31138746; PMCID: PMC6538783.
  80. Wu D, Kittana H, Shu J, Kachman SD, Cui J, Ramer-Tait AE, Zempleni J. Dietary Depletion of Milk Exosomes and Their MicroRNA Cargos Elicits a Depletion of miR-200a-3p and Elevated Intestinal Inflammation and Chemokine (C-X-C Motif) Ligand 9 Expression in Mdr1a(-/-) Mice. Curr Dev Nutr. 2019;3(12):nzz122. Epub 2020/03/11. doi: 10.1093/cdn/nzz122. PubMed PMID: 32154493; PMCID: PMC7053579.
  81. Yang Y, Zeng B, Sun Z, Esfahani AM, Hou J, Jiao ND, Liu L, Chen L, Basson MD, Dong L, Yang R*, Xi N. Optimization of Protein-Protein Interaction Measurements for Drug Discovery Using AFM Force Spectroscopy. IEEE Trans Nanotechnol. 2019;18:509-17. Epub 2020/02/14. doi: 10.1109/tnano.2019.2915507. PubMed PMID: 32051682; PMCID: PMC7015265.
  82. Zempleni J, Sukreet S, Zhou F, Wu D, Mutai E. Milk-Derived Exosomes and Metabolic Regulation. Annu Rev Anim Biosci. 2019;7:245-62. Epub 2018/10/05. doi: 10.1146/annurev-animal-020518-115300. PubMed PMID: 30285461.
  83. Zhang L*. X-Ray Absorption Spectroscopy of Metalloproteins. Methods Mol Biol. 2019;1876:179-95. Epub 2018/10/15. doi: 10.1007/978-1-4939-8864-8_12. PubMed PMID: 30317482.
  84. Zhou C, Bhinderwala F, Lehman MK, Thomas VC, Chaudhari SS, Yamada KJ, Foster KW, Powers R, Kielian T, Fey PD. Urease is an essential component of the acid response network of Staphylococcus aureus and is required for a persistent murine kidney infection. PLoS Pathog. 2019;15(1):e1007538. Epub 2019/01/05. doi: 10.1371/journal.ppat.1007538. PubMed PMID: 30608981; PMCID: PMC6343930.
  85. Zhou F, Paz HA, Sadri M, Cui J, Kachman SD, Fernando SC, Zempleni J. Dietary bovine milk exosomes elicit changes in bacterial communities in C57BL/6 mice. Am J Physiol Gastrointest Liver Physiol. 2019;317(5):G618-G24. Epub 2019/09/12. doi: 10.1152/ajpgi.00160.2019. PubMed PMID: 31509432; PMCID: PMC6879888.
  86. Zinniel DK, Sittiwong W, Marshall DD, Rathnaiah G, Sakallioglu IT, Powers R, Dussault PH, Barletta RG. Novel Amphiphilic Cyclobutene and Cyclobutane cis-C18 Fatty Acid Derivatives Inhibit Mycobacterium avium subsp. paratuberculosis Growth. Vet Sci. 2019;6(2). Epub 2019/05/30. doi: 10.3390/vetsci6020046. PubMed PMID: 31137605; PMCID: PMC6631517.


01/2020 – 9/2020 (Total: 69; junior investigators: 16)

*Project leader; **Pilot and/or seed grant recipient


  1. Aghamiri SS, Singh V, Niarakis A, Naldi A, Helikar T, Soliman S. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics. 2020; ahead of print. doi: 10.1093/bioinformatics/btaa484.
  2. Agrawal NK, Allen P, Song YH, Wachs RA*, Du Y, Ellington AD, Schmidt CE. Oligonucleotide-functionalized hydrogels for sustained release of small molecule (aptamer) therapeutics. Acta Biomater. 2020;102:315-25. Epub 2019/11/25. doi: 10.1016/j.actbio.2019.11.037. PubMed PMID: 31760222.
  3. Bai N, Li GH, Luo SL, Du L, Hu QY, Xu HK, Zhang KQ, Zhao PJ. Vib-PT, an Aromatic Prenyltransferase Involved in the Biosynthesis of Vibralactone from Stereum vibrans. Appl Environ Microbiol. 2020;86(10). Epub 2020/03/08. doi: 10.1128/AEM.02687-19. PubMed PMID: 32144102; PMCID: PMC7205494.
  4. Barrett ST, Thompson BM, Emory JR, Larsen CE, Pittenger ST, Harris EN, Bevins RA. Sex Differences in the Reward-Enhancing Effects of Nicotine on Ethanol Reinforcement: A Reinforcer Demand Analysis. Nicotine Tob Res. 2020;22(2):238-47. Epub 2019/04/16. doi: 10.1093/ntr/ntz056. PubMed PMID: 30982885; PMCID: PMC7297098.
  5. Bennett SJ, Chunda-Liyoka C, Poppe LK, Meinders K, Chileshe C, West JT, Wood C. High NNRTI resistance levels in HIV-1 infected Zambian mother-infant pairs. AIDS. 2020. Epub 2020/08/01. doi: 10.1097/QAD.0000000000002614. PubMed PMID: 32732629.
  6. Bhinderwala F, Evans P, Jones K, Laws BR, Smith TG, Morton M, Powers R. Phosphorus NMR and Its Application to Metabolomics. Anal Chem. 2020;92(14):9536-45. Epub 2020/06/13. doi: 10.1021/acs.analchem.0c00591. PubMed PMID: 32530272.
  7. Bousalis D, Lacko CS, Hlavac N, Alkassis F, Wachs RA*, Mobini S, Schmidt CE, Kasahara H. Extracellular Matrix Disparities in an Nkx2-5 Mutant Mouse Model of Congenital Heart Disease. Front Cardiovasc Med. 2020;7:93. Epub 2020/06/18. doi: 10.3389/fcvm.2020.00093. PubMed PMID: 32548129; PMCID: PMC7272573.
  8. Brooks J, Jaberi A, Yang R*. Microfluidic Device for Localized Electroporation. Methods Mol Biol. 2020;2050(Electroporation Protocols):91-7. Epub 2019/08/31. doi: 10.1007/978-1-4939-9740-4_10. PubMed PMID: 31468483.
  9. Campbell AC, Becker DF, Gates KS, Tanner JJ. Covalent Modification of the Flavin in Proline Dehydrogenase by Thiazolidine-2-Carboxylate. ACS Chem Biol. 2020;15(4):936-44. Epub 2020/03/12. doi: 10.1021/acschembio.9b00935. PubMed PMID: 32159324; PMCID: PMC7166166.
  10. Casey GR, Zhou X, Lesiak L, Xu B, Fang Y, Becker DF, Stains C. An Evolutionary Strategy for Identification of Higher Order, Green Fluorescent Host-Guest Pairs Compatible with Living Systems. Chemistry. 2020. Epub 2020/07/30. doi: 10.1002/chem.202002423. PubMed PMID: 32725914.
  11. Chunda-Liyoka C, Lubeya MK, Imakando M, Kisling S, Majid S, Willis MS, Wood C, Kankasa C, DiRusso CC. Healthy pregnancies and essential fats: focus group discussions with Zambian women on dietary need and acceptability of a novel RUSF containing fish oil DHA. BMC Pregnancy Childbirth. 2020;20(1):93. Epub 2020/02/12. doi: 10.1186/s12884-020-2783-8. PubMed PMID: 32041569; PMCID: PMC7011535.
  12. Derakhshandeh H, Aghabaglou F, McCarthy A, Mostafavi A, Wiseman C, Bonick Z, Ghanavati I, Harris S, Kreikemeier-Bower C, Basri SMM, Rosenbohm J, Yang R*, Mostafalu P, Orgill D, Tamayol A. A Wirelessly Controlled Smart Bandage with 3D-Printed Miniaturized Needle Arrays. Advanced Functional Materials. 2020;30(13):1905544. doi: 10.1002/adfm.201905544. PubMed PMID: WOS:000512956200001.
  13. Fang Y, Gong H, Yang R*, Lai KWC, Quan M. An Active Biomechanical Model of Cell Adhesion Actuated by Intracellular Tensioning-Taxis. Biophys J. 2020;118(11):2656-69. Epub 2020/05/08. doi: 10.1016/j.bpj.2020.04.016. PubMed PMID: 32380000; PMCID: PMC7264853.
  14. Furlan AL, Bianucci E, Giordano W, Castro S, Becker DF. Proline metabolic dynamics and implications in drought tolerance of peanut plants. Plant Physiol Biochem. 2020;151:566-78. Epub 2020/04/23. doi: 10.1016/j.plaphy.2020.04.010. PubMed PMID: 32320942.
  15. Gallagher LA, Shears RK, Fingleton C, Alvarez L, Waters EM, Clarke J, Bricio-Moreno L, Campbell C, Yadav AK, Razvi F, O'Neill E, O'Neill AJ, Cava F, Fey PD, Kadioglu A, O'Gara JP. Impaired Alanine Transport or Exposure to d-Cycloserine Increases the Susceptibility of MRSA to beta-lactam Antibiotics. J Infect Dis. 2020;221(6):1000-16. Epub 2019/10/20. doi: 10.1093/infdis/jiz542. PubMed PMID: 31628459; PMCID: PMC7050987.
  16. Ganesan M, Mathews S, Makarov E, Petrosyan A*, Kharbanda KK, Kidambi S*, Poluektova LY, Casey CA, Osna NA. Acetaldehyde suppresses HBV-MHC class I complex presentation on hepatocytes via induction of ER stress and Golgi fragmentation. Am J Physiol Gastrointest Liver Physiol. 2020;319(4):G432-G42. Epub 2020/08/07. doi: 10.1152/ajpgi.00109.2020. PubMed PMID: 32755306.
  17. Gopal T, Kumar N, Perriotte-Olson C, Casey CA, Donohue TM, Jr., Harris EN, Talmon G, Kabanov AV, Saraswathi V. Nanoformulated SOD1 ameliorates the combined NASH and alcohol-associated liver disease partly via regulating CYP2E1 expression in adipose tissue and liver. Am J Physiol Gastrointest Liver Physiol. 2020;318(3):G428-G38. Epub 2020/01/14. doi: 10.1152/ajpgi.00217.2019. PubMed PMID: 31928222; PMCID: PMC7099493.
  18. Grove RA, Madhavan D, Boone CHT, Braga CP, Papackova Z, Kyllo H, Samson K, Simeone K, Simeone T, Helikar T, Hanson CK, Adamec J. Aberrant energy metabolism and redox balance in seizure onset zones of epileptic patients. J Proteomics. 2020;223:103812. Epub 2020/05/19. doi: 10.1016/j.jprot.2020.103812. PubMed PMID: 32418907.
  19. Harris EN, Baker E. Role of the Hyaluronan Receptor, Stabilin-2/HARE, in Health and Disease. Int J Mol Sci. 2020;21(10). Epub 2020/05/21. doi: 10.3390/ijms21103504. PubMed PMID: 32429122; PMCID: PMC7279005.
  20. Heller DA, Jena PV, Pasquali M, Kostarelos K, Delogu LG, Meidl RE, Rotkin SV, Scheinberg DA, Schwartz RE, Terrones M, Wang Y, Bianco A, Boghossian AA, Cambre S, Cognet L, Corrie SR, Demokritou P, Giordani S, Hertel T, Ignatova T, Islam MF, Iverson NM**, Jagota A, Janas D, Kono J, Kruss S, Landry MP, Li Y, Martel R, Maruyama S, Naumov AV, Prato M, Quinn SJ, Roxbury D, Strano MS, Tour JM, Weisman RB, Wenseleers W, Yudasaka M. Banning carbon nanotubes would be scientifically unjustified and damaging to innovation. Nat Nanotechnol. 2020;15(3):164-6. Epub 2020/03/12. doi: 10.1038/s41565-020-0656-y. PubMed PMID: 32157238.
  21. Hofferber EM, Stapleton JA, Iverson NM**. Review-Single Walled Carbon Nanotubes as Optical Sensors for Biological Applications. Journal of the Electrochemical Society. 2020;167(3):37530. doi: 10.1149/1945-7111/ab64bf. PubMed PMID: WOS:000506633400001.
  22. Howell ME, Booth CS, Sikich SM, Helikar T, van Dijk K, Roston RL, Couch BA. Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships. Biochem Mol Biol Educ. 2020;48(4):356-68. Epub 2020/06/27. doi: 10.1002/bmb.21362. PubMed PMID: 32590880.
  23. Joel S, Eastwick PW, Allison CJ, Arriaga XB, Baker ZG, Bar-Kalifa E, Bergeron S, Birnbaum GE, Brock RL, Brumbaugh CC, Carmichael CL, Chen S, Clarke J, Cobb RJ, Coolsen MK, Davis J, de Jong DC, Debrot A, DeHaas EC, Derrick JL, Eller J, Estrada MJ, Faure R, Finkel EJ, Fraley RC, Gable SL, Gadassi-Polack R, Girme YU, Gordon AM, Gosnell CL, Hammond MD, Hannon PA, Harasymchuk C, Hofmann W, Horn AB, Impett EA, Jamieson JP, Keltner D, Kim JJ, Kirchner JL, Kluwer ES, Kumashiro M, Larson G, Lazarus G, Logan JM, Luchies LB, MacDonald G, Machia LV, Maniaci MR, Maxwell JA, Mizrahi M, Muise A, Niehuis S, Ogolsky BG, Rebecca C, Overall NC, Perrez M, Peters BJ, Pietromonaco PR, Powers SI, Prok T, Pshedetzky-Shochat R, Rafaeli E, Ramsdell EL, Reblin M, Reicherts M, Reifman A, Reis HT, Rhoades GK, Rholes WS, Righetti F, Rodriguez LM, Rogge R, Rosen NO, Saxbe D, Sened H, Simpson JA, Slotter EB, Stanley SM, Stocker S, Surra C, Kuile HT, Vaughn AA, Vicary AM, Visserman ML, Wolf S. Machine learning uncovers the most robust self-report predictors of relationship quality across 43 longitudinal couples studies. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(32):19061-71. doi: 10.1073/pnas.1917036117. PubMed PMID: WOS:000561789200028.
  24. Johnson TB, Mechels K, Anderson RH, Cain JT, Sturdevant DA, Braddock S, Pinz H, Wilson MA, Landsverk M, Roux KJ, Weimer JM. Author Correction: Characterization of a recurrent missense mutation in the forkhead DNA-binding domain of FOXP1. Sci Rep. 2020;10(1):6635. Epub 2020/04/17. doi: 10.1038/s41598-020-62950-8. PubMed PMID: 32296074; PMCID: PMC7160118.
  25. Kelly MI, Dodds ED. Parallel Determination of Polypeptide and Oligosaccharide Connectivities by Energy-Resolved Collison-Induced Dissociation of Protonated O-Glycopeptides Derived from Nonspecific Proteolysis. J Am Soc Mass Spectrom. 2020;31(3):624-32. Epub 2020/03/05. doi: 10.1021/jasms.9b00065. PubMed PMID: 32126781; PMCID: PMC7164384.
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