Publications

• Shih YM, Cooke MS, Pan CH, Chao MR, Hu CW. (2019, Jan.). Clinical relevance of guanine-derived urinary biomarkers of oxidative stress, determined by LC-MS/MS. Redox Biol. 20:556-565. doi: 10.1016/j.redox.2018.11.016. Epub 2018 Nov 26. PubMed PMID: 30508700; PubMed Central PMCID: PMC6279954.

• Jeanne Dit Fouque K, Bisram V, Hegemann JD, Zirah S, Rebuffat S, Fernandez-Lima F. (2019, Feb 1). Structural signatures of the class III lasso peptide BI-32169 and the branched-cyclic topoisomers using trapped ion mobility spectrometry-mass spectrometry and tandem mass spectrometry. Anal Bioanal Chem. doi:10.1007/s00216-019-01613-8. [Epub ahead of print] PubMed PMID: 30707269.

• Mittal R, Patel AP, Nguyen D, Pan DR, Jhaveri VM, Rudman JR, Dharmaraja A, Yan D, Feng Y, Chapagain P, Lee DJ, Blanton SH, Liu XZ. (2018). Genetic basis of hearing loss in Spanish, Hispanic and Latino populations. Gene. 647:297-305. doi: 10.1016/j.gene.2018.01.027.

• Delinasios GJ, Karbaschi M, Cooke MS, Young A,R. (2018). Vitamin E inhibits the UVAI induction of "light" and "dark" cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes. Sci Rep.,8(1):423. doi: 10.1038/s41598-017-18924-4.

• Ioannou D, Tempest HG. (2018). Does genome organization matter in spermatozoa? A refined hypothesis to awaken the silent vessel. Syst Biol Reprod Med, 1-17. doi: 10.1080/19396368.2017.1421278

• Flora P, Schowalter S, Wong-Deyrup S, DeGennaro M, Nasrallah MA, Rangan P. (2018). Transient transcriptional silencing alters the cell cycle to promote germline stem cell differentiation in Drosophila. Dev Biol. 434(1):84-95. doi: 10.1016/j.ydbio.2017.11.014.

• Annamalai T, Cheng B, Keswani N, Tse-Dinh YC. (2018). A Fluorescence-Based Assay for Identification of Bacterial Topoisomerase I Poisons. Methods Mol Biol, 1703:259-268. doi: 10.1007/978-1-4939-7459-7_18.

• Liu Y, Hua ZC, Leng F. (2018). DNA Supercoiling Measurement in Bacteria. Methods Mol Biol, 1703:63-73. doi: 10.1007/978-1-4939-7459-7_4

• Beaver JM, Lai Y, Rolle SJ, Weng L, Greenberg MM, Liu Y. (2018). An oxidized abasic lesion inhibits base excision repair leading to DNA strand breaks in a trinucleotide repeat tract. PLoS One, 13(2):e0192148. doi: 10.1371/journal.pone.0192148

• Benigni P, Porter J, Ridgeway ME, Park MA, Fernandez-Lima, F. (2018). Increasing Analytical Separation and Duty Cycle with Nonlinear Analytical Mobility Scan Functions in TIMS-FT-ICR MS. Anal Chem, 90 (4), pp 2446–2450. doi: 10.1021/acs.analchem.7b04053

• Yan Y, Leng F, Finzi L, Dunlap D. (2018). Protein-mediated looping of DNA under tension requires supercoiling. Nucleic Acids Res. 46(5):2370-2379. doi: 10.1093/nar/gky021.

• Sandhaus S, Chapagain PP, Tse-Dinh YC (2018). Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assays. Sci Rep, 8(1):1437. doi: 10.1038/s41598-018-19944-4.

• Damaso N, Mendel J, Mendoza M, von Wettberg EJ, Narasimhan G, Mills D. (2018). Bioinformatics Approach to Assess the Biogeographical Patterns of Soil Communities: The Utility for Soil Provenance. J Forensic Sci. 63(4):1033-1042. doi: 10.1111/1556-4029.13741.

• Molano-Arevalo JC, Gonzalez W, Jeanne Dit Fouque K, Miksovska J, Maitre P, Fernandez-Lima F. (2018). Insights from ion mobility-mass spectrometry, infrared spectroscopy, and molecular dynamics simulations on nicotinamide adenine dinucleotide structural dynamics: NAD(+)vs. NADH. Phys Chem Chem Phys. 20(10):7043-7052. doi: 10.1039/c7cp05602h.

• Adams KJ, Smith NF, Ramirez CE, Fernandez-Lima F. (2018). Discovery and targeted monitoring of polychlorinated biphenyl metabolites in blood plasma using LC-TIMS-TOF MS. Int J Mass Spectrom. 427:133-140. doi: 10.1016/j.ijms.2017.11.009.

• Adams KJ, Ramirez CE, Smith NF, Muñoz-Muñoz AC, Andrade L, Fernandez-Lima F. (2018). Analysis of isomeric opioids in urine using LC-TIMS-TOF MS. Talanta, 83:177-183. doi:10.1016/j.talanta.2018.02.077

• Yan Y, Ding Y, Leng F, Dunlap D, Finzi L. (2018). Protein-mediated loops in supercoiled DNA create large topological domains. Nucleic Acids Res. 46(9):4417-4424. doi: 10.1093/nar/gky153.

• Ahmed MS, Annamalai T, Li X, Seddek A, Teng P, Tse-Dinh YC, Moon JH. (2018). Synthesis of Antimicrobial Poly(guanylurea)s. Bioconjug Chem. 29(4):1006-1009. doi: 10.1021/acs.bioconjchem.8b00057.

• Nouzova M, Michalkova V, Hernández-Martínez S, Rivera-Perez C, Ramirez CE, Fernandez-Lima F, Noriega FG. (2018). JH biosynthesis and hemolymph titers in adult male Aedes aegypti mosquitoes. Insect Biochem Mol Biol. 95:10-16. doi:10.1016/j.ibmb.2018.02.005.

• Guo J, Pan J, Chang S, Wang X, Kong N, Yang W, He J. (2018). Monitoring the Dynamic Process of Formation of Plasmonic Molecular Junctions during Single Nanoparticle Collisions. Small. (15):e1704164. doi: 10.1002/smll.201704164.

• Corda E, Du X, Shim SY, Klein AN, Siltberg-Liberles J, Gilch S. (2018). Interaction of Peptide Aptamers with Prion Protein Central Domain Promotes α-Cleavage of PrP(C). Mol Neurobiol. doi: 10.1007/s12035-018-0944-9.

• Mathivathanan L, Yang G, Leng F, Raptis RG. (2018). Crystal structure and conformational analysis of doxorubicin nitrate. Acta Crystallogr E Crystallogr Commun. 74(Pt 3):400-405. doi: 10.1107/S2056989018002955.

• Abood S, Veisaga ML, López LA, Barbieri MA. (2018). Dehydroleucodine inhibits mitotic clonal expansion during adipogenesis through cell cycle arrest. Phytother Res. doi: 10.1002/ptr.6089. 

• Nouzova, M., Etebari, K., Noriega, F.G., Asgari, S. (2018). A comparative analysis of corpora allata-corpora cardiaca microRNA repertoires revealed significant changes during mosquito metamorphosis. Insect Biochem Mol Biol., 96:10-18. doi: 10.1016/j.ibmb.2018.03.007

• Del Vecchio K, Frick CT, Gc JB, Oda SI, Gerstman BS, Saphire EO, Chapagain PP, Stahelin RV (2018). A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine. J Biol Chem., 293(9):3335-3349. doi: 10.1074/jbc.M117.816280

• Butcher D, Bernad S, Derrien V, Sebban P, Miksovska J, Fernandez-Lima F. (2018). Non-symbiotic hemoglobin conformational space dependence on the heme coordination using nESI-TIMS-TOF MS. International Journal of Mass Spectrometry, 430:37-43. doi.org/10.1016/j.ijms.2018.03.008

• Wang L, Feng Y, Yan D, Qin L, Grati M, Mittal R, Li T, Sundhari AK, Liu Y, Chapagain P, Blanton SH, Liao S, Liu X. (2018). A dominant variant in the PDE1C gene is associated with nonsyndromic hearing loss. Hum Genet. 137(6-7):437-446. doi: 10.1007/s00439-018-1895-y.

• Zhang M, Krause WC, Agoulnik IU. (2018). Techniques for Evaluation of AR Transcriptional Output and Recruitment to DNA. Methods Mol Biol., 1786:219-236. doi: 10.1007/978-1-4939-7845-8_13

• Tose LV, Benigni P, Leyva D, Sundberg A, Ramírez CE, Ridgeway ME, Park MA, Romão W, Jaffé R, Fernandez-Lima F. (2018). Coupling trapped ion mobility spectrometry to mass spectrometry: trapped ion mobility spectrometry-time-of-flight mass spectrometry versus trapped ion mobility spectrometry-Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom. 32(15):1287-1295. doi: 10.1002/rcm.8165.

• Zhou Q, Gomez Hernandez, ME, Fernandez-Lima F, Tse-Dinh YC (2018). Biochemical Basis of E. coli Topoisomerase I Relaxation Activity Reduction by Nonenzymatic Lysine Acetylation. Int J Mol Sci. 19(5). pii: E1439. doi: 10.3390/ijms19051439.

• Suzol SH, Howlader AH, Wen Z, Ren Y, Laverde EE, Garcia C, Liu Y, Wnuk SF. (2018). Pyrimidine Nucleosides with a Reactive (β-Chlorovinyl) sulfone or (β-Keto)sulfone Group at the C5 Position, Their Reactions with Nucleophiles and Electrophiles, and Their Polymerase-Catalyzed Incorporation into DNA. ACS Omega, 3(4):4276-4288. doi: 10.1021/acsomega.8b00584

• Li W, Sun J, Ling J, Li J, He C, Liu Y, Chen H, Men M, Niu Z, Deng Y, Li M, Li T, Wen J, Sang S, Li H, Wan Z, Richard EM, Chapagain PP, Yan D, Liu X., Mei L, Feng Y. (2018). ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss. Hum Genet., 137(4):329-342. doi: 10.1007/s00439-018-1885-0.

• Pavadai E, Gerstman B S, Chapagain PP. (2018). A cylindrical assembly model and dynamics of the Ebola virus VP40 structural matrix. Scientific Reports, 8, 9776. doi.org/10.1038/s41598-018-28077-7

• Chang Y, Cooke M, Hu C, Chao M. (2018). Novel approach to integrated DNA adductomics for the assessment of in vitro and in vivo environmental exposures. Arch Toxicol, 92(8):2665-2680. doi: 10.1007/s00204-018-2252-6

• Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh YC. (2018). Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site. Nucleic Acids Res. June 14, doi: 10.1093/nar/gky492. [Epub ahead of print]

• Mathivathanan L, Boudalis AK, Turek P, Pissas M, Sanakis Y, Raptis RG. (2018). Interactions between H-bonded [Cu(μ(3)-OH)] triangles; a combined magnetic susceptibility and EPR study. Phys Chem Chem Phys. 20(25):17234-17244. doi: 10.1039/c8cp02643b.

• Jalal AH, Alam F, Roychoudhury S, Umasankar Y, Pala N, Bhansali S.   (2018). Prospects and Challenges of Volatile Organic Compound Sensors in Human Healthcare. ACS  Sens. 3(7):1246-1263. doi: 10.1021/acssensors.8b00400.

• Delgado C, Florez L, Lollett I, Lopez C, Kangeyan S, Kumari H, Stylianou M, Smiddy RJ, Schneper L, Sautter RT, Smith D, Szatmari G, Mathee K. (2018). Pseudomonas aeruginosa Regulated Intramembrane Proteolysis: Protease MucP Can Overcome Mutations in the AlgO Periplasmic Protease To Restore Alginate Production in Nonmucoid Revertants. J Bacteriol. 200(16). pii: e00215-18. doi: 10.1128/JB.00215-18.

• Delinasios GJ, Karbaschi M, Cooke MS, Young AR (2018). Author Correction: Vitamin E inhibits the UVAI induction of “light” and “dark” cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes. Scientific Reports, 8, 4998. doi.org/10.1038/s41598-018-23048-4

• Gupta R, Rodrigues Felix C, Akerman MP, Akerman KJ, Slabber CA, Wang W, Adams J, Shaw LN, Tse-Dinh YC, Munro OQ, Rohde KH. (2018). Evidence for Inhibition of Topoisomerase 1A by Gold(III) Macrocycles and Chelates Targeting Mycobacterium tuberculosis and Mycobacterium abscessus. Antimicrob Agents Chemother. 62(5). pii: e01696-17. doi: 10.1128/AAC.01696-17

• Alam F, RoyChoudhury S, Jalal AH, Umasankar Y, Forouzanfar S, Akter N, Bhansali S, Pala N. (2018). Lactate biosensing: The emerging point-of-care and personal health monitoring. Biosens Bioelectron. 117:818-829. doi: 10.1016/j.bios.2018.06.054.

• Garabedian A, Benigni P, Ramirez CE, Baker ES, Liu T, Smith RD, Fernandez-Lima F. (2018). Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS. J Am Soc Mass Spectrom. (5):817-826. doi: 10.1007/s13361-017-1787-8.

• Rodríguez-Santiago AJ, Nicole Cortés, Khoa Pham, Jaroslava Miksovska, Raptis RG. (2018). 4,40-Dihydroxy-2,20-bipyridine complexes of Co(III), Cu(II) and Zn(II); structural and spectroscopic characterization. Polyhedron 150, 61–68. doi.org/10.1016/j.poly.2018.04.039.

• Babic-Samardzija K, Baran P, Boca R, Herchel R, Raptis RG, Vélez CL. (2018). Structural and magnetic susceptibility study of an octanuclear MnIII-oxo-pyrazolido complex. Polyhedron 149, 142–147. doi.org/10.1016/j.poly.2018.04.033.

• Kandel S, Stenger-Smith J, Chakraborty I, Raptis RG. (2018). Syntheses and X-ray crystal structures of a family of dinuclear silver(I) pyrazolates: Assessment of their antibacterial efficacy against P. aeruginosa with a soft tissue and skin infection model. Polyhedron 154, 390–397. doi.org/10.1016/j.poly.2018.08.015

• Yanhao Lai, Yossi Weizmann, Yuan Liu (2018). The deoxyribose phosphate lyase of DNA polymerase β suppresses a processive DNA synthesis to prevent trinucleotide repeat instability. Nucleic Acids Research, gky700, doi.org/10.1093/nar/gky700.

• Yoshinaga, M.,  How, S.,  Blanco, D.,  Murdoch, I.,  Grudny, M.,  Powers, S.,  Molina, N., Rosen, B.,  Welch, A. (2018). Directed Evolution of Saccharomyces cerevisiae for Increased Selenium Accumulation. Microorganisms, 6(3), 81; doi.org/10.3390/microorganisms6030081

• Garabedian, A., Bolufer, A., Leng, F., & Fernandez-Lima, F. (2018). Peptide Sequence Influence on the Conformational Dynamics and DNA binding of the Intrinsically Disordered AT-Hook 3 Peptide. Scientific Reports, 8, 10783. doi.org/10.1038/s41598-018-28956-z.

• Choudhary, A., George T.,  Li, G. (2018). Conjugation of Nanomaterials and Nematic Liquid Crystals for Futuristic Applications and Biosensors. Biosensors, 8(3), 69; doi.org/10.3390/bios8030069.

• Hu, C., Cooke, M., Chang, YJ., Chao, MR. (2018). Direct-acting DNA ethylating agents associated with tobacco use primarily originate from the tobacco itself, not combustion. Journal of Hazardous Materials, 358:397-404. doi: 10.1016/j.jhazmat.2018.07.011.

• Tiwari, P. B., Chapagain, P. P., & Üren, A. (2018). Investigating molecular interactions between oxidized neuroglobin and cytochrome c. Scientific Reports, 8, 10557. doi.org/10.1038/s41598-018-28836-6.

• Chao MR, Cooke MS, Kuo CY, Pan CH, Liu HH, Yang HJ, Chen SC, Chiang YC, Hu CW. (2018). Children are particularly vulnerable to environmental tobacco smoke exposure: Evidence from biomarkers of tobacco-specific nitrosamines, and oxidative stress. Environ Int. 120:238-245. doi: 10.1016/j.envint.2018.08.006.

• Dages S, Dages K, Zhi X, Leng F. (2018 Oct 3). Inhibition of the gyrA promoter by transcription-coupled DNA supercoiling in Escherichia coli. Sci Rep. 8(1):14759. doi: 10.1038/s41598-018-33089-4. PubMed PMID: 30282997; PubMed Central PMCID: PMC6170449.

• Zhang M, Suarez E, Vasquez JL, Nathanson L, Peterson LE, Rajapakshe K, Basil P, Weigel NL, Coarfa C, Agoulnik IU. (2018 Sep 18.) Inositol polyphosphate 4-phosphatase type II regulation of androgen receptor activity. Oncogene.  doi:10.1038/s41388-018-0498-3. PubMed PMID: 30228349.

• Alam F, RoyChoudhury S, Jalal AH, Umasankar Y, Forouzanfar S, Akter N,Bhansali S, Pala N. (2018 Oct 15). Lactate biosensing: The emerging point-of-care and personal health monitoring. Biosens Bioelectron. 117:818-829. doi: 10.1016/j.bios.2018.06.054.  Review. PubMed PMID: 30096736.

• Cooke MS, Hu CW, Chang YJ, Chao MR. (2018 Nov 1). Urinary DNA adductomics - A novel approach for exposomics. Environ Int.  pii: S0160-4120(18)31833-6. doi: 10.1016/j.envint.2018.10.041. [Epub ahead of print] PubMed PMID: 30392940.

• Mills M, Tse-Dinh YC, Neuman KC. (2018 Nov 26). Direct observation of topoisomerase IA gate dynamics. Nat Struct Mol Biol.  doi: 10.1038/s41594-018-0158-x.  [Epubahead of print] PubMed PMID: 30478267.

• Shih YM, Cooke MS, Pan CH, Chao MR, Hu CW. (2018 Nov 26).  Clinical relevance of guanine-derived urinary biomarkers of oxidative stress, determined by LC-MS/MS. Redox Biol. 20:556-565. doi: 10.1016/j.redox.2018.11.016. [Epub ahead of print] PubMed PMID: 30508700.

• Porter JE, Chapagain P, Fernandez-Lima F. (2018 Dec 3). Single stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation. Rapid Commun Mass Spectrom. doi: 10.1002/rcm.8367. [Epub ahead of print] PubMed PMID: 30506977.

• Paudel I, Hernandez SM, Portalatin GM, Chambers TP, Chambers JW. (2018 Nov 15). Sab concentrations indicate chemotherapeutic susceptibility in ovarian cancer cell lines. Biochem J. 475(21):3471-3492. doi: 10.1042/BCJ20180603. PubMed PMID: 30322886.

• Chen F, Manandhar P, Ahmed MS, Chang S, Panday N, Zhang H, Moon JH, He J. (2018 Dec 13). Extracellular Surface Potential Mapping by Scanning Ion Conductance Microscopy Revealed Transient Transmembrane Pore Formation Induced by Conjugated Polymer Nanoparticles. Macromol Biosci. e1800271. doi: 10.1002/mabi.201800271. [Epub ahead of print]

• Wang L, Yan D, Qin L, Li T, Liu H, Li W, Mittal R, Yong F, Chapagain P, Liao S, Liu X. (2018, April). Amino acid 118 in the Deafness Causing (DFNA20/26) ACTG1 gene is a Mutational Hot Spot. Gene Rep. 2018 Jun;11:264-269. doi: 10.1016/j.genrep.2018.04.011. Epub 2018 Apr 28. PubMed PMID: 30599039; PubMedCentral PMCID: PMC6309262.

• Noriega FG, Oliveira PL. (2018, September). Editorial overview: Molecular physiology: from omics data encyclopedia to physiology 'short stories'. Curr Opin Insect Sci. 2018 Oct;29:vi-viii. doi: 10.1016/j.cois.2018.08.004. Epub 2018 Sep 10. PubMed PMID: 30551834.

• Nouzova M, Rivera-Pérez C, Noriega FG. (2018, Oct). Omics approaches to study juvenile hormone synthesis. Curr Opin Insect Sci. 29:49-55. doi:10.1016/j.cois.2018.05.013. Epub 2018 May 26. Review. PubMed PMID: 30551825.

• Deshpande SA, Meiselman M, Hice RH, Arensburger P, Rivera-Perez C, Kim DH, Croft RL, Noriega FG, Adams ME. (2018, Dec 10.) Ecdysis triggering hormone receptors regulate male courtship behavior via antennal lobe interneurons in Drosophila. Gen Comp Endocrinol. pii: S0016-6480(18)30323-X. doi:10.1016/j.ygcen.2018.12.003. [Epub ahead of print] PubMed PMID: 30543770.

• Adams, K.J., Smith, N.F., Ramirez, C,E., Fernandez-Lima, F. (2017). Discovery and targeted monitoring of polychlorinated biphenyl metabolites in blood plasma using LC-TIMS-TOF MS. Int. J. Mass Spectrom., https:/doi.org10.1016/j.ijms.2017.11.009.
• Flora, P., Schowalter, S., Wong-Deyrup, S., DeGennaro, M., Nasrallah, M.A,, Rangan, P. (2017). Transient transcriptional silencing alters the cell cycle to promote germline stem cell differentiation in Drosophila. Dev Biol, https:/doi.org10.1016/j.ydbio.2017.11.014.
• Qu, Z., Bendena, W.G., Nong, W., Siggens, K.W., Noriega, F.G., Kai, Z.P., Zang, Y.Y., Koon, A.C., Chan, H.Y.E., Chan, T.F., Chu, K.H., Lam, H.M., Akam, M., Tobe, S.S., Lam Hui, J.H. (2017). MicroRNAs regulate the sesquiterpenoid hormonal pathway in Drosophila and other arthropods. Proc Biol Sci, 284(1869). doi: 10.1098/rspb.2017.1827.
• De Jesus, C.L., Bartley, A., Welch, A.Z., Berry, J.P. (2017). High Incidence and Levels of Ochratoxin A in Wines Sourced from the United States. Toxins (Basel), 10(1). doi: 10.3390/toxins10010001.
• Fernandez, R.E., Umasankar, Y., Manickam, P., Nickel, J.C., Iwasaki, L.R., Kawamoto, B.K., Todoki, K.C., Scott, J.M., Bhansali, S. (2017). Disposable aptamer-sensor aided by magnetic nanoparticle enrichment for detection of salivary cortisol variations in obstructive sleep apnea patients. Sci Rep, 7(1):17992. doi: 10.1038/s41598-017-17835-8.
• Mittal, R., Nguyen, D., Debs, L.H., Patel, A.P., Liu, G., Jhaveri, V.M., S Kay S.I., Mittal, J., Bandstra, E.S., Younis, R.T., Chapagain, P., Jayaweera, D.T., Liu, X.Z. (2017). Zika Virus: An Emerging Global Health Threat. Front Cell Infect Microbiol, 7:486. doi: 10.3389/fcimb.2017.00486.
• Olinski, R., Gackowski, D., Cooke, M.S. (2017). Endogenously generated DNA nucleobase modifications source, and significance as possible biomarkers of malignant transformation risk, and role in anticancer therapy. Biochim Biophys Acta, 1869(1):29-41. doi: 10.1016/j.bbcan.2017.11.002.
• Niu, G., Franc̨a, C., Zhang, G., Roobsoong, W., Nguitragool, W., Wang, X., Prachumsri, J., Butler, B.S., Li, J. (2017). The fibrinogen-like domain of FREP1 protein is a broad-spectrum malaria transmission-blocking vaccine antigen. JBC, doi: 10.1074/jbc.M116.773564.
• Niu, G., Zhang, G., Franca, C., Cui, Y., Munga, S., Afrane, Y., Li, J. (2017). FBN30 in wild Anopheles gambiae functions as a pathogen recognition molecule against clinically circulating Plasmodium falciparum in malaria endemic areas in Kenya. Sci Rep, 7(1):8577. doi: 10.1038/s41598-017-09017-3. 
• Banda, S., Cao, N., Tse-Dinh, Y.C. (2017). Distinct Mechanism Evolved for Mycobacterial RNA Polymerase and Topoisomerase I Protein-Protein Interaction. J Mol Biol, 429(19):2931-2942. doi: 10.1016/j.jmb.2017.08.011. 
• Boudalis, A.K., Rogez, G., Heinrich, B., Raptis, R.G., Turek, P. (2017). Towards ionic liquids with tailored magnetic properties: bmim+ salts of ferro- and antiferromagnetic Cu triangles. Dalton Trans, 46(36):12263-12273. doi: 10.1039/c7dt02472j. 
• Liu, Y., Berrido, A.M., Hua, Z.C., Tse-Dinh, Y.C., Leng, F. (2017). Biochemical and biophysical properties of positively supercoiled DNA. Biophys Chem, 230:68-73. doi: 10.1016/j.bpc.2017.08.008. 
• Garabedian, A., Benigni, P., Ramirez, C.E., Baker, E.S., Liu, T., Smith, R.D., Fernandez-Lima, F. (2017). Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS. J Am Soc Mass Spectrom, doi: 10.1007/s13361-017-1787-8.
• Gc, J.B., Pokhrel, R., Bhattarai, N., Johnson, K.A., Gerstman, B.S., Stahelin, R.V., Chapagain, P.P. (2017). Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments. Biochem Biophys Res Commun, 493(1):176-181. doi: 10.1016/j.bbrc.2017.09.052. 
• Gu, S., Lai, Y., Chen, H., Liu, Y., Zhang, Z. (2017). miR-155 mediates arsenic trioxide resistance by activating Nrf2 and suppressing apoptosis in lung cancer cells. Sci Rep, 7(1):12155. doi: 10.1038/s41598-017-06061-x.
• Rivera-Pérez, C., Clifton, M.E., Noriega, F.G. (2017). How micronutrients influence the physiology of mosquitoes. Curr Opin Insect Sci, 23:112-117. doi: 10.1016/j.cois.2017.07.002. 
• Zhi, X., Dages, S., Dages, K., Liu, Y., Hua, Z.C., Makemson, J., Leng, F. (2017). Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli. J Biol Chem, 292(35):14566-14575. doi: 10.1074/jbc.M117.794628. 
• Molano-Arevalo, J.C., Dit Fouque, K.J., Khoa, N.P., Miksovska, J., Ridgeway, M.E., Park, M.A., Fernandez-Lima, F. (2017). Characterization of Intramolecular Interactions of Cytochrome c Using Hydrogen Deuterium Exchange - Trapped Ion Mobility Spectrometry – Mass Spectrometry and Molecular Dynamics. Anal. Chem., 89(17):8757-8765. doi: 10.1021/acs.analchem.7b00844
• Chen, W., Tuladhar, A., Rolle, S., Lai, Y., Del Rey, F.R., Zavala, C.E., Liu, Y., Rein, K.S. (2017). Brevetoxin-2, is a unique inhibitor of the C-terminal redox center of mammalian thioredoxin reductase-1. Toxicol Appl Pharmacol, doi: 10.1016/j.taap.2017
• Ranjan, N., Story, S., Fulcrand, G., Leng, F., Ahmad, M., King, A., Sur, S., Wang, W., Tse-Dinh, Y.C., Arya, D.P. (2017). Selective Inhibition of Escherichia coli RNA and DNA Topoisomerase I by Hoechst 33258 Derived Mono- and Bisbenzimidazoles. J Med Chem, doi: 10.1021/acs.jmedchem.7b00191

• Benigni, P., Sandoval, K., Thompson, C.J., Ridgeway, M.E., Park, M.A., Gardinali, P., Fernandez-Lima, F.(2017). Analysis of Photoirradiated Water Accommodated Fractions of Crude Oils Using Tandem TIMS and FT-ICR MS. Environ. Sci. Technol., doi 1021/acs.est.7b00508

• Ren, Y., Lai, Y., Laverde, E.E., Lei, R., Rein, H.L., Liu, Y. (2017). Modulation of trinucleotide repeat instability by DNA polymerase β polymorphic variant R137Q. PLoS One., 12(5):e0177299. doi: 10.1371/journal.pone.0177299
• Wijesinghe, K.J., Urata, S., Bhattarai, N., Kooijman, E.E., Gerstman, B.S., Chapagain, P.P., Li, S., Stahelin, R.V. (2017). Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry. J Biol Chem, 292(15):6108-6122. doi: 10.1074/jbc.M116.758300
• Zhou, Q., Zhou, Y.N., Jin, D.J., Tse-Dinh, Y.C. (2017). Deacetylation of topoisomerase I is an important physiological function of E. coli CobB. Nucleic Acids Res, 45(9):5349-5358. doi: 10.1093/nar/gkx250
• Hernández-Martínez, S., Sánchez-Zavaleta, M., Brito, K., Herrera-Ortiz, A., Ons, S., Noriega, F.G. (2017). Allatotropin: A pleiotropic neuropeptide that elicits mosquito immune responses. PLoS One, 12(4):e0175759. doi: 10.1371/journal.pone.0175759

• Raji, J.I., DeGennaro, M. (2017). Genetic Analysis of Mosquito Detection of Humans. Curr Opin Insect Sci, 20:34–38. doi: 10.1016/j.cois.2017.03.003
• Meiselman, M., Lee, S.S., Tran, R.T., Dai, H., Ding, Y., Rivera-Perez, C., Wijesekera, T.P., Dauwalder, B., Noriega, F.G., Adams, M.E. (2017). Endocrine network essential for reproductive success in Drosophila melanogaster. Proc Natl Acad Sci U S A, doi: 10.1073/pnas.1620760114

• White, P.M., Serbus, L.R., Debec, A., Codina, A., Bray, W., Guichet, A., Lokey, R.S., Sullivan, W. (2017). Reliance of Wolbachia on High Rates of Host Proteolysis Revealed by a Genome-Wide RNAi Screen of Drosophila Cells. Genetics, 205(4):1473-1488. doi: 10.1534/genetics.116.198903
• Liu, D., Shao, Y., Chen, G., Tse-Dinh, Y.C., Piccirilli, J.A., Weizmann, Y. (2017). Synthesizing topological structures containing RNA. Nat Commun, 8:14936. doi: 10.1038/ncomms14936
• Chambers, T.P., Santiesteban, L., Gomez, D., Chambers, J.W. (2017). Sab mediates mitochondrial dysfunction involved in imatinib mesylate-induced cardiotoxicity. Toxicology, 382:24-35. doi: 10.1016/j.tox.2017.03.006

• Luo, Q., Beaver, J.M., Liu, Y., Zhang, Z. (2017). Dynamics of p53: A Master Decider of Cell Fate. Genes (Basel), 8(2): 66. doi: 10.3390/genes8020066

• Mittal, R., Aranke, M., Debs, L.H., Nguyen, D., Patel, A.P., Grati, M., Mittal, J., Yan, D., Chapagain, P., Eshraghi, A.A., Liu, X.Z. (2016). Indispensable Role of Ion Channels and Transporters in the Auditory System. J Cell Physiol, doi: 10.1002/jcp.25631
• Martínez-Rincón R.O., Rivera-Pérez C., Diambra, L., Noriega, F.G. (2017). Modeling the flux of metabolites in the juvenile hormone biosynthesis pathway using generalized additive models and ordinary differential equations. PLoS One, 12(2):e0171516 doi: 10.1371/journal.pone.0171516
• Ioannou, D., Millan, N. M., Jordan, E., Tempest, H. G. (2017). A new model of sperm nuclear architecture following assessment of the organization of centromeres and telomeres in three-dimensions. Scientific Reports,(7) 41585. doi:10.1038/srep41585
• Cheng, B., Zhou, Q., Weng, L., Leszyk, J.D., Greenberg, M.M., Tse-Dinh, Y.C. (2017). Identification of proximal sites for unwound DNA substrate in E. coli topoisomerase I with oxidative crosslinking. FEBS Lett, 591(1):28-38 doi: 10.1002/1873-3468.12517

• Butcher, D., Bernad, S., Derrien, V., Sebban, P., Miksovska, J. (2017). Role of Ionic Strength and pH in Modulating Thermodynamic Profiles Associated with CO Escape from Rice Nonsymbiotic Hemoglobin 1. J Phys Chem B, 121(2):351-364 doi: 10.1021/acs.jpcb.6b06933

• Yu, X., Zhang, M., Annamalai, T., Bansod, P., Narula, G., Tse-Dinh, Y.C., Sun, D. (2017). Synthesis, evaluation, and CoMFA study of fluoroquinophenoxazine derivatives as bacterial topoisomerase IA inhibitors. Eur J Med Chem, 125:515-527

• Jalal, A.H., Umasankar, Y., Gonzalez, P.J., Alfonso, A., Bhansali, S. (2017). Multimodal technique to eliminate humidity interference for specific detection of ethanol. Biosens Bioelectron, 87:522-530

• T. M. Jonah, L. Mathivathanan, A. N. Morozov, A . M. Mebel, R. G. Raptis, K. Kavallieratos* (2017). Remarkably selective NH4+ binding and fluorescence sensing by tripodal tris(pyrazolyl) receptors derived from 1,3,5-triethylbenzene: structural and theoretical insights on the role of ion pairing. New J. Chem. 41, 14835-8.

• Benigni, P., Bravo, C., Quirke, J.M.E., DeBord, J.H., Mebel, A.M.,Fernandez-Lima, F. (2016). Analysis of geologically relevant metal-porphyrins using Trapped Ion Mobility Spectrometry-Mass Spectrometry and theoretical calculations. Energy & Fuels, doi 10.1021/acs.energyfuels.6b02388

• Panday, N., Qian, G., Wang, X., Chang, S., Pandey, P., He, J. (2016). Simultaneous Ionic Current and Potential Detection of Nanoparticles by a Multifunctional Nanopipette. ACS Nano, 10(12),11237–11248. doi: 10.1021/acsnano.6b06307

• Dos Santos, H.G., Siltberg-Liberles, J. (2016). Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family. Genome Biol Evol, 8(9):2806-25

• Jani, M., Mathee, K., Azad, R.K. (2016). Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering. Front Microbiol, 7:1210

• Gc., J.B., Gerstman, B.S., Stahelin, R.V., Chapagain, P.P. (2016). The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P2 lipids in the plasma membrane. Phys Chem Chem Phys, 18(41):28409-28417

• Chen, C., Jiang, X., Gu, S., Lai, Y., Liu, Y., Zhang, Z. (2016). Protection of Nrf2 against arsenite-induced oxidative damage is regulated by the cyclic guanosine monophosphate-protein kinase G signaling pathway. Environ Toxicol, doi: 10.1002/tox.22374
• Beaver, J.M., Lai, Y., Rolle, S.J., Liu, Y. (2016). Proliferating cell nuclear antigen prevents trinucleotide repeat expansions by promoting repeat deletion and hairpin removal. DNA Repair (Amst), 48:17-29

• Rahaman, J., Siltberg-Liberles, J. (2016). Avoiding regions symptomatic of conformational and functional flexibility to identify antiviral targets in current and future coronaviruses. Genome Biol Evol, 8(11):3471-3484. doi: 10.1093/gbe/evw246

• Gu, M., Berrido, A., Gonzalez, W.G., Miksovska, J., Chambers, J.W., Leng, F. (2016). Fluorescently labeled circular DNA molecules for DNA topology and topoisomerases. Sci Rep, 6:36006

• Mittal, R., Lisi, C.V., Kumari, H., Grati, M., Blackwelder, P., Yan, D., Jain, C., Mathee, K., Weckwerth, P.H., Liu, X.Z. (2016). Otopathogenic Pseudomonas aeruginosa Enters and Survives Inside Macrophages. Front Microbiol, 7: 1828

• Adams, K.J., Montero, D., Aga, D., Fernandez-Lima, F. (2016). Isomer Separation of Polybrominated Diphenyl Ether Metabolites using nanoESI-TIMS-MS. Int J Ion Mobil Spectrom, 19(2):69-76

• Adams, K.J., DeBord, J.D., Fernandez-Lima, F. (2016). Lipid specific molecular ion emission as a function of the primary ion characteristics in TOF-SIMS. J Vac Sci Technol B Nanotechnol Microelectron, 34(5):051804

• Garabedian, A., Butcher, D., Lippens, J.L., Miksovska, J., Chapagain, P.P., Fabris, D., Ridgeway, M.E., Park, M.A., Fernandez-Lima, F. (2016). Structures of the kinetically trapped i-motif DNA intermediates. Phys Chem Chem Phys, 18(38):26691-26702

• Benigni, P., Marin, R., Molano-Arevalo, J.C., Garabedian, A., Wolff, J.J., Ridgeway, M.E., Park, M.A., Fernandez-Lima, F. (2016). Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS. Int J Ion Mobil Spectrom, 19(2):95-104

• Vanbellingen, Q.P., Castellanos, A., Rodriguez-Silva, M., Paudel, I., Chambers, J.W., Fernandez-Lima, F. (2016). Analysis of Chemotherapeutic Drug Delivery at the Single Cell Level Using 3D-MSI-TOF-SIMS. J Am Soc Mass Spectrom, 27(12):2033-2040

• Lai, Y., Budworth, H., Beaver, J.M., Chan, N.L.S., Zhang, Z., McMurray, C., Liu, Y. (2016). Crosstalk between MSH2–MSH3 and pol β promotes trinucleotide repeat expansion during base excision repair. Nat Commun, 7:12465. doi: 10.1038/ncomms12465

• Benigni, P., Fernandez-Lima, F. (2016). Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry Coupled to FT-ICR MS: Fundamentals and Applications. Anal Chem, 88(14):7404-12
• Tiwari, P.B., Chapagain, P.P., Banda, S., Darici, Y., Üren, A., Tse-Dinh, Y.C. (2016). Characterization of molecular interactions between E. coli RNA polymerase and topoisomerase I by molecular simulations. FEBS Lett,590(17):2844-51
• Ramirez, C.E., Nouzova, M., Benigni, P., Quirke, J.M., Noriega, F.G., Fernandez-Lima, F. (2016). Fast, ultra-trace detection of juvenile hormone III from mosquitoes using mass spectrometry. Talanta, 159:371-8

• Christensen, S., Pérez Dulzaides, R., Hedrick, V.E., Momtaz, A.J., Nakayasu, E.S., Paul, L.N., Serbus, L.R.(2016). Wolbachia endosymbionts modify Drosophila ovary protein levels in a context-dependent manner. Appl Environ Microbiol, doi: 10.1128/AEM.01255-16

• Dos Santos, H.G., Nunez-Castilla J., Siltberg-Liberles, J. (2016). Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73. PLoS One, 11(3):e0151961. doi: 10.1371/journal.pone.0151961

• Ahrens, J., Dos Santos, H.G., Siltberg-Liberles, J. (2016). The Nuanced Interplay of Intrinsic Disorder and Other Structural Properties Driving Protein Evolution. Mol Biol Evol, doi: 10.1093/molbev/msw092
• Benigni, P., DeBord J.D., Thompson, C.J., Gardinali, P., Fernandez-Lima, F. (2016). Increasing Polyaromatic Hydrocarbon (PAH) Molecular Coverage during Fossil Oil Analysis by Combining Gas Chromatography and Atmospheric-Pressure Laser Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS). Energy Fuels, 30(1):196-203

• Aguiar-Pulido, V., Huang, W., Suarez-Ulloa, V., Cickovski, T., Mathee, K., Narasimhan, G. (2016). Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. Evol Bioinform Online, 12(1):5-16

• Lopez, S.M., Agoulnik, A.I., Zhang, M., Peterson, L.E., Suarez, E., Gandarillas, G.A., Frolov, A., Li, R., Rajapakshe, K., Coarfa, C., Ittmann, M.M., Weigel, N.L., Agoulnik, I.U. (2016). Nuclear Receptor Corepressor 1 Expression and Output Declines with Prostate Cancer Progression. Clin Cancer Res, doi:10.1158/1078-0432.CCR-15-1983
• Mittal, R., Patel, A.P., Debs, L.H., Nguyen, D,, Patel, K., Grati, M., Mittal, J., Yan, D., Chapagain, P., Liu, X.Z. (2016). Intricate functions of matrix metalloproteinases in physiological and pathological conditions. J Cell Physiol, doi: 10.1002/jcp.25430

• GC, J.B., Johnson K.A., Husby M.L., Frick, C.T., Gerstman, B.S., Stahelin, R.V, Chapagain, P.P. (2016). Interdomain salt-bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization. Protein Sci. doi:10.1002/pro.2969
• Lai, Y., Jiang, Z., Zhou, J., Osemota, E., Liu, Y. (2016). AP endonuclease 1 prevents the extension of a T/G mismatch by DNA polymerase β to prevent mutations in CpGs during base excision repair. DNA Repair, 43: 89-97
• Leng, F., (2016). Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects. Biophysical Reviews, doi: 10.1007/s12551-016-0204-z
• Ahmad, M., Xue, Y., Lee. S.K., Martindale, J.L., Shen, W., Li, W., Zou, S., Ciaramella, M., Debat, H., Nadal, M., Leng, F., Zhang, H., Wang, Q., Siaw, G.E., Niu, H., Pommier, Y., Gorospe, M., Hsieh, T.S., Tse-Dinh, Y.C., Xu, D., Wang, W. (2016). RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. Nucleic Acids Res, doi: 10.1093/nar/gkw508
• Tse-Dinh, Y.C. (2016). Targeting bacterial topoisomerases - how to counter mechanisms of resistance. Future Med Chem, doi:10.4155/fmc-2016-0042

• Villalobos-Sambucaro, M.J., Diambra, L.A., Noriega, F.G., Ronderos, J.R. (2016). Allatostatin-C antagonizes the synergistic myostimulatory effect of allatotropin and serotonin in rhodnius prolixus (stal). Gen Comp Endocrinol, 233:1-7

• Zhang, Y., Liu, J., Li, D., Dai, X., Yan, F., Conlan, X.A., Zhou, R., Barrow, C.J., He, J., Wang, X., Yang, W. (2016). Self-Assembled Core-Satellite Gold Nanoparticle Networks for Ultrasensitive Detection of Chiral Molecules by Recognition Tunneling Current. ACS Nano,10(5):5096-103.

• Pham, K., Miksovska, J. (2016). Molecular insight of DREAM and presenilin 1 C-terminal fragment interactions. FEBS Lett, 590(8):1114-22.

• Dos Santos, H.G., Nunez-Castilla, J., Siltberg-Liberles, J. (2016). Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73. PLoS One, 11(3):e0151961. doi: 10.1371/journal.pone.0151961.

• Banda, S., Tiwari, P.B., Darici, Y., Tse-Dinh, Y.C. (2016). Investigating direct interaction between Escherichia coli topoisomerase I and RecA. Gene,585(1):65-70.

• Huang, W., Kazmierczak, K., Zhou, Z., Aguiar-Pulido, V., Narasimhan. G., Szczesna-Cordary, D. (2016). Gene expression patterns in transgenic mouse models of hypertrophic cardiomyopathy caused by mutations in myosin regulatory light chain. Arch Biochem Biophys, 601:121-32
• Gonzalez, W.G., Ramos, V., Diaz, M., Garabedian, A., Molano-Arevalo, J.C., Fernandez-Lima, F., Miksovska, J. (2016). Characterization of the Photophysical, Thermodynamic, and Structural Properties of the Terbium(III)-DREAM Complex. Biochemistry, 55(12):1873-86.

• Shan, Y., Panday, N., Myoung, Y., Twomey, M., Wang, X., Li, W., Celik, E., Moy, V., Wang, H., Moon, J.H., He, J. (2016). Scanning Ion Conductance Microscopic Study for Cellular Uptake of Cationic Conjugated Polymer Nanoparticles. Macromol Biosci,16(4):599-607.

• Sandhaus, S., Taylor, R., Edwards, T., Huddleston, A., Wooten, Y., Venkatraman, R., Weber, R.T., González-Sarrías, A., Martin, P.M., Cagle, P., Tse-Dinh, Y.C., Beebe, S.J., Seeram, N., Holder, A.A. (2016). A novel copper(II) complex identified as a potent drug against colorectal and breast cancer cells and as a poison inhibitor for human topoisomerase IIα. Inorg Chem Commun,64:45-49.

• Matthews, B.J., McBride, C.S., DeGennaro, M., Despo, O., Vosshall, L.B. (2016). The neurotranscriptome of the Aedes aegypti mosquito. BMC Genomics, 17:32. doi: 10.1186/s12864-015-2239-0.

• Mittal, R., Chan, B., Grati, M., Mittal, J., Patel, K., Debs, L.H., Patel, A.P., Yan, D., Chapagain, P., Liu, X. Z. (2016). Molecular Structure and Regulation of P2X Receptors With a Special Emphasis on the Role of P2X2 in the Auditory System. J Cell Physiol, (8):1656-70.

• Twomey, M., Mendez, E., Manian, R.K., Lee, S., Moon J.H. (2016). Mitochondria-specific conjugated polymer nanoparticles. Chem Commun (Camb), 52(27): 4910–4913.

• Sandhaus, S., Annamalai, T., Welmaker, G., Houghten, R. A., Paz, C., Garcia, P. K., Andres, A., Narula, G., Rodrigues Felix, C., Geden, S., Netherton, M., Gupta, R., Rohde, K. H., Giulianotti, M.A., and Tse-Dinh, Y.C. (2016). Small Molecule Inhibitors Targeting Topoisomerase I as Novel Antituberculosis Agents. Antimicrob Agents Chemother, 60 (7):4028-4036.

• Ioannou, D., Miller, D., Griffin, D. K., Tempest H.G. (2016). Impact of sperm DNA chromatin in the clinic. J Assist Reprod Genet,33(2):157-66.

• Fulcrand, G., Chapagain, P., Dunlap, D., and Leng, F. (2016). Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope. FEBS Letters, 590(5):613-61.

• Fulcrand, G., Dages, S., Zhi, X., Chapagain, P., Gerstman, B. S., Dunlap, D., and Leng, F. (2016). DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli. Scientific Reports, 6:19243.

• Agoulnik, I.U., Agoulnik, A.I. (2015). Long-Lasting Consequences of Testosterone Exposure. Endocrinology, 156(10):3488-9.

• Rodriguez Pino, M., Castillo, B., Kim, B., Kim, L.W. (2015). PP2A/B56 and GSK3/Ras suppress PKB activity during Dictyostelium chemotaxis. Mol Biol Cell, 26(24):4347-57.

• Yang, J., Annamalai, T., Cheng, B., Banda, S., Tyagi, R., Tse-Dinh, Y.C. (2015). Antimicrobial Susceptibility and SOS-Dependent Increase in Mutation Frequency Are Impacted by Escherichia coli Topoisomerase I C-Terminal Point Mutation. Antimicrob Agents Chemother, 59(10):6195-202.

• Chambers, T.P., Portalatin, G.M., Paudel, I, Robbins, C.J., Chambers, J.W. (2015). Sub-chronic administration of LY294002 sensitizes cervical cancer cells to chemotherapy by enhancing mitochondrial JNK signaling. Biochem Biophys Res Commun,463(4):538-44.
• Mathee, K., Silver, L.L, Tatke, G. (2015). 70th Anniversary Collection for the Microbiology Society: Journal of Medical Microbiology. J Med Microbiol, 64(12):1457-61.
• Tan, K., Cao, N., Cheng, B., Joachimiak, A., Tse-Dinh, Y.C. (2015). Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold. J Mol Biol, 428(1):182-933.

• Mustafi, S., Veisaga, M.L., López L.A, Barbieri, M.A. (2015). A Novel Insight into Dehydroleucodine Mediated Attenuation of Pseudomonas aeruginosa Virulence Mechanism. Biomed Res Int., 216097. doi: 10.1155/2015/216097.
• Tan, K., Zhou, Q., Cheng, B., Zhang, Z., Joachimiak, A., Tse-Dinh, Y.C. (2015). Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I. Nucleic Acids Res, 43(22):11031-46.

• Roy, U., Barber, P., Tse-Dinh, Y.C., Batrakova, E.V., Mondal, D., Nair, M. (2015). Role of MRP transporters in regulating antimicrobial drug inefficacy and oxidative stress-induced pathogenesis during HIV-1 and TB infections. Front Microbiol,6:948. doi: 10.3389/fmicb.2015.00948.
• Frost, L., Baez, M. A., Harrilal, C., Garabedian, A., Fernandez-Lima F., and Leng, F. (2015). The dimerization state of the mammalian high mobility group protein AT-hook-2 (HMGA2). PLOS ONE, 10(6): e0130478.

• Saldana-Caboverde A., Perera E.M., Watkins-Chow D., Hansen N.F., Vemulapalli M., Mullikin J.C., Nisc Comparative Sequencing Program, Pavan W.J., Kos L. (2015). The transcription factors Ets1 and Sox10 interact during murine melanocyte development. Dev Biol 407: 300-312.

• DeGennaro, M. (2015). The mysterious multi-modal repellency of DEET. Fly, 9:1, 45-51.

• Jiang, Z., Xu, M., Lai, Y., Laverde, E.E., Terzidis, M.A., Masi, A., Chatgilialoglu, C., & Liu, Y. (2015). Bypass of a 5 ,8-cyclopurine-2 -deoxynucleoside by DNA polymerase during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks. DNA Repair 33:24-34.

• Ioannou, D., Kandukuri, L., Simpson, J. L., & Tempest, H. G. (2015). Chromosome territory repositioning induced by PHA-activation of lymphocytes: A 2D and 3D appraisal. Molecular Cytogenetic 8 (47): doi:10.1186/s13039-015-0146-3.
• Beaver J.M., Lai Y., Meng X., Casin A.H., Laverde E.E., & Liu Y. (2015). AP endonuclease 1 prevents trinucleotide repeat expansion via a novel mechanism during base excision repair. Nucl. Acids Res. doi: 10.1093/nar/gkv530.
• Benigni P., Thompson C.J., Ridgeway M.E., Park M.A., & Fernandez-Lima F. (2015). Targeted high-resolution ion mobility separation coupled to ultrahigh-resolution mass spectrometry of endocrine disruptors in complex mixtures. Anal Chem 87(8):4321-4325.

• Tiwari P.B., Wang X., He J., & Darici Y. (2015). Analyzing surface plasmon resonance data: Choosing a correct biphasic model for interpretation. Rev Sci Instrum. 86(3):035001 doi.10.1063/1.4914027.

• Chengzhi C., Jiang X., Lai Y., Liu Y., & Zhang Z. (2015). Resveratrol protects against arsenic trioxide-induced oxidative damage through maintenance of glutathione homeostasis and inhibition of apoptotic progression. Environ. Mol. Mutagen 56(3): 333–346.

• Schenk E.R., Almeida R., Miksovska J., Ridgeway M.E., Park M. A., & Fernandez-Lima F. (2015). Kinetic Intermediates of Holo- and Apo-Myoglobin Studied Using HDX-TIMS-MS and Molecular Dynamic Simulations. J. Am. Soc. Mass Spectrom 26(4):555-563.

• Schenk E.R., Nau F., Fernandez-Lima F. (2015). Theoretical predictor for candidate structure assignment from IMS data of biomolecule-related conformational space. Int. J. Ion Mobil. Spec. doi: 10.1007/s12127-015-0165-0.
• Alonso N., Guillen R., Chambers J.W., & Leng F. (2015). A rapid and sensitive high-throughput screening method to identify compounds targeting protein–nucleic acids interactions. Nucleic Acids Res 43(8):e52. doi: 10.1093/nar/gkv069

• Twomey M., Vokatá T., Kumar M.R., & Moon J.H. (2015). Differential interactions of conjugated polymer nanoparticles with glycosaminoglycans in synthetic urine. The Royal Society of Chemistry 51(19):4065-4068

• Chayaratanasin P., Barbieri M.A., Suanpairintr N., & Adisakwattana S. (2015). Inhibitory effect of Clitoria ternatea flower petal extract on fructose-induced protein glycation and oxidation-dependent damages to albumin in vitro. BMC Complement Altern Med 15 (27) doi:10.1186/s12906-015-0546-2.

• Tse-Dinh Y.C. (2015). Targeting bacterial topoisomerase I to meet the challenge of finding new antibiotics. Future Med Chem 7(4); 459-471.

• Serbus L.R., White P.M., Silva J. P., Rabe A., Teixeira L., Albertson R., & Sullivan W. (2015). The impact of host diet on wolbachia titer in Drosophila. PLoS Pathog 11(3):1-25 
• Christensen S., & Serbus L.R. (2015). Comparative Analysis of Wolbachia Genomes Reveals Streamlining and Divergence of Minimalist Two-Component Systems. G3 Journal. doi:10.1534/g3.115.017137.

• Cheng B., Annamalai T., Sandhaus S., Bansod P., & Tse-Dinh Y.C. (2015). Inhibition of Zn(II) Binding Type IA Topoisomerases by Organomercury Compounds and Hg(II). PLoS ONE 10(3):1-14.

• Ioannou D., Kandukuri L., Quadri A., Becerra V., Simpson J.L & Tempest H.G. (2015). Spatial Positioning of all 24 Chromosomes in the Lymphocytes of Six Subjects: Evidence of Reproducible Positioning and Spatial Repositioning following DNA Damage with Hydrogen Peroxide and Ultraviolet B. PLoS ONE 10(3):1-24.

• Molano-Arevalo J.C., Hernandez D.R., Gonzalez W.G., Miksovska J., Ridgeway M.E., Park M.A., & Fernandez-Lima F. (2014). Flavin adenine dinucleotide structural motifs: from solution to gas phase. Anal Chem 86(20):10223-30.

• Xu M., Lai Y., Jiang Z., Terzidis M.A., Masi A., Chatgilialoglu C., & Liu Y. (2014). A 5', 8-cyclo-2'-lesion induces trinucleotide repeat deletion via a unique lesion bypass by DNA polymerase β. Nucleic Acids Research 42(22):13749-13763.

• Feng L., Maddox M.M., Alam M.Z., Tsutsumi L.S., Narula G., Bruhn D.F., Wu X., Sandhaus S., Lee R.B., Simmons C.J., Tse-Dinh Y.C., Hurdle J.G., Lee R.E, & Sun D. (2014). Synthesis, Structure-Activity Relationship Studies, and Antibacterial Evaluation of 4-Chromanones and Chalcones, as Well as Olympicin A and Derivatives. Journal of Medicinal Chemistry 57(20):8398-8420.

• Schenk E.R., Nau F., Thompson C.J., Tse-Dinh Y.C., & Fernandez-Lima F. (2014). Changes in lipid distribution in E. coli strains in response to norfloxacin. Journal of Mass Spectrometry 50:88-94.

• Tiwari P.B., Astudillo L., Miksovska J., Wang X., Li W., Darici Y., & He J.(2014). Quantitative study of protein-protein interactions by quartz nanopipettes. The Royal Society of Chemistry 6:10255-10263.

• Ryu M.H., Kang I.H., Nelson M.D., Jensen T.M., Lyuksyutova A.I., Siltberg-Liberles J., Raizen D.M., & Gomelsky M.(2014). Engineering adenylate cyclases regulated by near-infrared window light. Proc Natl Acad Sci 111(28):10167-10172.