Publications

Shih YM, Cooke MS, Pan CH, Chao MR, Hu CW. (2019). 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). 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.

Hernández-Martínez S, Cardoso-Jaime V, Nouzova M, Michalkova V, Ramirez CE, Fernandez-Lima F, Noriega FG. (2019). Juvenile hormone controls ovarian development in female Anopheles albimanus mosquitoes. Sci Rep. 9(1):2127. doi: 10.1038/s41598-019-38631-6. PubMed PMID: 30765796; PubMed Central PMCID: PMC6375968.

Garcia PK, Annamalai T, Wang W, Bell RS, Le D, Martin Pancorbo P, Sikandar S, Seddek A, Yu X, Sun D, Uhlemann AC, Tiwari PB, Leng F, Tse-Dinh YC. (2019). Mechanism and resistance for antimycobacterial activity of a fluoroquinophenoxazine compound. PLoS One. 14(2):e0207733. doi: 10.1371/journal.pone.0207733. eCollection 2019. PubMed PMID: 30794538.

Jeanne Dit Fouque K,  Garabedian A, Leng F, Tse-Dinh YC, Fernandez-Lima F. (2019). Microheterogeneity of Topoisomerase IA/IB and Their DNA-Bound States. ACS Omega, 2019, 4 (2), pp 3619–3626. DOI: 10.1021/acsomega.8b02887.

Pokhrel R, Pavadai E, Gerstman BS, Chapagain PP. (2019). Membrane pore formation and ion selectivity of the Ebola virus delta peptide. Phys Chem Chem Phys. doi: 10.1039/c8cp07323f. [Epub ahead of print] PubMed PMID: 30785432.

Tangar A, Derrien V, Lei R, Santiago Estevez MJ, Sebban P, Bernad S, Miksovska J. (2019). Utility of fluorescent heme analogue ZnPPIX to monitor conformational heterogeneity in vertebrate hexa-coordinated globins. Metallomics.  doi: 10.1039/c8mt00332g. [Epub ahead of print] PubMed PMID: 30734813.

Oranzi NR, Kemperman RHJ, Wei MS, Petkovska VI, Granato SW, Rochon B, Kaszycki J, La Rotta A, Jeanne Dit Fouque K, Fernandez-Lima F, Yost RA. (2019). Measuring the Integrity of Gas-Phase Conformers of Sodiated 25-Hydroxyvitamin D3 by Drift Tube, Traveling Wave, Trapped, and High-Field Asymmetric Ion Mobility. Anal Chem. doi: 10.1021/acs.analchem.8b05723. [Epub ahead of print] PubMed PMID: 30807105.

Masi A, Sabbia A, Ferreri C, Manoli F, Lai Y, Laverde E, Liu Y, Krokidis MG, Chatgilialoglu C, Faraone Mennella MR. (2019). Diastereomeric Recognition of 5',8-cyclo-2'-Deoxyadenosine Lesions by Human Poly(ADP-ribose) Polymerase 1 in a Biomimetic Model. Cells. 8(2). pii: E116. doi: 10.3390/cells8020116. PubMed PMID: 30717407.

Butcher D, Miksovska J, Ridgeway ME, Park MA, Fernandez-Lima F. (2019). The effects of solution additives and gas-phase modifiers on the molecular environment and conformational space of common heme proteins. Rapid Commun Mass Spectrom. 33(5):399-404. doi: 10.1002/rcm.8347. PubMed PMID: 30421840.

Raji JI, Melo N, Castillo JS, Gonzalez S, Saldana V, Stensmyr MC, DeGennaro M. (2019). Aedes aegypti Mosquitoes Detect Acidic Volatiles Found in Human Odor Using the IR8a Pathway. Curr Biol. pii: S0960-9822(19)30215-5. doi:10.1016/j.cub.2019.02.045. [Epub ahead of print] PubMed PMID: 30930038.

Lugo-Martinez J, Ruiz-Perez D, Narasimhan G, Bar-Joseph Z. (2019). Dynamic interaction network inference from longitudinal microbiome data. Microbiome. 7(1):54. doi: 10.1186/s40168-019-0660-3. PubMed PMID: 30940197; PubMed Central PMCID: PMC6446388.

Bhushan P, Umasankar Y, Hutcheson JD, Bhansali S. (2019). Toxicity assessment of wearable wound sensor constituents on keratinocytes. Toxicol In Vitro. 58:170-177. doi: 10.1016/j.tiv.2019.03.034. [Epub ahead of print] PubMed PMID: 30928693.

Lazarou KA, González-Nieves K, Chakraborty I, Raptis RG. (2019). Spontaneous Resolution by Crystallization of an Octanuclear Iron(III) Complex Using Only Racemic Reagents. Angew Chem Int Ed Engl. doi:10.1002/anie.201901877. [Epub ahead of print] PubMed PMID: 30891840.

Duan W, Gao L, Kalvala A, Aguila B, Brooks C, Mo X, Ding H, Shilo K, Otterson GA, Villalona-Calero MA. (2019). Type of TP53 mutation influences oncogenic potential and spectrum of associated K-ras mutations in lung-specific transgenic mice. Int J Cancer. doi: 10.1002/ijc.32279. [Epub ahead of print] PubMed PMID: 30873587.

Lucero M, Suarez AE, Chambers JW. (2019). Phosphoregulation on mitochondria: Integration of cell and organelle responses. CNS Neurosci Ther. doi: 10.1111/cns.13141. [Epub ahead of print] Review. PubMed PMID: 31025544.

Jia Y, Karbaschia M, Cooke M. (2019). Mycoplasma infection of cultured cells induces oxidative stress and attenuates cellular base excision repair activity. Science Direct, Received 16 August 2018, Revised 11 April 2019, Accepted 19 May 2019, Available online 20 May 2019.

Deshpande SA, Meiselman M, Hice RH, Arensburger P, Rivera-Perez C, Kim DH, Croft RL, Noriega FG, Adams ME. (2019). Ecdysis triggering hormone receptors regulate male courtship behavior via antennal lobe interneurons in Drosophila. Gen Comp Endocrinol. 278:79-88. doi: 10.1016/j.ygcen.2018.12.003. Epub 2018 Dec 10. PubMed PMID: 30543770.

Moon JH, Manandhar P, Torabi H, Rohman MR, Mathivathanan L, Lee KH, Irle S. (2019). Phenyleneethynylene trimer-based rigid-flexible [2+2] macrocycles for nucleic acid labelling in live cells. Chem Commun (Camb). 55(42):5930-5933. doi: 10.1039/c9cc02162k. PubMed PMID: 31049491.

Shi K, Mathivathanan L, Boudalis AK, Turek P, Chakraborty I, Raptis RG. (2019). Nitrite Reduction by Trinuclear Copper Pyrazolate Complexes: An Example of a Catalytic, Synthetic Polynuclear NO Releasing System. Inorg Chem. doi: 10.1021/acs.inorgchem.9b00748. [Epub ahead of print] PubMed PMID: 31091082.

Rodriguez-Silva, M, Ashourian, KT, Smith, AD, and Chambers JW. (2019). Assessment of Mitochondrial Stress in Neurons: Proximity Ligation Assays to Detect Recruitment of Stress-Responsive Proteins to Mitochondria. Neuromethods: Cell Culture Techniques. DOI: 10.1007/978-1-4939-9228-7_6.

Dit Fouquea KJ, Fernandez-Lima F. (2019). Recent Advances in Biological Separations using Trapped Ion Mobility Spectrometry – Mass Spectrometry. TrAC Trends in Analytical Chemistry, Volume 116, Pages 308-315.

Cickovski T, Aguiar-Pulido V, Narasimhan G. (2019). MATria: a unified centrality algorithm. BMC Bioinformatics. 20(Suppl 11):278. doi:10.1186/s12859-019-2820-7. PubMed PMID: 31167635; PubMed Central PMCID: PMC6551236.

Pokhrel R, Bhattarai N, Baral P, Gerstman BS, Park JH, Handfield M, Chapagain PP. (2019). Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140. Phys Chem Chem Phys. doi: 10.1039/c9cp01558b. [Epub ahead of print] PubMed PMID: 31147666.

Chatgilialoglu C, Ferreri C, Geacintov NE, Krokidis MG, Liu Y, Masi A, Shafirovich V, Terzidis MA, Tsegay PS. (2019). 5',8-Cyclopurine Lesions in DNA Damage: Chemical, Analytical, Biological, and Diagnostic Significance. Cells. 8(6). pii: E513. doi: 10.3390/cells8060513. Review. PubMed PMID: 31141888.

Leyva D, Tose LV, Porter J, Wolff J, Jaffé R, Fernandez-Lima F. (2019). Understanding the structural complexity of dissolved organic matter: isomeric diversity. Faraday Discuss. doi: 10.1039/c8fd00221e. [Epub ahead of print] PubMed PMID: 31134248.

Silverman JA, Mathivathanan L, Govor EV, Raptis RG, Kavallieratos K. (2019). Coordination polymers of Cd(II) and Pb(II) with croconate show remarkable differences in coordination patterns: a structural and spectroscopic study. Acta Crystallogr C Struct Chem. 75(Pt 7):935-940. doi: 10.1107/S2053229619007277. Epub 2019 Jun 14. PubMed PMID: 31271382.

Ioannou D, Tempest HG. (2019). Human Sperm Chromosomes: To Form Hairpin-Loops, Or Not to Form Hairpin-Loops, That Is the Question. Genes (Basel). 10(7). pii: E504. doi: 10.3390/genes10070504. PubMed PMID: 31277336

Jeanne Dit Fouque K, Moreno J, Fernandez-Lima F. (2019). Exploring the Conformational Space of Growth-Hormone-Releasing Hormone Analogues Using Dopant Assisted Trapped Ion Mobility Spectrometry-Mass Spectrometry. J Phys Chem B. doi: 10.1021/acs.jpcb.9b03777. [Epub ahead of print] PubMed PMID: 31299151.

Ahmed MS, Dutta RK, Manandhar P, Li X, Torabi H, Barrios A, Wang P, Chinnapaiyan S, Unwalla HJ, Moon JH. (2019). A guanylurea-functionalized conjugated polymer enables RNA interference in ex vivo human airway epithelium. Chem Commun (Camb). 55(54):7804-7807. doi: 10.1039/c9cc02856k. PubMed PMID: 31214678.

Ma T, Guo J, Chang S, Wang X, Zhou J, Liang F, He J. (2019). Modulating and probing the dynamic intermolecular interactions in plasmonic molecule-pair junctions. Phys Chem Chem Phys. doi: 10.1039/c9cp02030f. [Epub ahead of print] PubMed PMID: 31263809.

Nouzova M, Michalkova V, Ramirez CE, Fernandez-Lima F, Noriega FG. (2019). Inhibition of juvenile hormone synthesis in mosquitoes by the methylation inhibitor 3-deazaneplanocin A (DZNep). Insect Biochem Mol Biol. 103183. doi: 10.1016/j.ibmb.2019.103183. [Epub ahead of print] PubMed PMID: 31265905.

Gabelica V, Shvartsburg AA, Afonso C, Barran P, Benesch JLP, Bleiholder C, Bowers MT, Bilbao A, Bush MF, Campbell JL, Campuzano IDG, Causon T, Clowers BH, Creaser CS, De Pauw E, Far J, Fernandez-Lima F, Fjeldsted JC, Giles K, Groessl M, Hogan CJ Jr, Hann S, Kim HI, Kurulugama RT, May JC, McLean JA, Pagel K, Richardson K, Ridgeway ME, Rosu F, Sobott F, Thalassinos K, Valentine SJ, Wyttenbach T. (2019). Recommendations for reporting ion mobility Mass Spectrometry measurements. Mass Spectrom Rev. 38(3):291-320. doi: 10.1002/mas.21585. Epub 2019 Feb 1. Review. PubMed PMID: 30707468.

Wang W, Tse-Dinh YC. (2019). Recent Advances in Use of Topoisomerase Inhibitors in Combination Cancer Therapy. Curr Top Med Chem. 19(9):730-740. doi: 0.2174/1568026619666190401113350. Review. PubMed PMID: 30931861.

Nouzova M, Clifton ME, Noriega FG. (2019). Mosquito adaptations to hematophagia impact pathogen transmission. Curr Opin Insect Sci. 34:21-26. doi:10.1016/j.cois.2019.02.002. [Epub ahead of print] Review. PubMed PMID: 31247413.

Lai Y, Lei R, Ren Y, Liu Y. (2019). Methods to Study Trinucleotide Repeat Instability Induced by DNA Damage and Repair. Methods Mol Biol. 1999:87-101. doi: 10.1007/978-1-4939-9500-4_5. PubMed PMID: 31127571.

Castellanos A, Ramirez CE, Michalkova V, Nouzova M, Noriega FG, Fernández-Lima F. (2019). Three Dimensional Secondary Ion Mass Spectrometry Imaging (3D-SIMS) of Aedes aegypti ovarian follicles. J. Anal. At. Spectrom. DOI: 10.1039/c8ja00425k

Valdes C, Stebliankin V, Narasimhan G. (2019). Large scale microbiome profiling in the cloud. Bioinformatics. 35(14):i13-i22. doi:10.1093/bioinformatics/btz356. PubMed PMID: 31510682; PubMed Central PMCID: PMC6612844.

Christensen S, Camacho M, Sharmin Z, Momtaz AJMZ, Perez L, Navarro G, Triana J, Samarah H, Turelli M, Serbus LR. (2019). Quantitative methods for assessing local and bodywide contributions to Wolbachia titer in maternal germline cells of Drosophila. BMC Microbiol. 19(1):206. doi: 10.1186/s12866-019-1579-3. PubMed PMID: 31481018; PubMed Central PMCID: PMC6724367.

Dages S, Zhi X, Leng F. (2019). Fis protein forms DNA topological barriers to confine transcription-coupled DNA supercoiling in Escherichia coli. FEBS Lett.  doi: 10.1002/1873-3468.13643. [Epub ahead of print] PubMed PMID: 31639222.

Alhegaili AS, Ji Y, Sylvius N, Blades MJ, Karbaschi M, Tempest HG, Jones GDD, Cooke MS. (2019). Genome-Wide Adductomics Analysis Reveals Heterogeneity in the Induction and Loss of Cyclobutane Thymine Dimers across Both the Nuclear and Mitochondrial Genomes. Int J Mol Sci. 20(20). pii: E5112. doi: 10.3390/ijms20205112. PubMed PMID: 31618917.

Wang W, Rodriguez-Silva M, Acanda de la Rocha AM, Wolf AL, Lai Y, Liu Y, Reinhold WC, Pommier Y, Chambers JW, Tse-Dinh YC. (2019). Tyrosyl-DNA Phosphodiesterase 1 and Topoisomerase I Activities as Predictive Indicators for Glioblastoma Susceptibility to Genotoxic Agents. Cancers (Basel). 11(10). pii: E1416. doi: 10.3390/cancers11101416. PubMed PMID: 31547492.

Pandey P, Garcia J, Guo J, Wang X, Yang D, He J. (2019). Differentiation of metallic and dielectric nanoparticles in solution by single-nanoparticle collision events at the nanoelectrode. Nanotechnology.31(1):015503. doi:10.1088/1361-6528/ab4445. [Epub ahead of print] PubMed PMID: 31519013.

Tenenbaum R, Agarwal R, Cooke MS, Agrawal MM, Maddux M, Burke SL. (2019). Utilization of Complementary and Alternative Therapies in Youth with Developmental Disabilities. Evid Based Complement Alternat Med. 3630509. doi: 10.1155/2019/3630509. eCollection 2019. PubMed PMID: 31341491; PubMed Central PMCID: PMC6614975.

Wang Y, Rakela S, Chambers JW, Hua ZC, Muller MT, Nitiss JL, Tse-Dinh YC, Leng F. (2019). Kinetic Study of DNA Topoisomerases by Supercoiling-Dependent Fluorescence Quenching. ACS Omega. 4(19):18413-18422. doi: 10.1021/acsomega.9b02676. eCollection 2019 Nov 5. PubMed PMID: 31720544; PubMed Central PMCID: PMC6844113.

Tsegay PS, Lai Y, Liu Y. (2019). Replication Stress and Consequential Instability of the Genome and Epigenome. Molecules. 24(21). pii: E3870. doi: 10.3390/molecules24213870. Review. PubMed PMID: 31717862.

Raji JI, Gonzalez S, DeGennaro M. (2019). Aedes aegypti Ir8a mutant female mosquitoes show increased attraction to standing water. Commun Integr Biol. 12(1):181-186. doi: 10.1080/19420889.2019.1681063. eCollection 2019. PubMed PMID: 31700566; PubMed Central PMCID: PMC6824317.

Hu CW, Chang YJ, Cooke MS, Chao MR. (2019). DNA Crosslinkomics: A Tool for the Comprehensive Assessment of Interstrand Crosslinks Using High Resolution Mass Spectrometry. Anal Chem.  doi: 10.1021/acs.analchem.9b04068. [Epub ahead of print] PubMed PMID: 31670503.

Castellanos A, Ramirez CE, Michalkova V, Nouzova M, Noriega FG, Francisco FL. (2019). Three Dimensional Secondary Ion Mass Spectrometry Imaging (3D-SIMS) of Aedes aegypti ovarian follicles. J Anal At Spectrom. 34(5):874-883. doi: 10.1039/C8JA00425K. Epub 2019 Feb 21. PubMed PMID: 31680712; PubMed Central PMCID: PMC6824543.

Cooke MS, Hu CW, Chao MR. (2019). Editorial: Mass Spectrometry for Adductomic Analysis. Front. Chem. doi: 10.3389/fchem.2019.00794

Karbaschi M, Ji Y, Abdulwahed AMS, Alohaly A, Bedoya JF, Burke SL, Boulos TM, Tempest HG, Cooke MS. (2019). Evaluation of the Major Steps in the Conventional Protocol for the Alkaline Comet Assay. Int J Mol Sci. 20(23). pii: E6072. doi: 10.3390/ijms20236072. PubMed PMID: 31810189.

Ramirez CE, Nouzova M, Michalkova V, Fernandez-Lima F, Noriega FG. (2019). Common structural features facilitate the simultaneous identification and quantification of the five most common juvenile hormones by liquid chromatography-tandem mass spectrometry. Insect Biochem Mol Biol. 116:103287. doi: 10.1016/j.ibmb.2019.103287. [Epub ahead of print] PubMed PMID: 31760138.

Vasquez JL, Lai Y, Annamalai T, Jiang Z, Zhang M, Lei R, Zhang Z, Liu Y, Tse-Dinh YC, Agoulnik IU. (2019). Inhibition of base excision repair by natamycin suppresses prostate cancer cell proliferation. Biochimie. 168:241-250. doi: 10.1016/j.biochi.2019.11.008. [Epub ahead of print] PubMed PMID: 31756402.

Pavadai E, Bhattarai N, Baral P, Stahelin RV, Chapagain PP, Gerstman BS. (2019). Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament. J Phys Chem B. 123(43):9045-9053. doi: 10.1021/acs.jpcb.9b04674. Epub 2019 Oct 16. PubMed PMID: 31576755.

Melo N, Wolff GH, Costa-da-Silva AL, Arribas R, Triana MF, Gugger M, Riffell JA DeGennaro M, Stensmyr MC. (2019). Geosmin Attracts Aedes aegypti Mosquitoes to Oviposition Sites.Curr Biol. pii: S0960-9822(19)31441-1. doi: 10.1016/j.cub.2019.11.002. [Epub ahead of print] PubMed PMID: 31839454.

Silverman JA, Mathivathanan L, Govor EV, Raptis RG, Kavallieratos K. (2019 ). Coordination polymers of Cd(II) and Pb(II) with croconate show remarkable differences in coordination patterns: a structural and spectroscopic study. Acta Crystallogr C Struct Chem. 75(Pt 7):935-940. doi: 10.1107/S2053229619007277. Epub 2019 Jun 14. PubMed PMID: 31271382.

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.

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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]

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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

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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.

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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.

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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.

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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.

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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]

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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.

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Mathee K. (2018). Forensic investigation into the origin of Pseudomonas aeruginosa PA14 - old but not lost. J Med Microbiol. 67(8):1019-1021. doi: 10.1099/jmm.0.000778. PubMed PMID: 30067168.

Pandey S, Delgado C, Kumari H, Florez L, Mathee K. (2018). Outer-membrane protein LptD (PA0595) plays a role in the regulation of alginate synthesis in Pseudomonas aeruginosa. J Med Microbiol. 67(8):1139-1156. doi: 10.1099/jmm.0.000752. Epub 2018 Jun 20. Erratum in: J Med Microbiol. 2018 Oct;67(10):1533. PubMed PMID: 29923820; PubMed Central PMCID: PMC6557146.

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. 46(14):7296-7308. doi: 10.1093/nar/gky492. PubMed PMID: 29905859; PubMed Central PMCID: PMC6101483.

Rodríguez-Santiago AJ, Nicole Cortés, Khoa Pham, Jaroslava Miksovska, Raptis RG. (2018). 4,4′-Dihydroxy-2,2′-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.

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

Jeanne Dit Fouque K, Salgueiro LM, Cai R, Sha W, Schally AV, Fernandez-Lima F. (2018). Structural Motif Descriptors as a Way To Elucidate the Agonistic or Antagonistic Activity of Growth Hormone-Releasing Hormone Peptide Analogues. ACS Omega. 3(7):7432-7440. doi: 10.1021/acsomega.8b00375. eCollection. PubMed PMID: 31458901; PubMed Central PMCID: PMC6644384.

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.

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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.