Publications

Andre M, Kolishetti N, Yndart A, Vashist A, Nair M, Raymond AD. Magnetoelectric Extracellular Vesicle Latency-Targeting (MELT) Nanotherapeutic for the Block-Lock-and-Kill HIV Eradication Strategy. Biomedicines. 2025 Jan 9;13(1):147. doi: 10.3390/biomedicines13010147. PMID: 39857731; PMCID: PMC11762476.

Shirali A, Stebliankin V, Karki U, Shi J, Chapagain P, Narasimhan G.A comprehensive survey of scoring functions for protein docking models. BMC Bioinformatics. 2025 Jan 22;26(1):25. doi: 10.1186/s12859-024-05991-4. PMID: 39844036; PMCID: PMC11755896.

Linjia Su, Zifang Deng, Miguel Santos-Fernandez, Kevin Jeanne Dit Fouque, Prem P Chapagain, Jeremy W Chambers, Francisco Fernandez-Lima,Fenfei Leng, Inhibition of HMGA2 binding to AT-rich DNA by its negatively charged C-terminus, Nucleic Acids Research, Volume 53, Issue 3, 10 February 2025, gkaf035, https://doi.org/10.1093/nar/gkaf035

Rezaei S, Moncada-Restrepo M, Leng S, Chambers JW, Leng F.Synthesizing unmodified, supercoiled circular DNA molecules in vitro. bioRxiv [Preprint]. 2025 Jan 25:2025.01.24.634800. doi: 10.1101/2025.01.24.634800. PMID: 39896529; PMCID: PMC11785245.

Holmes CJ, Chakraborty S, Ajayi OM, Uhran MR, Frigard R, Stacey CL, Susanto EE, Chen SC, Rasgon JL, DeGennaro M, Xiao Y, Benoit JB. Multiple blood feeding bouts in mosquitoes allow for prolonged survival and are predicted to increase viral transmission during dry periods. iScience. 2025 Jan 9;28(2):111760. doi: 10.1016/j.isci.2025.111760. PMID: 39935457; PMCID: PMC11810705.

Howlader AH, Fernandez R, Tsegay PS, Liu Y, Wnuk SF. Synthesis of Adenine Nucleosides with a Reactive (β-Iodovinyl)sulfone or (β-Keto)sulfone Group at the C2 Position and Their Polymerase-Catalyzed Incorporation into DNA. Molecules. 2025 Mar 18;30(6):1358. doi: 10.3390/molecules30061358. PMID: 40142132; PMCID: PMC11944392.

Jibowu M, Vigilant M, Costa-da-Silva AL, Nelson A, Essigmann HT, Brown EL, Gunter SM. Spatial and seasonal dynamics of mosquito species in Harris County, Texas, highlight risk of arbovirus introduction and transmission. Sci Rep. 2025 Mar 25;15(1):10330. doi: 10.1038/s41598-025-92175-6. PMID: 40133319; PMCID: PMC11937572.

Barton LJ, Sanny J, Packard Dawson E, Nouzova M, Noriega FG, Stadtfeld M, Lehmann R. Juvenile hormones direct primordial germ cell migration to the embryonic gonad. Curr Biol. 2024 Jan 8:S0960-9822(23)01733-5. doi: 10.1016/j.cub.2023.12.033. Epub ahead of print. PMID: 38215744.

Costa-da-Silva AL, Cabal S, Lopez K, Boloix J, Rodriguez BG, Marrero KM, Bellantuono AJ, DeGennaro M.Female Aedes aegypti mosquitoes use communal cues to manage population density at breeding sites. Commun Biol. 2024 Jan 31;7(1):143. doi: 10.1038/s42003-024-05830-5. PMID: 38297108; PMCID: PMC10830494.

Nayman EI, Schwartz BA, Polmann M, Gumabong AC, Nieuwdorp M, Cickovski T, Mathee K.Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus. Sci Rep. 2024 Feb 26;14(1):4585. doi: 10.1038/s41598-024-54769-4. PMID: 38403716; PMCID: PMC10894869.

Gomes Souza F Jr, Bhansali S, Pal K, Silveira Maranhão FD, Santos Oliveira M, Valladão VS, Brandão E Silva DS, Silva GB. A 30-Year Review on Nanocomposites: Comprehensive Bibliometric Insights into Microstructural, Electrical, and Mechanical Properties Assisted by Artificial Intelligence. Materials (Basel). 2024 Feb 27;17(5):1088. doi: 10.3390/ma17051088. PMID: 38473560; PMCID: PMC10934506.

Hamsanathan S, Anthonymuthu T, Prosser D, Lokshin A, Greenspan SL, Resnick NM, Perera S, Okawa S, Narasimhan G, Gurkar AU. A molecular index for biological age identified from the metabolome and senescence-associated secretome in humans. Aging Cell. 2024 Mar 7:e14104. doi: 10.1111/acel.14104. Epub ahead of print. PMID: 38454639.

Ortega-Insaurralde I, Latorre-Estivalis JM, Costa-da-Silva AL, Cano A, Insausti TC, Morales HS, Pontes G, de Astrada MB, Ons S, DeGennaro M, Barrozo RB. The pharyngeal taste organ of a blood-feeding insect functions in food recognition. BMC Biol. 2024 Mar 13;22(1):63. doi: 10.1186/s12915-024-01861-w. PMID: 38481317; PMCID: PMC10938694.

Shaver M, Gomez K, Kaiser K, Hutcheson JD. Mechanical stretch leads to increased caveolin-1 content and mineralization potential in extracellular vesicles from vascular smooth muscle cells. BMC Mol Cell Biol. 2024 Mar 14;25(1):8. doi: 10.1186/s12860-024-00504-w. PMID: 38486163; PMCID: PMC10938675.

Cioffi MD, Husby ML, Gerstman BS, Stahelin RV, Chapagain PP.Role of phosphatidic acid lipids on plasma membrane association of the Ebola virus matrix protein VP40. Biochim Biophys Acta Mol Cell Biol Lipids. 2024 Apr;1869(3):159464. doi: 10.1016/j.bbalip.2024.159464. Epub 2024 Feb 14. PMID: 38360201.

Motsa BB, Sharma T, Chapagain PP, Stahelin RV. Minor changes in electrostatics robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. bioRxiv [Preprint]. 2024 Jan 31:2024.01.30.578092. doi: 10.1101/2024.01.30.578092. PMID: 38352396; PMCID: PMC10862912.

Fan RZ, Sportelli C, Lai Y, Salehe SS, Pinnell JR, Brown HJ, Richardson JR, Luo S, Tieu K.A partial Drp1 knockout improves autophagy flux independent of mitochondrial function. Mol Neurodegener. 2024 Mar 19;19(1):26. doi: 10.1186/s13024-024-00708-w. PMID: 38504290; PMCID: PMC10953112.

Tan K, Tse-Dinh YC. Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life. Cells. 2024 Mar 21;13(6):553. doi: 10.3390/cells13060553. PMID: 38534397; PMCID: PMC10969213.

Sharmin Z, Samarah H, Aldaya Bourricaudy R, Ochoa L, Serbus LR.Cross-validation of chemical and genetic disruption approaches to inform host cellular effects on Wolbachia abundance in Drosophila. Front Microbiol. 2024 Mar 25;15:1364009. doi: 10.3389/fmicb.2024.1364009. PMID: 38591028; PMCID: PMC10999648.

Motsa BB, Sharma T, Cioffi MD, Chapagain PP, Stahelin RV. Minor electrostatic changes robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. J Biol Chem. 2024 May;300(5):107213. doi: 10.1016/j.jbc.2024.107213. Epub 2024 Mar 24. PMID: 38522519; PMCID: PMC11061732.

Narkhede Y, Saxena R, Sharma T, Conarty JP, Ramirez VT, Motsa BB, Amiar S, Li S, Chapagain PP, Wiest O, Stahelin RV. Computational and experimental identification of keystone interactions in Ebola virus matrix protein VP40 dimer formation. Protein Sci. 2024 May;33(5):e4978. doi: 10.1002/pro.4978. PMID: 38591637; PMCID: PMC11002992.

Colbert BM, Lanting C, Smeal M, Blanton S, Dykxhoorn DM, Tang PC, Getchell RL, Velde H, Fehrmann M, Thorpe R, Chapagain P, Elkhaligy H, Kremer H, Yntema H, Haer-Wigman L, Redfield S, Sun T, Bruijn S, Plomp A, Goderie T, van de Kamp J, Free RH, Wassink-Ruiter JK, Widdershoven J, Vanhoutte E, Rotteveel L, Kriek M, van Dooren M, Hoefsloot L, de Gier HHW; DOOFNL Consortium; Schaefer A, Kolbe D, Azaiez H, Rabie G, Aburayyan A, Kawas M, Kanaan M, Holder J, Usami SI, Chen Z, Dai P, Holt J, Nelson R, Choi BY, Shearer E, Smith RJH, Pennings R, Liu XZ. The natural history and genotype-phenotype correlations of TMPRSS3 hearing loss: an international, multi-center, cohort analysis. Hum Genet. 2024 May;143(5):721-734. doi: 10.1007/s00439-024-02648-3. Epub 2024 Apr 30. PMID: 38691166; PMCID: PMC11098735.

Work HM, Hackett JC, Lampe JN. HCV Antiviral Drugs Have the Potential to Adversely Perturb the Fetal-Maternal Communication Axis through Inhibition of CYP3A7 DHEA-S Oxidation. Drug Metab Dispos. 2024 May 16;52(6):516-525. doi: 10.1124/dmd.123.001434. PMID: 38267095; PMCID: PMC11114604.

Hernández-Martínez G, Ares MA, Rosales-Reyes R, Soria-Bustos J, Yañez-Santos JA, Cedillo ML, Girón JA, Martínez-Laguna Y, Leng F, Ibarra JA, De la Cruz MA. The nucleoid protein HU positively regulates the expression of type VI secretion systems in Enterobacter cloacae. mSphere. 2024 May 29;9(5):e0006024. doi: 10.1128/msphere.00060-24. Epub 2024 Apr 22. PMID: 38647313.

Johnson KA, Budicini MR, Bhattarai N, Sharma T, Urata S, Gerstman BS, Chapagain PP, Li S, Stahelin RV. PI(4,5)P2 binding sites in the Ebola virus matrix protein VP40 modulate assembly and budding. J Lipid Res. 2024 Mar;65(3):100512. doi: 10.1016/j.jlr.2024.100512. Epub 2024 Jan 29. PMID: 38295986; PMCID: PMC10909612.

Qi Z, Etebari K, Nouzova M, Noriega FG, Asgari S. Differential gene expression and microRNA profile in corpora allata-corpora cardiaca of Aedes aegypti mosquitoes with weak juvenile hormone signalling. BMC Genomics. 2024 Jan 25;25(1):113. doi: 10.1186/s12864-024-10007-9. PMID: 38273232; PMCID: PMC10811912.

Shah S, Dougan KE, Chen Y, Lo R, Laird G, Fortuin MDA, Rai SK, Murigneux V, Bellantuono AJ, Rodriguez-Lanetty M, Bhattacharya D, Chan CX. Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates. ISME J. 2024 Jan 8;18(1):wrae059. doi: 10.1093/ismejo/wrae059. PMID: 38655774; PMCID: PMC11114475.

Miller SA, Jeanne Dit Fouque K, Hard ER, Balana AT, Kaplan D, Voinov VG, Ridgeway ME, Park MA, Anderson GA, Pratt MR, Fernandez-Lima F.Top/Middle-Down Characterization of α-Synuclein Glycoforms. Anal Chem. 2023 Dec 12;95(49):18039-18045. doi: 10.1021/acs.analchem.3c02405. Epub 2023 Dec 4. PMID: 38047498; PMCID: PMC10836061.

Mantica F, Iñiguez LP, Marquez Y, Permanyer J, Torres-Mendez A, Cruz J, Franch-Marro X, Tulenko F, Burguera D, Bertrand S, Doyle T, Nouzova M, Currie PD, Noriega FG, Escriva H, Arnone MI, Albertin CB, Wotton KR, Almudi I, Martin D, Irimia M. Evolution of tissue-specific expression of ancestral genes across vertebrates and insects. Nat Ecol Evol. 2024 Jun;8(6):1140-1153. doi: 10.1038/s41559-024-02398-5. Epub 2024 Apr 15. PMID: 38622362.

Hackett JC, Krueger S, Urban VS, Zárate-Pérez F. Small angle scattering reveals the orientation of cytochrome P450 19A1 in lipoprotein nanodiscs. J Inorg Biochem. 2024 Aug;257:112579. doi: 10.1016/j.jinorgbio.2024.112579. Epub 2024 May 1. PMID: 38703512.

Costa-da-Silva AL, Dye-Braumuller KC, Wagner-Coello HU, Li H, Johnson-Carson D, Gunter SM, Nolan MS, DeGennaro M.Landscape and meteorological variables associated with Aedes aegypti and Aedes albopictus mosquito infestation in two southeastern USA coastal cities. bioRxiv [Preprint]. 2024 Jun 9:2024.06.06.597792. doi: 10.1101/2024.06.06.597792. PMID: 38895389; PMCID: PMC11185711.

Chen J, Nouzova M, Noriega FG, Tatar M. Gut-to-brain regulation of Drosophila aging through neuropeptide F, insulin and juvenile hormone. bioRxiv [Preprint]. 2024 Jun 30:2024.06.26.600832. doi: 10.1101/2024.06.26.600832. PMID: 38979180; PMCID: PMC11230353.

Helgoe J, Davy SK, Weis VM, Rodriguez-Lanetty M.Triggers, cascades, and endpoints: connecting the dots of coral bleaching mechanisms. Biol Rev Camb Philos Soc. 2024 Jun;99(3):715-752. doi: 10.1111/brv.13042. Epub 2024 Jan 12. PMID: 38217089.

David OG, Arce AV, Costa-da-Silva AL, Bellantuono AJ, DeGennaro M.Fertility decline in Aedes aegypti (Diptera: Culicidae) mosquitoes is associated with reduced maternal transcript deposition and does not depend on female age. J Med Entomol. 2024 Jul 12;61(4):1064-1070. doi: 10.1093/jme/tjae058. PMID: 38757780; PMCID: PMC11239790.

Dougan KE, Bellantuono AJ, Kahlke T, Abbriano RM, Chen Y, Shah S, Granados-Cifuentes C, van Oppen MJH, Bhattacharya D, Suggett DJ, Rodriguez-Lanetty M, Chan CX. Whole-genome duplication in an algal symbiont bolsters coral heat tolerance. Sci Adv. 2024 Jul 19;10(29):eadn2218. doi: 10.1126/sciadv.adn2218. Epub 2024 Jul 19. PMID: 39028812; PMCID: PMC11259175.

Mamun Y, Tse-Dinh YC, Chapagain P.Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations. J Chem Inf Model. 2024 Jul 18. doi: 10.1021/acs.jcim.4c00472. Epub ahead of print. PMID: 39024468.

Sklenicka J, Tran T, Ramirez MS, Donow HM, Magaña AJ, LaVoi T, Mamun Y, Jimenez V, Chapagain P, Santos R, Pinilla C, Giulianotti MA, Tolmasky ME. Structure-Activity Relationship of Pyrrolidine Pentamine Derivatives as Inhibitors of the Aminoglycoside 6'-N-Acetyltransferase Type Ib. Antibiotics (Basel). 2024 Jul 19;13(7):672. doi: 10.3390/antibiotics13070672. PMID: 39061354; PMCID: PMC11274322.

Tariq U, Saeed F.Predicting peptide properties from mass spectrometry data using deep attention-based multitask network and uncertainty quantification. bioRxiv [Preprint]. 2024 Aug 22:2024.08.21.609035. doi: 10.1101/2024.08.21.609035. PMID: 39229185; PMCID: PMC11370541.

Ruiz-Perez D, Gimon I, Sazal M, Mathee K, Narasimhan G.Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA. mSystems. 2024 Sep 6:e0130323. doi: 10.1128/msystems.01303-23. Epub ahead of print. PMID: 39240096.

Delinasios GJ, Karbaschi M, Cooke MS, Young AR. Author Correction: Vitamin E inhibits the UVAI induction of "light" and "dark" cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes. Sci Rep. 2024 Sep 6;14(1):20862. doi: 10.1038/s41598-024-70946-x. Erratum for: Sci Rep. 2018 Jan 11;8(1):423. doi: 10.1038/s41598-017-18924-4. PMID: 39242736; PMCID: PMC11379699.

Adams PE, Thies JL, Sutton JM, Millwood JD, Caldwell GA, Caldwell KA, Fierst JL. Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing. PeerJ. 2024 Sep 13;12:e18100. doi: 10.7717/peerj.18100. PMID: 39285918; PMCID: PMC11404476.

Chen J, Nouzová M, Noriega FG, Tatar M. Gut-to-brain regulation of Drosophila aging through neuropeptide F, insulin, and juvenile hormone. Proc Natl Acad Sci U S A. 2024 Oct 22;121(43):e2411987121. doi: 10.1073/pnas.2411987121. Epub 2024 Oct 16. PMID: 39413128.

Fierst JL, Eggers VK. Regulatory logic and transposable element dynamics in nematode worm genomes. bioRxiv [Preprint]. 2024 Sep 16:2024.09.15.613132. doi: 10.1101/2024.09.15.613132. PMID: 39345564; PMCID: PMC11429677.

Lawson A, Annunziato M, Bashirova N, Eeza MNH, Matysik J, Alia A, Berry JP.High-Resolution Magic-Angle Spinning Nuclear Magnetic Resonance Identifies Impairment of Metabolism by T-2 Toxin, in Relation to Toxicity, in Zebrafish Embryo Model. Toxins (Basel). 2024 Oct 1;16(10):424. doi: 10.3390/toxins16100424. PMID: 39453200; PMCID: PMC11511446.

Nasim S, Abujamra BA, Chaparro D, Nogueira PDS, Riva A, Hutcheson JD, Kos L.Multiple cell types including melanocytes contribute to elastogenesis in the developing murine aortic valve. Sci Rep. 2024 Oct 26;14(1):25481. doi: 10.1038/s41598-024-73673-5. PMID: 39461968; PMCID: PMC11513076.

Vashist A, Perez Alvarez G, Andion Camargo V, Raymond AD, Arias AY, Kolishetti N, Vashist A, Manickam P, Aggarwal S, Nair M. Recent advances in nanogels for drug delivery and biomedical applications. Biomater Sci. 2024 Nov 1. doi: 10.1039/d4bm00224e. Epub ahead of print. PMID: 39484856; PMCID: PMC11528912.

Cioffi MD, Sharma T, Motsa BB, Bhattarai N, Gerstman BS, Stahelin RV, Chapagain PP.Ebola Virus Matrix Protein VP40 Single Mutations G198R and G201R Significantly Enhance Plasma Membrane Localization. J Phys Chem B. 2024 Nov 21;128(46):11335-11344. doi: 10.1021/acs.jpcb.4c02700. Epub 2024 Sep 26. PMID: 39326870; PMCID: PMC11586905.

Chadni SH, Young MA, Igorra P, Bhuiyan MAR, Kenyon V, Tse-Dinh YC.Small Molecule Inhibitors of Mycobacterium tuberculosis Topoisomerase I Identified by Machine Learning and In Vitro Assays. Int J Mol Sci. 2024 Nov 15;25(22):12265. doi: 10.3390/ijms252212265. PMID: 39596331; PMCID: PMC11594364.

Dargam V, Sanchez A, Kolengaden A, Perez Y, Arias R, Valentin Cabrera AM, Chaparro D, Tarafa C, Coba A, Yapaolo N, da Silva Nogueira P, Todd EA, Williams MM, Shehadeh LA, Hutcheson JD. Sex-Specific Changes in Cardiac Function and Electrophysiology During Progression of Adenine-Induced Chronic Kidney Disease in Mice. J Cardiovasc Dev Dis. 2024 Nov 7;11(11):362. doi: 10.3390/jcdd11110362. PMID: 39590205; PMCID: PMC11594452.

Chandler KB, Marrero Roche DE, Sackstein R. Multidimensional separation and analysis of alpha-1-acid glycoprotein N-glycopeptides using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and nano-liquid chromatography tandem mass spectrometry. (2023) Anal Bioanal Chem;415(3):379-390. doi: 10.1007/s00216-022-04435-3. Epub 2022 Nov 19. PMID: 36401639.

Tsegay PS, Hernandez D, Qu F, Olatunji M, Mamun Y, Chapagain P, Liu Y. RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation. (2023) Nucleic Acids Res;51(1):166-181. doi: 10.1093/nar/gkac1178. PMID: 36533524; PMCID: PMC9841414.

Ferdous S, Dasgupta T, Annamalai T, Tan K, Tse-Dinh YC. The interaction between transport-segment DNA and topoisomerase IA-crystal structure of MtbTOP1 in complex with both G- and T-segments. (2023) Nucleic Acids Res;51(1):349-364. doi: 10.1093/nar/gkac1205. PMID: 36583363; PMCID: PMC9841409.

Benoit JB, McCluney KE, DeGennaro MJ, Dow JAT. Dehydration Dynamics in Terrestrial Arthropods: From Water Sensing to Trophic Interactions. (2023) Annu Rev Entomol;68:129-149. doi: 10.1146/annurev-ento-120120-091609. Epub 2022 Oct 21. PMID: 36270273; PMCID: PMC9936378.

Kandoor A, Fierst J.Dauer fate in a Caenorhabditis elegans Boolean network model. (2023) PeerJ;11:e14713. doi: 10.7717/peerj.14713. PMID: 36710867; PMCID: PMC9879150.

Chen P, Zhang M, Zhang Y, Li J, Wan X, Lv T, Chen Y, Zhao Z, Ma Z, Zhu Z, Chen L, Li Z, Wang Z, Qiao G. Cyprinid herpesvirus 2 infection changes microbiota and metabolites in the gibel carp (Carassius auratus gibelio) midgut. (2023) Front Cell Infect Microbiol;12:1017165. doi: 10.3389/fcimb.2022.1017165. PMID: 36817692; PMCID: PMC9933507.

Leyva D, Usman Tariq M, Jaffé R, Saeed F, Fernandez-Lima F.Description of Dissolved Organic Matter Transformational Networks at the Molecular Level. (2023) Environ Sci Technol;57(6):2672-2681. doi: 10.1021/acs.est.2c04715. Epub 2023 Feb 1. PMID: 36724500.

Martin HR, Sales Martinez S, Stebliankin V, Tamargo JA, Campa A, Narasimhan G, Hernandez J, Rodriguez JAB, Teeman C, Johnson A, Sherman KE, Baum MK. Diet Quality and Liver Health in People Living with HIV in the MASH Cohort: A Multi-Omic Analysis of the Fecal Microbiome and Metabolome. (2023) Metabolites;13(2):271. doi: 10.3390/metabo13020271. PMID: 36837890; PMCID: PMC9962547.

Bose D, Stebliankin V, Cickovski T, Saha P, Trivedi A, Roy S, More M, Tuteja A, Mathee K, Narasimhan G, Chatterjee S. Microbiome Dysbiosis Shows Strong Association of Gut-Derived Altered Metabolomic Profile in Gulf War Chronic Multisymptom Illness Symptom Persistence Following Western Diet Feeding and Development of Obesity. (2023) Int J Mol Sci;24(4):4245. doi: 10.3390/ijms24044245. PMID: 36835663; PMCID: PMC9962797.

Costa-da-Silva AL.Artificial Membrane Feeding Mosquitoes in the Laboratory with Glytube. (2023) Cold Spring Harb Protoc;2023(3):pdb.prot108013. doi: 10.1101/pdb.prot108013. PMID: 36223987.

Costa-da-Silva AL.Membrane Feeding Devices to Blood Feed Mosquitoes in the Laboratory. (2023) Cold Spring Harb Protoc;2023(3):pdb.top107655. doi: 10.1101/pdb.top107655. PMID: 36223989.

Adams PE, Eggers VK, Millwood JD, Sutton JM, Pienaar J, Fierst JL. Genome Size Changes by Duplication, Divergence, and Insertion in Caenorhabditis Worms. (2023) Mol Biol Evol;40(3):msad039. doi: 10.1093/molbev/msad039. PMID: 36807460; PMCID: PMC10015627.

Sesena-Rubfiaro A, Prajapati NJ, Paolino L, Lou L, Cotayo D, Pandey P, Shaver M, Hutcheson JD, Agarwal A, He J. Membrane Remodeling of Human-Engineered Cardiac Tissue by Chronic Electric Stimulation. (2023)ACS Biomater Sci Eng.;9(3):1644-1655. doi: 10.1021/acsbiomaterials.2c01370. Epub 2023 Feb 10. PMID: 36765460.

Chandler KB, Pavan CH, Cotto Aparicio HG, Sackstein R. Enrichment and nLC-MS/MS Analysis of Head and Neck Cancer Mucinome Glycoproteins. (2023) J Proteome Res. doi: 10.1021/acs.jproteome.2c00746. Epub ahead of print. PMID: 36971183.

Alam MS, Leyva D, Michelin W, Fernandez-Lima F, Miksovska J.Distinct mechanism of Tb3+ and Eu3+ binding to NCS1. (2023) Phys Chem Chem Phys;25(13):9500-9512. doi: 10.1039/d2cp05765d. PMID: 36938969.

Bakhshian Nik A, Ng HH, Ashbrook SK, Sun P, Iacoviello F, Shearing PR, Bertazzo S, Mero D, Khomtchouk BB, Hutcheson JD. Epidermal growth factor receptor inhibition prevents vascular calcifying extracellular vesicle biogenesis. (2023) Am J Physiol Heart Circ Physiol;324(4):H553-H570. doi: 10.1152/ajpheart.00280.2022. Epub 2023 Feb 24. PMID: 36827229; PMCID: PMC10042607.

Castillo JS, Bellantuono AJ, DeGennaro M.Building a Uniport Olfactometer to Assess Mosquito Responses to Odors. (2023) Cold Spring Harb Protoc. doi: 10.1101/pdb.prot108174. Epub ahead of print. PMID: 37019609.

Castillo JS, Bellantuono AJ, DeGennaro M.Quantifying Mosquito Attraction Using a Uniport Olfactometer. (2023)Cold Spring Harb Protoc. doi: 10.1101/pdb.prot108175. Epub ahead of print. PMID: 37019611.

Castillo JS, Bellantuono AJ, DeGennaro M.Quantifying Mosquito Attraction Behavior Using Olfactometry. (2023) Cold Spring Harb Protoc. doi: 10.1101/pdb.top107660. Epub ahead of print. PMID: 37024240.

Chandler KB, Pavan CH, Cotto Aparicio HG, Sackstein R. Enrichment and nLC-MS/MS Analysis of Head and Neck Cancer Mucinome Glycoproteins. (2023) J Proteome Res;22(4):1231-1244. doi: 10.1021/acs.jproteome.2c00746. Epub 2023 Mar 27. PMID: 36971183.

Thapa B, Adhikari NP, Tiwari PB, Chapagain PP.A 5'-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA. (2023) J Chem Inf Model;63(7):2095-2103. doi: 10.1021/acs.jcim.2c01294. Epub 2022 Dec 23. PMID: 36563044.

Mejia G, Su L, Pandey P, Jeanne Dit Fouque K, McGoron AJ, Fernandez-Lima F, He J, Mebel AM, Leng F.Anticancer Drug Doxorubicin Spontaneously Reacts with GTP and dGTP. (2023) Chem Res Toxicol;36(4):660-668. doi: 10.1021/acs.chemrestox.2c00367. Epub 2023 Mar 31. PMID: 37000908.

Prapharsavat R, Kittikongnapang R, Smithkittipol C, Udomrat W, Numsawat S, Hernandez-Koutoucheva A, Naemiratch B, Chomkatekaew C, Amaratunga C, Bleho J, Mathee K, Schneiders ML, Khirikoekkong N, Kanthawang N, Sumpradit N, Suveeranont R, Asarath SA, Poomchaichote T, Schilling W, Chan XHS, Osterrieder A, Cheah PY, Limmathurotsakul D. Raising awareness of antimicrobial resistance: development of an 'antibiotic footprint calculator'. (2023) J Antimicrob Chemother:dkad113. doi: 10.1093/jac/dkad113. Epub ahead of print. PMID: 37071582.

Jobson J, Tsegay PS, Beltran MT, Taher EA, Rein SR, Liu Y, Rein KS. Brevetoxin induces a shift in the redox state of the proteome and unfolded protein response in human lymphoblast cells that can be alleviated with the acrolein scavenger MESNA. Environ Toxicol Pharmacol. 2023 Apr 29;100:104137. doi: 10.1016/j.etap.2023.104137. Epub ahead of print. PMID: 37127110.

Ghimire G, Guo J, Halmagian R, He J.Reversibly Modulating Plasmon-mediated Chemical Reaction via Electrode Potential on Reliable Copper Nanoelectrode. Angew Chem Int Ed Engl. 2023 May 8;62(20):e202302215. doi: 10.1002/anie.202302215. Epub 2023 Apr 12. PMID: 36929628.

Ramelow J, Keleta Y, Niu G, Wang X, Li J. Plasmodium parasitophorous vacuole membrane protein Pfs16 promotes malaria transmission by silencing mosquito immunity. J Biol Chem. 2023 May 15;299(6):104824. doi: 10.1016/j.jbc.2023.104824. Epub ahead of print. PMID: 37196765.

Vashist A, Raymond AD, Chapagain P, Vashist A, Arias AY, Kolishetti N, Nair M. Multi-functional auto-fluorescent nanogels for theranostics. J Neurovirol. 2023 May 29. doi: 10.1007/s13365-023-01138-y. Epub ahead of print. PMID: 37248372.

Prapharsavat R, Kittikongnapang R, Smithkittipol C, Udomrat W, Numsawat S, Hernandez-Koutoucheva A, Naemiratch B, Chomkatekaew C, Amaratunga C, Bleho J, Mathee K, Schneiders ML, Khirikoekkong N, Kanthawang N, Sumpradit N, Suveeranont R, Asarath SA, Poomchaichote T, Schilling W, Chan XHS, Osterrieder A, Cheah PY, Limmathurotsakul D. Raising awareness of antimicrobial resistance: development of an 'antibiotic footprint calculator'. J Antimicrob Chemother. 2023 Jun 1;78(6):1317-1321. doi: 10.1093/jac/dkad113. PMID: 37071582; PMCID: PMC10232231.

Santos-Fernandez M, Jeanne Dit Fouque K, Fernandez-Lima F. Integration of Trapped Ion Mobility Spectrometry and Ultraviolet Photodissociation in a Quadrupolar Ion Trap Mass Spectrometer. Anal Chem. 2023 Jun 6;95(22):8417-8422. doi: 10.1021/acs.analchem.3c01220. Epub 2023 May 23. PMID: 37220214.

David OG, Sanchez KM, Arce AV, Costa-da-Silva AL, Bellantuono AJ, DeGennaro M.Fertility decline in female mosquitoes is regulated by the orco olfactory co-receptor. iScience. 2023 May 13;26(6):106883. doi: 10.1016/j.isci.2023.106883. PMID: 37275523; PMCID: PMC10239028.

 Valdes C, Stebliankin V, Ruiz-Perez D, Park JI, Lee H, Narasimhan G.Microbiome maps: Hilbert curve visualizations of metagenomic profiles. Front Bioinform. 2023 Jun 19;3:1154588. doi: 10.3389/fbinf.2023.1154588. PMID: 37405310; PMCID: PMC10317073.

Ray G, Huff RM, Castillo JS, Bellantuono AJ, DeGennaro M, Pitts RJ. Carboxylic acids that drive mosquito attraction to humans activate ionotropic receptors. PLoS Negl Trop Dis. 2023 Jun 20;17(6):e0011402. doi: 10.1371/journal.pntd.0011402. PMID: 37339129; PMCID: PMC10313001.

Yoshinaga M, Niu G, Yoshinaga-Sakurai K, Nadar VS, Wang X, Rosen BP, Li J.Arsinothricin Inhibits Plasmodium falciparum Proliferation in Blood and Blocks Parasite Transmission to Mosquitoes. Microorganisms. 2023 May 3;11(5):1195. doi: 10.3390/microorganisms11051195. PMID: 37317169; PMCID: PMC10222646.

Moura AS, Costa-da-Silva AL, Peixoto PS, Maciel C, Cardoso AF. Vitellogenin genes are transcribed in Culex quinquefasciatus ovary. Mem Inst Oswaldo Cruz. 2023 Jul 17;118:e220143. doi: 10.1590/0074-02760220143. PMID: 37466532; PMCID: PMC10368008.

Cickovski T, Mathee K, Aguirre G, Tatke G, Hermida A, Narasimhan G, Stollstorff M. Attention Deficit Hyperactivity Disorder (ADHD) and the gut microbiome: An ecological perspective. PLoS One. 2023 Aug 18;18(8):e0273890. doi: 10.1371/journal.pone.0273890. PMID: 37594987; PMCID: PMC10437823.

Bakhshian Nik, A., Kaiser, K., Sun, P., Khomtchoul BB, Hutchenson JD, et al. Altered Caveolin-1 Dynamics Result in Divergent Mineralization Responses in Bone and Vascular Calcification. Cel. Mol. Bioeng. (2023). https://doi.org/10.1007/s12195-023-00779-7

Angel J. Magañaa, Jan Sklenickaa, Clemencia Pinillab, Marc Giulianottib, Prem Chapagain, Radleigh Santose, Maria Soledad Ramireza and Marcelo E. Tolmasky. Restoring susceptibility to aminoglycosides: identifying small molecule inhibitors of enzymatic inactivation. DOI: 10.1039/D3MD00226H.

Sharma T, Gerstman B, Chapagain P.Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding. Int J Mol Sci. 2023 Aug 9;24(16):12586. doi: 10.3390/ijms241612586. PMID: 37628766; PMCID: PMC10454900.

Yogesh B. Narkhede, Atul Bhardwaj, Balindile B. Motsa, Roopashi Saxena, Tej Sharma, Prem P. Chapagain, Robert V. Stahelin, and Olaf Wiest. Elucidating Residue-Level Determinants Affecting Dimerization of Ebola Virus Matrix Protein Using High-Throughput Site Saturation Mutagenesis and Biophysical Approaches. The Journal of Physical Chemistry B 2023 127 (29), 6449-6461
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Lucchini R, Tieu K. Manganese-Induced Parkinsonism: Evidence from Epidemiological and Experimental Studies. Biomolecules. 2023 Jul 30;13(8):1190. doi: 10.3390/biom13081190. PMID: 37627255; PMCID: PMC10452806.

Sweeney DT, Zárate-Pérez F, Stokowa-Sołtys K, Hackett JC. Induced fit describes ligand binding to membrane-associated cytochrome P450 3A4. Mol Pharmacol. 2023 Aug 3:MOLPHARM-AR-2023-000698. doi: 10.1124/molpharm.123.000698. Epub ahead of print. PMID: 37536953.

Leyria J, Guarneri AA, Lorenzo MG, Nouzova M, Noriega FG, Benrabaa SAM, Fernandez-Lima F, Valadares Tose L, Orchard I, Lange AB. Effects of mating on female reproductive physiology in the insect model, Rhodnius prolixus, a vector of the causative parasite of Chagas disease. PLoS Negl Trop Dis. 2023 Sep 20;17(9):e0011640. doi: 10.1371/journal.pntd.0011640. Epub ahead of print. PMID: 37729234.

Clarke RD, Garba NA, Barbieri MA, Acuna L, Baum M, Rodriguez MS, Frias H, Saldarriaga P, Stefano T, Mathee K, Narasimhan G, R Brown D. Detection of SARS-CoV-2 in high-efficiency particulate air (HEPA) filters of low-cost air purifiers in community-based organizations. Environ Monit Assess. 2023 Oct 14;195(11):1320. doi: 10.1007/s10661-023-11950-y. PMID: 37837468; PMCID: PMC10576720.

Susana Herrera, Masafumi Yoshinaga, Raphael G. Raptis,“Antibacterial properties of nine indium(III) complexes of substituted pyrazoles/pyrazolate and the structural and solution characterization of the mer- and trans‑indium(III) complexes of 4-Me-pzH”, Journal of Inorganic Biochemistry, Volume 250, 2024, 112402,ISSN 0162-0134,https://doi.org/10.1016/j.jinorgbio.2023.112402.

Deng Z, Chapagain P, Leng F.Macromolecular Crowding Potently Stimulates DNA Supercoiling Activity of Mycobacterium tuberculosis DNA Gyrase. J Biol Chem. 2023 Nov 7:105439. doi: 10.1016/j.jbc.2023.105439. Epub ahead of print. PMID: 37944619.

Veisaga ML, Ahumada M, Soriano S, Acuna L, Zhang W, Leung I, Barnum R, Barbieri MA.Anti-proliferative effect of Annona extracts on breast cancer cells. Biocell. 2023 Aug 28;47(8):1835-1852. PMID: 37771344; PMCID: PMC10538365.

Zhang M, Ceyhan Y, Mei S, Hirz T, Sykes DB, Agoulnik IU.Regulation of EZH2 Expression by INPP4B in Normal Prostate and Primary Prostate Cancer. Cancers (Basel). 2023 Nov 15;15(22):5418. doi: 10.3390/cancers15225418. PMID: 38001678; PMCID: PMC10670027.

Hutcheson JD.From Flow to Pharmaceuticals: Single-Cell Mechanobiology and Drug Efficacy. Arterioscler Thromb Vasc Biol. 2023 Dec;43(12):2282-2284. doi: 10.1161/ATVBAHA.123.320117. Epub 2023 Nov 9. PMID: 37942613.

Santosh Khatri, Popular Pandey, German Mejia, Govinda Ghimire, Fenfei Leng, and Jin He. Nanoconfinement and Crowding Enhanced Single-Molecule Detection of Small Molecules with Nanopipettes. Journal of the American Chemical Society Article. DOI: 10.1021/jacs.3c09311. PMID: 37996390.

Zhou J, Guo J, Ghimire G, Mebel AM, Chang S, He J.Plasmon-mediated dehydrogenation of the aromatic methyl group and benzyl radical formation. Chem Sci. 2023 Nov 28;14(47):13951-13961. doi: 10.1039/d3sc05847f. PMID: 38075667; PMCID: PMC10699572.

Kurogi Y, Imura E, Mizuno Y, Hoshino R, Nouzova M, Matsuyama S, Mizoguchi A, Kondo S, Tanimoto H, Noriega FG, Niwa R. Female reproductive dormancy in Drosophila is regulated by DH31-producing neurons projecting into the corpus allatum. Development. 2023 May 15;150(10):dev201186. doi: 10.1242/dev.201186. Epub 2023 May 23. PMID: 37218457; PMCID: PMC10233717.

Truman JW, Riddiford LM, Konopová B, Nouzova M, Noriega F, Herko M. The embryonic role of juvenile hormone in the firebrat, Thermobia domestica, reveals its function before its involvement in metamorphosis. bioRxiv [Preprint]. 2023 Oct 10:2023.10.06.561279. doi: 10.1101/2023.10.06.561279. PMID: 37873170; PMCID: PMC10592639.

Castro, K.D., Tose, L.V., Willetts, M., Park, M.A., Nouzova, M., Noriega, F.G., Fernandez-Lima, F.Tracing de novo Lipids using Stable Isotope Labeling LC-TIMS-TOF MS/MS. J. Vis. Exp. (), e65590, doi:10.3791/65590 (2023).

Ruiz-Perez D, Gimon I, Sazal M, Mathee K, Narasimhan G.Unfolding and De-confounding: Biologically meaningful causal inference from longitudinal multi-omic networks using METALICA. bioRxiv [Preprint]. 2023 Dec 13:2023.12.12.571384. doi: 10.1101/2023.12.12.571384. PMID: 38168315; PMCID: PMC10760167.

Costa-da-Silva AL, Cabal S, Lopez K, Boloix J, Rodriguez BG, Marrero KM, Bellantuono AJ, DeGennaro M.Female Aedes aegypti mosquitoes use communal cues to manage population density at breeding sites. Commun Biol. 2024 Jan 31;7(1):143. doi: 10.1038/s42003-024-05830-5. PMID: 38297108; PMCID: PMC10830494.

Nayman EI, Schwartz BA, Polmann M, Gumabong AC, Nieuwdorp M, Cickovski T, Mathee K.Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus. Sci Rep. 2024 Feb 26;14(1):4585. doi: 10.1038/s41598-024-54769-4. PMID: 38403716; PMCID: PMC10894869.

Gomes Souza F Jr, Bhansali S, Pal K, Silveira Maranhão FD, Santos Oliveira M, Valladão VS, Brandão E Silva DS, Silva GB. A 30-Year Review on Nanocomposites: Comprehensive Bibliometric Insights into Microstructural, Electrical, and Mechanical Properties Assisted by Artificial Intelligence. Materials (Basel). 2024 Feb 27;17(5):1088. doi: 10.3390/ma17051088. PMID: 38473560; PMCID: PMC10934506.

Hamsanathan S, Anthonymuthu T, Prosser D, Lokshin A, Greenspan SL, Resnick NM, Perera S, Okawa S, Narasimhan G, Gurkar AU. A molecular index for biological age identified from the metabolome and senescence-associated secretome in humans. Aging Cell. 2024 Mar 7:e14104. doi: 10.1111/acel.14104. Epub ahead of print. PMID: 38454639.

Ortega-Insaurralde I, Latorre-Estivalis JM, Costa-da-Silva AL, Cano A, Insausti TC, Morales HS, Pontes G, de Astrada MB, Ons S, DeGennaro M, Barrozo RB. The pharyngeal taste organ of a blood-feeding insect functions in food recognition. BMC Biol. 2024 Mar 13;22(1):63. doi: 10.1186/s12915-024-01861-w. PMID: 38481317; PMCID: PMC10938694.

Shaver M, Gomez K, Kaiser K, Hutcheson JD.Mechanical stretch leads to increased caveolin-1 content and mineralization potential in extracellular vesicles from vascular smooth muscle cells. BMC Mol Cell Biol. 2024 Mar 14;25(1):8. doi: 10.1186/s12860-024-00504-w. PMID: 38486163; PMCID: PMC10938675.

Cioffi MD, Husby ML, Gerstman BS, Stahelin RV, Chapagain PP. Role of phosphatidic acid lipids on plasma membrane association of the Ebola virus matrix protein VP40. Biochim Biophys Acta Mol Cell Biol Lipids. 2024 Apr;1869(3):159464. doi: 10.1016/j.bbalip.2024.159464. Epub 2024 Feb 14. PMID: 38360201.

Motsa BB, Sharma T, Chapagain PP, Stahelin RV. Minor changes in electrostatics robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. bioRxiv [Preprint]. 2024 Jan 31:2024.01.30.578092. doi: 10.1101/2024.01.30.578092. PMID: 38352396; PMCID: PMC10862912.

Fan RZ, Sportelli C, Lai Y, Salehe SS, Pinnell JR, Brown HJ, Richardson JR, Luo S, Tieu K.A partial Drp1 knockout improves autophagy flux independent of mitochondrial function. Mol Neurodegener. 2024 Mar 19;19(1):26. doi: 10.1186/s13024-024-00708-w. PMID: 38504290; PMCID: PMC10953112.

Tan K, Tse-Dinh YC.Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life. Cells. 2024 Mar 21;13(6):553. doi: 10.3390/cells13060553. PMID: 38534397; PMCID: PMC10969213.

Hejníková M, Nouzova M, Ramirez CE, Fernandez-Lima F, Noriega FG, Doležel D. (2022). Sexual dimorphism of diapause regulation in the hemipteran bug Pyrrhocoris apterus. Insect Biochem Mol Biol. 142:103721. doi: 10.1016/j.ibmb.2022.103721. Epub ahead of print. PMID: 35007710.

Barrios A, Estrada M, Moon JH. (2022). Carbamoylated Guanidine-Containing Polymers for Non-Covalent Functional Protein Delivery in Serum-Containing Media. Angew Chem Int Ed Engl. e202116722. doi: 10.1002/anie.202116722. Epub ahead of print. PMID: 34995405.

Leyva D, Tariq MU, Jaffé R, Saeed F, Lima FF. (2022). Unsupervised Structural Classification of Dissolved Organic Matter Based on Fragmentation Pathways. Environ Sci Technol. 56(2):1458-1468. doi: 10.1021/acs.est.1c04726. Epub 2022 Jan 4. PMID: 34981937.

Leung I, Veisaga ML, Espinal M, Zhang W, Barnum R, Barbieri MA. (2022). Anti-lipid droplets accumulation effect of Annona montana (mountain soursop) leaves extract on differentiation of preadipocytes. Biocell. 46(3):567-578. doi: 10.32604/biocell.2022.014009. Epub 2021 Nov 18. PMID: 34970018; PMCID: PMC8713457.

Tsegay PS, Hernandez D, Brache C, Chatgilialoglu C, Krokidis MG, Chapagain P, Liu Y. (2022). Incorporation of 5',8-cyclo-2'deoxyadenosines by DNA repair polymerases via base excision repair. DNA Repair (Amst). 109:103258. doi: 10.1016/j.dnarep.2021.103258. Epub 2021 Nov 24. PMID: 34871863.

Pandey P, Bhattarai N, Su L, Wang X, Leng F, Gerstman B, Chapagain PP, He J. (2022). Detecting Individual Proteins and Their Surface Charge Variations in Solution by the Potentiometric Nanoimpact Method. ACS Sens. doi: 10.1021/acssensors.1c02385. Epub ahead of print. PMID: 35060380.

Zhang C, Kim AJ, Rivera-Perez C, Noriega FG, Kim YJ. (2022). The insect somatostatin pathway gates vitellogenesis progression during reproductive maturation and the post-mating response. Nat Commun. 13(1):969. doi: 10.1038/s41467-022-28592-2. PMID: 35181671.

Cintron-Diaz YL, Gomez-Hernandez ME, Verhaert MMHA, Verhaert PDEM, Fernandez-Lima F. (2022). Spatially Resolved Neuropeptide Characterization from Neuropathological Formalin-Fixed, Paraffin-Embedded Tissue Sections by a Combination of Imaging MALDI FT-ICR Mass Spectrometry Histochemistry and Liquid Extraction Surface Analysis-Trapped Ion Mobility Spectrometry-Tandem Mass Spectrometry. J Am Soc Mass Spectrom.  doi: 10.1021/jasms.1c00376. Epub ahead of print. PMID: 35258288.

Garabedian A, Jeanne Dit Fouque K, Chapagain PP, Leng F, Fernandez-Lima F. (2022). AT-hook peptides bind the major and minor groove of AT-rich DNA duplexes. Nucleic Acids Res. gkac115. doi: 10.1093/nar/gkac115. Epub ahead of print. PMID: 35212375.

Eeza MNH, Bashirova N, Zuberi Z, Matysik J, Berry JP, Alia A. (2022). An integrated systems-level model of ochratoxin A toxicity in the zebrafish (Danio rerio) embryo based on NMR metabolic profiling. Sci Rep. 12(1):6341. doi: 10.1038/s41598-022-09726-4. PMID: 35428752.

Tose LV, Ramirez CE, Michalkova V, Nouzova M, Noriega FG, Fernandez-Lima F. (2022). Coupling Stable Isotope Labeling and Liquid Chromatography-Trapped Ion Mobility Spectrometry-Time-of-Flight-Tandem Mass Spectrometry for De Novo Mosquito Ovarian Lipid Studies. Anal Chem. doi: 10.1021/acs.analchem.1c05090. Epub ahead of print. PMID: 35420029.

Hossen ML, Baral P, Sharma T, Gerstman B, Chapagain P. (2022), Significance of the RBD mutations in the SARS-CoV-2 omicron: from spike opening to antibody escape and cell attachment. Phys Chem Chem Phys. doi: 10.1039/d2cp00169a. Epub ahead of print. PMID: 35395667.

Sweeney DT, Krueger S, Sen K, Hackett JC. (2022). Structures and Dynamics of Anionic Lipoprotein Nanodiscs. J Phys Chem B. doi: 10.1021/acs.jpcb.2c00758. Epub ahead of print. PMID: 35393859.

Seddek A, Madeira C, Annamalai T, Mederos C, Tiwari PB, Welch AZ, Tse-Dinh YC. (2022). A Yeast-Based Screening System for Differential Identification of Poisons and Suppressors of Human Topoisomerase I. Front Biosci (Landmark Ed). 27(3):93. doi: 10.31083/j.fbl2703093. PMID: 35345325.

Bourguignon N, Kamat V, Perez M, Mathee K, Lerner B, Bhansali S. (2022). New dynamic microreactor system to mimic biofilm formation and test anti-biofilm activity of nanoparticles. Appl Microbiol Biotechnol. 106(7):2729-2738. doi: 10.1007/s00253-022-11855-9. Epub 2022 Mar 24. PMID: 35325273.

Rue KL, Niu G, Li J, Raptis RG. (2022). Crystal Structure Determination and Hirshfeld Analysis of a New Alternariol Packing Polymorph. Crystals. 12(5):579. https://doi.org/10.3390/cryst12050579

Qiao G, Li X, Li J, Zhang M, Shen Y, Zhao Z, Zhang Y, Qi Z, Chen P, Sun Y, Cang P, Liu P, Wangkahart E, Wang Z.  (2022). An Eco-Friendly Conversion of Aquaculture Suspended Solid Wastes Into High-Quality Fish Food by Improving Poly-β-Hydroxybutyrate Production. Front Physiol. 13:797625. doi: 10.3389/fphys.2022.797625. PMID: 35721543; PMCID: PMC9205610.

Bakhshian Nik A, Ng HH, Garcia Russo M, Iacoviello F, Shearing PR, Bertazzo S, Hutcheson JD. (2022). The Time-Dependent Role of Bisphosphonates on Atherosclerotic Plaque Calcification. J Cardiovasc Dev Dis. 9(6):168. doi: 10.3390/jcdd9060168. PMID: 35735797; PMCID: PMC9225625.

Elkhaligy H, Balbin CA, Siltberg-Liberles J. (2022). Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions. Pathogens. 11(5):583. doi: 10.3390/pathogens11050583. PMID: 35631103; PMCID: PMC9147284.

Jeanne Dit Fouque K, Sipe SN, Garabedian A, Mejia G, Su L, Hossen Md L, Chapagain PP, Leng F, Brodbelt JS, and Fernandez-Lima F. (2022). Exploring the Conformational and Binding Dynamics of HMGA2·DNA Complexes Using Trapped Ion Mobility Spectrometry–Mass Spectrometry.
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Saha P, Bose D, Stebliankin V, Cickovski T, Seth RK, Porter DE, Brooks BW, Mathee K, Narasimhan G, Colwell R, Scott GI, Chatterjee S. (2022). Prior exposure to microcystin alters host gut resistome and is associated with dysregulated immune homeostasis in translatable mouse models. Sci Rep. 12(1):11516. doi: 10.1038/s41598-022-15708-3. PMID: 35799048; PMCID: PMC9262933.

Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. (2022). Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience. 2022 Aug 19;25(8):104685. doi: 10.1016/j.isci.2022.104685. Epub. PMID: 35789750; PMCID: PMC9242679.

Barrios A, Milan M, Perozo E, Hossen ML, Chapagain P, Moon JH. (2022). Effects of sidechain isomerism on polymer-based non-covalent protein delivery. Chem Commun (Camb). 58(59):8246-8249. doi: 10.1039/d2cc02343a. PMID: 35786710.

Ceyhan Y, Zhang M, Sandoval CG, Agoulnik AI, Agoulnik IU. (2022). Expression pattern and the roles of phosphatidylinositol phosphatases in testis. Biol Reprod. :ioac132. doi: 10.1093/biolre/ioac132. Epub ahead of print. PMID: 35766372.

Dargam V, Ng HH, Nasim S, Chaparro D, Irion CI, Seshadri SR, Barreto A, Danziger ZC, Shehadeh LA, Hutcheson JD. (2022). S2 Heart Sound Detects Aortic Valve Calcification Independent of Hemodynamic Changes in Mice. Front Cardiovasc Med. 9:809301. doi: 10.3389/fcvm.2022.809301. PMID: 35694672; PMCID: PMC9174427.

Sipe SN, Jeanne Dit Fouque K, Garabedian A, Leng F, Fernandez-Lima F, Brodbelt JS. (2022). Exploring the Conformations and Binding Location of HMGA2·DNA Complexes Using Ion Mobility Spectrometry and 193 nm Ultraviolet Photodissociation Mass Spectrometry. J Am Soc Mass Spectrom. 33(7):1092-1102. doi: 10.1021/jasms.2c00083. Epub 2022 Jun 10. PMID: 35687872; PMCID: PMC9274541.

Miller SA, Jeanne Dit Fouque K, Ridgeway ME, Park MA, Fernandez-Lima F. (2022). Trapped Ion Mobility Spectrometry, Ultraviolet Photodissociation, and Time-of-Flight Mass Spectrometry for Gas-Phase Peptide Isobars/Isomers/Conformers Discrimination. J Am Soc Mass Spectrom. 33(7):1267-1275. doi: 10.1021/jasms.2c00091. Epub 2022 Jun 5. PMID: 35658468; PMCID: PMC9262853.

Alam MS, Azam S, Pham K, Leyva D, Fouque KJD, Fernandez-Lima F, Miksovska J. (2022). Nanomolar affinity of EF-hands in neuronal calcium sensor 1 for bivalent cations Pb2+, Mn2+, and Hg2. Metallomics. 14(7):mfac039. doi: 10.1093/mtomcs/mfac039. PMID: 35657675.

Nunez-Castilla J, Stebliankin V, Baral P, Balbin CA, Sobhan M, Cickovski T, Mondal AM, Narasimhan G, Chapagain P, Mathee K, Siltberg-Liberles J. (2022). Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins. Viruses. 14(7):1415. doi: 10.3390/v14071415. PMID: 35891400.

Pokhrel R, Shakya R, Baral P, Chapagain P. (2022). Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus. J Chem Inf Model. doi: 10.1021/acs.jcim.2c00437. Epub ahead of print. PMID: 35981320.

Diaz B, Mederos C, Tan K, Tse-Dinh YC. (2022). Microbial Type IA Topoisomerase C-Terminal Domain Sequence Motifs, Distribution and Combination. Int J Mol Sci. 23(15):8709. doi: 10.3390/ijms23158709. PMID: 35955842; PMCID: PMC9369019.

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 Ambreetha S, Marimuthu P, Mathee K, Balachandar D. (2022). Plant-associated Pseudomonas aeruginosa strains harbour multiple virulence traits critical for human infection. J Med Microbiol. 71(8). doi: 10.1099/jmm.0.001493. PMID: 35947528.

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Garcia PK, Martinez Borrero R, Annamalai T, Diaz E, Balarezo S, Tiwari PB, Tse-Dinh YC. Localization of Mycobacterium tuberculosis topoisomerase I C-terminal sequence motif required for inhibition by endogenous toxin MazF4. (2022) Front Microbiol;13:1032320. doi: 10.3389/fmicb.2022.1032320. PMID: 36545199; PMCID: PMC9760754.

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Leyria J, Benrabaa S, Nouzova M, Noriega FG, Tose LV, Fernandez-Lima F, Orchard I, Lange AB. Crosstalk between Nutrition, Insulin, Juvenile Hormone, and Ecdysteroid Signaling in the Classical Insect Model, Rhodnius prolixus. (2022) Int J Mol Sci;24(1):7. doi: 10.3390/ijms24010007. PMID: 36613451; PMCID: PMC9819625.

Thapa B, Adhikari NP, Tiwari PB, Chapagain PP. A 5'-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA. (2022) J Chem Inf Model. doi: 10.1021/acs.jcim.2c01294. Epub ahead of print. PMID: 36563044.

Laverde EE, Polyzos AA, Tsegay PP, Shaver M, Hutcheson JD, Balakrishnan L, McMurray CT, Liu Y. Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair. (2022) Genes (Basel);14(1):98. doi: 10.3390/genes14010098. PMID: 36672839; PMCID: PMC9859040.

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Sazal M, Stebliankin V, Mathee K, Yoo C, Narasimhan G. (2021). Causal effects in microbiomes using interventional calculus. Sci Rep. 11(1):5724. doi: 10.1038/s41598-021-84905-3. PMID: 33707536; PMCID: PMC7970971.

Huang SN, Michaels SA, Mitchell BB, Majdalani N, Vanden Broeck A, Canela A, Tse-Dinh YC, Lamour V, Pommier Y. (2021). Exonuclease VII repairs quinolone-induced damage by resolving DNA gyrase cleavage complexes. Sci Adv. 7(10):eabe0384. doi: 10.1126/sciadv.abe0384. PMID: 33658195; PMCID: PMC7929499.

Guo J, Yan X, Xu M, Ghimire G, Pan X, He J. (2021). Effective Electrochemical Modulation of SERS Intensity Assisted by Core-Shell Nanoparticles. Anal Chem. 93(10):4441-4448. doi: 10.1021/acs.analchem.0c04398. Epub 2021 Mar 2. PMID: 33651586.

Duan W, Tang S, Gao L, Dotts K, Fink A, Kalvala A, Aguila B, Wang QE, Villalona-Calero MA. (2021). MiRNA-200C expression in Fanconi anemia pathway functionally deficient lung cancers. Sci Rep. 11(1):4420. doi: 10.1038/s41598-021-83884-9. PMID: 33627769; PMCID: PMC7904768.

Olanrewaju CA, Ramirez CE, Fernandez-Lima F. (2021). Comprehensive Screening of Polycyclic Aromatic Hydrocarbons and Similar Compounds Using GC-APLI-TIMS-TOFMS/GC-EI-MS. Anal Chem. 93(15):6080-6087. doi: 10.1021/acs.analchem.0c04525. Epub 2021 Apr 9. PMID: 33835784.

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Inglis TJJ, Mathee K. (2021). JMM Profile: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Med Microbiol. 70(3). doi: 10.1099/jmm.0.001336. Epub 2021 Mar 23. PMID: 33759741.

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Tose LV, Weisbrod CR, Michalkova V,  Nouzova M, Noriega FG, Fernandez-Lima F. (2021). Following de novo triglyceride dynamics in ovaries of Aedes aegypti during the previtellogenic stage. Sci Rep. 11(1):9636. doi: 10.1038/s41598-021-89025-6. PMID: 33953286; PMCID: PMC8099868.

Qu F, Tsegay PS, Liu Y. (2021). N6-Methyladenosine, DNA Repair, and Genome Stability. Front Mol Biosci. 8:645823. doi: 10.3389/fmolb.645823. PMID: 33898522; PMCID: PMC8062805.

Burke SL, Cobb J, Agarwal R, Maddux M, Cooke MS. (2021). How Robust is the Evidence for a Role of Oxidative Stress in Autism Spectrum Disorders and Intellectual Disabilities? J Autism Dev Disord. 51(5):1428-1445. doi: 10.1007/s10803-020-04611-3. PMID: 32929662; PMCID: PMC8084796.

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Kong N, Guo J, Chang S, Pan J, Wang J, Zhou J, Liu J, Zhou H, Pfeffer FM, Liu J, Barrow CJ, He J, Yang W. (2021). Direct Observation of Amide Bond Formation in a Plasmonic Nanocavity Triggered by Single Nanoparticle Collisions. J Am Chem Soc. doi: 10.1021/jacs.1c02426. Epub ahead of print. PMID: 34164979.

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Mathee K, Logan HF, Fry NK. (2021). Journal of Medical Microbiology: global footprint and appointment of a regional Editorial Board. J Med Microbiol. 70(6). doi: 10.1099/jmm.0.001391. PMID: 34128782.

Huang M, Zhou Q, Liang F, Yu L, Xiao B, Li Y, Zhang M, Chen Y, He J, Xiao S, Chang S. (2021). Detecting Individual Bond Switching within Amides in a Tunneling Junction. Nano Lett. 21(12):5409-5414. doi: 10.1021/acs.nanolett.1c01882. Epub 2021 Jun 14. PMID: 34124909.

Jeanne Dit Fouque K, Hegemann JD, Santos-Fernandez M, Le TT, Gomez-Hernandez M, van der Donk WA, Fernandez-Lima F. (2021). Exploring structural signatures of the lanthipeptide prochlorosin 2.8 using tandem mass spectrometry and trapped ion mobility-mass spectrometry. Anal Bioanal Chem. doi: 10.1007/s00216-021-03437-x. Epub ahead of print. PMID: 34105020.

Büttner P, Feistner L, Lurz P, Thiele H, Hutcheson JD, Schlotter F. (2021). Dissecting Calcific Aortic Valve Disease-The Role, Etiology, and Drivers of Valvular Fibrosis. Front Cardiovasc Med. 8:660797. doi: 10.3389/fcvm.2021.660797. PMID: 34041283; PMCID: PMC8143377.

Amiar S, Husby ML, Wijesinghe KJ, Angel S, Bhattarai N, Gerstman BS, Chapagain PP, Li S, Stahelin RV. (2021). Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. J Biol Chem. 296:100796. doi: 10.1016/j.jbc.2021.100796. Epub ahead of print. PMID: 34019871; PMCID: PMC8191294.

Niu G, Cui Y, Wang X, Keleta Y, Li J. (2021). Studies of the Parasite-Midgut Interaction Reveal Plasmodium Proteins Important for Malaria Transmission to Mosquitoes. Front Cell Infect Microbiol. 11:654216. doi: 10.3389/fcimb.2021.654216. PMID: 34262880; PMCID: PMC8274421.

Koirala RP, Pokhrel R, Baral P, Tiwari PB, Chapagain PP, Adhikari NP. (2021). Structural insights into the repair mechanism of AGT for methyl-induced DNA damage. Biol Chem. doi: 10.1515/hsz-2021-0198. Epub ahead of print. PMID: 34192828.

Bhattarai N, Baral P, Gerstman BS, Chapagain PP. (2021). Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B.1.1.7 and B.1.351. J Phys Chem B. acs.jpcb.1c01626. doi: 10.1021/acs.jpcb.1c01626. Epub ahead of print. PMID: 34110159; PMCID: PMC8204914.

Freitas JT, Lopez J, Llorian C, Boroni M, Kos L. (2021). The immunosuppressive role of Edn3 over-expression in the melanoma microenvironment. Pigment Cell Melanoma Res. doi: 10.1111/pcmr.13002. Epub ahead of print. PMID: 34288510.

Mathivathanan L, Sanakis Y, Raptis RG, Turek P, Boudalis AK. (2021). Observation and deconvolution of a unique EPR signal from two cocrystallized spin triangles. Phys Chem Chem Phys. 23(26):14415-14421. doi: 10.1039/d1cp01965a. PMID: 34180472.

Jeanne Dit Fouque K, Kaplan D, Voinov VG, Holck FHV, Jensen ON, Fernandez-Lima F. (2021). Proteoform Differentiation using Tandem Trapped Ion Mobility, Electron Capture Dissociation, and ToF Mass Spectrometry. Anal Chem. 93(27):9575-9582. doi: 10.1021/acs.analchem.1c01735. Epub 2021 Jun 25. PMID: 34170114.

Rubfiaro AS, Tsegay PS, Lai Y, Cabello E, Shaver M, Hutcheson J, Liu Y, He J. (2021). Scanning Ion Conductance Microscopy Study Reveals the Disruption of the Integrity of the Human Cell Membrane Structure by Oxidative DNA Damage. ACS Appl Bio Mater. 4(2):1632-1639. doi: 10.1021/acsabm.0c01461. Epub 2021 Jan 13. PMID: 34430802; PMCID: PMC8382241.

Hutcheson JD, Schlotter F, Creager MD, Li X, Pham T, Vyas P, Higashi H, Body SC, Aikawa M, Singh SA, Kos L, Aikawa E. (2021). Elastogenesis Correlates With Pigment Production in Murine Aortic Valve Leaflets. Front Cardiovasc Med. 8:678401. doi: 10.3389/fcvm.2021.678401. PMID: 34239903; PMCID: PMC8257952.

Baral P, Bhattarai N, Hossen ML, Stebliankin V, Gerstman BS, Narasimhan G, Chapagain PP. (2021). Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B.1.617.2 and implications for immune evasion. Biochem Biophys Res Commun. ;574:14-19. doi: 10.1016/j.bbrc.2021.08.036. Epub ahead of print. PMID: 34425281; PMCID: PMC8364676.

Bhattarai N, Pavadai E, Pokhrel R, Baral P, Hossen ML, Stahelin RV, Chapagain PP, Gerstman BS. (2021). Ebola Virus Protein VP40 Binding to Sec24c for Transport to the Plasma Membrane. Proteins. doi: 10.1002/prot.26221. Epub ahead of print. PMID: 34431571.

Johnson KA, Bhattarai N, Budicini MR, LaBonia CM, Baker SCB, Gerstman BS, Chapagain PP, Stahelin RV. Cysteine Mutations in the Ebolavirus Matrix Protein VP40 Promote Phosphatidylserine Binding by Increasing the Flexibility of a Lipid-Binding Loop. Viruses. 2021 Jul 15;13(7):1375. doi: 10.3390/v13071375. PMID: 34372582; PMCID: PMC8310056.

Tose LV, Weisbrod CR, Michalkova V, Nouzova M, Noriega FG, Fernandez-Lima F. (2021). Author Correction: Following de novo triglyceride dynamics in ovaries of Aedes aegypti during the previtellogenic stage. Sci Rep. 11(1):16319. doi: 10.1038/s41598-021-95696-y. Erratum for: Sci Rep. 2021 May 5;11(1):9636. PMID: 34354221; PMCID: PMC8342491.

Haseeb, M., Saeed, F. (2021). High performance computing framework for tera-scale database search of mass spectrometry data. Nat Comput Sci 1, 550–561. https://doi.org/10.1038/s43588-021-00113-z

Lucas-Barbosa D, DeGennaro M, Mathis A, Verhulst NO. (2021). Skin bacterial volatiles: propelling the future of vector control. Trends Parasitol. S1471-4922(21)00208-7. doi: 10.1016/j.pt.2021.08.010. Epub ahead of print. PMID: 34548253.

Conway NB, Tempest HG, Fortun J. (2021). Remote Learning and Its Impact on Newly Matriculated Medical Students. Cureus. 13(8):e17223. doi: 10.7759/cureus.17223. PMID: 34540450; PMCID: PMC8442805.

Amente S, Scala G, Majello B, Azmoun S, Tempest HG, Premi S, Cooke MS. (2021). Genome-wide mapping of genomic DNA damage: methods and implications. Cell Mol Life Sci. doi: 10.1007/s00018-021-03923-6. Epub ahead of print. PMID: 34463773.

Nouzova M, Edwards MJ, Michalkova V, Ramirez CE, Ruiz M, Areiza M, DeGennaro M, Fernandez-Lima F, Feyereisen R, Jindra M, Noriega FG. (2021). Epoxidation of juvenile hormone was a key innovation improving insect reproductive fitness. Proc Natl Acad Sci U S A. 118(45):e2109381118. doi: 10.1073/pnas.2109381118. PMID: 34697248.

Ambreetha S, Marimuthu P, Mathee K, Balachandar D. (2021). Rhizospheric and endophytic Pseudomonas aeruginosa in edible vegetable plants share molecular and metabolic traits with clinical isolates. J Appl Microbiol. doi: 10.1111/jam.15317. Epub ahead of print. PMID: 34608722.

Anifandis G, Taylor TH, Messini CI, Chatzimeletiou K, Daponte A, Ioannou D, Tempest HG. (2021). The Impact of SARS-CoV-2 on Sperm Cryostorage, Theoretical or Real Risk? Medicina (Kaunas). 57(9):946. doi: 10.3390/medicina57090946. PMID: 34577870; PMCID: PMC8467274.

Rocha K, Magallon J, Reeves C, Phan K, Vu P, Oakley-Havens CL, Kwan S, Ramirez MS, LaVoi T, Donow H, Chapagain P, Santos R, Pinilla C, Giulianotti MA, Tolmasky ME. (2021). Inhibition of Aminoglycoside 6'-N-acetyltransferase Type Ib (AAC(6')-Ib): Structure-Activity Relationship of Substituted Pyrrolidine Pentamine Derivatives as Inhibitors. Biomedicines. 9(9):1218. doi: 10.3390/biomedicines9091218. PMID: 34572404; PMCID: PMC8471502.

Annunziato M, Eeza MNH, Bashirova N, Lawson A, Matysik J, Benetti D, Grosell M, Stieglitz JD, Alia A, Berry JP. (2021). An integrated systems-level model of the toxicity of brevetoxin based on high-resolution magic-angle spinning nuclear magnetic resonance (HRMAS NMR) metabolic profiling of zebrafish embryos. Sci Total Environ. 803:149858. doi: 10.1016/j.scitotenv.2021.149858. Epub ahead of print. PMID: 34482148.

Pham KN, Fernandez-Lima F. (2021). Structural Characterization of Human Histone H4.1 by Tandem Nonlinear and Linear Ion Mobility Spectrometry Complemented with Molecular Dynamics Simulations. ACS Omega. 6(44):29567-29576. doi: 10.1021/acsomega.1c03744. PMID: 34778628; PMCID: PMC8582071.

Al Mamun A, Tanvir RB, Sobhan M, Mathee K, Narasimhan G, Holt GE, Mondal AM. (2021). Multi-Run Concrete Autoencoder to Identify Prognostic lncRNAs for 12 Cancers. Int J Mol Sci. 22(21):11919. doi: 10.3390/ijms222111919. PMID: 34769351; PMCID: PMC8584911.

Jeanne Dit Fouque K, Wellmann M, Leyva Bombuse D, Santos-Fernandez M, Cintron-Diaz YL, Gomez-Hernandez ME, Kaplan D, Voinov VG, Fernandez-Lima F. (2021). Effective discrimination of gas-phase peptide conformers using TIMS-ECD-ToF MS/MS. Anal Methods. 13(43):5216-5223. doi: 10.1039/d1ay01461g. PMID: 34698320; PMCID: PMC8596503.

Elkhaligy H, Balbin CA, Gonzalez JL, Liberatore T, Siltberg-Liberles J. (2021). Dynamic, but Not Necessarily Disordered, Human-Virus Interactions Mediated through SLiMs in Viral Proteins. Viruses. 13(12):2369. doi: 10.3390/v13122369. PMID: 34960638; PMCID: PMC8703344.

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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.

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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.

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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.

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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.

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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. 

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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.

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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]

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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.

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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.

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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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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.

Mittal R, Parrish JM, Soni M, Mittal J, Mathee K. (2018). Microbial otitis media: recent advancements in treatment, current challenges and opportunities. J Med Microbiol. 67(10):1417-1425. doi: 10.1099/jmm.0.000810. Epub 2018 Aug 7. Review. PubMed PMID: 30084766.

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.