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Faculty Publications, Fall 2021

BCMB Faculty published more than 80 papers in the academic year 2020-2021.

  1.       Acharya A, Agarwal R, Baker M , Baudry J, Bhowmik D, Boehm S, Byler KG, Chen SY, Coates L, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller DW, Kovalevsky A, Larkin J, Lawrence TJ, LeGrand S, Liu S-H, Mitchell JC, Park G, Parks JM, Pavola A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedove A, Shen S, Smith JC, Smith MD, Soto C, Tsaris A, Thavappiragasm M, Tillack AF, Vermaas JV, Vuong VQ, Yin J, Yoo S, Zahran M , Zanetti-Polzi L. (2020) Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. Journal of Chemical Information and Modeling, 60(12): 5832-5852.
  2.   Adams EE, He Q, McKee BD. How noncrossover homologs are conjoined and segregated in Drosophila male meiosis I: Stable but reversible homolog linkers require a novel Separase target protein. PLoS Genet. 2020 Oct 1;16(10):e1008997. doi: 10.1371/journal.pgen.1008997. PMID: 33002007; PMCID: PMC7529219.
  3.       Agarwal R, Bensing BA, Mi D, Baudry J, Iverson TM, Smith JC. (2020) Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Has. Biochemical Journal, 477(19): 3695-3707.
  4.   Ajina R, Malchiodi ZX, Fitzgerald AA, Zuo A, Wang S, Moussa M, Cooper CJ, Shen Y, Johnson QR, Parks JM, Smith JC, Catalfamo M, Fertig EJ, Jablonski SA, Weiner LM. (2021) Anti-tumor T- Cell immunity contributes to pancreatic cancer immune resistance . Cancer Immunology Research, 9(4): 386-400. 10.1158/2326-6066.CIR-20-0272. Al Temimi, AHK A, Tran, V, Teeuwen, RS, Altunc, AJ, Amatdjais-Groenen, HIV, White, PB, . . . , Guo, H and Mecinović, J (2020). Examining sterically demanding lysine analogs for histone lysine methyltransferase catalysis. Scientific Reports, 10(1). doi:10.1038/s41598-020-60337-3
  5.       Aranha MP, Jewel YSM, Beckman RA, Weiner LM, Mitchell JC, J. M. Parks, Smith JC. (2020) Combining three-dimensional modeling with artificial intelligence to increase specificity and precision in peptide:MHC binding predictions. Journal of Immunology 205(7): 1962-1977.
  6.   Aranha MP, Penfound TA, Salehi S, Botteaux A, Smeesters P, Dale JB, Smith JC. Design of Broadly Cross-Reactive M Protein-Based Group A Streptococcal Vaccines. J Immunol. 2021 Aug 15;207(4):1138-1149. doi: 10.4049/jimmunol.2100286. Epub 2021 Aug 2. PMID: 34341168.
  7.   Ashkar R, Doktorova M, Heberle FA, Scott HL, Barrera FN, Katsaras J, Khelashvili G, Brown MF. Reply to Nagle et al.: The universal stiffening effects of cholesterol on lipid membranes. Proc Natl Acad Sci U S A. 2021 May 18;118(20):e2102845118. doi: 10.1073/pnas.2102845118. PMID: 33952694; PMCID: PMC8157964.
  8.   Azim MF, Burch-Smith TM. Organelles-nucleus-plasmodesmata signaling (ONPS) an update on its roles in plant physiology, metabolism and stress responses. Curr Opin Plant Biol. 2020 Dec;58:48-59. doi: 10.1016/j.pbi.2020.09.005. Epub 2020 Nov 13. PMID: 33197746.
  9.   Bidon B, Kabbara S, Courdavault V, Glevarec G, Oudin A, Hericourt F, Carpin S, Spichal L, Binder BM, Cock JM, Papon, N. (2020) Cytokinin and ethylene cell signalling pathways from prokaryotes to eukaryotes. Cells. 9: 2526.
  10.   Brady, N.G., Workman, C., Cawthon, B.J., Bruce, B.D., and Long, B. (2021) Protein Extraction Efficiency and Selectivity of Esterified Styrene–Maleic Acid Copolymers in Thylakoid Membranes. ACS Biomacromolecules, 22:6, 2544-2253. https://doi.org/10.1021/acs.biomac.1c00274
  11. Chakraborty S, Doktorova M, Molugu TR, Heberle FA, Scott HL, Dzikovski B, Nagao M, Stingaciu LR, Standaert RF, Barrera FN, Katsaras J, Khelashvili G, Brown MF, Ashkar R. How cholesterol stiffens unsaturated lipid membranes. Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):21896-21905. doi 10.1073/pnas.2004807117. Epub 2020 Aug 25. PMID: 32843347; PMCID: PMC7486787.
  12.   Das P, Shen T, McCord RP. Inferring chromosome radial organization from Hi-C data. BMC Bioinformatics. 2020 Nov 10;21(1):511. doi: 10.1186/s12859-020-03841-7. PMID: 33167851; PMCID: PMC7654587.
  13.   Davis, M.M., Lamichhane, R., and Bruce, B.D. (2021) Single-Molecule Approaches on the Structure and Dynamics of Protein Translocons. Trends in Cell Biology. 31:7, 569-583. doi.org/10.1016/j.tcb.2021.03.009
  14.   Deng H, Ma Y, Ren WS, Vuong VQ, Qian P, Guo H (2021) Structure and dynamics of the reactive state for the histidine methylation process and catalytic mechanism of SETD3: insights from quantum mechanics/molecular mechanics investigation. ACS Catalysis 10(22):13314-13322. doi:10.1021/acscatal.0c03390
  15.   Deng, Y.S., Hammond, J., Pauszek, R., Ozog, S., Chai, I. 2 , Rabuck-Gibbons, J., Lamichhane, R., Henderson, S.C., Millar, D.P., Torbett, B.E., and Williamson, J.R. Discrimination between functional and non-functional cellular Gag complexes involved in HIV-1 assembly. J Mol Biol, 2021, 433 (8), 166842 (1-21): DOI: 10.1016/j.jmb.2021.166842
  16.   Devarajan D, Liang L, Gu B, Brooks SC, Parks JM, Smith JC. (2020) Molecular dynamics simulation of the structures, dynamics, and aggregation of dissolved organic matter. Environmental Science and Technology. 54(21): 13527-13537.
  17.   Doppler, D., Rabbani, M.T, Villarreal, J.C., Kim, D.H., Gandhi, S., Egatz-Gomez, A., Chen, J., Oberthür, D., Schön, S., Youssef, M.H., Bajt, S., Shelby, M.L., Coleman, M.A., Wiedorn, M.O., Juraj Knoska, J., Mazalova, V., Gevorkov, Y., Sato, T., Hunter, M.S., Hosseinizadeh, A., Kupitz, C., Letrun, R., Campanile, G.T., Zhang, S., Zook, J.D., Nazari, R., Ayyer, K., Holl, M.R., Fromme, R., Moore, A.L., Moore, T.A., Dobson, Z., Roy-Chowdhury, S., Ketawala, G.K., Stander, N.E., Kuoa, F., Olson, T., Morin,K., Mondal, J., Nyugen, J., Meza-Aguilar, J.D., Bruce, B.D., Garcia, J.K.M., Yefanov, O.N., Mariani, V., Schwander, P., Schmidt, M., Mancuso, A.P., Messerschmidt, M., Zatsepin, N., Weierstall, U.. Grant, U.T., Barty, A., Chapman, H., Frank, M., Spence, J.C.W., Botha, S., Fromme, P., Kirian, R., Ros, A. (2021) Co-flow Injection for Serial Crystallography at X-Ray Free Electron Lasers. Journal of Applied Crystallography (in press)
  18.   Easton, A., Gao, S., Lawton, S.P., Bennuru, S., Khan, A., Dahlstrom, E., Oliveira, R.G., Kepha, S., Porcella, S.F., Webster, J., Anderson R.M., Grigg M.E., Davis R.E., Wang J., Nutman T.B. (2020). Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans. eLife 9. https://doi.org/10.7554/eLife.61562.
  19.   Fan H, Wei G, Chen X, Guo H, Crandall-Stotler B, Köllner TG, Chen F (2021) Sesquiterpene biosynthesis in a leafy liverwort Radula lindenbergiana Gottsche ex C. Hartm. Phytochemistry 190 01 Oct 2021. Doi:10.1016/j.phytochem.2021.112847.
  20.   Foutch D, Pham B, Shen T. Protein conformational switch discerned via network centrality properties. Comput Struct Biotechnol J. 2021 Jun 5;19:3599-3608. doi: 10.1016/j.csbj.2021.06.004. PMID: 34257839; PMCID: PMC8246261.
  21.   Francis O, Joshi A, Prince T, Krishnaswamy G, Patel NC. Subcutaneous Immunoglobulin Therapy with IgPro20 in Patients with Stiff Person Syndrome and Primary Immunodeficiency Disease. J Neuromuscul Dis. 2021 May 18. doi: 10.3233/JND-200616. Epub ahead of print. PMID: 34024772.
  22.   Ganusova, E.E. Vo, T.L., Mukherjee, T. and G. Alexandre. 2021. Multiple CheY proteins control surface-associated lifestyles of Azospirillum brasilense. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2021.664826
  23.   Ganusova, E.E., Vo, T. L., Paul E. Abraham, Lindsey O’Neal Yoder, Robert L. Hettich, and G. Alexandre. 2021.The Azospirillum brasilense core chemotaxis proteins CheA1 and CheA4 link chemotaxis signaling with nitrogen metabolism. mSystems 6:e01354 20. https://doi.org/10.1128/mSystems.01354-20.
  24.   Gerhard, A.P., Krucken, J., Heitlinger, E., Janssen, I.J.I., Basiaga, M., Kornas, S., Beier, C., Nielsen, M.K., Davis, R.E., Wang, J., and von Samson-Himmelstjerna, G. (2020). The P-glycoprotein repertoire of the equine parasitic nematode Parascaris univalens. Scientific Reports 10, 13586. https://doi.org/10.1038/s41598-020-70529-6.
  25.   Gerhardt, E., Parize, E., Gravina, F., Pontes, F., Santos, A., Araújo, G., Goedert, A., Urbanski, A., Steffens, M., Chubatsu, L., Pedrosa, F., Souza, E., Forchhammer, K., Ganusova, E., Alexandre, G., Souza, G. and Huergo, L. 2020. The protein-protein interaction network reveals a novel role of the signal transduction protein PII in the control of c-di-GMP homeostasis in Azospirillum brasilense 5 (6) e00817-20; DOI: 10.1128/mSystems.00817-20
  26.   Grieb ZA, Ford EG, Yagan M, Lau BYB, Manfredsson FP, Krishnan K, Lonstein JS. Oxytocin receptors in the midbrain dorsal raphe are essential for postpartum maternal social and affective behaviors. Psychoneuroendocrinology. 2021 Jun 18;131:105332. doi: 10.1016/j.psyneuen.2021.105332. Epub ahead of print. PMID: 34182251.
  27.   Gupta M, Ha K, Quarles LD, Smith JC. (2020) Molecular dynamics analysis of the binding of human Interleukin-6 with Interleukin-6 alpha-Receptor. (2021) PROTEINS: Structure, Function and Bioinformatics. 89(2): 163-173.
  28.   Gupta M, Rawal B, Dupree P, Smith JC, Petridis L. (2021) Spontaneous rearrangement of acetylated xylan on hydrophilic cellulose surfaces. Cellulose, 28: 3327-3345.
  29.   Hernandez-Esquivel, A.A., Castro-Mercado, E., Valencia-Cantero, E., Alexandre, G. and E. Garcia-Pineda (2020). Application of Azospirillum brasilense Lipopolysaccharides to Promote Early Wheat Plant Growth and Analysis of Related Biochemical Responses. Frontiers In Sustainable Food Systems. https://doi.org/10.3389/fsufs.2020.579976
  30.   Hsu SJ, Stow EC, Simmons JR, Wallace HA, Lopez AM, Stroud S, Labrador M. Mutations in the insulator protein Suppressor of Hairy wing induce genome instability. Chromosoma. 2020 Dec;129(3-4):255-274. doi: 10.1007/s00412-020-00743-8. Epub 2020 Nov 2. PMID: 33140220.
  31.   Ishida T, Parks JM, Smith JC. (2020) Insight into the catalytic mechanism of GH11 Xylanase: Computational analysis of substrate distortion based on a neutron structure Journal of the American Chemical Society. 142(42): 17966-17980.
  32.   Joshi AS, Ragusa JV, Prinz WA, Cohen S. Multiple C2 domain-containing transmembrane proteins promote lipid droplet biogenesis and growth at specialized endoplasmic reticulum subdomains. Mol Biol Cell. 2021 Jun 1;32(12):1147-1157. doi: 10.1091/mbc.E20-09-0590. Epub 2021 Apr 7. PMID: 33826368.
  33.   Kapoor K, Pi M, Nishimoto SK, Quarles LD, Baudry J, Smith JC. (2020) The carboxylation status of osteocalcin has Important consequences for its structure and dynamics. BBA – General Subjects, 1865(3):129809. 10.1016/j.bbagen.2020.129809.
  34.   Korotych, O.I, Nguyen, T.T., Reagan, B.C., Burch-Smith, T.M., and Bruce, B.D. (2021) Poly(styrene-co-maleic acid)-mediated isolation of supramolecular membrane protein complexes from plant thylakoids. BBA Bioenergetics, 1862:3, 148347. https://doi.org/10.1016/j.bbabio.2020.148347
  35. Lee G, Park JH. Programmed cell death reshapes the central nervous system during metamorphosis in insects. Curr Opin Insect Sci. 2021 Feb;43:39-45. doi: 10.1016/j.cois.2020.09.015. Epub 2020 Oct 14. PMID: 33065339.
  36.   LeGrand S, Thavappiragasam M, Larkin J, Solis-Vasquez L, Hernandez O, Scheinberg A, Vermaas JV, Poole D, Koch A, Tillack F, Agarwal R, Santos-Martins D, Forli S, Smith JC, Sedova A. (2020) GPU-accelerated drug discovery with docking on the Summit Supercomputer: Porting, optimization, and application to COVID-19 Research. Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB 20), September 21–24, 2020, Virtual Event, USA. ACM, New York, NY, USA, 10 pages. 10.1145/3388440.3412472.
  37.   Li C-J, Liau ES, Lee Y-H, Haung Y-Z, Liu Z, Willems A, Garside V, McClinn E, Chen J-A, Hong T. (2021) MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback. Mol Syst Biol, 17:e9945
  38.   Li J, Hu X, Neusius T, Cheng X, Smith MD, Godec A, Hong L, Metzler R, Smith JC. (2021) Insufficient evidence for ageing in protein dynamics Nature Physics, 17: 773-774.
  39.   Lindsay RJ, Mansbach RA, Gnanakaran S, Shen T. Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation. Biophys Chem. 2021 Apr;271:106552. doi: 10.1016/j.bpc.2021.106552. Epub 2021 Jan 26. PMID: 33581430; PMCID: PMC8024028.
  40.   Liu Z, Shpak E, Hong T. (2020) A mathematical model for understanding synergy and tradeoff in gene expression patterns of the shoot apical meristem. Comput Struct Biotechnol J , 18:1878
  41.   Nebenführ A. Tracking organelle movements in plant cells. Methods Cell Biol. 2020;160:83-97. doi: 10.1016/bs.mcb.2020.03.003. Epub 2020 Apr 21. PMID: 32896334.
  42.   O’Banion, B., O’Neal, L., Alexandre, G., and Lebeis, S. (2020) Bridging the gap between single-strain and community-level plant-microbe chemical interactions. Mol. Plant-Microbe Interact. 33(2):124-134. doi: 10.1094/MPMI-04-19-0115-CR.
  43.   O’Neal, L., Vo, L. and G. Alexandre (2020) Specific root exudates compounds sensed by dedicated chemoreceptors shape A. brasilense chemotaxis in the rhizosphere. Appl. Environ. Microbiol. 86(15):e01026-20. doi: 10.1128/AEM.01026-20.
  44.   Onwubiko UN, Rich-Robinson J, Mustaf RA, Das ME. Cdc42 promotes Bgs1 recruitment for septum synthesis and glucanase localization for cell separation during cytokinesis in fission yeast. Small GTPases. 2021 Jul;12(4):257-264. doi: 10.1080/21541248.2020.1743926. Epub 2020 Mar 22. PMID: 32182184; PMCID: PMC8205068.
  45.   Panchy N, von Arnim AG, Hong T. (2020) Early detection of daylengths with a feedforward circuit coregulated by circadian and diurnal cycles. Biophys J , 119 (9), 1878-1895
  46.   Park Y-J, Kim S, Shim H-P, Park JH, Lee G, Kim T-Y, Jo M-C, Kwon A-Y, Lee M, Lee S, Yeo J, Chung H-L, Bellen HJ, Kwon S-H, Jeon S-H. 2021. Phosphatidylserine synthase (PSS) plays an essential role in glia and affects development as well as the maintenance of neuronal function. iScience 24, 102899. https://doi.org/10.1016/j.isci.2021.102899
  47.   Pauszek, R.F., Lamichhane, R., Rajkarnikar Singh, A., and Millar, D.P. Single-molecule view of co-ordination in a multi-functional DNA polymerase. eLife, 2021, 10: e62046: DOI: 10.7554/eLife.62046
  48.   Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, A. A. Golosov, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, Acharya A, Parks JM, Smith JC, Gumbart JC. (2020) Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Chemical Science, 12(4) 10.1039/DOSCO4942E.
  49.   Phan, M. Korotych, O. Brady, N.G., Davis, M., Akner, J. and Bruce, B.D. (2020) X-ray and neutron reflectivity studies of styrene-maleic acid copolymer interactions with galactolipid-containing monolayers. Langmuir 36:14, 3970-3980.
  50.   Pingali SV, Smith MD, Liu SH, Rawal TB, Pu Y, Shah R, Evans BR, Urban VS, Davison BH, Cai CM, Ragauskas AJ, O’Neill HM, Smith JC, Petridis L. Deconstruction of biomass enabled by local demixing of cosolvents at cellulose and lignin surfaces. Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):16776-16781. doi: 10.1073/pnas.1922883117. Epub 2020 Jul 7. PMID: 32636260; PMCID: PMC7382264.
  51.   Pino MR, Nuñez I, Chen C, Das ME, Wiley DJ, D’Urso G, Buchwald P, Vavylonis D, Verde F. Cdc42 GTPase Activating Proteins (GAPs) Regulate Generational Inheritance of Cell Polarity and Cell Shape in Fission Yeast. Mol Biol Cell. 2021 Jul 21:mbcE20100666. doi: 10.1091/mbc.E20-10-0666. Epub ahead of print. PMID: 34288736.
  52.   Rawal T, Smith MD, Ozcan A, Smith JC, Tetard L, Santra S, Petridis L. (2020) Role of capping agents in the synthesis of salicylate-capped zinc oxide nanoparticles. ACS Applied Nano Materials 3(10): 9951-9960.
  53.   Ren, WS, Jiang, KB, Deng, H, Lu, N, Yu, T, Guo, H, & Qian, P (2020). catalytic mechanism and product specificity of protein arginine methyltransferase PRMT7: a study from QM/MM molecular dynamics and free energy simulations.. J Chem Theory Comput. doi:10.1021/acs.jctc.0c00156
  54.   Rhee JE, Choi JH, Park JH, Lee G, Pak B, Kwon SH, Jeon SH. CG11426 gene product negatively regulates glial population size in the Drosophila eye imaginal disc. Dev Neurobiol. 2021 May 27. doi: 10.1002/dneu.22838. PMID: 34047015.
  55.   Saleheen A, Acharyya D, Prosser RA, Baker CA. (2021) A microfluidic bubble perfusion device for brain slice culture. Analytical Methods 13: 1364-1373. doi: 10.1039/d0ay02291h. Epub 2021 Mar 1. PMID: 33644791.
  56.   Sanders JT, Freeman TF, Xu Y, Golloshi R, Stallard MA, Hill AM, San Martin R, Balajee AS, McCord RP. (2020) Radiation-Induced DNA Damage and Repair Effects on 3D Genome Organization. Nature Communications. 11(1):6178.
  57.   Schaefer KG, Pittman AE, Barrera FN, King GM. Atomic force microscopy for quantitative understanding of peptide-induced lipid bilayer remodeling. Methods. 2020 Oct 24:S1046-2023(20)30229-2. doi: 10.1016/j.ymeth.2020.10.014. Epub ahead of print. PMID: 33164792.
  58.   Semchonok, D.A, Mondal, J, Cooper, C.S., Li, M., Schlum, K., Amin, M, Sorzano, C.O.S., Ramírez-Aportela, E., Kastritis, P., Boekema, E.J., Guskof, A., and Bruce, B.D. (2020) Structure of a Tetrameric Photosystem I from Chroococcidiopsis TS-821, A Thermophilic, Non-heterocyst Forming Cyanobacteria. Europe PMC. DOI: 10.21203/rs.3.rs-81702/v1
  59.   Shrestha UR, Smith JC, Petridis L. Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations. Commun Biol. 2021 Feb 23;4(1):243. doi: 10.1038/s42003-021-01759-1. PMID: 33623120; PMCID: PMC7902620.
  60.   Smith JC. Locking out water at 100°C. Biophys J. 2021 Jul 22:S0006-3495(21)00599-3. doi: 10.1016/j.bpj.2021.07.013. Epub ahead of print. PMID: 34358450.
  61.   Smith MD, Pingali SV, Elkins JG, Bolmatov D, Standaert RF, Nichels JD, Urban VS, Katsaras J, Davidson JB, Smith JC, Petridis L. (2020) Solvent-induced membrane stress in biofuel production: Molecular insights from small-angle scattering and all-atom molecular dynamics simulations. Green Chemistry 22: 8278-8288.
  62.   Smith MD, Smith JC. (2020) Repurposing therapeutics for COVID-19: Supercomputer-based docking to the SARS-CoV-2 viral spike protein and viral spike protein-human ACE2 interface ChemRX 10.26434/chemrxiv.11871402.v4.
  63.   Smith MD, Smith JC. Effects of sodium and calcium chloride ionic stresses on model yeast membranes revealed by molecular dynamics simulation. Chem Phys Lipids. 2020 Nov;233:104980. doi: 10.1016/j.chemphyslip.2020.104980. Epub 2020 Oct 8. PMID: 33038307.
  64.   Sorzano, C.O.S., Semchonok, D., Lin, S.-C., Lo, Y.-C., Vilase, J.L., Jimenez-Morenoa, A., Grageraa, M., Maluendaa, D., M. Martinez, M., Ramirez-Aportela, E., Melero, R., Cuervo, A., Conesa, J., Conesa, P., Losanaa,P., del Canoa, L., Jimenez de la Morenaa, L., Fonseca, Y.C., Sanchez-Garcia. R., Strelaka, D., Fernandez-Gimenez, E., de Isidro,F., Herreros, D., Kastritis ,P., Marabini, R., Bruce. B.D., and Carazo, J.M. (2021) Algorithmic robustness to preferred orientations in Single Particle Analysis by CryoEM. J. Structural Biol. 213:1, 107695. doi.org/10.1016/j.jsb.2020.107695
  65.   Spencer J, Penfound T, Salehi S, Aranha M, Agarwal R, Smith JC, Dale J, Wade L, Baudry J. (2021) Cross-reactive immunogenicity of group A streptococcal vaccines designed using a recurrent neural network to identify conserved M protein linear epitopes. Vaccine 39(12): 1773-1779.
  66.   Stefanski, K.M., Russell, C.M., Westerfield, J.M., Lamichhane, R.*, and Barrera, F.N*., PIP2 promotes conformation-specific dimerization of the EphA2 membrane region. J Biol Chem, 2021 296 (100149):1-12 (* Co-corresponding authors): DOI: 10.1074/jbc.RA120.016423
  67.   Stevenson PK, Casenhiser DM, Lau BYB, Krishnan K. Systematic analysis of goal-related movement sequences during maternal behaviour in a female mouse model for Rett syndrome. Eur J Neurosci. 2021 Jul;54(2):4528-4549. doi: 10.1111/ejn.15327. Epub 2021 Jun 22. PMID: 34043854.
  68.   Tan, J.H., Lautens, M., Romanelli-Cedrez, L., Wang, J., Schertzberg, M.R., Reinl, S.R., Davis, R.E., Shepherd, J.N., Fraser, A.G., and Salinas, G. (2020). Alternative splicing of coq-2 controls the levels of rhodoquinone in animals. eLife 9. https://doi.org/10.7554/eLife.56376.
  69.   Teodor, A.H., Ooi, E., Medina, J., Alarcon, M.l, Vaughn, M.D.,Bruce, B.D., and Bergkamp, J.J. (2021) Functional Characterization of Bipyridine Cobalt (II/III) Redox Mediator Complexes as Photosystem I Electron Donors for Biophotovoltaic Applications. RCS Advances, 11, 10434-10450.   DOI: 10.1039/D0RA10221K
  70.   Teodor, A.H., Sherman, B.D., Ison, Z.Y., Ooi, E., Bergkamp, J.J., and Bruce, B.D. (2020) Green Catalysts: Applied and Synthetic Photosynthesis. Catalysts, 10(9), 1016-1046. https://doi.org/10.3390/catal10091016
  71.   Teodor, A.H., Thal, L.B., Vijayakumar, S., Chan, M., Little, G., and Bruce, B.D. (2021) Encapsulation and Stabilization of Cyanobacterial Photosystem I into Aqueous Mesoporous Microspheres using Calcium Carbonate Templates Materials Today Bio.11: 100122 (https://doi.org/10.1016/j.mtbio.2021.100122)
  72.   Topham CM, Smith JC. (2021) Peptide nucleic acid hoogsteen strand linker design for major groove recognition of DNA thymine bases. Journal of Computer-Aided Molecular Design, 35: 355-369.
  73.   Vermaas JV, Sedova A, Baker MB, Boehm S, Rogers DM, Larkin J, Glaser J, Smith MD, Hernandez O, Smith JC. (2021) Supercomputing pipelines search for therapeutics against COVID-19 IEEE Computing in Science & Engineering, 23(1): 7-16.
  74.   Wang, J. (2021). Genome Analysis of Programmed DNA Elimination in Parasitic Nematodes. Methods Mol Biol 2369, 251-261. https://doi.org/10.1007/978-1-0716-1681-9_14.
  75.   Wang, J. (2021). Genomics of the Parasitic Nematode Ascaris and Its Relatives. Genes (Basel) 12. https://doi.org/10.3390/genes12040493.
  76.   Ward AE, Ye Y, Schuster JA, Wei S, Barrera FN. Single-molecule fluorescence vistas of how lipids regulate membrane proteins. Biochem Soc Trans. 2021 Aug 4:BST20201074. doi: 10.1042/BST20201074. Epub ahead of print. PMID: 34346484.
  77.   Westerfield JM, Sahoo AR, Alves DS, Grau B, Cameron A, Maxwell M, Schuster JA, Souza PCT, Mingarro I, Buck M, Barrera FN. Conformational Clamping by a Membrane Ligand Activates the EphA2 Receptor. J Mol Biol. 2021 Jul 3;433(18):167144. doi: 10.1016/j.jmb.2021.167144. Epub ahead of print. PMID: 34229012.
  78.   Xi, J., Yang, N., Perez-Aguilar, J.M., Selling, B., Grothusen, J., Lamichhane, R., Saven, J.G., and Liu, R. Novel Variants of Engineered Water Soluble mu Opioid Receptors with Extensive Mutations and Removal of Cysteines. Proteins, 2021 (Online): DOI: 10.1002/prot.26160
  79.   Xu Y, McCord RP. (2021) CoSTA: Unsupervised Convolutional Neural Network Learning for Spatial Transcriptomics Analysis. BMC Bioinformatics. Accepted.
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