Research
The HPRC supports the research computing needs for many sponsored research projects supported by the National Science Foundation and the National Institutes of Health, among others.
The following research publications were supported by the HPRC
2022
- P. Gandhi, M. A. Robert, J. Palacios, D. Chan. Effects of contact tracing and self-reporting in a network disease model. Lett. Biomath., 9(1), 23–39 (2022).
- Copeland WE, Shanahan L, McGinnis EW, Aberg KA, van den Oord EJCG. Early adversities accelerate epigenetic aging into adulthood: a 10-year, within-subject analysis. J Child Psychol Psychiatry. 2022 Feb 9. doi: 10.1111/jcpp.13575. Epub ahead of print. PMID: 35137412.
- Guintivano J, Aberg KA, Clark SL, Rubinow DR, Sullivan PF, Meltzer-Brody S, van den Oord EJCG. Transcriptome-wide association study for postpartum depression implicates altered B-cell activation and insulin resistance. Mol Psychiatry. 2022 Apr 1. doi: 10.1038/s41380-022-01525-7. Epub ahead of print. PMID: 35365803.
- van den Oord CLJD, Copeland WE, Zhao M, Xie LY, Aberg KA, van den Oord EJCG. DNA methylation signatures of childhood trauma predict psychiatric disorders and other adverse outcomes 17 years after exposure. Mol Psychiatry. 2022 May 11. doi: 10.1038/s41380-022-01597-5. Epub ahead of print. PMID: 35546634.
- van den Oord EJCG, Xie LY, Zhao M, Aberg KA, Clark SL. A single-nucleus transcriptomics study of alcohol use disorder in the nucleus accumbens. Addict Biol. 2023 Jan;28(1):e13250. doi: 10.1111/adb.13250. PMID: 36577731.
- Bono RS, Pan Z, Dahman B, Deng Y, Kimmel AD. Urban-rural disparities in geographic accessibility to care for people living with HIV. AIDS Care, In press.
- Pan ZP*, Dahman B, Bono RS, Sabik LM, Belgrave FZ, Yerkes L, Nixon DE, Kimmel AD. Physician reimbursement and retention in HIV care: racial disparities in the US South. JAIDS 2023;92:1-5.
- Kiernan JS, Kimmel AD. Disparities in access to primary care, a key site for HIV prevention services, among gay and bisexual men in the United States. Revise and resubmit, AIDS Care.
- Kiernan JS, Bono RS, Mujwara D, Pan Z, Dahman B, Kimmel AD. Limited receipt of annual routine preventive care services among Medicaid enrollees living with HIV in the US South. Under review.
- Kimmel AD, Pan Z, Brazier E, Murenzi G, Rasnick R, Muhoza B, Yotebieng M, Anastos K, Nash D. Development and calibration of a mathematical model to inform HIV decision making in Rwanda. 25th International Workshop on HIV and Hepatitis Observational Databases, March 23 – 25, 2023, Athens, Greece.
- Rashid NS, Boyd DC, Olex AL et al. Transcriptomic changes underlying EGFR inhibitor resistance in human and mouse models of basal-like breast cancer. Sci Rep 2022;12:21248.
- W. Li, D. Wang, K. U. Lao, and X. Wang. Buffer concentration dramatically affects the stability of S-nitrosothiol in aqueous solutions. Nitric Oxide 118, 59 (2022).
- F. Ballesteros and K. U. Lao. Accelerating the convergence of self-consistent field calculations using the many-body expansion. J. Chem. Theory Comput. 18, 179 (2022).
- M. D. Word, H. A. L. Pena, D. A. Boateng, S. L. McPherson, G. L. Gutsev, L. G. Gutsev, K. U. Lao, and K. M. Tibbetts. Ultrafast dynamics of nitro-nitrite rearrangement and dissociation in nitromethane cation. J. Phys. Chem. A 126, 879 (2022).
- H. A. L. Pena, J. M. Shusterman, D. A. Boateng, K. U. Lao, and K. M. Tibbetts. Coherent control of molecular dissociation by selective excitation of nuclear wave packets. Front. Chem. 10, 859095 (2022).
- C. Villot, F. Ballesteros, D. Wang, and K. U. Lao. Coupled cluster bench- marking of large noncovalent complexes in L7 and S12L as well as the C60 dimer, DNA−ellipticine, and HIV−indinavir. J. Phys. Chem. A 126, 4326 (2022). [Featured on cover]
- K. C. Ng, T. Adel, K. U. Lao, M. Varmecky, Z. Liu, M. Arrad, and H. C. Allen. Iron (III) chloro complexation at the air-aqueous FeCl3 interface via second harmonic generation spectroscopy. J. Phys. Chem. C 126, 15386 (2022).
- Ke, C., Bandyopadhyay, D. and Sarkar, D. (2022) "Gene Screening for Prognosis of Non-Muscle-Invasive Bladder Carcinoma under Competing Risks Endpoints". Cancers, 15(2), 379.
- Ke, C., Bandyopadhyay, D., Acunzo M. and Winn R. (2022) "Gene screening in high-throughput right-censored lung cancer data". Onco, 2(4), 305-318.
- Li, L., Wang, Q. and Ke, C. (2022) "Local Support Vector Machine Based Dimension Reduction". Statistical Analysis and Data Mining: The ASA Data Science Journal, 15(6), 722-735.
- Li, L., Ke, C., Yin, X. and Yu, Z. (2022) "Generalized martingale difference divergence: Detecting independence in regression and quantile regression with applications in variable screening". Computational Statistics & Data Analysis, 107618.
- Yuan, Q., Chen, X., Ke, C. and Yin, X. (2022) "Independence Index Sufficient Variable Screening for Categorical Responses". Computational Statistics & Data Analysis, 107530.
- Hale, Melissa A., et al. "Dynamics and variability of transcriptomic dysregulation in congenital myotonic dystrophy during pediatric development." Human Molecular Genetics (2022).
- R. Secondo, A. Ball, B. T. Diroll, D. Fomra, K. Ding, V. Avrutin, Ü. Özgür, H. Morkoç, D. O. Demchenko, J. B. Khurgin, and N. Kinsey, “Deterministic modeling of hybrid nonlinear effects in epsilon-near-zero thin films”, Appl. Phys. Lett. 120, 031103 (2022).
- M. A. Reshchikov, O. Andrieiev, M. Vorobiov, D. Ye, D. O. Demchenko, K. Sierakowski, M. Bockowski, B. McEwen, V. Meyers, and F. Shahedipour-Sandvik, “Thermal annealing of GaN implanted with Be” J Appl. Phys. 131, 125704 (2022).
- M. A. Reshchikov, D. O. Demchenko, D. Ye, O. Andrieiev, M. Vorobiov, K. Grabianska, M. Zajac, P. Nita, M. Iwinska, M. Bockowski, B. McEwen, and F. Shahedipour-Sandvik, “The effect of annealing on photoluminescence from defects in ammonothermal GaN” J Appl. Phys. 131, 035704 (2022).
- B. McEwen, M. Reshchikov, E. Rocco, V. Meyers, K. Hogan, O. Andrieiev, M.Vorobiov, D. Demchenk2, and F. Shahedipour-Sandvik, “MOCVD Growth and Characterization of Be-Doped GaN” ACS Applied Electronic Materials 4, 3780 (2022).
- M. A. Reshchikov, D. O. Demchenko, M. Vorobiov, O. Andrieiev, B. McEwen, F. Shahedipour-Sandvik, K. Sierakowski, P. Jaroszynski, and M. Bockowski, “Photoluminescence related to Ca in GaN” Phys. Rev. B 106, 035206 (2022).
- M. A. Reshchikov and D. O. Demchenko, “Roadmap for Point Defects in GaN”, in Semiconductors and Semimetals, Roadmap for Skutterudites and Point Defects in GaN, edited by Z. Mi and H. H. Tan. Volume 111, p. 133 (2022).
- M. A. Reshchikov, M. Vorobiov, O. Andrieiev, B. McEwen, E. Rocco, V. Meyers, D. O. Demchenko, F. Shahedipour-Sandvik, “Photoluminescence from Be-Doped GaN Grown by Metal-Organic Chemical Vapor Deposition” Physica Status Solidi B, 2200487 (2022).
- Barr, P. B., Driver, M. N., Kuo, S. I. C., Stephenson, M., Aliev, F., Linnér, R. K., ... & Dick, D. M. (2022). Clinical, environmental, and genetic risk factors for substance use disorders: characterizing combined effects across multiple cohorts. Molecular Psychiatry, 27(11), 4633-4641.
- Barr, P. B., Mallard, T. T., Sanchez-Roige, S., Poore, H. E., Linnér, R. K., Waldman, I. D., ... & Dick, D. M. (2022). Parsing genetically influenced risk pathways: genetic loci impact problematic alcohol use via externalizing and specific risk. Translational psychiatry, 12(1), 420.
- Bigdeli, T. B., Voloudakis, G., Barr, P. B., Gorman, B. R., Genovese, G., Peterson, R. E., ... & Gill, S. (2022). Penetrance and pleiotropy of polygenic risk scores for schizophrenia, bipolar disorder, and depression among adults in the US Veterans Affairs health care system. JAMA psychiatry, 79(11), 1092-1101.
- Aliev, F., Barr, P. B., Davies, A. G., Dick, D. M., & Bettinger, J. C. (2022). Genes regulating levels of ω‐3 long‐chain polyunsaturated fatty acids are associated with alcohol use disorder and consumption, and broader externalizing behavior in humans. Alcoholism: Clinical and Experimental Research, 46(9), 1657-1664.
- Karlsson Linnér, R., Mallard, T. T., Barr, P. B., Sanchez-Roige, S., Madole, J. W., Driver, M. N., ... & Dick, D. M. (2021). Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. Nature neuroscience, 24(10), 1367-1376.
- Ksinan, A. J., Smith, R. L., Barr, P. B., & Vazsonyi, A. T. (2022). The associations of polygenic scores for risky behaviors and parenting behaviors with adolescent externalizing problems. Behavior genetics, 52(1), 26-37.
- T. M. Chu, M. Ross, H. Bindra, {\bf L. B. Carasik}, \emph{``Large Eddy Simulations of Low Prandtl Channel Flow with One Heated Wall for Developing Data-Driven Stochastic Emulators.''} Trans. of the ANS (Vol. 127(1), pp. 1284-1287), Phoenix, AZ. (2022).
- Sierra Tutwiler, {\bf L. B. Carasik}, Dillon R. Shaver, \emph{ “Determination of Aspect Ratio Influence on Flow and Heat Transfer Behavior in Twisted Elliptical Tubes for Molten Salt Applications.”} \textbf{ATH 2022}. Anaheim, CA, June 2022.
- James Vulcanoff, Joshua L. Gateley, {\bf L. B. Carasik}, \emph{ “Nek5000 Simulations for Thermal Performance Modeling of Helically Rifled Heat Transfer Enhancements.”} \textbf{ATH 2022}. Anaheim, CA, June 2022.
- Saeedi S, Serrano M, Yang D, Brooks JP, Buck G, Arodz T, 2022. Group Testing Matrix Design for PCR Screening with Real-Valued Measurements. Journal of Computational Biology 29(12):1397-1411
- Saeedi S, Serrano M, Yang D, Brooks JP, Buck G, Arodz T, 2022. Real-valued Group Testing for Quantitative Molecular Assays. Conference on Research in Computational Molecular Biology RECOMB'22.
- Cano, Alberto, and Bartosz Krawczyk. "ROSE: Robust online self-adjusting ensemble for continual learning on imbalanced drifting data streams." Machine Learning 111.7 (2022): 2561-2599.
- Alberghini, Gavin, Sylvio Barbon Junior, and Alberto Cano. "Adaptive ensemble of self-adjusting nearest neighbor subspaces for multi-label drifting data streams." Neurocomputing 481 (2022): 228-248.
- Forrest Baber, Jae-Woo Kim, Godfrey Sauti, Russell A Wincheski, Benjamin D Jensen, Kristopher E Wise, Emilie J Siochi, Ibrahim Guven, 2022, "Microstructural exploration of a carbon nanotube yarn reinforced composite using a peridynamic approach." Journal of Composite Materials, Vol. 56, No. 6, pp. 861-876.
2021
- M. K. Shehab, K. S. Weeraratne, T. Huang, K. U. Lao, and H. M. El-Kaderi. Exceptional sodium-ion storage by aza-covalent organic framework for high energy and power destiny sodium-ion batteries. ACS Appl. Mater. Interfaces 13, 15083 (2021).
- F. Ballesteros, S. Dunivan, and K. U. Lao. Coupled cluster benchmarks of large noncovalent complexes: The L7 dataset as well as DNA-ellipticine and buckycatcher-fullerene. J. Chem. Phys. 154, 154104 (2021).
- E. Epifanovsky et al. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J. Chem. Phys. 155, 084801 (2021).
- K. Carter-Fenk, K. U. Lao, and J. M. Herbert. Predicting and understanding noncovalent interactions using novel forms of symmetry-adapted perturbation theory. Acc. Chem. Res. 54, 3679 (2021).
- D. O. Demchenko, M. Vorobiov, O. Andrieiev, T. H. Myers, and M. A. Reshchikov, “Shallow and deep states of beryllium acceptor in GaN: why photoluminescence experiments do not reveal small polarons for defects in semiconductors”, Phys. Rev. Lett. 126, 027401 (2021).
- D. O. Demchenko and M. A. Reshchikov, “Passivation of the beryllium acceptor in GaN and a possible route for p-type doping”, Appl. Phys. Lett. 118, 142103 (2021).
- M. Vorobiov, O. Andrieiev, D. O. Demchenko, and M. A. Reshchikov, “Point defects in beryllium doped GaN”, Phys. Rev. B 104, 245203 (2021).
- M. A. Reshchikov, O. Andrieiev, M. Vorobiov, B. McEwen, F. Shahedipour-Sandvik, D. Ye, and D. O. Demchenko, “Stability of the CNHi complex and the BL2 luminescence band in GaN”, Phys. Status Solidi B, 258, 2100392 (2021).
- Panahi, Aliakbar, Seyran Saeedi, and Tom Arodz. "Shapeshifter: a parameter-efficient transformer using factorized reshaped matrices." Advances in Neural Information Processing Systems 34 (2021): 1337-1350.
- Roseberry, Martha, et al. "Self-adjusting k nearest neighbors for continual learning from multi-label drifting data streams." Neurocomputing 442 (2021): 10-25.
- Baber, F., Hall, R., Justusson, B., Ranatunga, V., Schaefer, J., Pankow, M., and Guven, I., “An Improved Peridynamic Approach for Prediction of Low Velocity Impact Damage in Fiber Reinforced Composites,” AIAA SciTech 2021 Forum, 2021.
2020
- K. A. Mason, A. C. Pearcy, K. U. Lao, Z. A. Christensen, and M. S. El- Shall. “Non-covalent interactions of hydrogen cyanide and acetonitrile with the quinoline radical cation via ionic hydrogen bonding”. Chem. Phys. Lett. 754, 137744 (2020).
- L. Alickovic*, C.-H. Bae*, W. Mai*, J. Rychtář and D. Taylor (2020). Decline of pollinators and attractiveness of the plants, Involve 13:3, 529-539. DOI: 10.2140/involve.2020.13.529 http://people.vcu.edu/~rychtarj/preprints/Alickovic_et_al_Involve2020.pdf
- Michael H. Peters, Oscar Bastidas, Daniel S. Kokron, Christopher Henze, Static All-Atom Energetic Mappings of the SARS-Cov-2 Spike Protein with Potential Latch Identification of the Down State Protomer bioRxiv 2020.05.12.091090; doi: https://doi.org/10.1101/2020.05.12.091090
- Tiwari, Vaibhav; Beer, Jacob C; Sankaranarayanan, Nehru Viji; Swanson-Mungerson, Michelle; Desai, Umesh R, Discovering small-molecule therapeutics against SARS-CoV-2. , Drug discovery today. 2020 08; 25 (8) :1535-1544
- Miles, L.S.; Ayoub, N.A.; Garb, J.E.; Haney, R.A.; Verrelli, B.C. Ovarian Transcriptomic Analyses in the Urban Human Health Pest, the Western Black Widow Spider. Genes 2020, 11, 87.
- S. G. Zamfir, F. Moucka, D. Bratko, High Pressure Infiltration/Expulsion of Aqueous NaCl in Planar Hydrophobic Nanopores, J. Phys. Chem. C, DOI: 10.1021/acs.jpcc.0c07184, (2020)
- N. Ojaghlou, D. Bratko, M. Salanne, M. Shafiei, A. Luzar, Solvent-Solvent Correlations across Graphene: The Effect of Image Charges, ACS Nano 14, 7987 (2020)
- D. O. Demchenko, M. Vorobiov, O. Andrieiev, T. H. Myers, and M. A. Reshchikov, “Shallow and deep states of beryllium acceptor in GaN: why photoluminescence experiments do not reveal small polarons for defects in semiconductors”, Phys. Rev. Lett, under review (2020).
- D. O. Demchenko and M. A. Reshchikov, “Koopmans’ tuning of HSE hybrid density functional for calculations of defects in semiconductors: A case study of carbon acceptor in GaN”, J. Appl. Phys 127, 155701 (2020).
- Tiwari V, Tandon R, Sankaranarayanan NV, Beer JC, Kohlmeir EK, Swanson-Mungerson M, et al. Preferential recognition and antagonism of SARS-CoV-2 spike glycoprotein binding to 3-O-sulfated heparan sulfate. BioRxiv. 2020.
- Tiwari V, Beer JC, Sankaranarayanan NV, Swanson-Mungerson M, Desai UR. Discovering small-molecule therapeutics against SARS-CoV-2. Drug discovery today. 2020.
- Sankaranarayanan NV, Bi Y, Kuberan B, Desai UR. Combinatorial virtual library screening analysis of antithrombin binding oligosaccharide motif generation by heparan sulfate 3-O-Sulfotransferase 1. Computational and Structural Biotechnology Journal. 2020.
- Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology. 2020.
- Boothello RS, Sankaranarayanan NV, Afosah DK, Karuturi R, Al-Horani RA, Desai UR. Studies on fragment-based design of allosteric inhibitors of human factor XIa. Bioorganic & Medicinal Chemistry. 2020:115762.
2019
- D. Ampadu Boateng, M.D. Word, and K. M. Tibbetts, “Probing Coherent Vibrations of Organic Phosphonate Radical Cations with Femtosecond Time-Resolved Mass Spectrometry”, Molecules 24 509 (2019)
- D. Ampadu Boateng, M.D. Word, L. G. Gutsev, P. Jena, and K. M. Tibbetts “Conserved Vibrational Coherence in the Ultrafast Rearrangement of 2-Nitrotoluene Radical Cation”, J. Phys. Chem. A 123 1140-1152 (2019)
- Rymer K, Shiang R, Hsiung, A., Pandya A, Bigdeli T, Webb BT, Rhodes, J. Expanding the Phenotype for the Recurrent p.Ala391Glu Variant in FGFR3: Beyond Crouzon Syndrome and Acanthosis Nigricans. Mol Genet Genomic Med 2019 Jun;7(6):e656. doi: 10.1002/mgg3.656. Epub 2019 Apr 23. PMID: 31016899
- Morla, Shravan; Sankaranarayanan, Nehru Viji; Afosah, Daniel K; Kumar, Megh; Kummarapurugu, Apparao B; Voynow, Judith A; Desai, Umesh R, On the Process of Discovering Leads That Target the Heparin-Binding Site of Neutrophil Elastase in the Sputum of Cystic Fibrosis Patients. Journal of Medicinal Chemistry. 2019 06 13; 62 (11) :5501-5511
- Boothello, Rio S; Patel, Nirmita J; Sharon, Chetna; Abdelfadiel, Elsamani I; Morla, Shravan; Brophy, Donald F; Lippman, H Robert; Desai, Umesh R; Patel, Bhaumik B, A Unique Nonsaccharide Mimetic of Heparin Hexasaccharide Inhibits Colon Cancer Stem Cells via p38 MAP Kinase Activation. Molecular cancer therapeutics. 2019 01; 18 (1) :51-61
- Mahoney CR, IR MacLachlan, BM Lind, JB Yoder, T Wang, S Aitken. Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study. Evolutionary Applications 00:1-16. 2019
- Friedline CJ, TM Faske, BM Lind, EM Hobson, P Dylan, R Dyer, D Johnson, L Thompson, K Grayson, AJ Eckert. Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient. Molecular Ecology 28:2206-2223. 2019
- M. Shafiei, N. Ojaghlou, S. Zamfir, D. Bratko, A. Luzar, Modulation of Structure and Dynamics of Water Under Alternating Electric Field and the Role of Hydrogen Bonding, Mol. Phys. 117, 3282 (2019)
- F. Moucka, S. Zamfir, D. Bratko, A. Luzar, Molecular Polarizability in Open Ensemble Simulations of Aqueous Nanoconfinements under Electric Field, J. Chem. Phys. 150,164702 (2019)
- M. von Domaros, D. Bratko, B. Kirchner, G. Hummer, A. Luzar, Multifaceted Water Dynamics in Spherical Nanocages, J. Phys. Chem. C 123, 5989 (2019)
- M. Shafiei, M. von Domaros, D. Bratko, A. Luzar, Anisotropic Structure and Dynamics of Water under Static Electric Fields, J. Chem. Phys. 150, 074505 (2019)
- M.A. Reshchikov, R. M. Sayeed, Ü. Ozgür, D. O. Demchenko, J. D. McNamara, V. Prozheeva, F. Tuomisto, H. Helava, A. Usikov, and Yu. Makarov, “Unusual properties of the RY3 center in GaN”, Phys. Rev. B, 100, 045204 (2019).
- E. H. Eladgham, D. O. Demchenko, T. A. Nakagawara, Ü. Özgür, and I. U. Arachchige, “Facile synthesis of highly luminescent lithium silicate nanocrystals with varying crystal structures and morphology”, CrystEngComm 21, 1974-1983 (2019).
- Nagarajan B, Sankaranarayanan NV, Desai UR. Molecular Dynamics Simulations of Glycosaminoglycan Oligosaccharide Using Newer Force Fields. BioRxiv. 2019:561969.
- Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. Wiley Interdisciplinary Reviews: Computational Molecular Science. 2019;9(2):e1388.
- Morla S, Sankaranarayanan NV, Afosah DK, Kumar M, Kummarapurugu AB, Voynow JA, et al. On the Process of Discovering Leads That Target the Heparin-Binding Site of Neutrophil Elastase in the Sputum of Cystic Fibrosis Patients. Journal of Medicinal Chemistry. 2019;62(11):5501-11.
- Majmudar H, Hao M, Sankaranarayanan NV, Zanotti B, Volin MV, Desai UR, et al. A synthetic glycosaminoglycan mimetic blocks HSV-1 infection in human iris stromal cells. Antiviral Research. 2019;161:154-62.
2018
- Menon MG, Bagley JC, Friedline C, Whipple A, Schoettle A, Sáenz AL, Wehenkel CA, Flores- Renteria LH, Sneizko R, Cushman S, Waring K, Eckert AJ (2018) “The role of hybridization during ecological divergence between southwestern white pine, Pinus strobiformis, and limber pine, P. flexilis.” Molecular Ecology, 27, 1245-1260.
- Zhu B, Macleod LC, Kitten T, Xu P*. “Streptococcus sanguinis biofilm formation & interaction with oral pathogens.” Future Microbiol. 2018 Jun7/24/2014Page 21;13:915-932. doi: 10.2217/fmb- 2018-0043. Epub 2018 Jun 8. PMID:29882414
- Zhu B, Song L, Kong X, Macleod LC, Xu P*. “A Novel Regulator Modulates Glucan Production, Cell Aggregation and Biofilm Formation in Streptococcus sanguinis SK36.” Front Microbiol. 2018 May 29;9:1154. doi: 10.3389/fmicb.2018.01154. eCollection 2018. PMID: 29896189 Free Article
- El-Rami F, Kong X, Parikh H, Zhu B, Stone V, Kitten T, Xu P*. “Analysis of essential gene dynamics under antibiotic stress in Streptococcus sanguinis.” Microbiology. 2018 Feb;164(2):173-185. doi: 10.1099/mic.0.000595.
- Ly C and Weinberg SH, “Analysis of heterogeneous cardiac pacemaker network models and traveling wave dynamics.” J. Theoretical Biology. In press. (2018)
- Sankaranarayanan NV, Nagarajan B, Desai UR. So You Think Computational Approaches to Understanding Glycosaminoglycan–Protein Interactions are Too Dry and Too Rigid? Think Again!. Current Opinion in Structural Biology. 2018, 50:91-100.
- Kummarapurugu AB*, Afosah DK*, Sankaranarayanan NV*, Zheng S, Kennedy T, Rubin BK, Voynow JA, Desai UR. Molecular principles for heparin oligosaccharide-based inhibition of neutrophil elastase in cystic fibrosis. Journal of Biological Chemistry. 2018
- Gangji RN, Sankaranarayanan NV, Elste J, Al-Horani RA, Afosah DA, Joshi R, Tiwari V, Desai UR. Inhibition of Herpes Simplex Virus-1 Entry into Human Cells by Non-Saccharide Glycosaminoglycan Mimetics. ACS Medicinal. Chemistry. Letters. 2018 (Accepted on 7/16/2018 – In production).
- Parchman, T. L., J. P. Jahner, K. Uckele, L. M. Galland, and A. J. Eckert. 2018. RADseq approaches and applications for forest tree genetics. Tree Genetics & Genomes 14: 39. doi: 10.1007/s11295-018- 1251-3
- Lind, B. M., M. Menon, C. E. Bolte, T. M. Faske, and A. J. Eckert. 2018. The genomics of local adaptation in trees: Are we out of the woods yet? Tree Genetics & Genomes 14: 29. doi:10.1007/s11295-017-1224-y
- V. Tallapally, T. A. Nakagawara, D. O. Demchenko, Ü. Özgür, and I. U. Arachchige, “Ge1-xSnx Alloy Quantum Dots with Composition-Tunable Energy Gaps and Near-Infrared Photoluminescence”, Nanoscale (accepted) (2018).
- M.A. Reshchikov, M. Vorobiov, D. O. Demchenko, Ü. Özgür, H. Morkoc, A. Lesnik, M. P. Hoffmann, F. Horich, A. Dadgar, and A. Strittmatter, “Two charge states of the CNacceptor in GaN: Evidence from photoluminescence”, Phys. Rev. B 98, 125207 (2018).
- M.A.Reshchikov, P. Ghimire, and D. O. Demchenko, “Magnesium acceptor in gallium nitride. I. Photoluminescence from Mg-doped GaN”, Phys. Rev. B 97, 205204 (2018).
- D. O. Demchenko, I. C. Diallo, and M. A. Reshchikov, “Magnesium acceptor in gallium nitride. II. Koopmans-tuned Heyd-Scuseria-Ernzerhof hybrid functional calculations of its dual nature and optical properties”, Phys. Rev. B 97, 205205 (2018).
- Miles LS, Dyer RJ, Verrelli BC. 2018. “Urban hubs of connectivity: Contrasting patterns of gene flow within and among cities in the Western black widow spider.” Proceedings of the Royal Society B, 285: 2018 1224.
- Miles LS, Johnson JC, Dyer RJ, Verrelli BC. 2018. “Urbanization as a facilitator of gene flow in a human health pest.” Molecular Ecology, 27(16):3219-3230.
- C. D. Daub, N. M. Cann, D. Bratko and A. Luzar, “Electrokinetic flow of aqueous electrolyte in amorphous silica nanotubes,” Physical Chemistry Chemical Physics 20, 27838 (2018).
- N. Ojaghlou, H. V. Tafreshi, D. Bratko and A. Luzar, “Dynamic insights into the mechanism of a droplet detachment from a fiber,” Soft Matter 14, 8924 (2018).
- B. S. Jabes, D. Bratko and A. Luzar, “Curvature dependence on the effect of ionic functionalization on the attraction among nanoparticles in dispersion,” J. Chem. Phys. 148, 222185 (2018).
- S. Gehrke, M. von Domaros, R. Clark, O. Holloczki, M. Brehm, T. Welton, A. Luzar and B. Kirchner,” Structure and lifetimes in ionic liquids and their mixtures,” Faraday Discuss. 206, 219 (2018).
- B. S. Jabes, D. Bratko and A. Luzar, “Extent of surface force additivity on chemically heterogeneous substrates at varied orientation,” J. Phys. Chem. B 122, 3596 (2018).
- Xia H, Jahr FM, Kim NK, Xie L, Shabalin AA, Bryois J, Sweet DH, Kronfol MM, Palasuberniam P, McRae M, Riley BP, Sullivan PF, van den Oord EJ, McClay JL (2018) “Building a schizophrenia genetic network: transcription factor 4 regulates genes involved in neuronal development and schizophrenia risk.” Human Molecular Genetics 27 (18): 3246-3256
- Ramezani A, Nolin TD, Barrows IR, Serrano MG, Buck GA, Regunathan-Shenk R, West RE 3rd, Latham PS, Amdur R, Raj DS. “Gut Colonization with Methanogenic Archaea Lowers Plasma Trimethylamine N-oxide Concentrations in Apolipoprotein e-/- Mice.” Sci Rep. 2018 Oct 3;8(1):14752. PMID: 30283097
- Salman A, Koparde V, Hall CE, Jameson-Lee M, Roberts C, Serrano M, AbdulRazzaq B, Meier J, Kennedy C, Manjili MH, Spellman SR, Wijesinghe D, Hashmi S, Buck G, Qayyum R, Neale M, Reed J, Toor AA. “Determining the Quantitative Principles of T Cell Response to Antigenic Disparity in Stem Cell Transplantation.” Front Immunol. 2018 Oct 11;9:2284. PMID: 30364159
- Costa-Martins AG, Lima L, Alves JMP, Serrano MG, Buck GA, Camargo EP, Teixeira MMG. “Genome-wide identification of evolutionarily conserved Small Heat-Shock and eight other proteins bearing α-crystallin domain-like in kinetoplastid protists.” PLoS One. 2018 Oct 22;13(10):e0206012. PMID: 30346990
- Bradwell KR, Koparde VN, Matveyev AV, Serrano MG, Alves JMP, Parikh H, Huang B, Lee V, Espinosa-Alvarez O, Ortiz PA, Costa-Martins AG, Teixeira MMG, Buck GA. “Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence.” BMC Genomics. 2018 Oct 24;19(1):770. PMID: 30355302
- Espinosa-Álvarez O, Ortiz PA, Lima L, Costa-Martins AG, Serrano MG, Herder S, Buck GA, Camargo EP, Hamilton PB, Stevens JR, Teixeira MMG. “Trypanosoma rangeli is phylogenetically closer to Old World trypanosomes than to Trypanosoma cruzi.” Int J Parasitol. 2018 Jun;48(7):569-584. PMID: 29544703.
- V. Chauhan, A.C. Reber, and S.N. Khanna. “Strong lowering of ionization energy of metallic clusters by organic ligands without changing shell filling,” Nature Communications 9, 2357 (2018).
- Y. Yang, A.C. Reber, S.E. Gilliland III, C.E. Castano, B.F. Gupton, and S.N. Khanna. “More than Just a Support: Graphene as a solid-state ligand for palladium catalyzed cross- coupling reactions,” Journal of Catalysis 360, 20-25 (2018).
- Y. Yang, A.C. Reber, S.E. Gilliland, C.E. Castano, B.F. Gupton, S.N. Khanna. “Donor/Acceptor Concepts for Developing Efficient Suzuki Cross-Coupling Catalysts Using Graphene Supported Ni, Cu, Fe, Pd, and Bimetallic Pd-Ni Clusters,” J. Phys. Chem. C, 122, 25396-25403 (2018).
- M. Jash, A.C. Reber, A. Ghosh, D. Sarkar, M. Bodiuzzaman, P. Basuri, A. Baksi, S.N. Khanna and T. Pradeep. “Preparation of Gas Phase Naked Silver Cluster Cations Outside the Mass Spectrometer from Ligand Protected Clusters in Solution,” Nanoscale 10, 15714-15722 (2018).
- SV. Chauhan, and S.N. Khanna. “Strong Effect of Organic Ligands on the Electronic Structure of Metal-Chalcogenide Clusters,” J. Phys. Chem A 122, 6014-6020 (2018).
- D. Bista, A.C. Reber, V. Chauhan, and S.N. Khanna. “Electronic and Magnetic Properties of Fe 2 Si n (1≤n≤12) +/0/- clusters,” Chemical Physics Letters, 706, 113-119 (2018).
- K.A. Kane, A.C. Reber, S.N. Khanna, and M.F. Bertino. “Laser synthesized nanoparticle alloys of metals with bulk miscibility gaps”, Progress in Natural Science: Materials International, 28, 456-463 (2018).
- Arthur C. Reber and Shiv N. Khanna. “The effect of chalcogen and metal on the electronic properties and stability of metal–chalcogenides clusters, TM 6 X n (PH 3 ) 6 (TM = Mo, Cr, Re, Co, Ni; X = Se, Te; n = 8,5),” Eur. Phys. J. D, 72, 199 (2018).
- N. Haddadine, S. Chalal, K. Abouzeid, N. Bouslah, A. Benaboura, M. S. El-Shall. “Preparation and Characterization of Carbopol-Silver Nanocomposites for Efficient Antimicrobial Applications,” Polymers for Advanced Technologies, v.30, 2018, p. 1107. doi:doi.org/10.1002/pat.4222
2017
- Zhu B, Ge X, Stone V, Kong X, El-Rami F, Liu Y, Kitten T, Xu P*. “ciaR impacts biofilm formation by regulating an arginine biosynthesis pathway in Streptococcus sanguinis SK36.” Sci Rep. 2017 Dec 7;7(1):17183. doi: 10.1038/s41598-017-17383-1.
- Aynapudi J, El-Rami F, Ge X, Stone V, Zhu B, Kitten T, Xu P*. “Involvement of Signal peptidase I in Streptococcus sanguinis biofilm formation.” Microbiology. 2017 Sep;163(9):1306-1318. doi: 10.1099/mic.0.000516. Epub 2017 Sep 4. PMID: 28869408
- Stone VN, Xu P*. “Targeted Antimicrobial Therapy in the Microbiome Era.” Mol Oral Microbiol. 2017 Jun 13. doi: 10.1111/omi.12190. [Epub ahead of print] Review. PubMed PMID: 28609586.
- El-Rami F, Nelson K, Xu P*. “Proteomic Approach for Extracting Cytoplasmic Proteins from Streptococcus sanguinis using Mass Spectrometry.” J Mol Biol Res. 2017;7(1):50-57. doi: 10.5539/jmbr.v7n1p50. PMID: 29152022
- Liu J, Stone VN, Ge X, Tang M, Elrami F, Xu P*. “TetR Family Regulator brpT Modulates Biofilm Formation in Streptococcus sanguinis.” PLoS One. 2017 Jan 3;12(1):e0169301. doi: 10.1371/journal.pone.0169301.PMID: 28046010
- Weinberg SH, “Ephaptic coupling rescues conduction failure in weakly coupled cardiac tissue with voltage-gated gap junctions.” Chaos. 27: 093908. (2017)
- Comlekoglu T# and Weinberg SH, “Memory in a fractional-order cardiomyocyte model alters properties of alternans and spontaneous activity.” Chaos. 27: 093904. (2017)
- Weinberg SH, Mair DB#, and Lemmon CA, “Mechanotransduction dynamics at the cell-matrix interface.” Biophysical J. 112: 1962-1974. (2017)
- Greer-Short A, George S, Poelzing S*, and Weinberg SH*, “Revealing the concealed nature of long QT type 3 syndrome.” Circulation: Arrhythm Electrophysiol. 10(2): e004400. (2017)
- Lemmon CA and Weinberg SH, “Multiple cryptic binding sites are necessary for robust fibronectin assembly: an in silico study.” Scientific Reports. 7: 18061. (2017)
- Zheng S, Kummarapurugu AB, Afosah DK, Sankaranarayanan NV, Boothello RS, Desai UR, et al. 2-O, 3-O Desulfated Heparin Blocks High Mobility Group Box 1 Release by Inhibition of p300 Acetyltransferase Activity. American journal of respiratory cell and molecular biology. 2017;56(1):90-8.
- Sankaranarayanan NV, Strebel TR, Boothello RS, Sheerin K, Raghuraman A, Sallas F, et al. A Hexasaccharide Containing Rare 2-O-Sulfate-Glucuronic Acid Residues Selectively Activates Heparin Cofactor II. Angewandte Chemie (International ed in English). 2017; 56(9):2312-2317.
- Nagarajan B, Sankaranarayanan NV, Patel BB, Desai UR. A molecular dynamics-based algorithm for evaluating the glycosaminoglycan mimicking potential of synthetic, homogenous, sulfated small molecules. PloS one. 2017;12(2):e0171619.
- Afosah DK, Al-Horani RA, Sankaranarayanan NV, Desai UR. Potent, Selective, Allosteric Inhibition of Human Plasmin by Sulfated Non-Saccharide Glycosaminoglycan Mimetics. Journal of Medicinal Chemistry. 2017; 60(2):641-57.
- Monneau YR, Luo L, Sankaranarayanan NV, Nagarajan B, Vivès R, Baleux F, Desai UR, Arenzana-Seidedos F, Lortat-Jacob H. Solution structure of CXCL13 and heparan sulphate binding show that GAG binding site and biological activity rely on distinct domains. Open Biol. 2017;7(10): 170133.
- D. O. Demchenko, S. A. Hafiz, R. J. A. Esteves, I. U. Arachchige, Ü. Özgür, “Optical Transitions and Excitonic Properties of Ge1–x Snx Alloy Quantum Dots.” J. Phys. Chem. C,121(33), 18299-18306 (2017).
- M. Toporkov, Md. B. Ullah, D. O. Demchenko, V. Avrutin, H. Morkoc, and Ü. Özgür, “Effect of oxygen-to-metal flux ratio on incorporation of metal species into quaternary BeMgZnO grown by plasma-assisted molecular beam epitaxy”, Journal of Crystal Growth, 467, 145-149 (2017).
- N. Izyumskaya, D. O. Demchenko, S. Das, Ü. Özgür, V. Avrutin, and H. Morkoc, “Recent Development of Boron Nitride towards Electronic Applications”, Advanced Electronic Materials, 3, 1600485, (2017).
- Dhindwal S, Lobo J, Cabra V, Santiago D, Nayak AR, Dryden K, Samsó M* (2017). “A cryo–EM–based model of phosphorylation- and FKBP12.6-mediated allosterism of the cardiac ryanodine receptor.” Sci. Signal. 10, eaai8842.
- Koparde V, Abdul Razzaq B, Suntum T, Sabo R, Scalora A, Serrano M, Jameson-Lee M, Hall C, Kobulnicky D, Sheth N, Feltz J, Contaifer D Jr, Wijesinghe D, Reed J, Roberts C, Qayyum R, Buck G, Neale M, Toor A. “Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation.” PLoS One. 2017 Dec 1;12(12):e0187771. PMID: 29194460.
- Brooks JP, Edwards DJ, Blithe DL, Fettweis JM, Serrano MG, Sheth NU, Strauss JF 3rd, Buck GA, Jefferson KK. “Effects of combined oral contraceptives, depot medroxyprogesterone acetate and the levonorgestrel-releasing intrauterine system on the vaginal microbiome.” Contraception. 2017; 95(4):405-413. PMID: 27913230.
- Abdelmaksoud AA, Girerd PH, Garcia EM, Brooks JP, Leftwich LM, Sheth NU, Bradley SP, Serrano MG, Fettweis JM, Huang B, Strauss JF 3rd, Buck GA, Jefferson KK. “Association between statin use, the vaginal microbiome, and Gardnerella vaginalis vaginolysin-mediated cytotoxicity.” PLoS One. 2017 Aug 28;12(8):e0183765. PMID: 28846702.
- Hall CE, Koparde VN, Jameson-Lee M, Elnasseh AG, Scalora AF, Kobulnicky DJ, Serrano MG, Roberts CH, Buck GA, Neale MC, Nixon DE, Toor AA. “Sequence homology between HLA-bound cytomegalovirus and human peptides: A potential trigger for alloreactivity.” PLoS One. 2017 Aug 11;12(8):e0178763. PMID: 28800601
- Castro J, Franca A, Bradwell KR, Serrano MG, Jefferson KK and Cerca N. “Comparative transcriptomic analysis of Gardnerella vaginalis biofilms vs. planktonic cultures using RNA-seq,” Biofilms and Microbiomes, (2017) 3:3. PMID: 28649404.
- Matveyev AV, Alves JM, Serrano MG, Lee V, Lara AM, Barton WA, Costa-Martins AG, Beverley SM, Camargo EP, Teixeira MM, Buck GA. “The evolutionary loss of RNAi key determinants in kinetoplastids as a multiple sporadic phenomenon,” J Mol Evol. 2017 Feb 16. doi: 10.1007/s00239- 017-9780-1. PMID: 28210761.
- Kyle Mason, Adam Pearcy, Isaac K. Attah, Sean P. Platt, Saaduullah G. Aziz, and M. Samy El- Shall. “Gas Phase Hydration of Halogenated Benzene Cations. Is It Hydrogen or Halogen Bonding?,” Physical Chemistry Chemical Physics, v.19, 2017, p. 18603. doi:DOI: 10.1039/C7CP03778C
- H. S. Rady, A. N Emam, M. B Mohamed, and M. S. El-Shall. “Graphene Oxide Interface Enhances the Photochemical Synthesis, Stability and Photothermal Effect of Plasmonic Gold Nanostructures,” Chemical Physics Letters, v.690, 2017, p. 153. doi:doi.org/10.1016/j.cplett.2017.09.069
- F. Awad, K. M AbouZeid, W. M Abou El-Maaty, A. M El-Wakil, and M. S. El-Shall. “Efficient Removal of Heavy Metals from Polluted Water with High Selectivity for Mercury(II) by 2-Imino-4- Thiobiuret Partially Reduced Graphene Oxide (IT-PRGO),” ACS Applied Materials & Interfaces, v.9, 2017, p. 34230. doi:10.1021/acsami.7b10021
- AA Ibrahim, A Lin, F Zhang, KM AbouZeid, M Samy El?Shall. “Palladium Nanoparticles Supported on a Metal? Organic Framework-Partially Reduced Graphene Oxide Hybrid for the Catalytic Hydrodeoxygenation of Vanillin as a Model for Biofuel Upgrade Reactions,” ChemCatChem, v.9, 2017, p. 469. doi:DOI: 10.1002/cctc.201600956
- Ahmed Benaboura and M. Samy El-Shall Nabila Haddadine, Karima Agoudjil, Khaled Abouzeid, Carlos E. Castano, Naima Bouslah. “Optical and Physical Properties of iridescent Photonic Crystals obtained by Self-Assembled Polymethyl methacrylate Nanospheres within Graphene Oxide Nanoplatelets,” Polymers for Advanced Technologies, 2017. doi:DOI: 10.1002/pat.4109
- Andrew Lin, Amr Awad Ibrahim, Pezhman Arab, Hani M. El-Kaderi, and M. Samy El- Shall. “Palladium Nanoparticles Supported on Ce-Metal Organic Framework for Efficient CO Oxidation and Low Temperature CO2 Capture,” ACS Appl. Mater. Interfaces, v.9, 2017, p. 17961. doi:DOI: 10.1021/acsami.7b03555
- Isaac Kwame Attah, Abdel-Rahman Soliman , Sean P. Platt , Michael Meot-Ner (Mautner), Saaudallah G. Aziz and M. Samy El-Shall. “Observation of Covalent and Electrostatic Bonds in Nitrogen-containing polycyclic Ions formed by Gas Phase Reactions of the Benzene Radical Cation with Pyrimidine,” Physical Chemistry Chemical Physics, v.19, 2017, p. 6422. doi:DOI: 10.1039/C6CP08731K
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