Recent Publications

Ball, J., Salvi, F., & Gadda, G. (2016). Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH: Quinone Reductases. Journal of Biological Chemistry, 291(40), 21160-21170.

Burrows, N. L., & Mooring, S. R. (2015). Using concept mapping to uncover students’ knowledge structures of chemical bonding concepts. Chemistry Education Research and Practice, 16(1), 53-66.

Mooring, S. R., Mitchell, C. E., & Burrows, N. L. (2016). Evaluation of a Flipped, Large-Enrollment Organic Chemistry Course on Student Attitude and Achievement. Journal of Chemical Education.

Ornelles, D. A., Gooding, L. R., Dickherber, M. L., Policard, M., & Garnett-Benson, C. (2016). Limited but durable changes to cellular gene expression in a model of latent adenovirus infection are reflected in childhood leukemic cell lines. Virology, 494, 67-77.

Huo, L., Davis, I., Liu, F., Andi, B., Esaki, S., Iwaki, H., … & Liu, A. (2015). Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action. Nature communications, 6.

Saxena, R.,… C. Garlapati,…., R. Aneja (2017). Preclinical development of a non-toxic oral formulation of monoethanolamine, a lipid precursor, for prostate cancer treatment. Clinical Cancer Research.

Rogovskyy, A. S., Gillis, D. C., Ionov, Y., Gerasimov, E., & Zelikovsky, A. (2016). Antibody response to Lyme disease spirochetes in the context of VlsE-mediated immune evasion. Infection and Immunity, IAI-00890.

Sahay, P., Ganju, A., Ghimire, H. M., Almabadi, H., Yallappu, M. M., Skalli, O., … & Pradhan, P. (2015). Probing intracellular mass density fluctuation through confocal microscopy: application in cancer diagnostics as a case study. arXiv preprint arXiv:1512.08583.

Ghimire, H. M., Shukla, P., Sahay, P., Almabadi, H., Tripathi, V., Skalli, O., … & Pradhan, P. (2015). Nanoscale intracellular mass-density alteration as a signature of the effect of alcohol on early carcinogenesis: A transmission electron microscopy (TEM) study. arXiv preprint arXiv:1512.08593.

Liu, F., Geng, J., Gumpper, R. H., Barman, A., Davis, I., Ozarowski, A., … & Liu, A. (2015). An Iron Reservoir to the Catalytic Metal: the Rubredoxin Iron in an Extradiol Dioxygenase. Journal of Biological Chemistry, 290(25), 15621-15634.

Harika, N. K., Paul, A., Stroeva, E., Chai, Y., Boykin, D. W., Germann, M. W., & Wilson, W. D. (2016). Imino proton NMR guides the reprogramming of Ao T specific minor groove binders for mixed base pair recognition. Nucleic acids research, 44(10), 4519-4527.

He, X., Lee, B., & Jiang, Y. (2016). Cell-ECM Interactions in Tumor Invasion. In Systems Biology of Tumor Microenvironment (pp. 73-91). Springer International Publishing.

He, X., Jiang. Y. (2017) “Substrate curvature regulates cell migration”. in press

He, Z., Cai, Z., Yu, J., Wang, X., Sun, Y. and Li, Y., (2016). Cost-efficient strategies for restraining rumor spreading in mobile social networks. IEEE Transactions on Vehicular Technology.

Cai, Z., He, Z., Guan, X. and Li, Y., (2016). Collective data-sanitization for preventing sensitive information inference attacks in social networks. IEEE Transactions on Dependable and Secure Computing.

He, Z., Cai, Z., Sun, Y., Li, Y. and Cheng, X., (2016). Customized privacy preserving for inherent data and latent data. Personal and Ubiquitous Computing, pp.1-12.

He, Z., Cai, Z., Han, Q., Tong, W., Sun, L. and Li, Y., (2016). An energy e_cient privacy-preserving content sharing scheme in mobile social networks. Personal and Ubiquitous Computing, 20(5), pp.833-846.

He, Z., Cai, Z., Cheng, S. and Wang, X., (2015). Approximate aggregation for tracking quantiles and range countings in wireless sensor networks. Theoretical Computer Science, 607, pp.381-390.

Wang, Y., Tong, X., Wang, K., Fan, B., He, Z. and Yin, G., (2017). A Novel Task Recommendation Model for Mobile Crowdsourcing Systems. International Journal of Sensor Networks.

Weber, I. T., Kneller, D. W., & Wong-Sam, A. (2015). Highly resistant HIV-1 proteases and strategies for their inhibition. Future Medicinal Chemistry, 7(8), 1023-1038.

S. Knyazev, V. Kalyakin, I. Deryabin, B. Fedorov, A. Smirnov, E. Stepanov, and Yu. Porozov (2015) Prediction of Protein Conformational Mobility and Evaluation of Its Reliability Using Small-Angle X-ray Scattering. Biophysics 60(6):pp.886-892

G. Tamazian, J. Ho Chang, S. Knyazev, E. Stepanov, K.J. Kim, Y. Porozov (2015) Modeling conformational redoxswitch modulation of human succinic semialdehyde dehydrogenase. Proteins: Structure, Function, and Bioinformatics 83(12):pp.2217-2229

E. Lutsenko, S. Knyazev, Yu. Porozov (2016) A new approach for modeling of conformational changes of multi chain proteins. 5th International Young Scientists Conference in High Performance Computing and Simulation (YSC) Procedia Computer Science, DOI: 10.1016/j.procs.2016.11.009

Musille, P.M., Kossmann, B.R., Kohn, J.A., Ivanov, I. & Ortlund, E.A. (2015). Unexpected Allosteric Network Contributes to LRH-1 Coregulator Selectivity. Journal of Biological Chemistry

Hudson, W.H., Kossmann, B.R., de Vera, I.M.S, Chuo, S., Weikum, E.R., Eick, G.N., Thornton, J.W., Ivanov, I.N., Kojetin, D.J. & Ortlund, E.A. (2015). Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space. Proceedings of the National Academy of Sciences, 113.2, 326-331

Kossmann, B.R., Abdelmalak, M., Lopez, S., Tender, G., Yan, C., Pommier, Y., Marchand, C., & Ivanov, I. (2016). Discovery of Selective Inhibitors of Tyrosyl-DNA Phosphodiesterase 2 by Targeting the Enzyme DNA-binding Cleft. Bioorganic and Medicinal Chemistry Letters.

Xu, X., Yan, C., Kossmann, B.R. & Ivanov, I. (2016). Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PolB from Polymerization to Editing. Journal of Physical Chemistry

Li, Y., Wang, D., Kvetny, M. M., Brown, W., Liu, J., & Wang, G. (2015). History-dependent ion transport through conical nanopipettes and the implications in energy conversion dynamics at nanoscale interfaces. Chemical Science, 6(1), 588-595.

Pett, L., Kiakos, K., Satam, V., Patil, P., Laughlin-Toth, S., Gregory, M., … & Lee, M. (2016). Modulation of topoisomerase IIα expression and chemosensitivity through targeted inhibition of NF-Y: DNA binding by a diamino p-anisyl-benzimidazole (Hx) polyamide. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms.

Li, B., Zhang, J., Yu, N., & Pan, Y. (2016). J2M: a Java to MapReduce translator for cloud computing. The Journal of Supercomputing, 72(5), 1928-1945.

Yu, N., Yu, Z., Li, B., Gu, F., & Pan, Y. (2016). A Comprehensive Review of Emerging Computational Methods for Gene Identification. Journal of Information Processing Systems, 12(1).

Makita, H., & Hastings, G. (2016). Time-resolved visible and infrared absorption spectroscopy data obtained using photosystem I particles with non-native quinones incorporated into the A 1 binding site. Data in brief, 7, 1463-1468.

Makita, H., & Hastings, G. (2016). Modeling electron transfer in photosystem I. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1857(6), 723-733.

Mandric, I., Lindsay, J., Mandoiu, I., Zelikovsky, A. (2016) Scaffolding Algorithms (book chapter in Computational Methods for Next Generation Sequencing Data Analysis, John Wiley \& Sons, Inc.).

Temate-Tiagueu, Y., Al Seesi, S., Mathew, M., Mandric, I. et al. (2016). Inferring metabolic pathway activity levels from RNA-Seq data, BMC Genomics.

Mandric, I., Zelikovsky, A. (2015). ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching, Bioinformatics.

Glebova, O., Knyazev, S., Melnyk, A., Artyomenko, A., Khudyakov, Y., Zelikovsky, A., Skums, P. (2016) Computational Inference of Transmission Characteristics between Viral Populations. ICCABS

Tork, B., Nenastyeva, E., Artyomenko, A., Mancuso, N., Khan, M. I., O’Neill, R., … & Zelikovsky, A. (2016). Reconstruction of infectious bronchitis virus quasispecies from ngs data. Computational Methods for Next Generation Sequencing Data Analysis, 383-400.

Mangul, S., Wu, N. C., Nenastyeva, E., Mancuso, N., Zelikovsky, A., Sun, R., & Eskin, E. (2016). Applications of High‐Fidelity Sequencing Protocol to RNA Viruses. Computational Methods for Next Generation Sequencing Data Analysis, 85-104.

Rogovskyy, A. S., Gillis, D. C., Ionov, Y., Gerasimov, E., & Zelikovsky, A. (2017). Antibody response to Lyme disease spirochetes in the context of VlsE-mediated immune evasion. Infection and Immunity, 85(1), e00890-16.

Pannu, V., Rida, P.C., Ogden, A., Turaga, R.C., Donthamsetty, S., Bowen, N.J., …& Aneja, R. (2015) HSET overexpression fuels tumor progression via centrosome clustering-independent mechanisms in breast cancer patients. Oncotarget. 20;6(8):6076-91.

Ogden, A., Rida, P.C., Reid, M.D., Kucuk, O., Aneja, R. (2015) Die-hard survivors: heterogeneity in apoptotic thresholds may underlie chemoresistance. Expert Review of Anticancer Therapy. 15(3):277-81.

Mittal, K., Ogden, A., Reid, M.D., Rida, P.C., Varambally, S., Aneja, R. (2015) Amplified centrosomes may underlie aggressive disease course in pancreatic ductal adenocarcinoma. Cell Cycle. 14(17):2798-809.

Rida PC, LiVecche D, Ogden A., Zhou J, Aneja R. (2015) The Noscapine Chronicle: A Pharmaco-Historic Biography of the Opiate Alkaloid Family and its Clinical Applications. Med Res Rev. 35(5):1072-96.

Ogden, A., Rida, P.C., Knudsen, B.S., Kucuk, O., Aneja, R. (2015) Docetaxel-induced polyploidization may underlie chemoresistance and disease relapse. Cancer Lett. 28;367(2):89-92.

Colley, H., Saxena, R., Ogden, A., Cantuaria, G., Reid, M. D., Li, X. B., … & Aneja, R. (2016). Abstract C50: Sensitivity of triple-negative breast cancer cell lines to cytotoxic and targeted agents as a function of molecular subtype. Cancer Epidemiology Biomarkers & Prevention, 25(3 Supplement), C50-C50.

Zhang, L., Ogden, A., Aneja, R., & Zhou, J. (2016). Diverse roles of HDAC6 in viral infection: Implications for antiviral therapy. Pharmacology & Therapeutics.

Xie, S., Ogden, A., Aneja, R., & Zhou, J. (2016). Microtubule‐Binding Proteins as Promising Biomarkers of Paclitaxel Sensitivity in Cancer Chemotherapy. Medicinal Research Reviews, 36(2), 300-312.

Ogden, A., Rida, P.C.G., Aneja R.(2017) Prognostic value of CA20, a score based on centrosome amplification-associated genes, in breast tumors. Sci Rep. 21;7:262.

Ogden A., Garlapati C., Li X.B., Turaga R.C., Oprea-Ilies G., Wright N., …& Aneja R. (2017) Multi-institutional study of nuclear KIFC1 as a biomarker of poor prognosis in African American women with triple-negative breast cancer. Sci Rep. 20;7:42289.

Mittal K., Choi D.H., Ogden A., Donthamsetty S., Melton B.D., Gupta M.V., …& Aneja R. (2017) Amplified centrosomes and mitotic index display poor concordance between patient tumors and cultured cancer cells. Sci Rep. 8;7:43984.

Sharma, M., Akhtar, N., Sambhav, K., Shete, G., K Bansal, A., & S Sharma, S. (2015). Emerging potential of citrus flavanones as an antioxidant in diabetes and its complications. Current Topics in Medicinal Chemistry, 15(2), 187-195.

Pu, F., Qiao, J., Xue, S., Yang, H., Pate,l A., Wei, L., Hekmatyar, K., Salarian, M., Grossniklaus, H.E., Liu, Z.R., Yang, J.J. (2015). GRPR-targeted protein contrast agents for molecular imaging of receptor expression in cancers by MRI. Scientific Reports, 5, 16214.

Xue, S., Yang, H., Qiao, J., Pu, F., Jiang, J., Hubbard, K., Hekmatyar, K., Langley, J., Salarian, M., …& Yang, J.J. (2015). Protein MRI contrast agent with unprecedented metal selectivity and sensitivity for liver cancer imaging. Proceedings of the National Academy of Sciences, 112, 6607-6612.

Behbahani, M., Salimi, S., Sadeghi, H., Abandansari, H.S., Omidi, F., Salarian, M., Esrafili, A. (2015). Application of a tailor-made polymer as a selective and sensitive colorimetric sensor for reliable detection of trace levels of uranyl ions in complex matrices. RSC Advances, 5, 59912-59920.

Pu, F., Salarian, M., Xue, S., Qiao, J., Feng, J., Tan, S., …& Yang, J.J. (2016). Prostate-specific membrane antigen targeted protein contrast agents for molecular imaging of prostate cancer by MRI. Nanoscale, 8, 12668-12682.

Behbahani, M., Bide, Y., Bagheri, S., Salarian, M., Omidi, F., Nabid, M.R. (2016). A pH responsive nanogel composed of magnetite, silica and poly(4-vinylpyridine) for extraction of Cd(II), Cu(II), Ni(II) and Pb(II). Microchimica Acta, 183, 111-121.

Turaga, R. C., Yin, L., Yang, J. J., Lee, H., Ivanov, I., Yan, C., … & Sun, L. (2016). Rational design of a protein that binds integrin [alpha] v [beta] 3 outside the ligand binding site. Nature Communications, 7.

Uluisik, R. C., Akbas, N., Lukat-Rodgers, G., Adrian, S.A., Allen, C., …& Dixon, D.W. (2017) Characterization of the Second Conserved Domain in the Heme Uptake Protein HtaA from Corynebacterium diphtheriae. Journal of Inorganic Biochemistry 167, 124-133