Listed below is a selection of some of our faculty’s recent publications.


Update in Progress…



  • M. Caponigro, M. Fornasier, B. Piccoli, E. Trelat: Sparse stabilization and control of alignment models, Mathematical Models and Methods in Applied Sciences, 25 (2015), 521{564.
  • N. Swaminathan, C. M. Grgicak, M. Medard, and D. S. Lun. NOCIt: A computational method to infer the number of contributors to DNA samples analyzed by STR genotyping. Forensic Sci. Int. Genet., 16:172-180, May 2015.
  • John Collins, Ting Zhang, Scott Huston, Fangfang Sun, Percival Zhang and Jinglin Fu* “A Hidden Transhydrogen Activity of A FMN-Bound Diaphorase under Anaerobic Conditions” PLoS One, accepted.
  • Minghui Liu, Jinglin Fu, Xiaodong Qi, Shaun Wootten, Neal W. Woodbury, Yan Liu, Hao Yan* “A three-enzyme pathway with an optimized geometric arrangement to facilitate substrate transfer” ChemBioChem, accepted.
  • Whitlow, J.W., Jr. & Loatman, P.A. (2015).  When patterning discriminations are harder than biconditional ones: A cue constellation approach.  Journal of Experimental Psychology: Animal Learning and Cognition, 41, 354-370.
  • Naddeo, J.J., Ratti, M., OMalley, S.M., Griepenburg, J.C., Bubb, D.M., Klein, E.A. Antibacterial properties of nanoparticles: a comparative review of chemically synthesized and laser-generated particles. Advanced Science, Engineering, and Medicine (2015), 7(12):1044-1057.
  • Interactions of  L-3,5,3?-triiodothyronine, Allopregnanolone, and Ivermectin with the GABA(A) receptor: Evidence for Overlapping Intersubunit Binding Modes, T. Westergard, R. Salari, J.V. Martin, G. Brannigan, PLOS ONE,  DOI: 10.1371/journal.pone.0139072 (2015). (Link)
  • Role of the fourth transmembrane-helix in the allosteric modulation of pentameric ligand-gated ion channels, C. Carswell, C.M Hénault, S. Murlidaran, J.P.D Therien, P.F. Juranka, J.A Surujballi, G. Brannigan, J. E. Baenziger,Structure, DOI:10.1016/j.str.2015.06.020 (2015). (Link)
  • Membrane protein structure, function, and dynamics: a perspective from experiments and theory, Z. Cournia…G. Brannigan…A-N. Bondar, Journal of Membrane Biology DOI:10.1007/s00232-015-9802-0 (2015). (Link)
  • Karaiskos, S., Naqvi, A., Swanson, K., Grigoriev, A. (2015) Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets. Biology Direct, 10 (1), 51.
  • Smith SD, Kawash JK, Grigoriev A: GROM-RD: resolving genomic biases to improve read depth detection of copy number variants. PeerJ, 2015, 3:e836


  • N. Bou-Rabee, A. Donev, E. Vanden-Eijnden. Metropolized Integration Schemes for Self-Adjoint Diffusions. Multiscale Modeling and Simulation, 12, 781–831, 2014.
  • N. Bou-Rabee. Time Integrators for Molecular Dynamics. Entropy, 16, 138–162, 2014.
  • B. Piccoli, F. Rossi: Generalized Wasserstein distance and its application to transport equation with source, Archive for Rational Mechanics and Analysis, 211 (2014), 335{358.
  • B. Weiser, R. Salari, R.G. Eckenhoff, G. Brannigan. Computational Investigation of Cholesterol Binding Sites on Mitochondrial VDAC ,  J Phys Chem B., 118 (33) 9852-9860, 2014. 
  • J. Hénin, R. Salari, S. Murlidaran, G. Brannigan. A Predicted binding site for cholesterol on the GABA(A) receptor ,  Biophys J, 106 (9) 1938–1949, 2014. 
  • R. Salari, S. Murlidaran, G. Brannigan, Pentameric ligand-gated ion channels : Insights from Computation , Mol Sim, DOI:10.1080/08927022.2014.896462, 2014.
  • H. Zhu H, J. Zhang, M. Kim, A. Boison, A. Sedykh, K. Moran. Big Data in Chemical Toxicity Research: the Use of High-Throughput Screening Assays to Identify Potential Toxicants. Chem. Res. Tox. 27(10): 1643-1651, October 2014
  • J. Zhang, J-H. Hsieh, H. Zhu. Profiling animal toxicants by automatically mining public bioassay data: a big data approach for computational toxicology. PLoS One 9(6): e99863, June 2014
  • M.G. Niepielko, R. A. Marmion, K. Kim, D. Luor, C. Ray, N. Yakoby. Chorion Patterning: A window into gene regulation and Drosophila species-relatedness. 2014. Molecular Biology & Evolution. 31 (1):154-164.
  • M.G. Niepielko and N. Yakoby. Evolutionary changes in TGF-alpha distribution underlie morphological diversity in Drosophila eggshells. 2014. Development 15;141(24):4710-4715.
  • E.W. Gachomo, T. Kefela, P. Houngnandan, L. Baba-Moussa and, S.O. Kotchoni. Bradyrhizobium japonicum IRAT FA3 increases biomass, yield and drought tolerance in plants. Journal of Biology and Nature, 1(1):12-23, December 2014.
  • Grigoriev, A.*, & Bonini, N. M.* Age-dependent patterns of microRNA RISC loading (2014) Aging, 6(9), 705–706.
  • Choudhari S.^, Lohia R.^, Grigoriev A. (2014) Comparative Metagenome Analysis of an Alaskan Glacier. J. Bioinform. Comput. Biol.
  • Jinglin Fu*, Yuhe Renee Yang, Alexander Johnson-Buck, Minghui Liu, Yan Liu, Nils G. Walter, Neal W. Woodbury and Hao Yan* “Multi-enzyme complexes on DNA scaffolds capable of substrate channeling with an artificial swinging arm” Nature Nanotechnology 2014, 9, 531–536.
  • H. Harikrishnan, V. Shanmugaiah, N. Balasubramanian, M.P. Sharma, S.O. Kotchoni, S. Huang, D.B. Szymanski and, C.J. Staiger. Antagonistic potential of native strain Streptomyces aurantiogriseus VSMGT1014 against sheath blight of rice disease. World Journal of Microbiology and Biotechnology, 30:3149-3161, December 2014.
  • Choi, Y. Ye, D. Salas de la Cruz, W. Liu, K. I. Winey, Y. A. Elabd, J. Runt, R. H. Colby, Macromolecules, 47 (2), 777-790, 2014.“Dielectric and viscoelastic responses of imidazolium-based ionomers with different counterions and side chain lengths.”
  • K. Ip, N. Donoghue, M. K. Kim, and D. S. Lun. Constraint-based modeling of heterologous pathways: Application and experimental demonstration for overproduction of fatty acids inEscherichia coli. Biotechol. Bioeng., 111(10):2056-2066, October 2014.