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Oklahoma State University
High Performance Computing Center

A unit in the Division of the Vice President for Research


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  1. Avery, A.S., & Jacob, J.D. (2017). Evaluation of low altitude icing conditions for small unmanned aircraft. 9th AIAA Atmospheric and Space Environments ConferenceAIAA Aviation Forum, (AIAA 2017-3929). DOI: 10.2514/6.2017-3929

  2. Ayalew, S., Confer, A.W., Hansen, R.D., & Couger, M.B. (2017). Genome sequence of Mannheimia haemolytica Serotype 1 Strain 16041065 BH. Genome Announcements, 5(14). DOI: 10.1128/genomeA.01721-16

  3. Ayalew, S., Confer, A.W., Hansen, R.D., & Couger, M.B. (2017). Genome sequence of a spontaneous nonhemolytic mutant of Mannheimia haemolytica 16041065 GH. Genome Announcements5(14). DOI: 10.1128/genomeA.01720-16

  4. Babu, K.S., Bajc, B., & Saad, S. (2017). Yukawa sector of minimal SO(10) unification. Journal of High Energy Physics. (available online 28 Feb 2017). DOI: 10.1007/JHEP02(2017)136

  5. Babu, K.S., Khanov, A., & Saad, S. (2017). Anarchy with hierarchy: A probabilistic appraisal. Physical Review D, 95(1). DOI: 10.1103/PhysRevD.95.055014

  6. Cho, J., Grogg, K., Min, C.H., Zhu, X., Paganetti, H., Lee, H.C., & El-Fakhri, G. (2017). Feasibility study of using fall-off gradients of early and late PET scans for proton range verification. Med. Phys., 44. 

  7. Chuba, D., Goyder, D., Chase, M.W., & Fishbein, M. (2017). Phylogenetics of the African Asclepias complex (Apocynaceae) based on three plastic DNA regions. Systematic Botany42(1), 148-159. DOI: 10.1600/036364417X694539

  8. Farag, I.F., Youssef, N.H., & Elshahed, M.S. (2017). Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). Applied and Environmental Microbiology, (available online 17 March 2017). DOI: 10.1128/AEM.00521-17

  9. Harris, A.J., Dee, J., & Palmer, M.W. (2017). The effects of taxonomic rank on climatic calibrations: A test using extant floras of United States counties. Review of Palaeobotany and Palynology, (available online 8 Feb 2017). DOI: 10.1016/j.revpalbo.2017.02.002 

  10. Hendershot, M.E., & Liang, Y. (2017). Estimating judicial accomplishment: Applying the legislative accomplishment strategy to the decisions of the Supreme Court. Justice System Journal, 1-21 (online 22 Mar 2017). DOI: 10.1080/0098261X.2017.1296386

  11. Kibble, G.A., Jacob, J.D., Alexander, A., Elbing, B.R., Ireland, P., & Black, B. (2017). Aerodynamic investigation of the conformal vortex generator, 47th AIAA Fluid Dynamics ConferenceAIAA AVIATION Forum, (AIAA 2017-3117). DOI: 10.2514/6.2017-3177 

  12. Moktan, H., & Zhou, D.H. (2017). Wing 1 of protein HOP2 is as important as helix 3 in DNA binding by MD simulation. Journal of Biomolecular Structure and Dynamics, 1-14, (online 08 Jun 2017). DOI: 10.1080/07391102.2017.1333458

  13. Passow, C.N., Brown, A.P., Arias-Rodriguez, L., Yee, M.C., Sockell, A., Schartl, M., Warren, W.C., Bustamante, C., Kelley, J.L, & Tobler, M. (2017). Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Molecular Ecology, (online 9 June 2017). DOI: 10.111/mec.14198

  14. Pleinert, M.O., Von Zanthier, J., & Agarwal, G.S. (2017). Hyperradiance-a new paradigm in 60 years of superradiance. arXiv: 1702.05392

  15. Shah, J.K., Marin-Rimoldi, E., Mullen, R.G., Keene, B.P., Khan, S., Paluch, A.S., et. al. (2017). Cassandra: An open source Monte Carlo package for molecular simulation. Journal of Computational Chemistry, (online 24 April 2017). DOI: 10.1002/jcc.24897



  1. Alderman, P.D., & Stanfill, B. (2016). Quantifying model-structure- and parameter-driven uncertainties in spring wheat phenology prediction with Bayesian analysis. European Journal of Agronomy, (online 6 October 2016). DOI: 10.1016/j/eja.2016.09.016

  2. Andreason, S.*, Schnieder, W., & Wayadande, A. (2016). Detection of plant pathogens within insect vector transcriptome sequencing datasets. Proceedings of: Entomological Society of America Southwestern Branch Meeting: Tyler, TX.

  3. Babu, K.S., Bajc, B., & Saad, S. (2016). New class of SO(10) models for flavor. American Physical Society, (online 25 July 2016). DOI: 10.1103/PhysRevD.94.015030. arXiv: 1605.05116v1 

  4. Blagden, T., Schneider, W., Melcher, U., Daniels, J.*, & Fletcher, J. (2016). Adaptation and validation of E-probe diagnostic nucleic acid analysis for detection of Escherichia coli O157:H7 in metagenomic data from complex food matrices. Journal of Food Protection79(4), 574-581. DOI: 10.4315/0362-028X.JFP-15-440

  5. Brini, E. Paranahewage, S.S., Fennell, C.J., & Dill, K.A. (2016). Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules. J. Comput. Aided Mol. Des. DOI: 10.1007/s10822-016-9961-9.

  6. Buchanan, J.W., Reecy, J.M., Garrick, D.J., Duan, Q., Beitz, D.C.,...Mateescu, R.G. (2016). Deriving gene networks from SNP associated with Triacylglycerol and Phospholipid fatty acid fractions from ribeyes of Angus cattle. Frontiers in Genetics7(116), 1-12. DOI: 10.3389/fgene.2016.00116.

  7. Cho, J., Campbell, P., Wang, M., Alqathami, M., Mawlawi, O., Kerr, M., & Cho, S.H. (2016). Feasibility of hydrogel fiducial markers for in vivo proton range verification using PET. Phys. Med. Biol.61, 2162-2176.

  8. Cho, J., Gonzalez-Lepera, C., Manohar, N., Kerr, M., Krishnan, S., Cho, S.H. (2016). Quantitative investigation of physical factors contributing to gold nanoparticle-mediated proton dose enhancement. Phys. Med. Biol.61(6), 2562-2581. DOI: 10.1088/0031-9155/61/6/2562.

  9. Cho, J., Ibbott, G., Kerr, M., Amos, R., Stingo, F., Mawlawi, O., et al. (2016). Characterizing proton-activated materials to develop PET-mediated proton range verification markers. Phys. Med. Biol.61, 291-310.

  10. Cho, J., Wang, M., Gonzalez-Lepera, C., Mawlawi, O., & Cho, S.H. (2016). Development of bimetallic (Zn@Au) nanoparticles as potential PET-imageable radiosensitizers. Phys. Med. Biol.43(8), 4775. DOI: 10.1118/1.4958961

  11. Couger, M.B., Wright, A., Lutter, E.I., & Youssef, N. (2016). Draft genome sequences of five Pseudomonas aeruginosa clinical strains isolated from Sputum samples from Cystic Fibrosis patients. Genome announcements4(1), e01528-15. DOI: 10.1128/genomeA.01528-15 

  12. Das, S. & Mykles, D.L. (2016). A comparison of resources for the annotation of a De Novo assembled transcriptome in the molting gland (Y-organ) of the Blackback Land Crab. Integrative and Comparative Biology, (online 22 Aug 2016). DOI: 10.1093/icb/icw107

  13. Das, S., Pitts, N.L., Mudron, M.R., Durica, D.S., & Mykles, D.L. (2016). Transcriptome analysis of the molting gland (Y-organ) from the Blackback Land Crab, Gecarninus lateralisComp. Biochem. Physiol.17D, 26-20. DOI: 10.1016/j/cbd.2015.11.003.

  14. Ding, T.*, & Melcher, U. (2016). Influences of plant species, season and location on leaf endophytic bacterial communities of non-cultivated plants. PLoS One11(3), e0150895. DOI: 10.1371/journal.pone.0150895

  15. Dipasquale, M., Francisco, C.A., Mermin, J., & Schweig, J. (2016).Free and non-free multiplicities on the A3 arrangement. (online 1 Sept 2016). arXiv: 1609.00337v1

  16. Frahm, K.A., Peffer, M.E., Zhang, J.Y., Luthra, S., Chakka, A.B., Couger, M.B., Chandran, U.R., Monoghan, A.P., & DeFranco, D.B. (2016). Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells. Biotechnol. Biofuels30(1), 144-154. DOI: 10.1210/me.2015-1258

  17. Harris, A.J., Fu, C., Xiang, Q.Y.J., Holland, L.R., & Wen, J. (2016). Testing the monophyly of Aesculus L. and Billia Peyr, woody genera of tribe Hippocastaneae of the Sapindaceae. Molecular Phylogenetics and Evolution, (online 3 June 2016). DOI: 10.1016/j.ympev.2016.06.001

  18. Kanost, M.R., Arrese, E.L., Cao, X., Chen, Y., Chellapilla, S., Goldsmith, M.R., Grosse-Wilde, E.,...Blissard, G.W. (2016). Multifacted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochemistry and Molecular Biology76, 118-147. DOI: 10.1016/j.ibmb.2016.07.005

  19. Kapoor, U., & Shah, J. (2016). Preferential ionic interactions and microscopic structural changes drive nonideality binary ionic liquid mixtures as revealed from molecular simulations. Industrial & Chemistry Engineering Research, (online 28 November 2016). DOI: 10.1021/acs.icer.6b03314.

  20. Liang, Ye. (2016). Bayesian nonparametric inference for panel count data with dependent observation times. Presented at: 2016 ICSA Applied Statistics Symposium: Atlanta, GA.

  21. Ma, J.* Pajouh, F.M., Balasundaram, B., & Boginski, V. (2016). The minimum spanning k-core problem with bounded CVaR under probabilistic edge failures. INFORMS Journal on Computing28(2), 295-307. 

  22. Maulik, R.*, & San, O.* (2016). A stable and scale-aware dynamic modeling framework for subgrid-scale parameterizations of two-dimensional turbulence. Computers & Fluids, (online 27 November 2016). DOI: 10.1016/j.compfluid.2016.11.015 

  23. Mortazavian, H., Fennell, C., & Blum, F.D. (2016). Surface bonding is stronger for poly(methyl methacrylate) than for poly(vinyl acetate). Macromolecule, (online 16 May 2016). DOI: 10.1021/acs.macromol.6b00521   

  24. Mortazavian, H., Fennell, C., & Blum, F.D. (2016). Structure of the interfacial region in adsorbed poly(vinyl acetate) on Silica. Macromolecules49(11), 4211-4219. DOI: 10.1021/acs.macromol.5b02214.

  25. Mykles, D.L., Burnett, K.G., Durica, D.S., Joyce, B.L., McCarthy, F.M., Schmidt, C.J., & Stillman, J.H. (2016). Resources and recommendations for using transcriptomics to address grand challenges in comparative biology. Integr. Comp. Biol., (advanced access published 17 September 2016). DOI: 10.1093/icb/icw083

  26. Neeman, H., Bergstrom, A., Brunson, D., Ganote, C., Gray, Z., Guilfoos, B., ...Voss, D. (2016). The Advanced Cyberinfrastructure Research and Education Facilitators Virtual Residency: Toward a national cyberinfrastructure workforce. Proceedings of the XSEDE16 Conference on Diversity, Big Data and Science at Scale, Article no. 57. DOI: 10.1145/2949550.2949584

  27. Pajouh, F.M., Balasundaram, B., & Hicks, I.V. (2016). On the 2-club polytope of graphs. Operations Research, (online 17 June 2016). DOI: 10.1287/opre.2016.1500

  28. Pajouh, F.M., Moradi, E.*, & Balasundaram, B. (2016). Detecting large risk-averse 2-clubs in graphs with random edge failures. Annals of Operations Research, (online 03 Aug 2016). DOI: 10.1007/s10479- 016-2279-0

  29. Paranhewage, S.S.*, Gierhart, C.S.**, & Fennell, C.J. (2016). Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields. J. Comput. Aided Mol. Des. DOI: 10.1007/s10822-016-9950-z.

  30. Pleinert, M., Zanthier, J., & Agarwal, G.S. (2016). Quantum signature of collective behavior of a coherently driven two atom system coupled to a single-mode of the electromagnetic field. (online 30 July 2016). arXiv: 1608.00137

  31. Pourhabib, A.* (2016). Empirical similarity for absent data generation in imbalanced classification. (online 12 May 2016). arXiv: 1508.01235v2 

  32. Schneider, W.D., Goncalves, T.A., Uchima, C.A., Couger, M.B., Prade, R., Squina, F.M.,...Camassola, M. (2016). Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass. Biotechnol. Biofuels, 9(66). DOI: 10.1186/s13068-016-0476-3

  33. Selvaraju, S., Adhikari, S., Hopson, R.A., Dai, S., Rheingold, A., Borunda, M., & Nelson, T. (2016). Effects of structural variations on the optical and electronic properties of eumelanin-inspired small molecules. Journal of Materials Chemistry C, (online 18 Jan 2016). DOI: 10.1039/C5TC03982G.

  34. Singh, A., Fennell, C., & Weaver, J.D. (2016). Photocatalyst size controls electron and energy transfer: Selectable E/Z isomer synthesis via C-F alkenylation. Chemical Science, (online 21 July 2016). DOI: 10/1039.C6SC02422J.

  35. Wang, B., Yi, H., Xu, K., & Wang, Q. (2016). Prediction of the self-accelerating decomposition temperature of organic peroxides using QSPR models. Journal of Thermal Analysis and Calorimetry, pp 1-8, (online 28 October 2016). DOI: 10.1007/s10973-016-5922-8


Dissertations & theses

  1. Andreason, Sharon. (2016). Discrimination and transcriptional response analysis of hemipteran phytopathogens [dissertation]. [Stillwater, OK]: Department of Entomology & Plant Pathology, Oklahoma State University. Advisor: Astri Wayadande.

  2. Miao, Z. (2016 May). Combinatorial and global optimization approaches to the maximum quasi-clique [dissertation]. [Stillwater, OK]: Department of Industrial Engineering & Management, Oklahoma State University. Advisor: Baski Balasundaram.

  3. Mohanty, R.P. (2016). Pollen biology and landscape ecology of Juniperus: An integrative study using quantitative molecular approaches, ultrastructure and habitat modeling [dissertation]. [Tulsa, OK]: Department of Biology, University of Tulsa. Advisor(s): Estelle Levetin & Mark Buccheim.

  4. Moradi, E. (2016 May). Decomposition algorithms for detecting low-diameter clusters in graphs [dissertation]. [Stillwater, OK]: Department of Industrial Engineering & Management, Oklahoma State University. Advisor: Baski Balasundaram.

  5. Mortazavian, H. (2016 May). Polymer adsorption on silica and wettability of graphene oxide surfaces, experiments and simulations [dissertation]. [Stillwater, OK]: Department of Chemistry, Oklahoma State University. Advisor: Frank Blum.

  6. Li, X. (2016 May). Microbial communities in soil ecosystems under different land uses [dissertation]. [Stillwater, OK]: Department of Plant & Soil Sciences, Oklahoma State University. Advisor: Shiping Deng.

  7. Sun, L. (2016 May). Modeling the Oklahoma Mesonet data with a multivariate spatial Dirichlet process mixture [master's thesis]. [Stillwater, OK]: Department of Statistics, Oklahoma State University. Advisor: Ye Liang.




  1. Al-Rubaye, A.A., Couger, M.B., Ojha, S., Pummill, J.F., Koon II, J.A., Wideman Jr., R.F., & Rhoads, D.D. (2015). Genome analysis of Staphylococcus agnetis, an agent of lameness in broiler chickens. PLoS One10(11), e0143336. DOI: 10.1371/journal.pone.0143336

  2. Andreason, S.*, Schneider, W., Davis, R.,  & Wayadande, A. (2015). E-probe diagnostic nucleic acid assay (EDNA) detection of Spiroplasma kunkelli in gray lawn leafhopper, Exitianus exitiosu, (Uhl.), transcriptome sequencing dataset. Proceedings of: Entomological Society of America National Meeting: Minneapolis, MN.

  3. Balasundaram, B. (2015, September 11). Cliques & Clubs. Presented at: Seminar Series, Department of Industrial & Systems Engineering, Texas A&M University: College Station, TX.

  4. Balasundaram, B. (2015, July 12-17). On the 2-club polytope of graphs. Presented at: 22nd International Symposium on Mathematical Programming: Proceedings of the 22nd International Symposium on Mathematical Programming: Pittsburgh, PA.

  5. Buchanan, J.W., Koltes, J.E., Reecy, J.M., & Mateescu, R.G. (2015, Jan. 12.) Deriving gene networks involving tenderness and sensory attributes in steaks from Angus beef cattle. Presented at: PAG XXIII. Proceedings of the 23rd International Plant and Animal Genome Conference: San Diego, CA.

  6. Cao, X., He, Y., Hu, Y., Wang, Y., Chen, Y., Bryant, B., Clem, R., Schwartz, L., Blissard, G., & Jiang, H. (2015). The immune signaling pathways of Manduca sexta. Insect Biochemistry and Molecular Biology62, 64-74. (online 7 April 2015). DOI: 10.1016/j.ibmb.2015.03.006

  7. Cao, X., & Jiang, H. (2015). Integrated modeling of protein-coding genes in Manduca sexta genome using RNA-Seq data from the biochemical model insect, Insect Biochemistry and Molecular Biology, 62, 2-10. (online 20 January 2015). DOI: 10.1016/j.ibmb.2015.01.007

  8. Couger, M.B., Hanafy, R.A., Edens, C., Budd, C., French, D.P., Hoff, W.D., Elshahed, M.S., & Youssef, N.H. (2015). Draft genome of the Arthrobacter sp. Strain Edens01. Genome announc.3(6), pii: e01475-15. DOI: 10.1128/genomeA.01475-15

  9. Couger, M.B., Hurlbut, A., Edens, C., Budd, C., French, D.P., Hoff, W.D., Elshahed, M.S., & Youssef, N.H. (2015). Draft genome sequence of the environmental isolate Chryseobacterium sp. Hurlbut01. Genome announc.3(5), pii: e01071-15. DOI: 10.1128/genomeA.01071-15

  10. Couger, M.B., Hanafy, R.A., Mitacek, R.M., Budd, C., French, D.P., Hoff, W.D., Elshahed, M.S., & Youssef, N.H. (2015). The draft genome sequence of Xanthomonas sp. Strain Mitacek01 expands the pangenome of a genus of plant pathogens. Genome announc.3(6), pii: e01450-15. DOI: 10.1128/genomeA.01450-15

  11. Couger, M.B., Youssef, N.H., Struchtemeyer, C.G., Liggenstoffer, A.S., & Elshahed, M.S. (2015). Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A. Biotechnol. Biofuels8, 208. DOI: 10.1186/s13068-015-0390-0

  12. Dutta, M.*, Ali, A., & Melcher, U. (2015). Detection, discrimination and discovery of a new Tobacco streak virus strain. J. Virol. Method221, 15-21. DOI: 10.1016/j.jviromet.2014.03.025

  13. Espindola, A.*, Schneider, W., Hoyt, P. R., Marek, S. M., & Garzon, C. (2015). A new approach for detecting fungal and oomycete plant pathogens in next generation sequencing metagenome data utilising electronic probes. International Journal of Data Mining and Bioinformatics12 (2), 115-128. DOI: 10.1504/IJDMB.2015.069422 PMID: 26510298

  14. Farmanesh, B., & Pourhabib, A.* (2015). Sparse pseudo-input local kriging for large non-stationary spatial datasets with exogenous variables. (online 5 August 2015). arXiv: 1508.01248v1

  15. He, Y., Cao, X., Li, K., Hu, Y., Chen, Y., Blissard, G., Kanost, M., & Jiang, H. (2015). A genome-wide analysis of antimicrobial effector genes and their transcription patterns in Manduca sexta. Insect Biochemistry and Molecular Biology62, 23-37. (online 3 February 2015). DOI10.1016/j.ibmb.2015.01.015

  16. Heisterkamp, D.R. (2015, December 9-11.) Lambda-Consensus Clustering. Presented at: ICMLA 2015. Proceedings of the 14th IEEE International Conference on Machine Learning and Applications; Miami, FL.

  17. Mandelli, F., Oliviera-Ramires, B., Couger, M.B., Paixao, D.A., Camilo, C.M., Polikarpov, I.,...Squina, F.M. (2015). Draft genome sequence of the Thermopile Thermis filiformis ATCC 43280, producer of carotenoid-(di)glucoside-branced fatty acid (di)esters and source of hyperthermostable enzymes of biotechnological interest. Genome announc., 3(3). doi:10.1128/genomeA.00475-15

  18. Matyi, S.A., Hoyt, P.R., Ayoubi-Canaan, P., Hasan, N.A., & Gustafson, J.E. (2015). Draft genome sequence of strain ATCC 33958, reported to be Elizabethkingia miricola. Genome Announcements, 3 (4), e00828-15. DOI: 10.1128/genomeA.00828-15

  19. Miao, Z. (2015, November 1-4). On the Lagrangian dual of the maximum quasiclique problem. Presented at: 2015 INFORMS Annual Meeting: Philadelphia, PA.

  20. Moradi, E.*, and Balasundaram, B. (2015). Finding a maximum k-club using the k-clique formulation and canonical hypercube cuts. Optimization Letters, 1-11. (online 14 November 2015). DOI: 10.1007/s11590-015-0971-7

  21. Mortazavaian, H., Fennel, C., & Blum, F. (2015). Structure of the interfacial region in adsorbed poly(vinyl acetate) on silica. Macromolecules, (online 31 December 2015). DOI: 10.1021/acs.macromol.5b02214

  22. Neeman, H., Adams, K., Alexander, J., Brunson, D., Calhous, S.P., Deaton, J., Fotou, F.F., Frinkle. K., Gray, Z., Lemley, E., Louthan, G., Monaco, G., Morris, M., Snow, J., & Zimmermann, B. (2015). On fostering a culture of research cyberinfrastructure grant proposals within a community of service providers in an EPSCoR state. Presented at: XSEDE '15. Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure. Article No. 19, ACM New York, NY. table of contents ISBN: 978-1-4503-3720-5 doi>10.1145/2792745.2792764

  23. Nicholson, S.J., Nickerson, M.L., Dean, M., Song, Y., Hoyt, P.R., Rhee, H., Kim, C., & Puterka, G.J. (2015). The genome of Diuraphis noxia, a global aphid pest of small grains. BMC Genomics16 (429). (online 5 June 2015). doi:10.1186/s12864-015-1525-1

  24. Prabhakaran, M., Couger, M.B., Jackson, C.A., Weirick, T., & Fathepure, B.Z. (2015). Genome sequences of the lignin-degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r isolated from decaying wood. Genome announc.3(2). doi:10.1128/genomeA.00019-15

  25. Shyamal, S., Bhaskaran, R., Priyadoss, G., Durica, D.S., & Anilkumar, G. (2015). Significant fluctuations in ecdysteroid receptor gene (EcR) expression in relation to seasons of molt and reproduction in the grapsid crab, Metapograpsus messor (Brachyura: Decapoda). Gen. Comp. Endocrinol.21, 39-51. doi:10.1016/j.ygcen.2014.11.006

  26. Sunetra, D. Pitts, N. L., Mudron, M., Durica, D., and Mykles, D. (2015). Transcriptome analysis of the molting gland (Y-organ) from the blackback land crab, Gecarcinus lateralisComparative Biochemistry and Physiology Part D: Genomics and Proteomics. (online 2 December 2015). doi:10.1016/j.cbd.2015.11.003

  27. Tetreau, G., Cao, X., Chen, Y., Muthkrishnan, S., Jian, K., Blissard, G., Kanost, M., & Wang, P. (2015). Overview of chitin metabolism enzymes in Manduca sexta: Identification, domain organization, phylogenetic analysis and gene expression. Insect Biochemistry and Molecular Biology62, 114-126.. (online 20 January 2015). doi:10.1016/j.ibmb.2015.01.006

  28. Utt, K.L., Rivero, P., Mehboudi, M., Harriss, E.O., Borunda, M.F., Pacheco-SanJuan, A.A., & Barraza-Lopez, S. (2015). Instrinsic defects, fluctuations of the local shape, and the photo-oxidation of black phosphorus. ACS Central Science1 (6), 320-327. (online 6, August 2015). doi:10.1021/acscentsci.5b00244

  29. Vemula, S., & Crick, C. (2015, June 27-July 2). Hadoop Image Processing Framework. Presented at the 4th IEEE International Congress on Big Data. Proceedings of the 2015 4th IEEE International Congress on Big Data: New York, NY. 

  30. Weitemier, K., Straub, S.C.K., Fishbein, M., & Liston, A. (2015). Intragenomic polymorphisms among high-copy loci: A genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae). PeerJ3 (e718). doi:10.7717/peerj.718

  31. Youssef, N.H., Couger, M.B., McCully, A.L., Criado, A.E., & Elshahed, M.S. (2015). Assessing the global phylum level diversity within the bacterial domain: A review. J. Adv. Res., 6(3), 269-282. doi:10.1016/j.jare.2014.10.005

  32. Yukihara, E. G., Doull, B. A., Ahmed, M., Brons, S., Tessonnier, T., Jäkel, O., & Greilich, S. (2015). Time-resolved optically stimulated luminescence of Al2O3:C for ion beam therapy dosimetry. Physics in Medicine and Biology, 60 (17). (online 13 August 2015). doi:10.1088/0031-9155/60/17/6613

  33. Zhang, X., He, Y., Cao, X., Gunaratna, R.T., Chen, Y., Blissard, G., Kanost, M.R., & Jiang, H. (2015). Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta. Insect Biochemistry and Molecular Biology62, 38-50. (online 18 February 2015). doi:10.1016/j.ibmb.2015.02.00


Dissertations & theses

  1. Buchanan, J.W. (2015, May). Genetic parameter estimation and gene network derivation for fatty acid traits in Angus beef cattle. [dissertation]. [Stillwater (OK)]: Department of Animal Science, Oklahoma State University. Advisor: Megan Rolf.

  2. Cavener, M. (2015, July). Vibrational Structural Markers for Infrared Structural Biology of Arginine in Proteins [senior thesis]. [Stillwater (OK)]: Department of Physics, Oklahoma State University. Advisor: Aihua Xie.

  3. Duan, L. (2015). Investigation of membrane protein structure by NMR [master's thesis]. [Stillwater (OK)]: Department of Physics, Oklahoma State University. Advisor: Donghua Zhou.

  4. Gipson, M. (2015). Betti numbers of edge ideals of cyclic graphs [senior honors thesis]. [Stillwater (OK)]: Department of Mathematics, Oklahoma State University. Advisor: Chris Francisco.

  5. Lin, P. (2015). Application of Nuclear Magnetic Resonance to protein structure and protin-ligand interaction studies [masters thesis]. [Stillwater (OK)]: Department of Physics, Oklahoma State University. Advisor: Donghua Zhou.

  6. Ma, J. (2015, December). Proactive approaches for system design under uncertainty applied to network synthesis and capacity planning [dissertation]. [Stillwater, OK]: Department of Industrial Engineering & Management, Oklahoma State University. Advisor: Baski Balasundaram.




  1. Buchanan, J.W.*, Koltes, J.E., Reecy, J.M., & Mateescu, R.G. (2014). Deriving gene networks underlying fatty acid composition of the triacylglycerol lipid fraction in Angus longissimus muscle. Proceedings: International Plant and Animal Genome Conference (2014 January 11). P769. 
  2. Cao, X., He, Y., Hu Y, Zhang, X., Wang, Y., Zou, Z., Chen, Y., Blissard, G.W., Kanost, M.R., & Jiang, H. (2014). Sequence conservation, phylogenetic relationships, and expression profiles of nondigestive serine proteases and serine protease homolugs in Manduca sexta. Insect Biochem Mol Biol. (online 2014 Dec 19).
  3. Couger, M.B., Pipes, L., Squina, F., Prade, R., Siepel, A., Palermo, R.,...Blood, P.D. (2014). Enabling large-scale next-generation sequence assembly with Blacklight. Concurr. Comput., 26(13), 2157-2166. doi:10.1002/cpe.3231
  4. Durica, D.S., Das, S., Najar, F., Roe, B., Phillips, B., Kappalli, S., & Anikumar, G. (2014). Alternative splicing in the fiddler crab cognate ecdysteroid reception: Variation in receptor isoform expression and DNA binding properties in response to hormone. Gen. Comp. Endocrinol.206, 80-95. DOI: 10.1016/j.ygcen.2014.05.034

  5. Dutta, M.*, Sokhandan-Bashir, N., Palmer, M.W., & Melcher, U. (2014). Genomic characterization of Ambrosia asymptomatic virus 1 and evidence of other Tymovirales members in the Oklahoma tallgrass prairie revealed by sequence analysis. Arch. Virol.159(7), 1755-1764. DOI: 10.1007/s00705-014-1985-7

  6. Farag, I.F., Davis J.P., Youssef N.H., & Elshahed M.S. (2014). Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8). PLoS One, 9(3):e92139. DOI: 10.1371/journal.pone.0092139.

  7. Khan, M.N.A.*, Fan, G., Heisterkamp, D.R., & Yu, L. (2014). Automatic Target Recognition in Infrared Imagery Using Dense HOG Features and Relevance Grouping of Vocabulary. Proceedings of: IEEE Workshop on Perception Beyond Visible Spectrum (in conjunction with CVPR 2014), (2014 June 23).

  8. Lin, P. H.*, Chen, X.*, Moktan, H.*, Arrese, E. L., Duan, L.*Wang, L. Y., Soulages, J. L., & Zhou, D. H. (2014). Membrane attachment and structure models of lipid storage droplet protein 1. BBA-Biomembranes, 1838, 874-881

  9. Ma, J*. (2014, November 9-12). The minimum spanning $k$-core problem with bounded CVaR under probabilistic edge failures. Presented at: 2014 INFORMS Annual Meeting: San Francisco, CA.

  10. Matyi S.A.*, Ramaraj, T., Sundararajan, A., Lindquist, I.E., Devitt, N.P., Schilkey, F.D., Lamichhane-Khadka, R., Hoyt, P.R., Mudge, J., & Gustafson J.E. (2014). Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels. Genome Announc2(4). (online 2014 July 10). pii: e00688-14. DOI: 10.1128/genomeA.00688-14.

  11. Melcher, U., Verma, R., & Schneider, W. (2014). Metagenomic search strategies for interactions among plants and multiple microbes. Frontiers in Plant Science5, article 268. DOI: 10.3389/fpls.2014.00268.

  12. Miao, Z*. (2014, November 9-12). A global optimization approach for the maximum quasi-clique problem. Presented at: 2014 INFORMS Annual Meeting: San Francisco, CA.

  13. Miao, Z.*, Balasundaram, B., & Pasiliao, E.L. (2014). An exact algorithm for the maximum probabilistic clique problem. Journal of Combinatorial Optimization28(1), 105–120. DOI: 10.1007/s10878-013-9699-4

  14. Moradi, E*. (2014, November 9-12). Finding a maximum $k$-club using the $k$-clique formation and lazy cuts. Presented at: 2014 INFORMS Annual Meeting: San Franciso, CA.

  15. Mushfiqual-Alam, Md., Vilankar, K.P., Field, D.J., & Chandler, D.M. (2014). Loca msking in natural images a database analysis. Journal of Vision, 4(8), article 22. (online 2014 July 29)

  16. Nouruzzadeh, P., Myles, C.W., & Vashaee, D. (2014). Structural, electronic, phonon and thermodynamic properties of hypothetical type-VIII clathrates, Ba8Si46 and Ba8Al16Si30 investigated by first principles. Journal of Alloys and Compounds587, 474-480. doi:10.1016/j.jallcom.2013.10.190

  17. Pajouh, F.M.*, Miao, Z.*, & Balasundaram, B. (2014). A branch-and-bound approach for maximum quasi-cliques. Annals of Operations Research, 216(1), 145-161. DOI: 10.1007/s10479-012-1242-y

  18. Ramaraj, T., Matyi, S.A.*, Sundararajan, A., Lindquist, I.E., Devitt, N.P., Schilkey, F.D., Lamichhane-Khadka, R., Hoyt, P.R., Mudge, J., & Gustafson, J.E. (2014). Draft genome sequences of vancomycin-susceptible Staphylococcus aureus related to heterogeneous vancomycin-intermediate S. aureus. Genome Announcements, 2(5), e01033-14. DOI: 10.1128.genomeA.00027-16

  19. Rao, X., Cao, X., He, Y., Hu, Y., Zhang, X., Chen, Y., Blissard, G., Kanost, M.R., Yu, X., & Jiang, H. (2014). Structural features, evolutionary relationships, and transcriptional regulation of C-type lectin-domain proteins in Manduca sexta. Insect Biochem Mol Biol62, 75-85. DOI: 10.1016/j.ibmb.2014.12.006

  20. Sahu, S.S.*, Weirick, T.* & Kaundal, R. (2014). Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches. BMC Bioinformatics, 15(S11): S13. DOI: 10.1186/1471-2105-15-S11-S13.

  21. Schönknecht, G., & Ternes, C. (2014). Gene transfers shaped the evolution of de novo NAD+ biosynthesis in eukaryotes. Genome Biology and Evolution6(9), 2335-2349. DOI: 10.1093/gbe/evu185

  22. Soufiani, A.R.,  Apblett, A., & Materer, N. (2014). DFT Studies of Dimethyl Peroxide Adsorption and Dissociation on MoO3(100) and H0.33MoO3(100) Surfaces. The Journal of Physical Chemistry C.  DOI: 10.1021/jp505258k

  23. Stobbe*, A.H., Schneider, W.L., Hoyt, P.R., & Melcher, U. (2014). Screening metagenomic data for viruses using the e-probe diagnostic nucleic acid Assay (EDNA). Phytopathology104(10):1125-1129. DOI: 10.1094/PHYTO-11-13-0310-R.

  24. Struchtemeyer, C.G., Ranganathan, A., Couger M.B., Liggenstoffer, A.S., Youssef, N.H., & Elshahed, M.S. (2014). Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure. Scientific Reports4: 6892. DOI: 10.1038/srep06892

  25. Ternes, C.M., & Schonknecht, G. (2014). Gene transfers shaped the evolution of de novo NAD+ biosynthesis in eukaryotes. Genome Biology and Evolution, 6(9), 2335-2349. DOI: 10.1093/gbe/evu185

  26. Tetreau, G., Dittmer, N., Xiaolong, C., Agrawal, S., Yun-Ru, C., Muthukrishnan, S., Haobo, J., Blissard, G., Kanost, M., Wang, P. (2014). Analysis of chitin-binding proteins from Manduca sexta provides new insights into evolution of peritrophin A-type chitin-binding domains in insects. Insect Biochemistry and Molecular Biology62, 127-141. DOI: 10.1016/j.ibmb.2014.12.002
  27. Weirick, T.*, Sahu, S.S.*, Mahalingam, R., & Kaundal, R. (2014). LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches. BMC Bioinformatics, 15(Suppl 11):S15. DOI: 10.1186/1471-2105-15-S11-S15

  28. Youssef, N.H., Couger, M.B.*, McCully, A.L., Guerrero-Criado, A.E., & Elshahed, M.S. (2014). Assessing the global phylum level diversity within the bacterial domain: A review. Journal of Advanced Research, 6(3), 269-282. DOI: 10.1016/j.jare.2014.10.005

  29. Zhang, X., Zheng, Y., Cao, X., Ren, R., Yu, X.Q., & Jiang, H. (2014). Identifiation and profiling of Maduca sexta microRNAs and their possible roles in regulating specific transcripts in fat body, hemocytes, and midgut. Insect Bochemistry and Molecular Biology62, 11-22. DOI: 1016.j.ibmb.2014.08.006.


Dissertations, theses & posters

  1. Kang, Z. (2014). Development and applications of infrared structural biology [dissertation]. [Stillwater, OK]: Department of Physics, Oklahoma State University. Advisor: Aihua Xie.

  2. Pennington, S. (2014). Pulsed induction: A method to identify genetic regulators of determination events [dissertation]. [Stillwater, OK]: Department of Biochemistry & Molecular Biology, Oklahoma State University. Advisor: Peter Hoyt.

  3. Soufiani, A.R. (2014). Computational studies of molybdenum oxide clusters and environmental corrosion of Iron and Zinc [dissertation]. [Stillwater, OK]: Departmet of Chemistry, Oklahoma State University. Advisor: Nicholas Materer.




  1. Couger, M.B.*, Pipes, L.*, Mason, C. & Blood, P.D. (2013). Enabling Large-scale Next-generation Sequence Assembly With Blacklight, Concurrency and Computation: Practice and Experience Special Bioinformatics Edition, 26, 2157-2166. DOI: 10.1002/cpe.3231

  2. Couger, M.B., Youssef, N.H., Struchtemeyer, C.G., Liggenstoffer, A.S., Prade, R.A., Najar, F.Z.,...Elshahed, M.S. (2013). The genome of anaerobic fungus Orpinomyces sp. strain C1A reveals the unique revolutionary history of a remarkable plant biomass degrade. Appl. Environ. Microbiol.79(15), 4620-4634. doi:10.1128/aem.00821-13

  3. Coyner, B.S., Braun, J.K., Mares, M.A., & Van Den Bussche, R.A. (2013). Taxonomic validity of species groups in the genus Akodon (Rodentia, Cricetidae). Zoologica Scripta42(4). DOI: 10.1111/zsc.12014

  4. Das. S.*, & Durica, D. (2013). Ecdysteroid receptor signaling disruption obstructs blastemal cell proliferation during limb regeneration in the fiddler crab Uca pugilator. Mol. Cell. Endocrinol.365(2), 249-259. DOI: 10/1016.j.mce.2012/10.026

  5. Davis, M.R., & Clarke, S.L. (2013). Influence of microRNA on the Maintenance of Human Iron Metabolism, Nutrients5, 2611-2628. DOI: 10.3390/nu5072611.

  6. Ding, T., Palmer, M. W., & Melcher, U. (2013). Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria, BMC Microbiology13(1). DOI: 10.1186/1471-2180-13-1.

  7. Francisco, C.A., Mermin, J., & Schweig, J. (2013). Generalizing the Borel property. J. London Math. Soc.87(3), 724-740. DOI: 10.1112/jlms/jds071

  8. Gao, Y., Harris, A.J., Zhou, S., & He, X., (2013). Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains, Molecular Phylogenetics and Evolution68(3), 443-460. DOI: 10.1016/j.ympev.2013.04.026

  9. Haas, B., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P., Bowden, J., Couger, M.B.*, ... Regev, A., (2013). De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity, Nature Protocols8, 1494-1512. DOI: 10.1038/nprot.2013.084

  10. Kaundal, R., Sahu, S.S.*, Verma, R. & Weirick, T.*. (2013). Identification and characterization of plastid-type proteins from sequence-attributed features using machine learning, BMC Bioinformatics, 14(S14): S7. DOI: 10.1186/1471-2105-14-S14-S7.

  11. Le, T., Cheng, C., Sangasoongsong, A., & Bukkapatnam, S.T.S. (2013). Prediction of sleep apnea episodes from wireless wearable multisensory suite. Proceedings of Point-of-Care Healthcare Technologies of the IEEE Engineering in Medicine and Biology Society, 152-155. DOI: 10.1109/PHT.2013.6461307

  12. Lu, H., Singh, R.P., Bardenhagen, S., & Komanduri, R. (2013). Simulations of failure via three-dimensional cracking in fuel cladding for advanced nuclear fuels. Nuclear Energy University Programs, U.S. Department of Energy. Project Number: 09-416.

  13. Ma, J., & Balasundaram, B., (2013). Solving chance-constrained spanning k-core problem via decomposition and integer programming. Proceedings of the 2013 Industrial and Systems Engineering Research Conference (ISERC 2013), 2774-2783. (ProQuest link)

  14. Matyi, S.A., Dupre, J.M., Johnson, W.L., Hoyt, P.R., White, D.G., Brody, T., Odenwald, W.F., & Gustafson, J.E. (2013). Isolation and characterization of Staphylococcus aureus strains from a Paso Del Norte dairy, J. Dairy Sci., 96(6), 3535-3542. DOI: 10.3168/jds-2013-6590.

  15. Matyi, S.A., Hoyt, P.R., Hosoyama, A., Yamazoe, A., Fujita, N., & Gustafson, J.E. (2013). Draft genome sequences of Elizabethkingia meningoseptica, Genome Announcements1(4):e00444-13. DOI: 10.1128/genomeA.00444-13.

  16. Mauro-Herrera, M., Wang, X., Barbier, H., Brutnell, T.P., Devos, K.M., & Doust, A.N. (2013). Genetic Control and Comparative Genomic Analysis of Flowering Time in Setaria (Poaceae), G3-Genes Genomes Genetics, 3(2), 283-295. DOI: 10.1534/g3.112.005207.

  17. Neeman, H., Brunson, D., Deaton, J., Gray, Z., Huebsch, E., Gentis, D., & Horton, D. (2013). The Oklahoma Cyberinfrastructure Initiative. Proc. XSEDE'13, article 70. DOI: 10.1145/2484762.2484793.

  18. Norouzzadeh, P., Myles, C.W., & Vashaee, D. (2013). Electronic, elastic, vibrational and thermodynamic properties of type-VIII clathrates Ba8Ga16Sn30 and Ba8Al16Sn30 by first principles. Journal of Applied Physics114. DOI: 10.1063/1.4826213

  19. Nguyen, M.T., & Rahnavard, N. (2013). Cluster-Based Energy-Efficient Data Collection in Wireless Sensor Networks Utilizing Compressive Sensing. 2013 Military Communications Conference, MILCOM 2013 - 2013 IEEE, 1708-1713, San Diego, CA. DOI: 10.1109/MILCOM.2013.289

  20. Pham, P.*, & Guo, Y. (2013). A Semiclassical Study of Cis-Trans Isomerization in HONO Using an Interpolating Moving Least-Squares Potential, Journal of Chemical Physics, 138(14), 144304. DOI: 10.1063.1.4799270

  21. Schoenknecht, G., Chen, W.H., Ternes, C.M., Barbier, G.G., Srestha, R.P., ... Weber, A.P. (2013). Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote, Science, 339(6124), 1207-1210. DOI: 10.1126/science.1231707

  22. Schrick, E.K., Forget, T.J., Roewe, K.D., Schrick, A.C., Moore, C.E., Golen, J.A., Rheingold, A.L., Materer, N.F, & Weinert, C.S. (2013). Substituent Effects in Digermanes: Electrochemical, Theoretical, and Structural Investigations, Organometallics32(7), 2245-2256. DOI: 10.1021/om400132z

  23. Schumacher, L.L., Love, B.C., Ferrell, M., DeSilva, U., Fernando, R., & Ritchey, J.R. (2013). Canine intestinal histoplasmosis containing Hyphal Forms, Journal of Veterinary Diagnostic Information, 25(2), 304-307. DOI: 10.1177/1040638713479604

  24. Stobbe, A.H.*, Daniels, J.*, Espindola, A.S.*, Verma, R., Melcher, U., Ochoa-Corona, F., Garzon, C., Fletcher, J., & Schneider, W. (2013). E-probe Diagnostic Nucleic acid Analysis (EDNA): A theoretical approach for handling of next generation sequencing data for diagnostics, J. Micro. Methods94(3), 356-366. DOI: 10.1016/j.mimet.2013.07.002

  25. Wang, S., & Rahnavard, N. (2013). Binary Compressive Sensing via Sum of L-1 norm and L-infinity norm Regularization, 2013 Military Communications Conference, MILCOM 2013 - 2013 IEEE, 1616-1621, San Diego, CA. DOI: 10.1109/MILCOM.2013.274

  26. Wasala, L., Talley, J.L., DeSilva, U., Fletcher, J., & Wayadande, A. (2013). Transfer of Escherichia coli O157:H7 to Spinach by House Flies, Musca domestica (Diptera: Muscidae), Phytopathology, 103(4), 373-380. DOI: 10.1094/PHYTO-09-12-0217-FL

  27. Youssef, N.H., Couger, M.B., Struchtemeyer, C.G., Liggenstoffer, A.S., Prade, R.A., Najar, F.Z., Atiyeh, H.K., Wilkins, M.R., & Elshahed, M.S. (2013). Genome of the anaerobic fungus Orpinomyces sp. C1A reveals the unique evolutionary history of a remarkable plant biomass degrader, Appl. Environ. Microbiol79(15), 4620-4634. DOI: 10.1128/AEM.00821-13.


Dissertations, theses & posters

  1. Borja, G. (2013). The evolutionary history of Paysonia (Brassicaceae) [master's thesis]. [Stillwater, OK]: Department of Botany, Oklahoma State University. Advisor: Andrew Doust.

  2. Chen, S. (2013). Nonparametric ANOVA using kernel methods [dissertation]. [Stillwater, OK]: Department of Statistics, Oklahoma State University. Advisor: Ibrahim Ahmad.

  3. Dai, S. (2013 July). The computational studies on Hydrogen bond switch in biological proton transfer [master's thesis]. [Stillwater, OK]: Department of Physics, Oklahoma State University. Advisor: Aihua Xie.

  4. Davis, M.R. (2013). Molecular coordination of Iron homeostasis by miRNA [dissertation]. [Stillwater, OK]: Deparment of Nutritional Sciences, Oklahoma State University. Advisor: Patricia Canaan.

  5. Kang, Z. (2013). Development and application of infrared structural biology [dissertation]. [Stillwater, OK]: Department of Physics, Oklahoma State University. Advisor: Aihua Xie.

  6. Li, X. (2013). A penalized maximum likelihood method for predicting phenotypes from genotypes of arbitrary related individuals [dissertation]. [Stillwater, OK]: Department of Statistics, Oklahoma State University. Advisor: Lan Zhu.    

  7. Nicholson, J. (2013). Methods of association for genome data with rare variants and a multinomal response [dissertation]. [Stillwater, OK]: Department of Statistics, Oklahoma State University. Advisor: Lan Zhu.

  8. Pham, P. (2013). Semiclassical calculations of tunneling using interpolating moving least-squares potentials [dissertation]. [Stillwater, OK]: Department of Physics, Oklahoma State University. Advisor: Yin Guo.

  9. Stobbe, A.H. (2013). Virus detection in a metagenomic sequence dataset, methods and applications [dissertation]. [Stillwater, OK]: Department of Biochemistry & Molecular Biology, Oklahoma State University. Advisor: Ulrich Melcher.

  10. Stowe, M. (2013). Neural network capacity with Delta learning and linear thresholds [master's thesis]. [Stillwater, OK]: Department of Computer Science, Oklahoma State University. Advisor: Subhash Kak.

  11. Weirick, T. (2013). In-silico approaches for the identification and characterization of lignin metabolism-related enzymes and pathways [master's thesis]. [Stillwater, OK]: Department of Biochemistry & Molecular Biology, Oklahoma State University. Advisor: Rakesh Kaundal.




  1. Bukkapatnam, S.T.S., Cheng, C, & Kumara, S. (2012). Time-series informatics for advanced laser based processing and nanomanufacturing. White Paper for Gavriel Salvendy International Symposium on Frontiers in Industrial Engineering.

  2. Cheng, C., Bukkapatnam, S.T.S, Raff, L.M., Hagan, M., & Komanduri, R. (2012). Scaling up Monte Carlo simulation of carbon nanotube nucleation and growth using nonlinear dynamic predictions, Chemical Physics Letters530, 81-85. DOI: 10.1016/j.cplett.2012.01.067.

  3. Cheng, C., Bukkapatnam, S.T.S, Raff, L.M., & Komanduri, R. (2012). Towards control of carbon nanotube synthesis process using prediction-based fast Monte Carlo simulations, Journal of Manufacturing Systems31(4): 438-443. DOI: 10.1016.j.jmsy.2012.06.006.

  4. Cheng, C., Bukkapatnam, S.T.S., Raff, L.M., & Komanduri, R. (2012). Novel Nanoinformatics methods for scaling up atomistic-scale simulation of carbon nanotube synthesis. Proceedings of the 2012 Industrial and Systems Engineering Research Conference.

  5. Constantin, P., Lai, M., Sharma, R., Tseng, Y., & Wu, J. (2012). New numerical results for the surface quasi-geostrophic equation. Journal of Scientific Computing5, 1-28. DOI: 10.1007/s10915-011-9471-9

  6. Davis, M.R., Rendina, E., Peterson, S.K., Lucas, E.A., Smith, B.J., & Clarke, S.L. (2012). Enhanced Expression of Lipogenic Genes May Contribute to Hyperglycemia and Alterations in plasma lipids in response to dietary iron deficiency, Genes & Nutrition, 7(3), 415-425.  (epub 2012 Jan 7). DOI: 10.1007/s12263-D11-0278-y

  7. Espindola, A.S.*, Garzon, C.D., Fletcher, J., & Schneider, W.L. (2012). Validation of EDNA, a newly developed bioinformatics tool, for the detection of Pythium ultimum from metagenomic samples, Phytopathology, 102(supplement), Annual Meeting of the American Phytopathological Society. 

  8. Fernando, B.R., Hermansky, S., Kim, H., Bible, M.R., Carter, S.D., & DeSilva, U. (2012). Impact of diet on swine fecal microbiome. Proceedings of the International Conference on the Status of Plant and Animal Genome Research, San Diego, USA.

  9. Handa, S., & Slaughter, L.M.* (2012). Enantioselective alkynylbenzaldehyde cyclizations catalyzed by chiral gold(I) acyclic diaminocarbene complexes containing weak Au-arene interactions.” Angewandte Chemie International Edition 2012, 51, 2912-2915. Designated a Very Important Paper (top 5%) by the referees and featured on the journal back cover for April 2012

  10. Pajouh, F.M., Miao, Z., & Balasundaram, B. (2012). A branch-and-bound approach for maximum quasi-cliques, Annals of Operations Research216(1), 145-161. DOI: 10.1007/s10479-012-1242-y.

  11. Pelser, P.B., Abbott, R.J, Comes, H.P., Milton, J.J., Moeller, M., Loosely, M.E., Cron, G.V., Barcelona, J.F., Kennedy, A.H., Watson, L.E., Barone, R., Hernández, F., & Kadereit, J.W. (2012). The genetic ghost of an invasion past: Ancient long-distance dispersal, colonization, and extinction revealed by historical hybridization in Senecio, Molecular Ecology, 21, 369-387. DOI: 10.1111/j.1365-294X.2011.05399.x

  12. Ray, A., Saykhedkar, S., Ayoubi-Canaan, P., Hartson, S.D., Prade, R., & Mort, A.J. (2012). Phanerochaete chrysosporium produces a diverse array of extracellular enzymes when grown on sorghum, Applied Microbiology and Biotechnology, 93(5), 2075-2089. DOI: 10.1007/s00253-012-3907-5

  13. Sattar, S., Addo-Quaye, C., Song, Y., Anstead, J.A., Sunkar, R., & Thompson, G.A. (2012). Expression of Small RNA in Aphis gossypii and Its Potential Role in the Resistance Interaction with Melon, PLoS ONE, 7(11), e48579. DOI:10.1371/journal.pone.0048579

  14. Sattar, S., Song, Y., Anstead, J.A., Sunkar, R., & Thompson, G.A. (2012). Cucumis melo microRNA expression profile during aphid herbivory in a resistant and susceptible interaction, Molecular Plant-Microbe Interactions25(6), 839-48. DOI: 10.1094/MPMI-09-11-0252.

  15. Saykhedkar, S., Ray, A., Ayoubi-Canaan, P., Hartson, S.D., Prade, R., & Mort, A.J. (2012). A time course analysis of the extracellular proteome of Aspergillus nidulans growing on sorghum stover, Biotechnology for Biofuels5(1), 52. DOI: 10.1186/1754-6834-5-52

  16. Schneider, W.L., Stobbe, A.H.*, Daniels, J.*, Espindola, A.S.*, Verma, R., & Blagden, T. (2012). Next-generation diagnostics: Eliminating the excessive sequence processing associated with next-generation sequencing using EDNA. Phytopathology 102 (supplement)

  17. Stobbe, A.H.*, Melcher, U.K., Fletcher, J., & Schneider, W.L. (2012). Validation of a unique sequence-based detection of plant pathogens using next-generation sequence data. Phytopathology 102 (supplement)

  18. Stobbe, A.H., Melcher, U., Palmer M.W., Roossinck, M.J., & Shen, G. (2012). Co-divergence and host-switching in the evolution of tobamoviruses, J. Gen. Virol93(Pt. 2), 408 - 418. DOI: 10.1099/vir.0.034280-0.

  19. Stobbe, A.H., Melcher U.K., & Schneider, W.L. (2012). Designing and validation of e-probes to strain type Plum pox virus, Phytopathology, 102 (supplement)

  20. Verma, R. & Melcher, U. (2012). A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins, BMC Bioinformatics13(S15):S9. DOI: 10.1186.1471-2105-13-S15-S9.

  21. Yerramsetty, K.M., Neely, B.J., & Gasem, K.A. (2012). A Non-Linear Structure-Property Model for Octanol-Water Partition Coeefficient, Fluid Phase Equilib., 332, 85–93. DOI: 10.1016/j.fluid.2012.07.001.

  22. Youssef, N.H., Ashlock-Savage, K.N., & Elshahed, M.S. (2012). Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats, Applied and Environmental Microbiology, 78(5),1332-1344. DOI: 10.1128/AEM.07420-11.

  23. Zhu, L., Chen, S., Jiang, Z., Zhang, Z., Ku, H., Li, X., McCann, M., Harris, S., Lust, G., Jones, P., & Todhunter, R. (2012). Identification of quantitative trait loci for canine hip dysplasia by two sequential multipoint linkage analyses, Journal of Applied Statistics39(8), 1719-1731. DOI: 10.1080/02664763.2012.673121.


Dissertations & theses

  1. Adhikari, S. (2012). Differential Gene Expression During Adipogenesis in Cultured Bovine Adipocytes [master's thesis]. [Stillwater, OK].

  2. Ding, T. (2012). The analysis of the diversity and distribution of leaf endophytic bacterial communities [dissertation]. [Stillwater, OK]: Department of Biochemistry & Molecular Biology, Oklahoma State University. Advisor: Ulrich Melcher.

  3. Fernando, B.R. (2012). Metagenomic analysis of microbial communities in the bovine rumen [dissertation]. [Stillwater, OK]: Department of Animal Science, Oklahoma State University. Advisor: Udaya Desilva. Vol. 3554905, Oklahoma State University. Gradworks: 3554905

  4. Krumm, B. (2012). Structural and Functional Studies on the Modulation of Interleukin-18 Activity [dissertation]. [Stillwater, OK]: Department of Biochemistry & Molecular Biology, Oklahoma State University. Advisor: Junpeng Deng.

  5. Ku, H. (2012). Penalized likelihood regression approach for quantitative trait loci mapping [dissertation]. [Stillwater, OK]: Department of Statistics, Oklahoma State University. Advisor: Lan Zhu.

  6. Pajouh, F.M. (2012). Polyhedral combinatorics, complexity & algorithms in k-clubs in graphs [dissertation]. [Stillwater, OK]: Department of Industrial Engineering & Management, Oklahoma State University. Advisor: Baski Balasundaram.




  1. Allred, B.W, Fuhlendorf, S.D., Engle, D.M., & Elmore, R.D. (2011). Ungulate preference for burned patches reveals strength of fire-grazing interaction. Ecology and Evolution, 1(2)132-144 DOI: 10.1002/ece3.12

  2. Allred, B.W., Fuhlendorf, S.D., & Hamilton, R.G. (2011). The role of herbivores in Great Plains conservation: comparative ecology of bison and cattle. Ecosphere, 2(3), 1-17. DOI: 10.1890/ES10-00152.1

  3. Daniels, J., Stobbe, T., Espindola, A., Schneider, W.L., Fletcher, J, et al. (2011). In silico simulation of massively parallel sequencing as a diagnostic tool for bacterial phytopathogens. Phytopathology 101: S41-S41.

  4. Espindola A.S., Stobbe A.H., Daniels J, Fletcher J, Garzon CD, et al. (2011). Design and validation of queries for the detection of Puccinia graminis in simulated metagenomes. Phytopathology 101: S50-S50.

  5. Fernando, B.R., & DeSilva. U. (2011). Phage biome of the bovine rumen. Proceedings of the International Conference on the Status of Plant and Animal Genome Research, San Diego, USA.

  6. Francisco, C.A., Mermin, J., & Schweig, J. (2011). Borel generators. Journal of Algebra, 332(1), 522-542. DOI: 10.1016/j.jalegbra.2010.09.042

  7. Friedenberg, S., Zhu, L., Zhang, Z., Foels, W., Schweitzer, P., et al. (2011). Evaluation of a Fibrillin 2 Gene Haplotype Associated with Hip Dysplasia and Incipient Osteoarthritis in Dogs. American Journal of Veterinary Research, 72(4), 530-540. DOI: 10.2460/ajvr.72.4.530

  8. Harris, A.J., & Xiang Q-Y(Jenny). (2011). The Bayes–DIVA method and its application for testing biogeographic origins of inter-continental disjunct endemics. International Botanical Congress, Melbourne, Australia. Page 278.

  9. Harris, A.J., & Xiang Q-Y(Jenny). (2011). Handling phylogenetic and reconstruction uncertainty in historical biogeographic analysis — The Bayes-DIVA approach and its application for testing biogeographic origins of inter-continental disjunct endemics. Journal of Systematics and Evolution Symposium, Lhasa, Tibet, China.

  10. Ku. H.*, & Zhu, L. (2011). Bayesian Regression Analysis of Quantitative Trait with Correlated Phenotypic Data. JSM proceedings 2011

  11. Ku, H.*, & Zhu, L. (2011). Bayesian regression analysis of quantitative trait with correlated phenotypic data. In JSM Proceedings, Statistical Computing Section. Alexandria, VA:American Statistical Association, pp.4909-4920. 2011.

  12. Link-Pérez, M.A., Watson, L.E., & Hickey, R.J. (2011). Redefinition of Adiantopsis Fée (Pteridaceae): Systematics, diversification, and biogeography. Taxon, 60(5), 1255-1268. (JSTOR link)

  13. Stobbe, A.H., Daniels, J., Espindola, A., Schneider, W.L., Fletcher, J., et. al. (2011). Use of massively parallel sequencing as a diagnostic tool. Phytopathology, 101: S171-S172.

  14. Struchtemeyer, C.G., Davis, J.P., & Elshahed, M.S. (2011). Influence of the Drilling Mud Formultion Prcess on the Bacterial Communities in Thermogenic Natural Gas Wells of the Barnett Shale, Applied and Environmental Microbiology, 77(14), 4744-53. (online 20 May 2011). DOI: 10.1128/AEM.00223-11

  15. Zhu, L., Feng, F., & Bustamante, C. (2011). A Regression-based Approach for Estimating Recombination Rate from Population Genomic Data. International conference on Bioinformatics & Computational Biology, BIOCOMP 2011, 1:215-221, 2011



Presentations, dissertations & theses

  1. Halpin, K.M. (2011). A chloroplast phylogeny of agavaceae subfamily chlorogaloideae with a focus on species relationships in hastingsia [master's thesis]. [Stillwater, OK]: Department of Botany, Oklahoma State University. Advisor: Mark Fishbein.




  1. Bukkapatnam, S.T.S., & Cheng, C. (2010). Forecasting the evolution of nonlinear and nonstationary systems using recurrence-based local Gaussian process models. Physical Review E, 82(5):056206, 2010. 

  2. Liggenstoffer A.S., Youssef, N.H., Couger, M.B.*, & Elshahed, M.S.* (2010). Phylogenetic diversity and community structure of anaerobic fungi (Phylum Neacallymastigales) in ruminant and non-ruminant herbivores The ISME Journal (2010), 1-11

  3. Youssef, N.H., Couger, M.B.*, & Elshahed, M.S.* (2010). Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone spring, OK, USA): the role of the rare biosphere PLoS One. 2010 Aug 26;5(8):e12414.


Dissertations, theses & posters

  1. Yunxing Li: Mechanism of Internal Proton Transfer in Proteins. Master Thesis in Physics, Oklahoma State University. July 2010 (Advisor: Professor Aihua Xie)

  2. Sharma, R.P. (2010). Global regularity or finite time singularity of the surface quasi-geostrophic equations [dissertation]. [Stillwater, OK]: Department of Mathematics, Oklahoma State University. Advisor: Jiahong Wu. 

  3. Monismith Jr., D.R. (2010). The Uses of the Slime Mold Lifecycle as a Model for Numerical Optimization [dissertation]. [Stillwater, OK]: Department of Computer Science, Oklahoma State University. Advisor: Blayne Mayfield.



  1. Zhang, W., & Guo, Y. (2009). First-principles of crystal structures of NO+NO3- under pressure. Solid State Communications, 149(33-34), 1342-1346. DOI: 10.1016/j.ssc.2009.05.027 

Dissertations & theses

  1. Chen S.(2009). Detecting Quantitative Trait Loci for Canine Hip Dysplasia by The Bayesian MCMC Method [master's thesis]. [Stillwater, OK]: Department of Statistics, Oklahoma State University. Advisor: Lan Zhu. 

  2. Zelnick L. (2009). An Evaluation of the SimWalk2 Method for Detecting Genotyping Error [master's thesis]. [Stillwater, OK]: Department of Statistics, Oklahoma State University. Advisor: Lan Zhu. 

  3. Wang Z. (2009). Identify Family ID for Linkage Disequilibrium Analysis [master's thesis]. [Stillwater, OK]: Department of Statistics, Oklahoma State University. Advisor: Lan Zhu.  

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