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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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  • Maulik, R., San, O. (2018). Explicit and Implicit LES Closures for Burgers Turbulence. Journal of Computational and Applied Mathematics, 327, 12-40. DOI: 10.1016/



  • Alderman, P. D., & Stanfill, B. (2017). Quantifying model-structure-and parameter-driven uncertainties in spring wheat phenology prediction with Bayesian analysis. European Journal of Agronomy, 88, 1-9. DOI: 10.1016/j.eja.2016.09.016.

  • 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), e01721-16. DOI: 10.1128/genomeA.01721-16.

  • 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 Announcements, 5(14), e01720-16. DOI: 10.1128/genomeA.01720-16.

  • Babu, K. S., Bajc, B., & Saad, S. (2017). Yukawa sector of minimal SO (10) unification. Journal of High Energy Physics, 2017(2), 136. DOI: 10.1007/JHEP02(2017)136.

  • Babu, K. S., Khanov, A., & Saad, S. (2017). Anarchy with hierarchy: A probabilistic appraisal. Physical Review D, 95(5), 55014. DOI: 10.1103/PhysRevD.95.055014.

  • Cao X., Jiang, H. (2017). An analysis of 67 RNA-seq datasets from various tissues at different stages of a model insect, Manduca sexta. BMC Genomics, 18(1), 796. DOI: 10.1186/s12864-017-4147-y.

  • Cao, X., Gulati, M., & Jiang, H. (2017). Serine protease-related proteins in the malaria mosquito, Anopheles gambiae. Insect Biochemistry and Molecular Biology, 88, 48-62. DOI: 10.1016/j.ibmb.2017.07.008.

  • 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. Medical Physics, 44(5), 1734-1746. DOI: 10.1002/mp.12191.

  • Chuba, D., Goyder, D., Chase, M. W., & Fishbein, M. (2017). Phylogenetics of the African Asclepias Complex (Apocynaceae) Based on Three Plastid DNA Regions. Systematic Botany, 42(1), 148-159. DOI: 10.1600/036364417X694539.

  • 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, 83(10), e00521-17. DOI: 10.1128/AEM.00521-17.

  • Feng, X., Castro, M. C., Linde, E., & Papeş, M. (2017). Armadillo Mapper: A Case Study of an Online Application to Update Estimates of Species’ Potential Distributions. Tropical Conservation Science, 10, 1.94E+15. DOI: 10.1177/1940082917724133.

  • Feng, X., Papes, M. (2017). Can Incomplete Knowledge of Species' Physiology Facilitate Ecological Niche Modelling? A Case Study with Virtual Species. Diversity and Distributions, 23(10), 1157-1168. DOI: 10.1111/ddi.12606.

  • Feng, Y., Zhao, J., Chen, X., Lin, J. (2017). An In Silico Subject-Variability Study of Upper Airway Morphological Influence on the Airflow Regime in a Tracheobronchial Tree. Bioengineering, 4(4), 90. DOI: 10.3390/bioengineering4040090.

  • Frazier, A. E., Hemingway, B., Brasher, J. (2017). Land Surface Heterogeneity and Tornado Formation: A Comparison of Tornado Alley and Dixie Alley. Journal of Climatology and Weather Forecasting, 5(2), 203. DOI: 10.4172/2332-2594.1000203.

  • 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., 244, 316-324. DOI: 10.1016/j.revpalbo.2017.02.002.

  • Harris, A.J., Chen, P.T., Xu, X.W., Zhang, J.Q., Yang, X., Wen, J. (2017). A Molecular Phylogeny of Staphyleaceae: Implications for Generic Delimitation and Classical Biogeographic Disjunctions in the Family. Journal of Systematics and Evolution, 55(2), 124-141. DOI: 10.1111/jse.12236.

  • 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. DOI: 10.1080/0098261X.2017.1296386.

  • Maulik, R., San, O. (2017). Resolution and Energy Dissipation Charactersitics of Implicit LES and Explicit Filtering Models for Compressible Turbulence. Fluids 2017, 2(2), 14. DOI: 10.3390/fluids2020014.

  • Melstrom, R.T. (2017). Where to Drill? The Petroleum Industry's Response to an Endangered Species Listing. Energy Economics, 66, 320-327. DOI: 10.1016/j.eneco.2017.06.028.

  • 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, 0(0), 1-14. DOI: 10.1080/07391102.2017.1333458.

  • Morrison, J.M., Baker, K.D., Zamor, R.M., Nikolai, S., Elshahed, M.S., Youssef, N.H. (2017). Spatiotemporal Analysis of Microbial Community Dynamics During Seasonal Stratification Events in a Freshwater Lake (Grand Lake, OK, USA). PLUS ONE, 12(5), e0177488. DOI: 10.1371/journal.pone.0177488.

  • Morrison, J.M., Murphy, C.L., Baker, K., Zamor, R.M., Nikolai, S.J., Wilder, S., Elshahed, M.S., Youssef, N.H. (2017). Microbial Communities Mediating Algal Deteritus Turnover Under Anaerobic Conditions. PeerJ, 5, e2803. DOI: 10.7717/peerj.2803.

  • Pajouh, F. M., Moradi, E., & Balasundaram, B. (2017). Detecting large risk-averse 2-clubs in graphs with random edge failures. Annals of Operations Research, 249(1-2), 55-73. DOI: 10.1007/s10479-016-2279-0.

  • Passow, C. N., Brown, A. P., Arias‐Rodriquez, L., Yee, M. C., Sockell, A., Schartl, M., ... & Tobler, M. (2017). Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Molecular Ecology, 26(16), 4211-4225. DOI: 10.1111/mec.14198.

  • Passow, C. N., Henpita C., Shaw, J. H., Quackenbush, C. R., Warren, W. C., Schartl, M., Arias-Rodriguez, L., Kelley, J. L., Tobler, M. (2017). The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Molecular Ecology, 1365(294X). DOI: 10.1111/mec.14360.

  • Pleinert, M. O., von Zanthier, J., & Agarwal, G. S. (2017). Hyperradiance from collective behavior of coherently driven atoms. Optica, 4(7), 779-785. DOI: 10.1364/OPTICA.4.000779.

  • Shah, J. K., Marin‐Rimoldi, E., Mullen, R. G., Keene, B. P., Khan, S., Paluch, A. S., ... & Maginn, E. J. (2017). Cassandra: An open source Monte Carlo package for molecular simulation. Journal of Computational Chemistry., 38(19), 1727-1739. DOI: 10.1002/jcc.24807.

  • Smith, P.M., Borunda, M.F. (2017). Torsional Potential Energy Surfaces of Dinitrobenzene Isomers. Advances in Condensed Matter Physics, 2017. DOI: 10.1155/2017/3296845.

  • Wang, B., Yi, H., Xu, K., & Wang, Q. (2017). Prediction of the self-accelerating decomposition temperature of organic peroxides using QSPR models. Journal of Thermal Analysis and Calorimetry, 128(1), 399-406. DOI: 10.1007/s10973-016-5922-8.



  • Babu, K. S., Bajc, B., & Saad, S. (2016). New class of SO (10) models for flavor. Physical Review D, 94(1), 15030. DOI: 10.1103/PhysRevD.94.015030.

  • 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 Protection, 79(4), 574-581. DOI: 10.4315/0362-028X.JFP-15-440.

  • 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. Journal of Computer-Aided Molecular Design, 30(11), 1067-1077. DOI: 10.1007/s10822-016-9961-9..

  • Buchanan, J. W., Reecy, J. M., Garrick, D. J., Duan, Q., Beitz, D. C., Koltes, J. E., ... & Mateescu, R. G. (2016). Deriving Gene Networks from SNP Associated with Triacylglycerol and Phospholipid Fatty Acid Fractions from Ribeyes of Angus Cattle. Frontiers in Genetics, 7, 116. DOI: 10.3389/fgene.2016.00116.

  • 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. Physics in Medicine and Biology, 61(5), 2162. DOI: 10.1088/0031-9155/61/5/2162.

  • 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. Physics in Medicine and Biology, 61(6), 2562. DOI: 10.1088/0031-9155/61/6/2562..

  • Cho, J., Ibbott, G. S., Kerr, M. D., Amos, R. A., Stingo, F. C., Marom, E. M., ... & DeGroot, P. M. (2016). Characterizing proton-activated materials to develop PET-mediated proton range verification markers. Physics in Medicine and Biology, 61(11), N291. DOI: 10.1088/0031-9155/61/11/n291.

  • Cho, J., Wang, M., Gonzalez‐Lepera, C., Mawlawi, O., & Cho, S. H. (2016). Development of bimetallic (Zn@ Au) nanoparticles as potential PET‐imageable radiosensitizers. Medical Physics, 43(8), 4775-4788. DOI: 10.1118/1.4958961.

  • 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 Announcements, 4(1), e01528-15. DOI: 10.1128/genomeA.01528-15.

  • 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, Gecarcinus lateralis. Integrative and Comparative Biology, 56(6), 1103-1112. DOI: 10.1093/icb/icw107.

  • 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, Gecarcinus lateralis. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 17, 26-40. DOI: 10.1016/j.cbd.2015.11.003.

  • Ding, T., & Melcher, U. (2016). Influences of plant species, season and location on leaf endophytic bacterial communities of non-cultivated plants. PLoS ONE, 11(3), e0150895. DOI: 10.1371/journal.pone.0150895.

  • Frahm, K. A., Peffer, M. E., Zhang, J. Y., Luthra, S., Chakka, A. B., Couger, M. B., ... & DeFranco, D. B. (2016). Research resource: the dexamethasone transcriptome in hypothalamic embryonic neural stem cells. Molecular Endocrinology, 30(1), 144-154. DOI: 10.1210/me.2015-1258.

  • Harris, A. J., Fu, C., Xiang, Q. Y. J., Holland, L., & Wen, J. (2016). Testing the monophyly of Aesculus L. and Billia Peyr., woody genera of tribe Hippocastaneae of the Sapindaceae. Molecular Phylogenetics and Evolution, 102, 145-151. DOI: 10.1016/j.ympev.2016.06.001.

  • Kanost, M. R., Arrese, E. L., Cao, X., Chen, Y. R., Chellapilla, S., Goldsmith, M. R., ... & Papanicolaou, A. (2016). Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochemistry and Molecular Biology, 76, 118-147. DOI: 10.1016/j.ibmb.2016.07.005.

  • Kapoor, U., & Shah, J. K. (2016). Preferential Ionic Interactions and Microscopic Structural Changes Drive Nonideality in Binary Ionic Liquid Mixtures as Revealed from Molecular Simulations. Industrial & Engineering Chemistry Research, 55(51), 13132-13146. DOI: 10.1021/acs.iecr.6b03314.

  • 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 Computing, 28(2), 295-307. DOI: 10.1287/ijoc.2015.0679.

  • Maulik, R., & San, O. (2016). A stable and scale-aware dynamic modeling framework for subgrid-scale parameterizations of two-dimensional turbulence. Computers & Fluids.

  • Mortazavian, H., Fennell, C. J., & Blum, F. D. (2016). Surface bonding is stronger for poly (methyl methacrylate) than for poly (vinyl acetate). Macromolecules, 49(11), 4211-4219. DOI: 10.1021/acs.macromol.6b00521.

  • 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. Integrative and Comparative Biology, 56(6), 1183-1191. DOI: 10.1093/icb/icw083.

  • Pajouh, F. M., Balasundaram, B., & Hicks, I. V. (2016). On the 2-club polytope of graphs. Operations Research, 64(6), 1466-1481. DOI: 10.1287/opre.2016.1500.

  • Paranahewage, S. S., Gierhart, C. S., & Fennell, C. J. (2016). Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields. Journal of Computer-Aided Molecular Design, 30(11), 1059-1065. DOI: 10.1007/s10822-016-9950-z..

  • Schneider, W. D. H., Gonçalves, 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. Biotechnology for Biofuels, 9(1), 66. DOI: 10.1186/s13068-016-0476-3.

  • Selvaraju, S., Adhikari, S., Hopson, R. A., Dai, S., Rheingold, A. L., Borunda, M. F., & Nelson, T. L. (2016). Effects of structural variations on the optical and electronic properties of eumelanin-inspired small molecules. Journal of Materials Chemistry C, 4(18), 3995-3999. DOI: 10.1039/C5TC03982G.

  • Singh, A., Fennell, C. J., & Weaver, J. D. (2016). Photocatalyst size controls electron and energy transfer: selectable E/Z isomer synthesis via C–F alkenylation. Chemical Science, 7(11), 6796-6802. DOI: 10.1039/C6SC02422J.


  • Andreason, S., Schneider, W., Wayadande, A. (2016, February). Detection of plant pathogens within insect vector transcriptome sequencing datasets. Presented at the 2016 annual meeting of the Entomological Society of America Southwestern Branch, Tyler, TX.

  • Liang, Y. (2016, June). Bayesian nonparametric inference for panel count data with dependent observation times. Presented at the 2016 ICSA Applied Statistics Symposium, Atlanta, GA.



  • 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 ONE, 10(11), e0143336. DOI: 10.1371/journal.pone.0143336.

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

  • Cao, X., He, Y., Hu, Y., Wang, Y., Chen, Y. R., Bryant, B., ... & Jiang, H. (2015). The immune signaling pathways of Manduca sexta. Insect Biochemistry and Molecular Biology, 62, 64-74. DOI: 10.1016/j.ibmb.2015.03.006.

  • Cao, X., He, Y., Hu, Y., Zhang, X., Wang, Y., Zou, Z., ... & Jiang, H. (2015). Sequence conservation, phylogenetic relationships, and expression profiles of nondigestive serine proteases and serine protease homologs in Manduca sexta. Insect Biochemistry and Molecular Biology, 62, 51-63. DOI: 10.1016/j.ibmb.2014.10.006.

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

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

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

  • 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. Biotechnology for Biofuels, 8(1), 208. DOI: 10.1186/s13068-015-0390-0.

  • Dutta, M., Ali, A., & Melcher, U. (2015). Detection, discrimination and discovery of a new Tobacco streak virus strain. Journal of Virological Methods, 221, 15-21. DOI: 10.1016/j.jviromet.2015.03.025.

  • 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 Bioinformatics, 12(2), 115-128. DOI: 10.1504/IJDMB.2015.069422.

  • He, Y., Cao, X., Li, K., Hu, Y., Chen, Y. R., Blissard, G., ... & Jiang, H. (2015). A genome-wide analysis of antimicrobial effector genes and their transcription patterns in Manduca sexta. Insect Biochemistry and Molecular Biology, 62, 23-37. DOI: 10.1016/j.ibmb.2015.01.015.

  • 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.

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

  • Mortazavian, H., Fennell, C. J., & Blum, F. D. (2015). Structure of the Interfacial Region in Adsorbed Poly (vinyl acetate) on Silica. Macromolecules, 49(1), 298-307. DOI: 10.1021/acs.macromol.5b02214.

  • Nicholson, S. J., Nickerson, M. L., Dean, M., Song, Y., Hoyt, P. R., Rhee, H., ... & Puterka, G. J. (2015). The genome of Diuraphis noxia, a global aphid pest of small grains. BMC Genomics, 16(1), 429. DOI: 10.1186/s12864-015-1525-1.

  • 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 Announcements, 3(2), e00019-15. DOI: 10.1128/genomeA.00019-15.

  • Rao, X. J., Cao, X., He, Y., Hu, Y., Zhang, X., Chen, Y. R., ... & Jiang, H. (2015). Structural features, evolutionary relationships, and transcriptional regulation of C-type lectin-domain proteins in Manduca sexta. Insect Biochemistry and Molecular Biology, 62, 75-85. DOI: 10.1016/j.ibmb.2014.12.006.

  • Shyamal, S., Anilkumar, G., Bhaskaran, R., Doss, G. P., & Durica, D. S. (2015). Significant fluctuations in ecdysteroid receptor gene (EcR) expression in relation to seasons of molt and reproduction in the grapsid crab, Metopograpsus messor (Brachyura: Decapoda). General and Comparative Endocrinology, 211, 39-51. DOI: 10.1016/j.ygcen.2014.11.006.

  • Tetreau, G., Cao, X., Chen, Y. R., Muthukrishnan, S., Jiang, H., Blissard, G. W., ... & Wang, P. (2015). Overview of chitin metabolism enzymes in Manduca sexta: identification, domain organization, phylogenetic analysis and gene expression. Insect Biochemistry and Molecular Biology, 62, 114-126. DOI: 10.1016/j.ibmb.2015.01.006.

  • Tetreau, G., Dittmer, N. T., Cao, X., Agrawal, S., Chen, Y. R., Muthukrishnan, S., ... & Wang, P. (2015). 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 Biology, 62, 127-141. DOI: 10.1016/j.ibmb.2014.12.002.

  • Utt, K. L., Rivero, P., Mehboudi, M., Harriss, E. O., Borunda, M. F., SanJuan, A. A. P., & Barraza-Lopez, S. (2015). Intrinsic defects, fluctuations of the local shape, and the photo-oxidation of black phosphorus. ACS Central Science, 1(6), 320-327. DOI: 10.1021/acscentsci.5b00244.

  • Weitemier, K., Straub, S. C., Fishbein, M., & Liston, A. (2015). Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae). PeerJ, 3, e718. DOI: 10.7717/peerj.718.

  • Youssef, N. H., Couger, M. B., McCully, A. L., Criado, A. E. G., & Elshahed, M. S. (2015). 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.

  • 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), 6613. DOI: 10.1088/0031-9155/60/17/6613.

  • Zhang, X., He, Y., Cao, X., Gunaratna, R. T., Chen, Y. R., Blissard, G., ... & 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 Biology, 62, 38-50. DOI: 10.1016/j.ibmb.2015.02.001.

  • Zhang, X., Zheng, Y., Cao, X., Ren, R., Yu, X. Q., & Jiang, H. (2015). Identification and profiling of Manduca sexta microRNAs and their possible roles in regulating specific transcripts in fat body, hemocytes, and midgut. Insect Biochemistry and Molecular Biology, 62, 11-22. DOI: 10.1016/j.ibmb.2014.08.006.


  • Balasundaram, B. (2015, September). Cliques & Clubs. Presented at a seminar series for the Department of Industrial and Systems Engineering at Texas A&M University, College Station, TX.

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

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

  • Heisterkamp, D.R. (2015, December). Lambda-Consensus Clustering. Presented at the 14th IEEE International Conference on Machine Learning and Applications, Miami, FL.

  • Miao, Z. (2015, November). On the Lagrangian dual of the maximum quasiclique problem. Presented at the 2015 INFORMS Annual Meeting, Philadelphia, PA.

  • Vemula, S., & Crick, C. (2015, June). Hadoop Image Processing Framework. Presented at the 4th IEEE International Congress on Big Data, New York, NY.



  • Alam, M. M., Vilankar, K. P., Field, D. J., & Chandler, D. M. (2014). Local masking in natural images: A database and analysis. Journal of Vision, 14(8), 22-22. DOI: 10.1167/14.8.22.

  • Brian Couger, M., Pipes, L., Squina, F., Prade, R., Siepel, A., Palermo, R., ... & Blood, P. D. (2014). Enabling large‐scale next‐generation sequence assembly with Blacklight. Concurrency and Computation: Practice and Experience, 26(13), 2157-2166. DOI: 10.1002/cpe.3231.

  • Durica, D. S., Das, S., Najar, F., Roe, B., Phillips, B., Kappalli, S., & Anilkumar, G. (2014). Alternative splicing in the fiddler crab cognate ecdysteroid receptor: Variation in receptor isoform expression and DNA binding properties in response to hormone. General and Comparative Endocrinology, 206, 80-95. DOI: 10.1016/j.ygcen.2014.05.034.

  • Dutta, M., Bashir, N. S., 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. Archives of Virology, 159(7), 1755-1764. DOI: 10.1007/s00705-014-1985-7.

  • 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.

  • Lin, P., Chen, X., Moktan, H., Arrese, E. L., Duan, L., Wang, L., ... & Zhou, D. H. (2014). Membrane attachment and structure models of lipid storage droplet protein 1. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1838(3), 874-881. DOI: 10.1016/j.bbamem.2013.12.003.

  • Matyi, S. A., Ramaraj, T., Sundararajan, A., Lindquist, I. E., Devitt, N. P., Schilkey, F. D., ... & Gustafson, J. E. (2014). Draft genomes of heterogeneous vancomycin-intermediate Staphylococcus aureus strain MM66 and MM66 derivatives with altered vancomycin resistance levels. Genome Announcements, 2(4), e00688-14. DOI: 10.1128/genomeA.00688-14.

  • Melcher, U., Verma, R., & Schneider, W. L. (2014). Metagenomic search strategies for interactions among plants and multiple microbes. Frontiers in Plant Science, 5, 268. DOI: 10.3389/fpls.2014.00268.

  • Miao, Z., Balasundaram, B., & Pasiliao, E. L. (2014). An exact algorithm for the maximum probabilistic clique problem. Journal of Combinatorial Optimization, 28(1), 105-120. DOI: 10.1007/s10878-013-9699-4.

  • Norouzzadeh, P., Myles, C. W., & Vashaee, D. (2014). Structural, electronic, phonon and thermodynamic properties of hypothetical type-VIII clathrates Ba 8 Si 46 and Ba 8 Al 16 Si 30 investigated by first principles. Journal of Alloys and Compounds, 587, 474-480. DOI: 10.1016/j.jallcom.2013.10.190.

  • 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.

  • Ramaraj, T., Matyi, S. A., Sundararajan, A., Lindquist, I. E., Devitt, N. P., Schilkey, F. D., ... & Gustafson, J. E. (2014). Draft genome sequences of vancomycin-susceptible Staphylococcus aureus related to heterogeneous vancomycin-intermediate Saureus. Genome Announcements, 2(5), e01033-14. DOI: 10.1128/genomeA.01033-14.

  • Sahu, S. S., Weirick, T., & Kaundal, R. (2014). Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches. BMC Bioinformatics, 15(11), S13. DOI: 10.1186/1471-2105-15-S11-S13.

  • 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. Phytopathology, 104(10), 1125-1129. DOI: 10.1094/PHYTO-11-13-0310-R.

  • 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 Reports, 4. DOI: 10.1038/srep06892.

  • Ternes, C. M., & Schönknecht, 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.

  • 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(11), S15. DOI: 10.1186/1471-2105-15-S11-S15.

NEUP Projects

  • Lu, H., Bukkapatnam, S., Harimkar, S., Singh, R., & Bardenhagen, S. (2014). Simulations of Failure via Three-Dimensional Cracking in Fuel Cladding for Advanced Nuclear Fuels (No. DOE/NEUP--09-818). Univ. of Texas, Dallas, TX (United States); Bardenhagen Consulting (United States); Oklahoma State Univ., OK (United States); Univ. of Tennessee, Knoxville (United States). DOI: 10.2172/1116513.


  • Buchanan, J.W., Koltes, J.E., Reecy, J.M., & Mateescu, R.G. (2014, January). Deriving gene networks underlying fatty acid composition of the triacylglycerol lipid fraction in Angus longissimus muscle. Presented at the International Plant and Animal Genome Conference, San Diego, CA.

  • Khan, M.N.A., Fan, G., Heisterkamp, D.R., & Yu, L. (2014, June). Automatic Target Recognition in Infrared Imagery Using Dense HOG Features and Relevance Grouping of Vocabulary. Presented at the 2014 IEEE Workshop on Perception Beyond Visible Spectrum (in conjunction with CVPR 2014), Columbus, OH.

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

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

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



  • Coyner, B. S., Braun, J. K., Mares, M. A., & Bussche, R. A. (2013). Taxonomic validity of species groups in the genus Akodon (Rodentia, Cricetidae). Zoologica Scripta, 42(4), 335-350. DOI: 10.1111/zsc.12014.

  • Das, S., & Durica, D. S. (2013). Ecdysteroid receptor signaling disruption obstructs blastemal cell proliferation during limb regeneration in the fiddler crab, Uca pugilator. Molecular and Cellular Endocrinology, 365(2), 249-259. DOI: 10.1016/j.mce.2012.10.026.

  • Davis, M., & Clarke, S. (2013). Influence of microRNA on the maintenance of human iron metabolism. Nutrients, 5(7), 2611-2628. DOI: 10.3390/nu5072611.

  • 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 Microbiology, 13(1), 1. DOI: 10.1186/1471-2180-13-1.

  • Gao, Y. D., Harris, A. J., Zhou, S. D., & He, X. J. (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 Evolution, 68(3), 443-460. DOI: 10.1016/j.ympev.2013.04.026.

  • Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., ... & MacManes, M. D. (2013). De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nature protocols, 8(8). DOI: 10.1038/nprot.2013.084.

  • 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(14), S7. DOI: 10.1186/1471-2105-14-S14-S7.

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

  • Matyi, S. A., Hoyt, P. R., Hosoyama, A., Yamazoe, A., Fujita, N., & Gustafson, J. E. (2013). Draft genome sequences of Elizabethkingia meningoseptica. Genome Announcements, 1(4), e00444-13. DOI: 10.1128/genomeA.00444-13.

  • 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.

  • Nof, S. Y., Cheng, G. J., Weiner, A. M., Chen, X. W., Bechar, A., Jones, M. G., ... & Bukkapatnam, S. T. (2013). Laser and photonic systems integration: Emerging innovations and framework for research and education. Human Factors and Ergonomics in Manufacturing & Service Industries, 23(6), 483-516. DOI: 10.1002/hfm.20555.

  • 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 Physics, 114(16), 163509. DOI: 10.1063/1.4826213.

  • Pham, P., & Guo, Y. (2013). A semiclassical study of cis-trans isomerization in HONO using an interpolating moving least-squares potential. The Journal of Chemical Physics, 138(14), 144304. DOI: 10.1063/1.4799270.

  • Schrick, E. K., Forget, T. J., Roewe, K. D., Schrick, A. C., Moore, C. E., Golen, J. A., ... & Weinert, C. S. (2013). Substituent effects in digermanes: electrochemical, theoretical, and structural investigations. Organometallics, 32(7), 2245-2256. DOI: 10.1021/om400132z.

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

  • Schönknecht, G., Chen, W. H., Ternes, C. M., Barbier, G. G., Shrestha, R. P., Stanke, M., ... & Carr, K. (2013). Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science, 339(6124), 1207-1210. DOI: 10.1126/science.1231707.

  • Stobbe, A. H., Daniels, J., Espindola, A. S., Verma, R., Melcher, U., Ochoa-Corona, F., ... & Schneider, W. (2013). E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics. Journal of Microbiological Methods, 94(3), 356-366. DOI: 10.1016/j.mimet.2013.07.002.

  • 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-FI.

  • Youssef, N. H., Couger, M. B., Struchtemeyer, C. G., Liggenstoffer, A. S., Prade, R. A., Najar, F. Z., ... & Elshahed, M. S. (2013). The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Applied and Environmental Microbiology, 79(15), 4620-4634. DOI: 10.1128/AEM.00821-13.


  • Ma, J., & Balasundaram, B. (2013, May). Solving chance-constrained spanning k-core problem via decomposition and integer programming. Presented at the 2013 Industrial and Systems Engineering Research Conference, San Juan, Puerto Rico.



  • Cheng, C., Bukkapatnam, S. T., Raff, L. M., & Komanduri, R. (2012). Towards control of carbon nanotube synthesis process using prediction-based fast Monte Carlo simulations. Journal of Manufacturing Systems, 31(4), 438-443. DOI: 10.1016/j.jmsy.2012.06.006.

  • Cheng, C., Bukkapatnam, S. T., Raff, L. M., Hagan, M., & Komanduri, R. (2012). Monte Carlo simulation of carbon nanotube nucleation and growth using nonlinear dynamic predictions. Chemical Physics Letters, 530, 81-85. DOI: 10.1016/j.cplett.2012.01.067.

  • Constantin, P., Lai, M. C., Sharma, R., Tseng, Y. H., & Wu, J. (2012). New numerical results for the surface quasi-geostrophic equation. Journal of Scientific Computing, 50(1), 1-28. DOI: 10.1007/s10915-011-9471-9.

  • 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. DOI: 10.1007/s12263-011-0278-y.

  • Francisco, C. A., Mermin, J., & Schweig, J. (2012). Generalizing the Borel property. Journal of the London Mathematical Society, 87(3), 724-740. DOI: 10.1112/jlms/jds071.

  • Handa, S., & Slaughter, L. M. (2012). Enantioselective alkynylbenzaldehyde cyclizations catalyzed by chiral gold (I) acyclic diaminocarbene complexes containing weak Au–arene interactions. Angewandte Chemie, 124(12), 2966-2969. DOI: 10.1002/ange.201107789.

  • Pelser, P. B., Abbott, R. J., Comes, H. P., Milton, J. J., Moeller, M., Looseley, M. E., ... & Barone, R. (2012). The genetic ghost of an invasion past: colonization and extinction revealed by historical hybridization in Senecio. Molecular Ecology, 21(2), 369-387. DOI: 10.1111/j.1365-294X.2011.05399.x.

  • 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.

  • 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.

  • 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 Interactions, 25(6), 839-848. DOI: 10.1094/MPMI-09-11-0252.

  • 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 Biofuels, 5(1), 52. DOI: 10.1186/1754-6834-5-52.

  • Stobbe, A. H., Melcher, U., Palmer, M. W., Roossinck, M. J., & Shen, G. (2012). Co-divergence and host-switching in the evolution of tobamoviruses. Journal of General Virology, 93(2), 408-418. DOI: 10.1099/vir.0.034280-0.

  • Stobbe, A., Melcher, U. K., Schneider, W. L. (2012). Designing and validation of e-probes to strain type Plum pox virus. Phytopathology, 102(7), 115.

  • Stobbe, A., 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(7), 114-115.

  • Verma, R., & Melcher, U. (2012). A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins. BMC Bioinformatics, 13(15), S9. DOI: 10.1186/1471-2105-13-S15-S9.

  • Yerramsetty, K. M., Neely, B. J., & Gasem, K. A. (2012). A non-linear structure–property model for octanol–water partition coefficient. Fluid Phase Equilibria, 332, 85-93. DOI: 10.1016/j.fluid.2012.07.001.

  • 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.

  • Zhu, L., Chen, S., Jiang, Z., Zhang, Z., Ku, H. C., Li, X., ... & Todhunter, R. (2012). Identification of quantitative trait loci for canine hip dysplasia by two sequential multipoint linkage analyses. Journal of Applied Statistics, 39(8), 1719-1731. DOI: 10.1080/02664763.2012.673121.


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

  • Espindola, A.S., Garzon, C.D., Fletcher, J., & Schneider, W.L. (2012, August). Validation of EDNA, a newly developed bioinformatics tool, for the detection of Pythium ultimum from metagenomic samples. Presented at the 2012 Annual Meeting of the American Phytopathological Society, Providence, RI.

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

  • Schneider, W.L., Stobbe, A.H., Daniels, J., Espindola, A.S., Verma, R., & Blagden, T., Fletcher, J., Ochoa Corona, F., Garzon, C., Hoyt, P. (2012, August). Next-generation diagnostics: Eliminating the excessive sequence processing associated with next-generation sequencing using EDNA. Presented at the 2012 Annual Meeting of the American Phytopathological Society, Providence, RI.



  • 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.

  • 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.

  • Daniels, J., Stobbe, T., Espindola, A., Schneider, W. L., Fletcher, J., Ochoa-Corona, F. (2011). In silico simulation of massively parallel sequencing as a diagnostic tool for bacterial phytopathogens. Phytopathology, 101(6), S41.

  • Espindola, A. S., Stobbe, A. H., Daniels, J., Fletcher, J., Garzon, C. D., Schneider, W. L. (2011). Design and validation of queries for the detection of Puccinia graminis in simulated metagenomes. Phytopathology, 101(6), S50.

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

  • Friedenberg, S. G., Zhu, L., Zhang, Z., van den Berg Foels, W., Schweitzer, P. A., Wang, W., ... & Jung, S. W. (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.

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

  • Stobbe, A. H., Daniels, J., Espindola, A., Schneider, W. L., Fletcher, J., Melcher, U. K. (2011). Use of massively parallel sequencing as a diagnostic tool. Phytopathology, 101(6), S171-S172.

  • Struchtemeyer, C. G., Davis, J. P., & Elshahed, M. S. (2011). Influence of the drilling mud formulation process on the bacterial communities in thermogenic natural gas wells of the Barnett Shale. Applied and Environmental Microbiology, 77(14), 4744-4753. DOI: 10.1128/AEM.00233-11.


  • Fernando, B.R., & DeSilva. U. (2011, January). Phage biome of the bovine rumen. Presented at the 2011 International Conference on the Status of Plant and Animal Genome Research, San Diego, CA.

  • Harris, A.J., & Xiang Q.Y. (2011, July). The Bayes–DIVA method and its application for testing biogeographic origins of inter-continental disjunct endemics. Presented at the 2011 International Botanical Congress, Melbourne, Australia.

  • Ku. H., & Zhu, L. (2011, August). Bayesian Regression Analysis of Quantitative Trait with Correlated Phenotypic Data. Presented at the 2011 Joint Statistical Meetings, Miami Beach, FL.

  • Zhu, L., Feng, F., & Bustamante, C. (2011, July). A Regression-based Approach for Estimating Recombination Rate from Population Genomic Data. Presented at the 2011 International conference on Bioinformatics & Computational Biology, Las Vegas, NV.



  • Bukkapatnam, S. T., & Cheng, C. (2010). Forecasting the evolution of nonlinear and nonstationary systems using recurrence-based local Gaussian process models. Physical Review E, 82(5), 56206. DOI: 10.1103/PhysRevE.82.056206.

  • 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. ISME Journal, 4(10), 1225-1235.

  • 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, 5(8), e12414. DOI: 10.1371/journal.pone.0012414.



  • Harris, A. J., & XIANG, Q. Y. J. (2009). Estimating ancestral distributions of lineages with uncertain sister groups: a statistical approach to Dispersal–Vicariance Analysis and a case using Aesculus L.(Sapindaceae) including fossils. Journal of Systematics and Evolution, 47(5), 349-368. DOI: 10.1111/j.1759-6831.2009.00044.x.

  • Zhang, W., & Guo, Y. (2009). First-principles study of crystal structures of under pressure. Solid State Communications, 149(33), 1342-1346. DOI: 10.1016/j.ssc.2009.05.027.



  • Andreason, S., Schneider, W., Davis, R., & Wayadande, A. (2008, November). E-probe diagnostic nucleic acid assay (EDNA) detection of Spiroplasma kunkelli in gray lawn leafhopper, Exitianus exitiosu, (Uhl.), transcriptome sequencing dataset. Presented at the 2008 annual meeting of the Entomological Society of America, Minneapolis, MN.

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