Publications

Doctor thesis

  • Herndon, N. (2016). Domain Adaptation Algorithms for Biological Sequence Classification. Kansas State University.

Master thesis

Refereed Journal Articles

  1.  Kanost, M. R., Arrese, E. L., Cao, X., Chen, Y.-R., Chellapilla, S., Goldsmith, M. R., Grosse-Wilde, E., Heckel, D. G., Herndon, N., Jiang, H., Papanicolaou, A., Qu, J., Soulages, J. L., Vogel, H., Walters, J., Waterhouse, R. M., Ahn, S.-J., Almeida, F. C., An, C., Aqrawi, P., Bretschneider, A., Bryant, W. B., Bucks, S., Chao, H., Chevignon, G., Christen, J. M., Clarke, D. F., Dittmer, N. T., Ferguson, L. C., Garavelou, S., Gordon, K. H., Gunaratna, R. T., Han, Y., Hauser, F., He, Y., Heidel-Fischer, H., Hirsh, A., Hu, Y., Jiang, H., Kalra, D., Klinner, C., König, C., Kovar, C., Kroll, A. R., Kuwar, S. S., Lee, S. L., Lehman, R., Li, K., Li, Z., Liang, H., Lovelace, S., Lu, Z., Mansfield, J. H., McCulloch, K. J., Mathew, T., Morton, B., Muzny, D. M., Neunemann, D., Ongeri, F., Pauchet, Y., Pu, L.-L., Pyrousis, I., Rao, X.-J., Redding, A., Roesel, C., Sanchez- Gracia, A., Schaack, S., Shukla, A., Tetreau, G., Wang, Y., Xiong, G.-H., Traut, W., Walsh, T. K., Worley, K. C., Wu, D., Wu, W., Wu, Y.-Q., Zhang, X., Zou, Z., Zucker, H., Briscoe, A. D., Burmester, T., Clem, R. J., Feyereisen, R., Grimmelikhuijzen, C. J., Hamodrakas, S. J., Hansson, B. S., Huguet, E., Jermiin, L. S., Lan, Q., Lehman, H. K., Lorenzen, M., Merzendorfer, H., Michalopoulos, I., Morton, D. B., Muthukrishnan, S., Oakeshott, J. G., Palmer, W., Park, Y., Passarelli, A. L., Rozas, J., Schwartz, L. M., Smith, W., Southgate, A., Vilcinskas, A., Vogt, R., Wang, P., Werren, J., Yu, X.-Q., Zhou, J.-J., Brown, S. J., Scherer, S. E., Richards, S., and Blissard, G. W.. (2016). Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochemistry and Molecular Biology 76 (2016): 118-147.
  2. Herndon, N., and Caragea, D. (2016). An evaluation of approaches for using unlabeled data with domain adaptation. Network Modeling Analysis in Health Informatics and Bioinformatics, 5(25):1-12, 2016.
  3. Raithel, S., Johnson, L., Galliart, M., Brown, S. J., Shelton, J. M., Herndon, N., and Bello, N. M. (2016). Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii. BMC Genomics, 17(140):1-16, 2016.
  4. Herndon, N. and Caragea, D. (2016). A Study of Domain Adaptation Classifiers Derived from Logistic Regression for the Task of Splice Site Prediction. IEEE Transactions on NanoBioscience, PP(99):1-9, 2016.
  5. Tangirala, K., Herndon, N., and Caragea, D. (2016). A Comparative Analysis between k-mers and Community Detection-based Features for the Task of Protein Classification. IEEE Transactions on NanoBioscience, PP(99):1-9, 2016.
  6. Shelton, J. M., Coleman, M. C., Herndon, N., Lu, N., Lam, E. T., Anantharaman, T., Sheth, P., and Brown, S. J. (2015). Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool. BMC Genomics 2015, 16(734):1-16, 2015.
  7. Zhao, C., Escalante, L., Chen, H., Benatti, T., Qu, J., Chellapilla, S., Waterhouse, R., Wheeler, D., Andersson, M., Bao, R., Batterton, M., Behura, S., Blankenburg, K., Caragea, D., Carolan, J., Coyle, M., El-Bouhssini, M., Francisco, L., Friedrich, M., Gill, N., Grace, T., Grimmelikhuijzen, C., Han, Y., Hauser, F., Herndon, N., Holder, M., Ioannidis, P., Jackson, L., Javaid, M., Jhangiani, S., Johnson, A., Kalra, D., Korchina, V., Kovar, C., Lara, F., Lee, S., Liu, X., Löfstedt, C., Mata, R., Mathew, T., Muzny, D., Nagar, S., Nazareth, L., Okwuonu, G., Ongeri, F., Perales, L., Peterson, B., Pu, L.-L., Robertson, H., Schemerhorn, B., Scherer, S., Shreve, J., Simmons, D., Subramanyam, S., Thornton, R., Xue, K., Weissenberger, G., Williams, C., Worley, K., Zhu, D., Zhu, Y., Harris, M., Shukle, R., Werren, J., Zdobnov, E., Chen, M.-S., Brown, S., Stuart, J., and Richards, S. (2015). A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor. Current Biology, 25(5):613-620, 2015.

Refereed Book Chapters

  1. Herndon, N. and Caragea, D. (2015). Empirical Study of Domain Adaptation Algorithms on the Task of Splice Site Prediction. In Biomedical Engineering Systems and Technologies, ser. Communications in Computer and Information Science, Springer Berlin Heidelberg, 2015, vol. 511, pp. 195-211.
  2. Herndon, N. and Caragea, D. (2014). Predicting Protein Localization Using a Domain Adaptation Approach. In Biomedical Engineering Systems and Technologies, ser. Communications in Computer and Information Science, Springer Berlin Heidelberg, 2014, vol. 452, pp. 191-206.

Refereed Conference Papers

  1. Herndon, N., Grau, E. S., Batra, I., Demurjian Jr., S. A., Vasquez-Gross, H. A., Staton, M. E., and Wegrzyn, J. L. (2016). CartograTree: Enabling Landscape Genomics for Forest Trees. In Proceedings of the Open Source Geospatial Research & Education Symposium (OGRS 2016), Perugia, Italy, pp. 1-7. [Short paper]
  2. Herndon, N. and Caragea, D. (2016). Ab initio Splice Site Prediction with Simple Domain Adaptation Classifiers. In Proceedings of the 7th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2016), Rome, Italy, pp. 245-252. [Short paper]
  3. Roy, S., DeLoach, J., Li, Y., Herndon, N., Caragea, D., Ou, X., Ranganath, V. P., Li, H., and Guevara, N. (2015). Experimental Study with Real-world Data for Android App Security Analysis using Machine Learning. In Proceedings of the 2015 Annual Computer Security Applications Conference (ACSAC 2015), Los Angeles, CA, pp. 81-90. [Regular paper; acceptance rate 25%]
  4. Herndon, N. and Caragea, D. (2015). An Evaluation of Self-training Styles for Domain Adaptation on the Task of Splice Site Prediction. In Proceedings of the 2015 International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics (HI-BI-BI 2015), Paris, France, pp. 1042-1047. [Regular paper; acceptance rate 35%; best paper award]
  5. Herndon, N. and Caragea, D. (2015). Domain Adaptation with Logistic Regression for the Task of Splice Site Prediction. In Proceedings of the 11th International Symposium on Bioinformatics Research and Applications (ISBRA 2015), Norfolk, VA, pp. 125-137. [Regular paper; acceptance rate 35%]
  6. Tangirala, K., Herndon, N., and Caragea, D. (2015). Community Detection-Based Feature Construction for Protein Sequence Classification. In Proceedings of the 11th International Symposium on Bioinformatics Research and Applications (ISBRA 2015), Norfolk, VA, pp. 331-342. [Regular paper; acceptance rate 35%;]
  7. Li, H., Guevara, N., Herndon, N., Caragea, D., Neppalli, K., Caragea, C., Squicciarini, A., and Tapia, A. (2015). Twitter Mining for Disaster Response: A Domain Adaptation Approach. In Proceedings of the 12th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2015), Kristiansand, Norway. [Short paper; acceptance rate 70%]
  8. Herndon, N., Tangirala, K., and Caragea, D. (2014). Predicting Protein Localization Using a Domain Adaptation Naive Bayes Classifier with Burrows Wheeler Transform Features. In Proceedings of the 6th IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), Belfast, UK, pp. 501-504. [Short paper; acceptance rate 38%]
  9. Herndon, N. and Caragea, D. (2014). Empirical Study of Domain Adaptation with Naive Bayes on the Task of Splice Site Prediction. In Proceedings of the 5th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2014), Angers, France, pp. 57-67. [Regular paper; acceptance rate 14%; nominated for best paper award]
  10. Herndon, N. and Caragea, D. (2013). Naive Bayes Domain Adaptation for Biological Sequences. In Proceedings of the 4th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2013), Barcelona, Spain, pp. 62-70. [Regular paper; acceptance rate 10%; nominated for best student paper award]
  11. Vert, G. and Herndon, N. (2006). Secure Simultaneous Search of Distributed, Heterogeneous Bioinformatics Databases. In Proceedings of the 2006 International Conference on Security & Management (SAM 2006), Las Vegas, NV, USA, pp. 384-389.

Posters and Presentations

  1. Herndon, N., Lin, Q., Wynne, M., Grau, E. S., Ficklin, S., Staton, M. E., Jung, S., Main, D., Feltus, A., Gessler, D., and Wegrzyn, J. L. (2017). CartograTree workflows with Tripal API for association mapping in forest trees. Computer demonstration, and poster presentation at the 25th International Plant and Animal Genome Conference (PAG XXV), January 14-18, 2017, San Diego, CA.
  2. Grau, E. S., Herndon, N., Demurjian Jr., S. A., Lin, Q., Wynne, M., Gessler, D., Feltus, A., Staton, M. E., Ficklin, S., Main, D., and Wegrzyn, J. L. (2017). TreeGenes: Genetic and Genomic Resources for Forest Trees. Poster presented by E. S. Grau at the 25th International Plant and Animal Genome Conference (PAG XXV), January 14-18, 2017, San Diego, CA.
  3. Lin, Q., Herndon, N., Grau, E. S., Ficklin, S., Staton, M. E., Jung, S., Main, D., Feltus, A., and Wegrzyn, J. L. (2017). A Novel Tripal Database Module and Workflow to Facilitate Variant Mapping and Detection in Non-Model Plant Species. Poster presented by Q. Lin at the 25th International Plant and Animal Genome Conference (PAG XXV), January 14-18, 2017, San Diego, CA.
  4. Herndon, N., Grau, E. S., Batra, I., Demurjian Jr., S. A., Vasquez-Gross, H. A., Staton, M. E., and Wegrzyn, J. L. (2016). CartograTree: Enabling Landscape Genomics for Forest Trees. Oral presentation at the Open Source Geospatial Research & Education Symposium (OGRS 2016), October 12-14, 2016, Perugia, Italy.
  5. Herndon, N. and Caragea, D. (2016). Ab initio Splice Site Prediction with Simple Domain Adaptation Classifiers. Oral presentation at the 7th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2016), February 21-23, 2016, Rome, Italy.
  6. Herndon, N. and Caragea, D. Domain Adaptation Algorithms for ab initio Splice Site Prediction. Poster presentation at the First Annual Midwest Bioinformatics Conference, October 15-16, 2015, Kansas City, MO.
  7. Herndon, N. and Caragea, D. An Evaluation of Self-training Styles for Domain Adaptation on the Task of Splice Site Prediction. Oral presentation at the 2015 International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics (HI-BI-BI 2015), August 26-27, Paris, France.
  8. Donghum, K., Herndon, N., Cheng, C., Nai, A. D. S., Jaworski, D., Ganta, R., and Park, Y. Transcriptome of the lone star tick, Amblyomma americanum, revealing the molecular interaction between the vector and the pathogen Ehrlichia chaffeensis. Poster presented by K. Donghum at the 9th Arthropod Genomics Symposium (AGS 2015), June 17-19, 2015, Manhattan, KS.
  9. Herndon, N., and Caragea, D. Domain Adaptation with Logistic Regression for the Task of Splice Site Prediction. Oral presentation at the 11th International Symposium on Bioinformatics Research and Applications (ISBRA 2015), June 7-10, 2015, Norfolk, VA.
  10. Tangirala, K., Herndon, N., and Caragea, D. Community Detection-Based Feature Construction for Protein Sequence Classification. Oral presentation at the 11th International Symposium on Bioinformatics Research and Applications (ISBRA 2015), June 7-10, 2015, Norfolk, VA.
  11. Herndon, N., Tangirala, K., and Caragea, D. Predicting Protein Localization Using a Domain Adaptation Naive Bayes Classifier with Burrows Wheeler Transform Features. Oral presentation at the 6th IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), November 2-5, 2014, Belfast, UK.
  12. Stanescu, A. and Caragea, D. Ensemble-based semi-supervised learning approaches for imbalanced splice site datasets. Regular paper presented by N. Herndon at the 6th IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), November 2-5, 2014, Belfast, UK.
  13. Herndon, N. and Caragea, D. Empirical Study of Domain Adaptation with Naive Bayes on the Task of Splice Site Prediction. Oral presentation at the 5th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2014), March 3-6, 2014, Angers, France.
  14. Tangirala, K. and Caragea, D. Generating Features Using Burrows Wheeler Transformation for Biological Sequence Classification. Short paper presented by N. Herndon at the 5th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2014), March 3-6, 2014, Angers, France.
  15. Herndon, N., Shelton, J. M., Andrews, W., Wang, W., and Brown, S. J. Improving the Tribolium draft Assembly with Physical Maps Based on Imaging Ultra-Long Single DNA Molecules. Poster presentation at the 22nd International Plant and Animal Genome Conference (PAG XXII), January 11-15, 2014, San Diego, CA.
  16. Shelton, J. M., Herndon, N., Gray, M. M., Liang, H., Durrett, T., Johnson, L., Akhunova, A., and Brown, S. J. Multi-K-Mer de novo Transcriptome Assembly, Validation, and Count Summarizing for Four Plant Taxa. Poster presented by J. M. Shelton at the 22nd International Plant and Animal Genome Conference (PAG XXII), January 11-15, 2014, San Diego, CA.
  17. Giraldo, M. C., Dalby, M., Herndon, N., Zhou, X., Jayasundera, K. B., Tao, A., Xu, J. R., and Valent, B. Identification of Rice Proteins Interacting with Magnaporthe oryzae Effector Proteins. Poster presented by M. C. Giraldo at the 6th International Rice Blast Conference (IRBC 2013), August 20-24, 2013, Jejudo, South Korea.
  18. Herndon, N. and Caragea, D. Naive Bayes Domain Adaptation for Biological Sequences. Oral presentation at the 4th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2013), Feb 11-14, 2013, Barcelona, Spain.
  19. Herndon, N. and Brown, S. J. Improving the T.castaneum genome assembly with 3 mate pairs jumping libraries. Oral presentation at K-INBRE Bioinformatics Core Minisymposium, Jan 2013.
  20. Shelton, J. M., Gray, M., Brown, S. J., Chellapilla, S., Herndon, N., Akhunova, A., Akhunov, E., Liang, H., and Johnson, L. C. De novo Transcriptome of Two Edaphically and Phenotypically Divergent Grasses: Dominant Forage Grass Big Bluestem Andropogon gerardii ssp. gerardii and Drought-Tolerant Sand Bluestem Andropogon gerardii ssp. hallii. Poster presented by J. M. Shelton at the 21st International Plant and Animal Genome Conference (PAG XXI), January 12-16, 2013, San Diego, CA.
  21. Herndon, N. and Caragea, D. Domain Adaptation for Genome-Wide Splice Site Prediction. Oral presentation at K-INBRE Bioinformatics GRA summit, Jan 2012.
  22. Herndon, N., Osei-Boadi, K., Jiang, D., Caragea, D., and Brown, S. J. MAKER and Apollo: tools for genome annotation. Oral presentation at the Fourth K-INBRE Bioinformatics GRA Summit, July 2010, Manhattan, KS.