Peer-reviewed Journal Articles

  1. C.M. Klinger, L. Paoli, R. Newby, M.Y. Wang, H.D. Carroll, J.D. Leblond, C.J. Howe, J.B. Dacks, B. Cahoon, R.G. Dorrell, and E.H. Richardson. 2017. Promiscuous origins and corrective selection underpin the evolution of transcript editing across dinoflagellate plastid lineages. Molecular Biology and Evolution. (Under review).
  2. H.D. Carroll, A.G. Davis, and R. Seipelt-Thiemann. 2017. Gene Family Visualization Server. In preparation.
  3. H.D. Carroll, J.L. Spouge, and M.W. Gonzalez. 2017. The MultiDomainBenchmark Suite: A Multiple-domain Query and Subject Database Suite. In preparation.
  4. H.D. Carroll, S.L. Sheetlin, M.W. Gonzalez, and J.L. Spouge. 2017. PSI-SemiGLOBAL: The Best of PSI-BLAST and GLOBAL. In preparation.
  5. A.B. Cahoon, H.D. Carroll, M.Y. Wang, R.C. Ewool, and R.F. Al-Tobasei. 2017. Analysis of the Karenia Brevis Transcriptome. In preparation.
  6. H.D. Carroll, A.C. Williams, A.G. Davis, and J.L. Spouge. 2015. Improving Retrieval Efficacy of Homology Searches using the False Discovery Rate. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12, 531-537. (web, pdf)
  7. B.T. Grimes, A.K. Sisay, H.D. Carroll, and A.B. Cahoon. 2014. Deep sequencing of the tobacco mitochondrial transcriptome reveals expressed ORFs and numerous editing sites outside coding regions. BMC Genomics 15:31. (web, pdf)
  8. T. O'Connor, K. Sundberg, H. Carroll, M. Clement, and Q. Snell. 2010. Analysis of long branch extraction and long branch shortening. BMC Genomics 11(Suppl 2):S14. (web, pdf)
  9. H.D. Carroll, M.G. Kann, S.L. Sheetlin, and J.L. Spouge. 2010. Threshold Average Precision (TAP-k): A Measure of Retrieval Efficacy Designed for Bioinformatics. Bioinformatics 26:14, 1708-1713. (web, pdf)
  10. K. Clement, N. Gustafson, A. Berbert, H. Carroll, C. Merris, A. Olsen, M. Clement, Q. Snell, J. Allen, and R.J. Roper. 2010. PathGen: A Transitive Gene Pathway Generator. Bioinformatics 26:3, 423-425. (web, pdf)
  11. H. Carroll, A.R. Teichert, J. Krein, K. Sundberg, Q. Snell, and M. Clement. 2009. An open source phylogenetic search and alignment package. International Journal of Bioinformatics Research and Applications 5:3, 349-364. (web, pdf)
  12. K. Sundberg, T. O'Connor, H. Carroll, M. Clement, and Q. Snell. 2008. Parsimony accelerated Maximum Likelihood searches. International Journal of Computational Biology and Drug Design 1:1, 74-87. (web, pdf)
  13. H.D. Carroll, P.G. Ridge, M.J. Clement, and Q.O. Snell. 2007. Phylogenies Scores for Exhaustive Maximum Likelihood and Parsimony Scores Searches. International Journal of Bioinformatics Research and Applications 3:4, 493-503. (web, pdf)
  14. H. Carroll, W. Beckstead, T. O'Connor, M. Ebbert, M. Clement, Q. Snell, and D. McClellan. 2007. DNA Reference Alignment Benchmarks Based on Tertiary Structure of Encoded Proteins. Bioinformatics 23:19, 2648-2649. (web, pdf)

Peer-reviewed Conference Articles

  1. A.C. Williams, A. Santarsiero, C. Meccariello, G. Verhasselt, H.D. Carroll, J.F. Wallin, D. Obbink, and J. Brusuelas. 2015. Proteus: A Platform for Born Digital Critical Editions of Literary and Subliterary Papyri. In 2015 Digital Heritage 2, 453-456. (web, pdf)
  2. A.C. Williams, H.D. Carroll, J.F. Wallin, J. Brusuelas, L. Fortson, A. Lamblin, and H. Yu. 2014. Identification of Ancient Greek Papyrus Fragments Using Genetic Sequence Alignment Algorithms. In 10th IEEE International Conference on e-Science 2, 5-10. (web, pdf)
  3. A.C. Williams, J.F. Wallin, H. Yu, M. Perale, H.D. Carroll, A. Lamblin, L. Fortson, D. Obbink, C.J. Lintott, and J.H. Brusuelas. 2014. A Computational Pipeline for Crowdsourced Transcriptions of Ancient Greek Papyrus Fragments. In IEEE International Conference on Big Data, 100-105. (web, pdf)
  4. H.D. Carroll, A.C. Williams, A.G. Davis, and J.L. Spouge. 2013. False Discovery Rate for Homology Searches. In Advances in Bioinformatics and Computational Biology, J. C. Setubal, and N. F. Almeida (Eds.) 8213, 194-201. (web, pdf)
  5. H. Carroll, M. Clement, Q. Snell, and D. McClellan. 2009. ChemAlign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties. In Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine, 70-73. (web, pdf)
  6. T. O'Connor, K. Sundberg, H. Carroll, M. Clement, and Q. Snell. 2009. Analysis of Long Branch Extraction. In International Conference on Bioinformatics and Computational Biology, 489-495. (pdf)
  7. K. Sundberg, H. Carroll, Q. Snell, and M. Clement. 2008. Incomparability of results between phylogenetic search programs. In International Conference on Bioinformatics and Computational Biology, 81-84. (pdf)
  8. N. Rungta, H. Carroll, E. Mercer, R. Roper, M. Clement, and Q. Snell. 2007. Analyzing Gene Relationships for Down Syndrome with Labeled Transition Graphs. In Proceedings of Formal Methods in Computer Aided Design, 216-219. (web, pdf)
  9. H. Carroll, M. Ebbert, M. Clement, and Q. Snell. 2007. PSODA: Better Tasting and Less Filling Than PAUP. In Proceedings of the 4th Biotechnology and Bioinformatics Symposium, 74-78. (pdf)
  10. J.L. Krein, A.R. Teichert, H.D. Carroll, M.J. Clement, and Q.O. Snell. 2007. PsodaScript: Applying Advanced Language Constructs to Open-source Phylogenetic Search. In Proceedings of the 4th Biotechnology and Bioinformatics Symposium, 89-94. (pdf)
  11. K. Sundberg, T. O'Connor, H. Carroll, M. Clement, and Q. Snell. 2007. Using Parsimony to Guide Maximum Likelihood Searches. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering II, 774-779. (web, pdf)
  12. H. Carroll, P. Ridge, M. Clement, and Q. Snell. 2006. Effects of Gap Open and Gap Extension Penalties. In Proceedings of the Third Biotechnology and Bioinformatics Symposium, 19-23. (pdf)
  13. P. Ridge, H. Carroll, D. Sneddon, M. Clement, and Q. Snell. 2006. Large Grain Size Stochastic Optimization Alignment. In Proceedings of the Sixth IEEE Symposium on BioInformatics and BioEngineering, 127-134. (web, pdf)
  14. H. Carroll, Q. Snell, M. Clement, and K. Crandall. 2005. Phylogenetic Analysis on Large Sequence Data Sets. In Proceedings of the Second Biotechnology and Bioinformatics Symposium, 20-24. (pdf)
  15. H. Carroll, J.K. Flanagan, and S. Baniya. 2005. A Trace-Driven Simulator For Palm OS Devices. In Proceedings of IEEE International Symposium on Performance Analysis of Systems and Software, 157-166. (web, pdf)

Dissertation, Thesis, Book Review and Poster

  1. A.B. Cahoon, H. Carroll, M.Y. Wang, R.J Newby, R.F. Al-Tobasei, R.C. Ewool, D. Evangelista, C.D. Stanley, and J. Leblond. 2015. Production of a complete library of the plastid derived transcripts of Karenia brevis and phylogenetic analysis of 6 proteins adds to the complex story of dinoflagellate endosymbiosis. Botany 2015. (web)
  2. F.H. Gebreyesus, and H.D. Carroll. 2014. RNA-seq Analysis of the Maize Leaf Using de-novo Genome Assemblies. MTSU Scholars' Week. (pdf)
  3. A.C. Williams, J.F. Wallin, and H.D. Carroll. 2014. Identification of Ancient Greek Papyrus Fragments Using Genetic Sequence Alignment Algorithms. MTSU Scholars' Week. (pdf)
  4. A.C. Williams, A.G. Davis, and H.D. Carroll. 2013. False Discovery Rates for Iterative Database Searching. MTSU Scholars' Week. (pdf)
  5. H.D. Carroll, M.G. Kann, S.L. Sheetlin, and J.L. Spouge. 2010. Threshold Average Precision (TAP-k): A Retrieval Efficacy Measure for Bioinformatics. Intelligent Systems for Molecular Biology. (web, pdf)
  6. H.D. Carroll. December 2008. Biologically Relevant Multiple Sequence Alignment. Ph.D. dissertation, Brigham Young University. (pdf)
  7. H. Carroll. 2008. Dynamic homology and phylogenetic systematics: a unified approach using POY. Cladistics 24:6, 1071-1072. (web, pdf)
  8. H.D. Carroll. December 2004. A Trace-Driven Simulator for Palm OS Devices. Master's thesis, Brigham Young University. (pdf)