Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., Duke University 2017
• Research
• 

  Selected Grants

  • Quantifying the genetic diversity of human regulatory element activity awarded by National Institutes of Health 2019 - 2023
  • Identifying Pathogenic Non-Coding Mutations in Rare Mendelian Disease awarded by National Institutes of Health 2019 - 2021
  • The function and regulation of the novel pregnancy-specific hexokinase HKDC1 2017 - 2020
  • Decoding and Reprogramming the Corticosteroid Transcriptional Regulatory Network awarded by National Institutes of Health 2015 - 2018
  • Genetics and Genomics of Maternal Glycemia During Pregnancy awarded by Northwestern University 2013 - 2018
  • Genetics and Evolution of Fetal Human Fat Accretion During Development awarded by Northwestern University 2013 - 2018
  • University of Utah awarded by University of Utah 2017 - 2018
  • EAGER: Graph-based Genome Annotation and Analyses for Plant Genomes awarded by University of Utah 2016 - 2017
  • Modeling the structure & evolution of regulatory regions in eukaryotic genomes awarded by National Institutes of Health 2007 - 2013
  • Function of alpha herpesvirus microRNAs awarded by National Institutes of Health 2010 - 2011
• Publications & Artistic Works
• 

  Selected Publications

  • Books

    • Majoros, William H. Methods for computational gene prediction. Cambridge Univ Pr, 2007.

  • Academic Articles

    • Majoros, William H., Young-Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang, Sarah J. Cunningham, Graham D. Johnson, et al. “Bayesian estimation of genetic regulatory effects in high-throughput reporter assays.” Bioinformatics 36, no. 2 (January 15, 2020): 331–38. https://doi.org/10.1093/bioinformatics/btz545.
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    • Edsall, Lee E., Alejandro Berrio, William H. Majoros, Devjanee Swain-Lenz, Shauna Morrow, Yoichiro Shibata, Alexias Safi, Gregory A. Wray, Gregory E. Crawford, and Andrew S. Allen. “Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach.” Genome Biol Evol 11, no. 10 (October 1, 2019): 3035–53. https://doi.org/10.1093/gbe/evz218.
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    • Johnson, Graham D., Alejandro Barrera, Ian C. McDowell, Anthony M. D’Ippolito, William H. Majoros, Christopher M. Vockley, Xingyan Wang, Andrew S. Allen, and Timothy E. Reddy. “Human genome-wide measurement of drug-responsive regulatory activity.” Nat Commun 9, no. 1 (December 21, 2018): 5317. https://doi.org/10.1038/s41467-018-07607-x.
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    • Majoros, William H., Carson Holt, Michael S. Campbell, Doreen Ware, Mark Yandell, and Timothy E. Reddy. “Predicting gene structure changes resulting from genetic variants via exon definition features.” Bioinformatics 34, no. 21 (November 1, 2018): 3616–23. https://doi.org/10.1093/bioinformatics/bty324.
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    • McDowell, Ian C., Alejandro Barrera, Anthony M. D’Ippolito, Christopher M. Vockley, Linda K. Hong, Sarah M. Leichter, Luke C. Bartelt, et al. “Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.” Genome Res 28, no. 9 (September 2018): 1272–84. https://doi.org/10.1101/gr.233346.117.
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    • D’Ippolito, Anthony M., Ian C. McDowell, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Luke C. Bartelt, Christopher M. Vockley, et al. “Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.” Cell Syst 7, no. 2 (August 22, 2018): 146-160.e7. https://doi.org/10.1016/j.cels.2018.06.007.
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    • Majoros, William H., Michael S. Campbell, Carson Holt, Erin K. DeNardo, Doreen Ware, Andrew S. Allen, Mark Yandell, and Timothy E. Reddy. “High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.” Bioinformatics 33, no. 10 (May 15, 2017): 1437–46. https://doi.org/10.1093/bioinformatics/btw799.
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    • Gussow, Ayal B., Brett R. Copeland, Ryan S. Dhindsa, Quanli Wang, Slavé Petrovski, William H. Majoros, Andrew S. Allen, and David B. Goldstein. “Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.” Plos One 12, no. 8 (2017): e0181604. https://doi.org/10.1371/journal.pone.0181604.
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    • Vockley, Christopher M., Anthony M. D’Ippolito, Ian C. McDowell, William H. Majoros, Alexias Safi, Lingyun Song, Gregory E. Crawford, and Timothy E. Reddy. “Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.” Cell 166, no. 5 (August 25, 2016): 1269-1281.e19. https://doi.org/10.1016/j.cell.2016.07.049.
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    • Snyder-Mackler, Noah, William H. Majoros, Michael L. Yuan, Amanda O. Shaver, Jacob B. Gordon, Gisela H. Kopp, Stephen A. Schlebusch, et al. “Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples.” Genetics 203, no. 2 (June 2016): 699–714. https://doi.org/10.1534/genetics.116.187492.
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    • Vockley, Christopher M., Cong Guo, William H. Majoros, Michael Nodzenski, Denise M. Scholtens, M Geoffrey Hayes, William L. Lowe, and Timothy E. Reddy. “Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.” Genome Res 25, no. 8 (August 2015): 1206–14. https://doi.org/10.1101/gr.190090.115.
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    • Ousterout, D. G., A. M. Kabadi, P. I. Thakore, P. Perez-Pinera, M. T. Brown, W. H. Majoros, T. E. Reddy, and C. A. Gersbach. “Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases.” Molecular Therapy 23, no. 3 (March 5, 2015): 523–32. https://doi.org/10.1038/mt.2014.234.
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    • Ousterout, David G., Ami M. Kabadi, Pratiksha I. Thakore, Pablo Perez-Pinera, Matthew T. Brown, William H. Majoros, Timothy E. Reddy, and Charles A. Gersbach. “Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases.” Mol Ther 23, no. 3 (March 2015): 523–32. https://doi.org/10.1038/mt.2014.234.
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    • Ousterout, David G., Ami M. Kabadi, Pratiksha I. Thakore, William H. Majoros, Timothy E. Reddy, and Charles A. Gersbach. “Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy.” Nat Commun 6 (February 18, 2015): 6244. https://doi.org/10.1038/ncomms7244.
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    • Majoros, William H., Niel Lebeck, Uwe Ohler, and Song Li. “Improved transcript isoform discovery using ORF graphs.” Bioinformatics 30, no. 14 (July 15, 2014): 1958–64. https://doi.org/10.1093/bioinformatics/btu160.
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    • Majoros, William H., Parawee Lekprasert, Neelanjan Mukherjee, Rebecca L. Skalsky, David L. Corcoran, Bryan R. Cullen, and Uwe Ohler. “MicroRNA target site identification by integrating sequence and binding information.” Nat Methods 10, no. 7 (July 2013): 630–33. https://doi.org/10.1038/nmeth.2489.
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    • Pruteanu-Malinici, Iulian, William H. Majoros, and Uwe Ohler. “Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields.” Bioinformatics 29, no. 13 (July 1, 2013): i27–35. https://doi.org/10.1093/bioinformatics/btt206.
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    • Majoros, W. H., P. Lekprasert, N. Mukherjee, R. L. Skalsky, D. L. Corcoran, B. R. Cullen, and U. Ohler. “MicroRNA target site identification by integrating sequence and binding information.” Nature Methods, May 26, 2013. https://doi.org/10.138/nmeth.2489.
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    • LaMonte, Gregory, Nisha Philip, Joseph Reardon, Joshua R. Lacsina, William Majoros, Lesley Chapman, Courtney D. Thornburg, et al. “Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance.” Cell Host Microbe 12, no. 2 (August 16, 2012): 187–99. https://doi.org/10.1016/j.chom.2012.06.007.
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    • Majoros, William H., and Uwe Ohler. “Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.” Plos Comput Biol 6, no. 12 (December 16, 2010): e1001037. https://doi.org/10.1371/journal.pcbi.1001037.
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    • Majoros, William H., and Uwe Ohler. “Complexity reduction in context-dependent DNA substitution models.” Bioinformatics 25, no. 2 (January 15, 2009): 175–82. https://doi.org/10.1093/bioinformatics/btn598.
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    • Rach, Elizabeth A., Hsiang-Yu Yuan, William H. Majoros, Pavel Tomancak, and Uwe Ohler. “Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.” Genome Biol 10, no. 7 (2009): R73. https://doi.org/10.1186/gb-2009-10-7-r73.
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    • Gottwein, Eva, Neelanjan Mukherjee, Christoph Sachse, Corina Frenzel, William H. Majoros, Jen-Tsan A. Chi, Ravi Braich, et al. “A viral microRNA functions as an orthologue of cellular miR-155.” Nature 450, no. 7172 (December 13, 2007): 1096–99. https://doi.org/10.1038/nature05992.
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    • Majoros, William H., and Uwe Ohler. “Spatial preferences of microRNA targets in 3' untranslated regions.” Bmc Genomics 8 (June 7, 2007): 152. https://doi.org/10.1186/1471-2164-8-152.
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    • Eisen, Jonathan A., Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R. Wortman, Jonathan H. Badger, et al. “Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.” Plos Biol 4, no. 9 (September 2006): e286. https://doi.org/10.1371/journal.pbio.0040286.
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    • Majoros, W. H., M. Pertea, and S. L. Salzberg. “Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.” Bioinformatics 21, no. 9 (May 1, 2005): 1782–88. https://doi.org/10.1093/bioinformatics/bti297.
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    • Anderson, I. J., R. F. Watkins, J. Samuelson, D. F. Spencer, William Majoros, M. W. Gray, and B. J. Loftus. “Gene discovery in the Acanthamoeba castellanii genome.” Protist 156 (2005): 203-214-203–14.
    • Majoros, William, Mihaela Pertea, Arthur Delcher, and Steven Salzberg. “Efficient decoding algorithms for generalized hidden Markov model gene finders.” Bmc Bioinformatics 6, no. 16 (2005).
    • Nierman, William, William author 51, William Majoros, and William 97 authors. “Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.” Nature 438 (2005): 1151-1156-1151–56.
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    • Majoros, W. H., M. Pertea, and S. L. Salzberg. “TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.” Bioinformatics 20, no. 16 (November 1, 2004): 2878–79. https://doi.org/10.1093/bioinformatics/bth315.
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    • ENCODE Project Consortium, J. I. “The ENCODE (ENCyclopedia Of DNA Elements) Project.” Science 306, no. 5696 (October 22, 2004): 636–40. https://doi.org/10.1126/science.1105136.
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    • Majoros, William, and Steven Salzberg. “An empirical analysis of training protocols for probabilistic gene finders.” Bmc Bioinformatics 5, no. 206 (2004).
    • Mi, H. “Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster.” Genome Research 13, no. 9 (September 1, 2003): 2118–28. https://doi.org/10.1101/gr.771603.
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    • Majoros, W. H. “GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders.” Nucleic Acids Research 31, no. 13 (July 1, 2003): 3601–4. https://doi.org/10.1093/nar/gkg527.
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    • Majoros, W. H., G. M. Subramanian, and M. D. Yandell. “Identification of key concepts in biomedical literature using a modified Markov heuristic.” Bioinformatics 19, no. 3 (February 12, 2003): 402–7. https://doi.org/10.1093/bioinformatics/btg010.
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    • Mural, Richard J., Eugene W. Myers, Hamilton Smith, George L. Gabor Miklos, Ron Wides, Aaron Halpern, Peter W. Li, et al. “A preliminary comparison of the mouse and human genomes.” International Congress Series 1246 (December 2002): 169–81. https://doi.org/10.1016/s0531-5131(02)01137-8.
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    • Yandell, Mark D., and William H. Majoros. “Genomics and natural language processing.” Nature Reviews Genetics 3, no. 8 (August 2002): 601–10. https://doi.org/10.1038/nrg861.
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    • Mural, R. J. “A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome.” Science 296, no. 5573 (May 31, 2002): 1661–71. https://doi.org/10.1126/science.1069193.
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    • Majoros, William. “Syntactic Structure in Birdsong: Memetic Evolution of Songs or Grammars?” Journal of Memetics 6 (2002).
    • Venter, J. C., J. C. author 249, William Majoros, and William 273 authors. “The sequence of the human genome.” Science 291 (2001): 1304-1351-1304–51.

  • Book Sections

    • Majoros, W. H., I. Korf, and U. Ohler. “Gene prediction methods.” In Bioinformatics: Tools and Applications, 99–119, 2007. https://doi.org/10.1007/978-0-387-92738-1_5.
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    • Majoros, William, and Uwe Ohler. “Advancing the State of the Art in Computational Gene Prediction.” In Proceedings of KDECB / Benelearn ’06. Springer-Verlag, 2007.
    • Majoros, William. “Dynamic programming for gene finders.” In Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics. Wiley, 2005.
    • Majoros, William. “Automatic concept identification in biomedical literature.” In Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics. Wiley, 2005.
• Teaching & Mentoring
• 

  Recent Courses

  • BIOSTAT 914: Graphical Models for Biological Data 2020
  • CBB 914: Graphical Models for Biological Data 2020

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