Bill Majoros
PhD Candidate
Program in Computational Biology & Bioinformatics
Center for Genomic & Computational Biology
Duke University Medical Center

contact: bmajoros@duke.ed
u
advisor: Dr. Tim Reddy

  




News

  • February 2016: An article I was interviewed for in "The Scientist" has just been published: Life after Sequencing
  • October 2015: I've been invited to serve on the program committee for AlCoB (Algorithms for Computational Biology)
  • April 2015: I received an Honorable Mention for my NSF Graduate Research Fellowship
  • February 2015: Passed my prelim - yay!

Summary Statistics

As of June, 2016:
  • Total publications: 36
  • Total citations: 19,953
  • h-index: 24
  • i10-index: 27
  • Journals I've published in as first author:
    • Nature Methods, Nucleic Acids Research, Genome Research, Bioinformatics, PLoS Computational Biology, BMC Genomics, BMC Bioinformatics
  • Journals I've published in as middle author:
    • Science, Nature, Cell, Genome Biology, PLoS Biology, Genetics, Nature Communications, Molecular Therapy, Bioinformatics, Cell Host and Microbe, Protist
  • Journals I've published in as last author:
    • Nature Reviews: Genetics
  • Years working in applied research: 20
  • Years working in genomics: 17
  • Years at Duke: 11
  • Patent applications: 2
  • Graduate lectures given: 34
  • Undergraduate lectures given: 2
  • Journals I've reviewed papers for: 11
  • Conferences I've reviewed papers for: 4
  • Conference program committees I've served on: 2
  • Invited talks: 1
  • Conference workshops organized: 1
  • People supervised: 3
  • Years programming in C++: 25
  • Years programming in Perl: 18
  • Lines of C++ code written: >>100,000
  • Cups of coffee consumed: +inf


Research Interests

  • The representation and transmission of information in living systems
  • Modeling of biological sequences
  • Grammars and parsing
  • Theory of languages and computation
  • Evolution of syntactic structure in complex bird song
  • Complex adaptive systems and nonlinear dynamics

Publications:

Books:

  1. Methods for Computational Gene Prediction (2007). Majoros WH.  Cambridge University Press.  430 pages.  Amazon.com: five stars.

Book Chapters:

  1. Gene Prediction Methods (2009) Majoros WH, Korf I, Ohler U.  In: Bioinformatics, Tools and Applications. Springer.  pp99-120.
  2. Dynamic programming for gene finders. (2005). Majoros WH.  In: Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics.  Wiley. 
  3. Automatic concept identification in biomedical literature. (2005). Majoros WH.  In: Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics.  Wiley.

Research Articles and Reviews:

  1. Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi AS, Song L, Crawford GE, Reddy TE (2016) - manuscript accepted and embargoed until publication
  2. Synder-Mackler N, Majoros WH, Yuan M, Shaver A, Gordon J, Kopp G, Schlebush S, Wall JD, Alberts SC, Mukherjee S, Xiang Z, Tung J (2016) Genome-wide sequencing and low coverage pedigree analysis from low quality, noninvasively collected samples. Genetics 203:699-714.
  3. Vockley CM*, Guo C*, Majoros WH* (co-1st author), Nodzenski M, Scholtens DM, Hayes MG, Lowe WL, Reddy TE (2015) Massively parallel quantification of the regulatory effects of non-coding genetic variation in a human cohortGenome Research 25:1206-1214.
  4. Ousterout DG, Kabadi AM, Thakore PI, Majoros WH, Reddy TE, Gersbach CA (2015) Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy. Nature Comm 6:6244.
  5. Ousterout DG, Kabadi AM, Thakore PI, Perez-Pinera P, Brown MT, Majoros WH, Reddy TE, Gersbach CA (2015) Correction of dystrophin expression in cells from duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases. Molecular Therapy 23:523-32.
  6. Majoros WH, Lebeck N, Ohler U, Li S (2014) Improved transcript isoform discovery using ORF graphs. Bioinformatics 30:1958-64.
  7. Majoros WH, Lekprasert P, Mukherjee N, Skalsky RL, Corcoran DL, Cullen BR, Ohler U (2013) MicroRNA target site identification by integrating sequence and binding information. Nature Methods 10:630-3.
  8. Pruteanu-Malinici I, Majoros WH, Ohler U (2013) Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields. Bioinformatics 29:i27-35.
  9. LaMonte G, Philip N, Reardon J, Lacsina JR, Majoros W, Chapman L, Thornburg CD, Telen MJ, Ohler U, Nicchitta CV, Haystead T, Chi JT (2012) Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance. Cell Host and Microbe 12:187-99.
  10. Majoros WH, Ohler U (2010) Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs. PLoS Computational Biology 6(12): e1001037
  11. Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U (2009) Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biology 10:R73.
  12. Majoros WH, Ohler U (2008) Complexity Reduction in Context-dependent DNA Substitution Models. Bioinformatics 25:185-82.
  13. Gottwein E, Mukherjee N, Sachse C, Frenzel C, Majoros WH, Chi J-T, Braich R, Manoharan M, Soutschek J, Ohler U, Cullen BR (2007) A viral microRNA functions as an ortholog of cellular miR-155. Nature 450:1096-1099.
  14. Majoros W, Ohler U (2007) Spatial preferences of microRNA targets in 3' untranslated regions. BMC Genomics 8:152.
  15. Majoros W, Ohler U (2007) Advancing the State of the Art in Computational Gene Prediction. Proceedings of KDECB / Benelearn '06, Springer-Verlag.
  16. Allen J, Majoros W, Pertea M, Salzberg SL (2006) JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions Genome Biology 7(Suppl 1):S9.
  17. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, and 37 others (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryotePLoS Biology 4(9).
  18. Nierman W, ... , Majoros WH (author 51 of 97), et al. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438:1151-1156.
  19. Majoros WH, Pertea M, Salzberg SL (2005) Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. Bioinformatics 21:1782-1788.
  20. Majoros W, Pertea M, Delcher A, Salzberg SL (2005) Efficient decoding algorithms for generalized hidden Markov model gene finders. BMC Bioinformatics 6:16.
  21. Anderson IJ, Watkins RF, Samuelson J, Spencer DF, Majoros WH, Gray MW, Loftus BJ (2005). Gene discovery in the Acanthamoeba castellanii genome. (2005). Protist 156:203-14.
  22. Majoros WH, Salzberg SL (2004) An empirical analysis of training protocols for probabilistic gene finders. BMC Bioinformatics 5:206.
  23. Majoros WH, Pertea M, Salzberg SL (2004) TIGRscan and GlimmerHMM : two open source ab initio eukaryotic gene finders. Bioinformatics 20:2878-2879. 
  24. The ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306:636-640.
  25. Majoros WH, Pertea M, Antonescu C, Salzberg SL (2003) GlimmerM, Exonomy, and Unveil: Three ab initio Eukaryotic Genefinders. Nucleic Acids Research 31:3601-3604.
  26. Mi H, Vandergriff J, Campbell M, Marechania A, Majoros WH, Lewis S, Thomas PD, Ashburner M (2003) Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Research 13:2118-2128.
  27. Majoros WH, Subramanian GM, Yandell MD (2002) Identification of Key Concepts in Biomedical Literature using a Modified Markov Heuristic. Bioinformatics 19:402-407.
  28. Yandell MD, Majoros WH (2002) Genomics and Natural Language Processing. Nature Reviews Genetics 3:601.
  29. Holt RA, ... , Majoros WH (author 14 of 123), et al. (2002) The Genome Sequence of the Malaria Mosquito Anopheles gambiaeScience 298:129-149.
  30. Mural RJ, ... , Majoros WH (author 87 of 180), et al. (2002) A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome. Science 296:1661-1671.
  31. Majoros WH (2002) Syntactic Structure in Birdsong: Memetic Evolution of Songs or Grammars? Journal of Memetics, vol 6.
  32. Venter JC, ..., Majoros WH (author 249 of 273), et al. (2001) The sequence of the human genome. Science 291:1304-1351.

Teaching - Computer Science / Computational Biology

  • Introduction to Computational Genomics (CS260 Duke University, Spring 2016) - two lectures
  • Computational and Regulatory Genomics (CBB561 Duke University, Fall 2015) - one lecture
  • Sequencing-based Genomics (CBB720 Duke University, Fall 2014) - two lectures
  • Computational Sequence Biology (CS261 Duke University, Spring 2014) - seven lectures
  • Computational Sequence Biology (CS261 Duke University, Spring 2012) - seven lectures
  • Computational Sequence Biology (CS261 Duke University, Spring 2010) - seven lectures
  • Computational Biology of Gene Regulation (CS261 Duke University, Spring 2008) - five lectures
  • Computational Biology of Gene Regulation (CS261 Duke University, Fall 2006) - five lectures

Employment

  • 2013-201x Duke University (PhD Student / Graduate Research Assistant)
  • 2005-2013 Duke University (Bioinformatics Researcher)
  • 2002-2005 TIGR - The Institute for Genomic Research (Bioinformatics Researcher)
  • 1999-2002 Celera Genomics (Computer Scientist)
  • 1996-1999 Thomson Labs / Reuters / ISI (Senior Researcher)
  • 1995-1996 Lockheed-Martin (Programmer/Analyst - TOP SECRET security clearance / U.S. Dept. of Defense)
  • 1992-1992 Teva Pharmaceuticals
  • 1991-1991 IBM
  • 1990-1990 Teva Pharmaceuticals

Education

Penn State University - B.Sc. in Computer Science, with High Distinction, spring 1994 (gpa=3.93/4.00; 4.00/4.00 in major); electives: Theory of Languages and Computation, Compiler Construction, Number Theory, Linear Programming. 

Duke University - PhD Program in Computational Biology (enrolled Aug. 2013, prelim Feb. 2015: passed)

Awards and Scholarships

  • Honorable Mention: NSF Graduate Research Fellowship (2015)
  • Chris Mader Memorial Scholarship (1992-1994)
  • Phi Kappa Phi Honor Society (1991-1994)

Supervisory Experience:

  • Mentor of graduate rotation student (spring, 2015)
  • Supervisor of undergraduate summer intern (two summers: 2011, 2012)
  • Software team leader (1998)

Invited Talks:

  • Knowledge Discovery and Emergent Complexity in Bioinformatics, Ghent, Belgium, 2006

Contributions as Peer Reviewer:

  • Journals I've reviewed papers for:
    • Bioinformatics
    • Nucleic Acids Research
    • PLoS Computational Biology
    • Journal of Theoretical Biology
    • Genomics
    • Journal of Computational Biology
    • European Journal of Human Genetics
    • PLoS ONE
    • BMC Bioinformatics
    • Plant Physiology
    • Computation
  • Conferences I've reviewed papers for:
    • ISMB
    • RECOMB
    • NIPS
    • WABI
  • Program Committees I've served on:
    • ISMB 2005 (Intelligent Systems for Molecular Biology)
    • AlCoB 2016 (Algorithms for Computational Biology)

Professional and Scientific Societies (past/present):

  • International Society for Computational Biology
  • Society for the Study of Evolution
  • American Ornithologists' Union

Patent Applications:

  • US 20050240583 - Literature mining pipeline - Applera Corp. (abandoned)
  • US 20060111915 - Hypothesis generation system - Applera Corp. (abandoned)





Click to buy my book:






This was supposed to be on the cover of my 2007 book, but the publisher of another book felt it was too similar to their title.



I took this photo of the Duke Chapel in winter using a Canon EOS 30D DSLR camera and a Tokina wide-angle lens. This is an HDR (High Dynamic Range) image, formed by merging multiple images at several exposure values.