Donald Seto, Ph.D.
Microbial Genomics and Diversity
(703) 993-8403, phone
Research Group News and Updates:
- S Dehghan, et al. (2013). Virology 443: 197-207 is Selected as a "Highlighted Article" by the Editors of Virology.
- Alumnus Postdoctoral Fellow, Raja Mazumder is an Associate Professor at George Washington University (School of Medicine), WA DC. August 2011.
- Alumnus PhD student, Padmanabhan Mahadevan is an Assistant Professor in the Dept. of Biology, University of Tampa, FL. August 2011.
- Alumnus Bioinformatics Analyst, Shoaleh Dehghan is a Professorial Lecturer at American University, September 2011.
- Alumnus Postdoctoral Fellow, Anjan Purkayastha is a Senior Computational Biologist at TessArae, LLC, VA, February 2011.
- Alumnus PhD student, Michael Walsh is a postdoc in Cancer Genomics at the Mayo Clinic in Jacksonville, FL. October 2010.
Areas of Scientific
Interest and Specialization:
sequencing and analysis of
viral genomes; phylogeny and mechanisms of adenovirus evolution.
Development of software tools
annotation; tools for whole genome comparisons/analysis.
Development and validation of
DNA-based molecular diagnostics/microarray pathogen detection (USAF,
SG/R: EOS Program)
(-ended Oct.31, 2004).
I have extensive experience and interests in
analysis, genomics and biochemistry. An additional expertise is
in nucleic acids core facilities development, operations and management
from my diverse opportunities.
Advisor to the Surgeon General and the Director of Molecular
Diagnostics for the USAF-EOS program, I have project management
experience, dealing with research groups at the USAF Surgeon General’s
Office, AFIP, NHRC, NRL and LAFB (see below for an acronym key), as
well as arranging, directing and managing contract work with
Commonwealth Biotechnologies, Inc. and Virapur, Inc. My lab’s
current focus is in software tools development for whole genome data
mining and analyses, and in the genomic and bioinformatics analysis of
adenovirus genomes, with emphasis on the evolution and natural
variation of these genomes.
Academic labs (my laboratory at GMU and Lee Hood laboratory at Caltech)
Government labs (Molecular Endocrinology Branch at NIDDK/NIH and at
Commercial labs (DuPont-Merck Pharm., Digital Genes Tech. and GeneSys
Software development for whole genome
comparisons and analyses
Using virus genome data, e.g., adenoviruses and poxviruses, the Seto
Research Group has developed, validated and implemented two
net-accessible interactive and “on-the-fly” genome comparison software
The first, GeneOrder, compares two genomes to determine synteny and
gene order by using a BLAST algorithm. The second, CoreGenes,
analyzes up to five genomes in order to catalogue genes that have
sequence relationships with each other- e.g., ‘alphabet’ of essential
genes within a family. One application of CoreGenes is that it
can rapidly predict the function for newly sequenced predicted or
hypothetical genes based on other members of the family. Another
application is the presentation of unique and common genes, which may
be realized as targets for pharmaceutical drug discovery and for
molecular diagnostics. Recently these tools have been redeveloped
for analyzing small bacterial genomes, up to 2Mb.
Genomics and bioinformatics of human
Several members of the adenoviruses family are important human
pathogens. They are agents in acute respiratory disease
(ARD). While ARD has a low mortality rate, especially in the
military training population, the morbidity rate is high. The
Seto Research Group and collaborators have sequenced genomes from
sixteen relevant serotypes (1, 4, 6, 7, 14, 16, 21, 34 and 50), and
have analyzed and annotated these genomes thoroughly. An
algorithm for annotation has been designed and optimized.
Bioinformatics analysis shows that serotype 4 arose from a zoonotic
event, transmission from a chimpanzee host. Three branches of
evolution are suggested, with one branch comprising the majority of the
serotypes and species; one branch comprising the species B serotypes;
and one ‘relatively recent’ branch comprising the sole member of
species E. Species B is subdivided into B1 and B2, with data
suggesting B1 is derived from a zoonotic event and B2 diverging from
the original human adenovirus branch and converging with the B1
branch. Current epidemic outbreak strains of adenoviruses are
being studied to determine epidemiology and evolution of pathogenic
Viral and molecular evolution; Natural
Current field strains of HAdV-4 isolated from epidemics appear to
contain two genome recombination events allowing this serotype to
become now the single agent of adenovirus-caused ARD in the military
trainee population (at 99%, NHRC Spring 05). Bioinformatics
analyses suggest these recombinations of critical regulatory sites
drove the adaptive evolution of this pathogen from a chimpanzee host to
a human host. (re-emerging in the absence of vaccines).
Genomic, bioinformatics and molecular
analyses of adenoviruses associated with previously vaccinated
During the course of studies, it was noted that archived strains from
the US Navy Health Research Center (Global Emerging Infectious Disease
Surveillance- GEIS), collected from individuals who were diagnosed with
ARD despite vaccinations (‘Breakthrough’ or ‘coinfection’ strains),
contained multiple serotypes of adenoviruses. One genome was
sequenced and analyzed. This, along with other ARD-relevant
adenovirus genomes analyzed earlier, shows that molecular evolution of
viral pathogens may be more rapid than earlier thought, and that
vaccination with unattenuated viruses may drive recombinations and
accelerate the evolution to more problematic substrains. These
genomic studies complement molecular and epidemiologic studies with the
collection of adenovirus field strains collected by NHRC.
Molecular recombination and co-infections may be major forces shaping
virus adaptive evolution, particularly of pathogenic strains.
Development of advanced molecular
diagnostics platforms for epidemic outbreaks surveillance (May 2002 to
As part of a Consortium (Epidemic Outbreak Surveillance- EOS) formed by
the US Air Force Surgeon General’s Office to develop molecular
diagnostics tools for the identification and surveillance of ARD
pathogens in the military, the Seto Research Group has provided unique
pathogen genome signatures for populating microarray chips. These
set of probes include signatures from several viral and bacterial
agents that are identified as pathogens in ARD. Currently, three
versions of the Affymetrix-based Respiratory Pathogen Microarray (RPM)
have been designed, and are being tested, validated and implemented in
a real-world test bed at LAFB. This Consortium includes
collaborating groups from the Armed Forces Institute of Pathology at
Walter Reed Army Medical Center (AFIP), Naval Research Laboratory
(NRL), and Wilford Hall/Lackland USAF base (LAFB). The goal has
been to support a rapid response to current epidemic challenges, so
methodology has been optimized for sequencing and analyzing viral
genomes rapidly, translating this into pathogen signatures for rapid
turnaround and for microarray inclusion. Current epidemic field
strains of adenoviruses have been sequenced and analyzed rapidly:
HAdV-4FS (US Air Force), HAdV-4FS (US Army), HAdV-7FS (US Navy),
HAdV-3FS (US Navy) and HAdV-5FS (US Army).
Seto., D., Jones, M.S., Dyer, D.W., J. Chodosh. (2013). Characterizing, typing and naming
human adenovirus type 55 in the era of whole genome data. J. Clin. Virol. 58: 741-2.
Dehghan, S., Seto, J., Jones, M.S., Dyer, D.W., Chodosh, J. and D. Seto. (2013). Simian
adenovirus type 35 has a recombinant genome comprising human and simian adenovirus
sequences, which predicts its potential emergence as a human respiratory pathogen. Virol.
Singh, G., Robinson, C.M., Dehghan, S., Jones, M.S., Dyer, D.W., D. Seto. and Chodosh, J.
(2013). Homologous recombination in E3 genes of human adenoviruses species D. J Virol.
Dehghan, S., Seto, J., Liu, E.B., Walsh, M.P., Dyer, D.W., Chodosh, J. and D. Seto. (2013). Computational analysis of four human adenovirus type 4 genomes reveals
molecular evolution through two interspecies recombination events. Virology 443: 197-207.
(NOTE: Selected as a "Highlighted Article" by the Editors of Virology).
Robinson, C.M., Singh, G., Lee, J.Y., Dehghan, S., Rajaiya, J., Liu, E.B., Yousuf, M.A., Betensky, R.A., Dyer, D.W., Jones, M.S., Seto, D. and J. Chodosh. (2013).
Molecular evolution of human adenoviruses. Scientific Reports 3:1812.
Tang, L., An, J., Xie, Z., Dehghan, S., Seto, D., Xu, W. and Y. Ji. (2013). Genome and bioinformatic analysis of a HAdV-B14p1 virus isolated from a baby with pneumonia in
Beijing, China. PLoS One 8(3): e60345.
Robinson, C., Zhou, X., Rajaiya, J., Yousuf, M.A., Singh, G., DeSerres, J.A., Walsh, M.P., Wong, S., Seto, D., Dyer, D.W., Chodosh, J.* and M.S. Jones. (2013).
Predicting the next pathogen: analysis of a novel human adenovirus. mBio 4(2): e00595-12. *corresponding author.
Turner, D., Reynolds, D., Seto, D.* and P. Mahadevan*. (2013). CoreGenes 3.5: A webserver for the determination of core genes from sets of viral and small bacterial
genomes. BMC Research Notes 6:140. *corresponding authors.
Zhang, Q., Seto, D., Cao, B., Zhao, S., Zhao, W., Zhu, L. and C. Wan. (2012). Genome sequence of human adenovirus type 55, a re-emergent acute respiratory disease pathogen in China. J Virol. 86: 12441-2.
Qurei, L., Seto, D., Salah, Z. and M. Azzeh. (2012). A molecular epidemiology survey of respiratory adenoviruses circulating in children residing in Southern Palestine. PLoS One 7(8): e42732.
Zhang, Q., Seto, D., Zhao, S., Zhu, L., Zhao, W. and C. Wan. (2012). Genome Sequence of the First Human Adenovirus Type 14 Isolated in China. J Virol. 86: 7019-20.
Zhou, X., Robinson, C.M., Rajaiya, J., Deghan, S., Seto, D., Jones, M.S., Dyer, D.W. and J. Chodosh. (2012). Analysis of human adenovirus type 19
associated with epidemic keratoconjunctivitis and its reclassification as adenovirus type 64. Invest Ophthalmol Vis Sci. 53: 2804-2811.
Liu, E.B., Wadford, D.A., Seto, J., Vu, M., Hudson, N.R., Thrasher, L., Torres, S., Messenger, S.L., Dyer, D.W., Chodosh, J., Seto, D. and M.S. Jones. (2012).
Computational and serologic analysis of novel and known viruses in species human adenovirus D in which serology and genomics do not correlate. PLoS One 7(3):
Zhang, Q., Zhang, X., Wu, H., Seto, D., Zhang, H-J, Chen, Z., Wan, C. and B-J. Zheng. (2012). Parental LTRs are important in a construct of a stable and
efficient replication-competent infectious molecular clone of HIV-1 CRF08_BC. PLoS One 7(2): e31233.
Singh, G., Robinson, C.M., Dehghan, S., Schmidt, T., Seto, D., Jones, M.S., Dyer, D.W. and Chodosh, J. (2012). Over-reliance on the hexon gene leading to
misclassification of human adenoviruses. J Virol. 86: 4693-4695. [Epub 02/01/12].
Dehghan, S., Liu, E.B., Seto, J., Torres, S., Hudson, N.R., Kajon, A., Metzgar, D.W., Dyer, D.W., Chodosh, J., Jones, M.S. and D. Seto. (2012). Five genome sequences of subspecies B1 human adenoviruses associated with acute respiratory disease. J Virol. 86: 635-636.
Dehghan, S., Seto, J., Hudson, N.R., Robinson, C.M., Jones, M.S., Dyer, D.W., Chodosh, J. and D. Seto. (2011). Complete genome sequence of human adenovirus prototype 17. J Virol. 85: 11540-11541. [Epub 10/07/11].
Liu, E.B., Ferreyra, L., Fischer, S.L., Pavan, J.V., Nates, S.V., Hudson, N.R., Tirado, D., Dyer, D.W., Chodosh, J., Seto, D. and M.S. Jones. (2011). Genomic and computational analysis of a novel human adenovirus with a serologically unique hexon and a recombinant fiber gene. PLoS One. 6(9):e24491
Akula, N., Baranova, A., Seto, D., Solka, J., Nalls, M.A., Singleton, A., Ferrucci, L., Tanaka, T., Bandinelli, S., Cho, Y.S., Kim, Y.J., Lee, J-Y., Han, B-G. and F.J. McMahon. (2011). A network-based approach to prioritize results from genome-wide association studies. PLoS One. 6(9):e24220
Walsh, M.P., Seto, J., Liu, E.B., Dehghan, S., Hudson, N.R., Lukashev, A.N., Ivanova, O., Chodosh, J., Dyer, D., Jones, M.S. and D. Seto. (2011). Computational analysis of two species C human adenoviruses provides evidence of a novel virus. J Clin Microbiol. 49: 3482-3490-993. [Epub 08/17/11].
Robinson, C.M., Seto, D., Jones, M.S., Dyer, D.W. and J. Chodosh. (2011). Molecular evolution of human species D adenoviruses. Infect, Genet Evol. 11:1208-17. [ePub 05/05/11]. (Invited review).
Seto, D., Chodosh, J., Brister, J.R., Jones, M.S. and members of the Adenovirus Research Community. (2011). Using the whole genome sequence to characterize and name human adenoviruses. J Virol. 85: 5701-2. [Epub 03/30/11]. (Editorial).
Robinson, C.M., Gurdeep, S., Henquell, C., Walsh, M.P., Peigue-Lafeuille, H., Seto, D., Jones, M.S., Dyer, D.W. and J. Chodosh. (2011). Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. Virology 409: 141-147. [Epub 11/05/10].
Mahadevan, P. and D. Seto. (2011). In silico bioinformatic tools for determining core genes from sets of genomes. Drug Development Research 72: 147-152. [Epub 12/16/10]. (Review).
Seto, D. (2010). Viral genomics and bioinformatics. Viruses 2: 2587-2593. (Editorial).
Mahadevan, P. and D. Seto. (2010). In silico bioinformatic tools for determining core genes from sets of genomes. Drug Development Research 72: 1-6. (Invited Review).
Brister, J.R., Bao, Y., Kuiken, C., Lefkowitz, E., Le Mercier, P., Leplae, R., Madupu, R., Scheuermann, R., Schobel, S., Seto, D., Shrivastava, S., Sterk, P., Zeng, Q., Klimke W. and T. Tatusova. (2010). Towards viral genome annotation standards, Report from the 2010 NCBI Annotation Workshop. Viruses 2(10): 2258-2268. (Editorial).
Mahadevan, P. and Seto, D. (2010). "Taxonomic parsing of bacteriophages using core genes and in silico proteome-based CGUG and applications to small bacterial genomes." Adv Exp Med Biol. 680: 379-385. in Advances in Experimental Medicine and Biology. Arabnia, H.R. (Ed.). ISBN 978-1-4419-5912-6. (Book chapter).
Torres, S., Chodosh, J., Seto, D. and M.S. Jones. (2010). The revolution in viral genomics as exemplified by the bioinformatic analysis of human adenoviruses. Viruses 2(7): 1367-1381.
Walsh, M.P., Seto, J., Tirado, D., Chodosh, J., Seto, D.* and Jones, M.S. (2010). Genomic analysis of human adenovirus type 18. Virology. in press 05/13/10. [Epub 06/09/10]. *corresponding author.
Seto, J*., Walsh, M.P*., Metzgar, D. and Seto, D. (2010). Computational analysis of adenovirus serotype 5 (HAdV-C5) from a HAdV coinfection shows genome stability after forty-five years of circulation. Virology. in press 05/13/10. [Epub 06/03/10]. *equal contributions.
Mahadevan, P. and Seto, D. (2010). Pairwise synteny analysis of bacterial genomes using web-based GeneOrder. BMC Research Notes 3:41. [Epub 02/23/10]
Arnold, J., Janoska, M., Kajon, A.E., Metzgar, D., Hudson, N.R., Torres, S., Harrach, B., Seto, D., Chodosh, J. and Jones, M.S. (2010). Genomic characterization of human adenovirus 36, a putative obesity agent. Virus Research 149: 152-161. [Epub 01/28/10].
Seto, J., Walsh, M.P., Mahadevan, P. , Zhang, Q. and D. Seto. (2010). Applying genomic and bionformatic resources to human adenovirus genomes for use in vaccine development and for applications in vector development for gene delivery. Viruses 2: 1-26.
Walsh, M.P., Seto, J., Jones, M.S., Chodosh, J., Xu, W.and D. Seto. (2010). Computational analysis identifies human adenovirus type 55 as a re-emergent acute respiratory disease pathogen. J Clin Microbiol. 48: 991-993. [Epub 12/30/09]
Mahadevan, P., Seto, J., Tibbetts, C. and D. Seto. (2010). Natural variants of human adenovirus type 3 provide evidence for relative genome stability across time and geographic space. Virology 397: 113-118. [Epub 11/23/09].
Lavigne, R., Darius, P., Summer, E.J., Seto, D., Madhadevan, P., Nilsson, A.S., Ackermann, H.W. and A.M. Kropinski. (2009). Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiology 9:224. [Epub 10/26/09]
Mahadevan, P., King, J.F. and D. Seto. (2009). CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb. BMC Research Notes 2:168. [Epub 08/25/09]
Mahadevan, P., King, J.F. and Seto, D. (2009). Data mining pathogen genomes using GeneOrder, CoreGenes and CGUG: gene order, synteny, and in silico proteomes. International Journal of Computational Biology and Drug Design 2:100-114.
Robinson, C.M., Rajaiya, J., Walsh, M.P., Dyer, D.W., Seto, D., Jones, M.S. and Chodosh, J. (2009). Computational analysis of human adenovirus type 22 provides evidence for recombination between human adenovirus species D in the penton base gene. J Virology. Jun 24 [Epub ahead of print].
Mahadevan, P. and Seto, D. (2009). In silico proteome parsing analysis to identify core sets of proteins in bacteriophages to aid in their classification. Proceedings of the 2009 International Conference on Bioinformatics and Computational Biology. CSREA Press. H. R. Arabnia and H. Valafar, eds. (Las Vegas, NV. July 13-16, 2009).
Kropinski, A.M., Borodovsky, M., Carver, T.J., Cerdeno-Tarraga, A.M., Darling, A., Lomsadze, A., Mahadevan, P., Stothard, P., Seto, D., van Domselaar, G. and Wishart, D.S. (2009). "In silico Identification of Genes in Bacteriophage DNA." Methods Mol Biol. 502: 57-89.
Walsh, M.P., Chintakuntlawar, A., Robinson, C.M., Madisch, I., Harrach, B., Hudson, N.R., Torres, S., Schnurr, D., Heim, A., Chodosh, J., Seto, D. and M.S. Jones. (2009). Evidence of molecular evolution driven by recombination events influencing tropism and virulence in a novel human adenovirus that causes epidemic keratoconjunctivitis. PLoS ONE 4(6):e5635.
Seto, J., Walsh, M.P., Mahadevan, P., Purkayastha, A., Clark, J.M., Tibbetts, C. and D. Seto (2009). Genomic and bioinformatics analyses of HAdV-14p, a member of the human adenovirus B2 species. Virus Research 143: 94-105. [Epub 4/2/09].
Zhang, Q., Su, X., Seto, D., Zheng, B-J., Tian, X., Sheng, H., Li, H., Wang, Y. and R. Zhou. (2009). Construction and characterization of a replication-competent human adenovirus type 3-based vector for use as a live-vaccine candidate and a gene therapy vector. Vaccine 27: 1145-1153. [Epub 1/13/09].
Lavigne, R., Seto, D., Madhadevan, P., Ackermann, H.W. and A.M. Kropinski. (2008). Unifying classical and molecular taxonomy-based classification: A rational classification system for the Podoviridae using BLASTP-based tools. Research in Microbiology 159: 406-414. [Epub 4/18/08].
Mahadevan, P. and Seto, D. (2008). Data mining pathogen genomes using GeneOrder and CoreGenes: gene order, synteny, and proteomes. Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology. CSREA Press. H. R. Arabnia and H. Valafar, eds. (Las Vegas, NV. July 14-17, 2008).
Mahadevan, P. and Seto, D. (2007). Comparative genomics using CoreGenes to analyze small bacterial genomes, with an application for the annotation of hypothetical proteins. Proceedings of the 2007 International Conference on Bioinformatics and Computational Biology. CSREA Press. H. R. Arabnia and H. Valafar, eds. (Las Vegas, NV. June 25-28, 2007).
Vora, G.J., Lin, B., Gratwick, K., Meador, C., Hansen, C., Tibbetts, C., Stenger, D.A., Irvine, M., Seto, D., Purkayastha, A., Freed, N., Gibson, M.L., Russell K.L. and Metzgar, D. (2006). Coinfections of multiple adenoviral species in previously vaccinated patients. Emerging Infectious Diseases 12: 921-930.
Lin, B., Wang, Z., Vora, G.J., Thornton, J.A., Schnur, J.M., Thach, D.C., Mueller, K.M., Ligler, A.G., Malanoski, A.P., Santiago, J., Walter, E.A., Agan, B.K., Metzgar, D., Seto, D., Daum, L.T., Kruzelock, R., Rowley, R.K., Hanson, E.H., Tibbetts, C. and Stenger, D.A. (2006). Broad spectrum respiratory tract pathogen identification using re-sequencing DNA microarrays. Genome Res. 16: 527-55.
Mahadevan, P. and Seto, D. (2006). Comparative genomics using web-based GeneOrder to determine synteny and to function as an annotation tool. Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology. CSREA Press. H. R. Arabnia and H. Valafar, eds. 566-570. (Las Vegas, NV. June 26-29, 2006).
Purkayastha, A., Su, J., McGraw, J., Ditty, S.E., Carlisle, S., Hadfield, T.L., Seto, J., Russell, K.L., Tibbetts, C. and Seto, D. (2005). Genomic and bioinformatics analysis of HAdV-4vac and HAdV-7vac, two human adenovirus (HAdV) strains that constituted original prophylaxis against HAdV-related acute respiratory disease, a reemerging epidemic disease. J Clin Microbiol. 43: 3083-3094.
Purkayastha, A., Ditty, S.E., Su, J., McGraw, J., Hadfield, T.L., Tibbetts, C. and Seto, D. (2005). Genomic and bioinformatics analysis of HAdV-4, a human adenovirus that causes acute respiratory disease (ARD). Implications for gene therapy and vaccine vector development. J Virol. 79: 2559-2572.
Purkayastha, A., Su, J., Carlisle, S., Tibbetts, C. and Seto, D. (2005). Genomic and bioinformatics analysis of HAdV-7, a human adenovirus of species B1 that causes acute respiratory disease (ARD). Implications for human gene therapy. Virology 332:114-129.
Lauer, K.P., Llorente, I., Blair, E., Seto, J., Krasnov, V., Purkayastha, A., Ditty, S.E., Hadfield, T.L., Buck, C., Tibbetts, C. and Seto, D. (2004). Natural variation among human adenoviruses: Genome sequence and annotation of human adenovirus serotype 1 (HAdV-1). J Gen Virol. 85: 2615-2625.
Celamkoti, S., Kundeti, S., Purkayastha, A, Mazumder, R., Buck, C. and Seto, D. (2004). GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes. BMC Bioinformatics 5:52.
Purkayastha, A., Celamkoti, S., Kundeti, S., Buck, C. and Seto, D. (2003). Comparative analyses of small bacterial genomes using global computational tools GeneOrder and CoreGenes. Proceedings of the Seventh Joint Conference on Information Sciences (Fifth Conference on Computational Biology and Genome Informatics). Research Triangle Park, NC. Sept 03. K. Chen, et. al., eds. 863-868.
Zafar, N., Mazumder, R. and Seto, D. (2002). Application of global computational tools GeneOrder and CoreGenes to comparative analyses of chordopoxvirus genomes. Proceedings of the Sixth Joint Conference on Information Sciences (Fourth Conference on Computational Biology and Genome Informatics). Durham, NC Mar 02. H. J. Caulfield, et. al., eds. 1186-1192. Also selected for reprinting @ Information Sciences 146 (1-4): 127-135.
Zafar, N., Mazumder, R. and Seto, D. (2002). CoreGenes: A computational tool for identifying and cataloging “core” genes in a set of small genomes. BMC Bioinformatics 3:12.
Zafar, N., Mazumder, R. and Seto, D. (2001). Comparisons of gene co-linearity in genomes using GeneOrder2.0. Trends in Biochemical Sciences 26: 514-516.
Mazumder, R., Kolaskar, A. and Seto, D. (2001). GeneOrder: Comparing the order of genes in small genomes. Bioinformatics 17: 162-166.
- Seto, D., Chodosh, J. and M.S. Jones. (2013). “Adenoviruses.” In: Stanley Maloy and Kelly Hughes, editors. Brenner's Encyclopedia of Genetics, 2nd edition, Vol 1.
San Diego: Academic Press; 2013. p. 31-33. ISBN: 978-0-08-096156-9.
- Seto, D., Chodosh, J., Dyer, D.W. and M.S. Jones. (2012). “The confluence of informatics and genomics and bioinformatics approaches provides a high-resolution method
for typing human adenoviruses.” in Second Workshop for Human Adenoviruses. K. Aoki. (ed.).
- Seto, D. (2012). “Using informatics-, bioinformatics-, and genomics-based approaches for the molecular surveillance and detection of bio-threat agents.” pp.
327-334. in Technological Innovations in Sensing and Detection of Chemical, Biological, Radiological, Nuclear Threats and Ecological Terrorism. (Series: NATO Science for Peace
and Security Series- A: Chemistry and Biology). Vaseashta, A.K., N. Enaki and P. Susmann (eds.). Springer Press (NYC, NY). ISBN: 978-94-007-2487-7.
- Mahadevan, P. and Seto, D. (2010). "Taxonomic parsing of bacteriophages using core genes and in silico proteome-based CGUG and applications to small bacterial genomes." in Advances in Computational Biology. Volume 680: Advances in Experimental Medicine and Biology. Arabnia, H.R. (Ed.), Vol. 502, 2009, ISBN 978-1-4419-5912-6. in press, Aug. 2010
- Kropinski, A.M., Borodovsky, M., Carver, T.J., Cerdeno-Tarraga, A.M., Darling, A., Lomsadze, A., Mahadevan, P., Stothard, P., Seto, D., van Domselaar, G. and Wishart, D.S.
(2009). "In silico Identification of Genes in Bacteriophage DNA." Methods Mol Biol. 502: 57-89. in Bacteriophages. Methods and Protocols, Volume 2: Molecular and Applied Aspects Clokie, M.R.J. and Kropinski, A.M. (Eds.), Vol. 502, 2009, ISBN 978-1-60327-564-4
Agan, B.K., Hanson, E.H., Kruzelock, R.P., Lin, B, Rowley, R.K., Seto, D., Stenger, D.A., Thornton, J., Tibbetts, C.J., Thach, D., Vora, G.J., Walter, E.A. and Wang, Z. (2005).
Re-sequencing pathogen microarray. United States Patent Office application number 11/177,646. U.S. patent (07/02/05; approved; royalties paid 07-13).
Foreign Patent (Filed January 2007; approved).
Epidemics Outbreak Surveillance Consortium (as a contributing member- see complete author listing in acknowledgements):
Liu, J., Walter, E., Stenger, D., Thach, D., and Epidemic Outbreak Surveillance Consortium. (2006). Effects of two globin mRNA reduction methods on gene expression profiles from whole blood. J Molec Diagnos. 8: 551-558.
Thach, D.C., Agan, B.K., Olsen, C., Diao, J., Lin, B., Gomez, J., Jesse, M., Jenkins, Rowley, R.K., Hanson, E., Tibbetts, C., Stenger, D.A, Walter, E., and Epidemic Outbreak Surveillance Consortium. (2005). Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes. Genes Immun. 6: 588–595.
Davignon, L., Walter, E., Mueller, K.M., Barrozo, C.P., Stenger, D.A., Lin, B. and Epidemic Outbreak Surveillance Consortium. (2005). Use of resequencing oligonucleotide microarrays for identification of Streptococcus pyogenes and associated antibiotic resistance determinants. J Clin Microbiol. 43: 5690-5695.triphosphohydrolase from E. coli. J. Biol. Chem. 263: 1494-1499.
Kuo, C. L., Chen, M. L., Wang, K., Chou, C. K., Vernooij, B., Seto,
D., Koop, B. F. and Hood, L. (1998). A conserved sequence block in
murine and human T-cell receptor (TCR) J alpha region is a composite
element that enhances TCR alpha enhancer activity and binds multiple
nuclear factors. Proc. Natl. Acad. Sci., USA 95: 3839-3844.
Bunville, J., Krakowski, K. and Seto, D. (1997). Cerium oxide removes
background fluorescent contaminants, "Green Smears," from glass plates
used for automated fluorescence-based DNA sequencing. BioTechniques 22:
Seto, D. and Weintraub, B. (1996). Rapid molecular diagnosis of
mutations associated with generalized thyroid hormone resistance by
PCR-coupled automated direct sequencing of genomic DNA: Detection of
two novel mutations. Human Mutation 8: 247-257.
Boisclair, Y., Seto, D., Hsieh, S., Hurst, K. R. and Ooi. G. (1996).
Organization and chromosomal localization of the gene encoding the
acid-labile subunit of the insulin-like growth factor binding complex.
Proc. Natl. Acad. Sci., USA 93: 10028-10033.
Ooi, G. T., Cohen, F. J., Hsieh, S., Seto, D., Rechler, M. M. and
Boisclair, Y. (1995). Structure and regulation of the ALS gene.
Progress in Growth Factor Research 6: 151-157.
Krakowski, K., Bunville, J., Seto, J., Baskin, D. and Seto, D.
(1995). Rapid purification of fluorescent dye-labeled products in a
96-well format for high-throughput automated DNA sequencing. Nucl.
Acids Res. 23: 4930-4931.
Seto, D., Seto, J., Deshpande, P. and Hood, L. (1995). Use of DMSO to
resolve banding artifacts in fluorescent DNA sequencing. DNA Sequence
Seto, D., Koop, B. F., Deshpande, P., Howard, S., Seto, J., Wilk, E.,
Wang, K. and Hood, L. (1994). Organization, sequence, and function of
34.5 kilobases of genomic DNA encompassing several murine T-cell
receptor a/d variable gene segments. Genomics 20: 258-266.
Koop, B. F., Rowen, L., Wang, K., Kuo, C.-L., Seto, D., Lenstra, J.
A., Howard, S., Shan, W., Deshpande, P. and Hood, L. (1994). The human
T-cell receptor TCRa/TCRd (Ca/Cd) region: organization, sequence and
evolution of 97.6 kb of DNA. Genomics 19: 478-493.
Seto, D., Koop, B. F. and Hood, L. (1993). An experimentally-derived
data set constructed for testing large-scale DNA sequence assembly
algorithms. Genomics 15: 673-676.
Seto, D., Koop, B. F., Seto, J. and Hood, L. (1992). Complete
nucleotide sequence of the cosmid vector pWE15A. Nucl. Acids Res. 20:
Koop, B. F., Wilson, R. K., Wang, K., Vernooij, B., Zaller, D., Kuo,
C. L., Seto, D., Toda, M. and Hood, L. (1992). Organization, structure,
and function of 95kb of DNA spanning the murine T-cell receptor Ca/Cd
region. Genomics 13: 1209-1230.
Seto, D. and Rohrabacher, C. (1991). Development and application of a
nonradioactive phosphorescent autoradiograph marker. BioTechniques 10:
Seto, D. (1991). A temperature regulator for microtiter plates. Nucl.
Acids Res. 19: 2506.
Seto, D. (1990). An improved method for sequencing double stranded
plasmid DNA from minipreps using DMSO and modified template
preparation. Nucl. Acids Res. 18: 5905-5906.
Seto, D., Rohrabacher, C., Seto, J. and Hood, L. (1990).
Phosphorescent zinc sulfide is a nonradioactive alternative for marking
autoradiograms. Analyt. Biochem. 189: 51-53.
Quirk, S., Seto, D., Bhatnagar, S. K., Gauss, P., Gold, L. and
Bessman, M. J. (1989). Location and molecular cloning of the structural
gene for the deoxyguanosine triphosphate triphosphohydrolase of E.
coli. Molec. Microbiol. 3: 1391-1395.
Wiederrecht, G., Seto, D. and Parker, C. S. (1988). Molecular
cloning, nucleotide sequencing, and characterization of the
Saccharomyces cerevisiae heat-shock transcription factor. Cell 54:
Seto, D., Bhatnagar, S. K. and Bessman, M. J. (1988). The
purification and properties of deoxyguanosine triphosphate
triphosphohydrolase from E. coli. J. Biol. Chem. 263: 1494-1499
BINF 633 Lecture 5
Adenovirus Genome Diversity Project
Poxvirus Genome Diversity Project
Human Adenovirus 1 data set as a "tar" download (upon