VBRC Publications


1)  Publications From Virology.ca (older refs are from VBRC members)

2) Publications From People Referencing the VBRC Tools  (out of date)

 



VBRC Publications

2012

Dunigan, D.D., Cerny, R.L., Bauman, A.T., Roach, J.C., Lane, L.C., Agarkova, I.V., Wulser, K., Yanai-Balser, G.M., Gurnon, J.R., Vitek, J.C., Kronschnabel, B.J., Jeanniard, A., Blanc, G., Upton, C., Duncan, G.A., McClung, O.W., Ma, F. and Van Etten, J.L.

Paramecium bursaria Chlorella Virus 1 proteome reveals novel architectural and regulatory features of a giant virus. 

2011

Hillary, W., Lin, S.H. and Upton, C.

Base-By-Base Version 2: Single nucleotide-level analysis of whole viral genome alignments.

Zhao G, Droit L, Tesh RB, Popov VL, Little NS, Upton C, Virgin HW, Wang D.

The genome of Yoka poxvirus. J Virol. 2011 Oct;85(19):10230-8. Epub 2011 Aug 3

Chapman DA, Darby AC, Da Silva M, Upton C, Radford AD, Dixon LK.

Genomic analysis of highly virulent Georgia 2007/1 isolate of African swine fever virus. Emerg Infect Dis. 2011 Apr;17(4):599-605.

Qin L, Upton C, Hazes B, Evans DH.

Genomic analysis of the vaccinia virus strain variants found in Dryvax vaccine. J Virol. 2011 Dec;85(24):13049-60. Epub 2011 Oct 5.

Coulson D, Upton C.

Characterization of indels in poxvirus genomes. Virus Genes. 2011 Apr;42(2):171-7.

2010

Sadeque A, Barsky M, Marass F, Kruczkiewicz P, Upton C.

JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences.

Viruses. 2010 Sep;2(9):1867-85. Epub 2010 Aug 31.

 

Gammon DB, Gowrishankar B, Duraffour S, Andrei G, Upton C, Evans DH.

Vaccinia virus-encoded ribonucleotide reductase subunits are differentially required for replication and pathogenesis. PLoS Pathog. 2010 Jul 8;6(7):e1000984.

de Villiers EP, Gallardo C, Arias M, da Silva M, Upton C, Martin R, Bishop RP.

Phylogenomic analysis of 11 complete African swine fever virus genome sequences. Virology. 2010 Apr 25;400(1):128-36. Epub 2010 Feb 20.

2009

Alzhanova D, Edwards DM, Hammarlund E, Scholz IG, Horst D, Wagner MJ, Upton C, Wiertz EJ, Slifka MK, Früh K.

Cowpox virus inhibits the transporter associated with antigen processing to evade T cell recognition. Cell Host Microbe. 2009 Nov 19;6(5):433-45.

Clifford M, Twigg J, Upton C.

Evidence for a novel gene associated with human influenza A viruses. Virol J. 2009 Nov 16;6:198.

Marass F, Upton C.

KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences. BMC Res Notes. 2009 May 20;2:91.

Da Silva M, Upton C.

Vaccinia virus G8R protein: a structural ortholog of proliferating cell nuclear antigen (PCNA). PLoS One. 2009;4(5):e5479. Epub 2009 May 7.

Marass F, Upton C.

Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences. BMC Res Notes. 2009 Jan 30;2:14.

2008

Barsky, M., Stege, U., Thomo, A., Upton, C.

A New Method for Indexing Genomes Using On-Disk Suffix Trees

Assarsson E, Greenbaum JA, Sundström M, Schaffer L, Hammond JA, Pasquetto V, Oseroff C, Hendrickson RC, Lefkowitz EJ, Tscharke DC, Sidney J, Grey HM, Head SR, Peters B, Sette A. 2008.

Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proceedings of the National Academy of Science USA. 2008 Feb 12;105(6):2140-5. 

 

Chapman DA, Tcherepanov V, Upton C, Dixon LK.

Comparison of the genome sequences of non-pathogenic and pathogenic African swine fever virus isolates. J Gen Virol. 2008 Feb;89(Pt 2):397-408.

2007

Summer, E.J., Gill, J.J., Upton, C., Gonzalez, C.F. and Young, R. 2007. 
Role of phages in the pathogenesis of Burkholderia or ‘Where are the toxin genes in Burkholderia phages?’ Curr Opin Microbiol. 10(4):410-7.

Eaton, H.E., Metcalf, J., Penny, E., Tcherepanov, V., Upton, C. and Brunetti, C.R. 2007. 
Comparative genomic analysis of the family Iridoviridae: re-annotating and defining the core set of iridovirus genes. Virology Journal. 4:11 doi:10.1186/1743-422X-4-11.

Thomas, J.M., Horspool, D., Brown, G., Tcherepanov, V., and Upton, C. 2007. 
GraphDNA: a Java program for graphical display of DNA composition analyses. BMC Bioinformatics. 8:21.

Butler-Cole,C., Wagner, M.J., Da Silva, M., Brown, G.D., Burke, R.D. and Upton, C. 2007 
An ectromelia virus profilin homolog interacts with cellular tropomyosin and viral A-type inclusion protein. Virology Journal 2007, 4:76 doi:10.1186/1743-422X-4-76

Osbourne, J.D., Da Silva, M., Frace, M., Sammons, S.A., Olsen-Rasmussen, M., Upton, C., Buller, R.M.L., Chen, N., Feng, Z., Roper, R.L., Lui, J., Pougatcheva, S., Chen, W., Wohlheuter, R.M. and Esposito, J.J. 2007. 
Genomic differences of Vaccinia virus clones from Dryvax smallpox vaccine: The Dryvax-like ACAM2000 and the mouse neurovirulent Clone-3.Vaccine 25(52):8807-8832.

Sajic R, Lee K, Asai K, Sakac D, Branch DR, Upton C, Cochrane A. 2007. 
Use of modified U1 snRNAs to inhibit HIV-1 replication. Nucleic Acids Res. 35:247-55.

Tyler, S.D., Peters, G.A., Severini, A., Gray, M.J., Upton, C. and Tipples, G.A. 2007.
Genomic Cartography of Varicella-Voster Virus: A Complete Genome Based Analysis of Strain Variability with Implications for Attenuation and Phenotypic Differences. Virology 359:447-58

Moutaftsi M, Bui HH, Peters B, Sidney J, Salek-Ardakani S, Oseroff C, Pasquetto V, Crotty S, Croft M, Lefkowitz EJ, Grey H, Sette A. 2007
Vaccinia virus-specific CD4+ T cell responses target a set of antigens largely distinct from those targeted by CD8+ T cell responses. J Immunol. 1;178(11):6814-20.

Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD. 2007
Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Journal of Virology. 15;365(1):60-9.

Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. 2007
National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infection and Immunity. 75(7):3212-9.

2006

Lefkowitz, E., Wang, C. and Upton, C. 2006. 
Poxviruses: past, present and future. Virus Research, 117, 105-118.

Tcherepanov, T., Ehlers, A. and Upton, C. 2006. 
Genome Annotation Transfer Utility (GATU): Rapid annotation of viral genomes using a closely related reference genome. BMC Genomics 7:150.

Peters,G.A., Tyler,S.D., Grose,C., Severini,A., Gray,M.J., Upton,C. and Tipples,G.A. 2006. 
A full-genome phylogenetic analysis of Varicella-Zoster Virus reveals a novel origin of recombination between major circulating clades. J. Virol. 80, 9850-9860.

Syed, A. and Upton, C. 2006.
Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis. BMC Bioinformatics. 7:462.

Da Silva, M., Shen, L., Tcherepanov, V., Watson C. and Upton C. 2006.
Predicted function of the vaccinia virus G5R protein. Bioinformatics. 22:2846-50.

Li, G., Chen, N., Feng, Z., Buller, R.M. L., Osborne, J., Harms, T., Damon, I., Upton, C. and Esteban, D.J. 2006. 
Genomic sequence and analysis of a vaccinia isolate from a patient with a smallpox vaccine-related complication. Virology Journal 3:88.

Parveen S, Sullender WM, Fowler K, Lefkowitz EJ, Kapoor SK, Broor S. 2006
Genetic variability in the G protein gene of group A and B respiratory syncytial viruses from India. J Clin Microbiol. 44(9):3055-64.

2005

Lefkowitz, E. J., Upton, C., Changayil, S. S., Buck, C., Traktman, P., Buller, R. M. L. 2005. 
Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. Nucleic Acids Res. 2005 33: p. D311-D316

Whitney, J., Esteban, D. J. and Upton C. 2005. 
Recent Hits Acquired by BLAST (ReHAB): A tool to identify new hits in sequence similarity searches. BMC Bioinformatics. 6(1):23.

Da Silva, M. and Upton C. 2005. 
Using purine skews to predict genes in AT-rich poxviruses. BMC Genomics. 6(1):22.

Da Silva, M. and Upton C. 2005. 
Host-derived pathogenicity islands in poxviruses. Virology Journal 2(1):30.

Esteban, D. J., Da Silva, M. and Upton C. 2005.
New Bioinformatics Tools for Viral Genome Analyses at Viral Bioinformatics – Canada. Pharmacogenomics 6, 271-280

Chen, N., Li, G., Liszewski, M.K., Atkinson, J.P., Jahrling, P.B., Feng, Z., Schriewer, J., Buck, C., Wang, C., Lefkowitz, E.J., Esposito, J.J., Harms, T., Damon, I.K., Roper, R.L., Upton, C. and Buller, R.M. 2005. 
Virulence differences between monkeypox virus isolates from West Africa and the Congo basin. Virology 340, 46-63.

Li, G., Chen, N., Roper, R.L., Feng, Z., Hunter, A., Danila, M., Lefkowitz, E.J., Buller, R.M. L. and Upton, C. 2005. 
Complete coding sequences of the rabbitpox virus genome. J. Gen. Virol. 86, 2969-2977.

Wang C, Lefkowitz EJ. 2005
Genomic multiple sequence alignments: refinement using a genetic algorithm.BMC Bioinformatics.  8;6:200.

Wang C, Lefkowitz EJ. 2004
SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.BMC Bioinformatics. 28;5:171.

2004

Brodie, R., R. L. Roper, and C. Upton. 2004 
JDotter: A Java Interface to Multiple DotPlots Generated by Dotter. Bioinformatics, 20, 279-281.

Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004. 
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5, 96.

Minion FC, Lefkowitz EJ, Madsen ML, Cleary BJ, Swartzell SM, Mahairas GG. 2004
The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J Bacteriol. 186(21):7123-33.

Pre-2004

Upton, C., Slack, S., Hunter, A.W., Ehlers, A. and R. L. Roper. 2003. 
Poxvirus Orthologous Clusters (POCs): Toward defining the minimum essential poxvirus genome. J. Virology, 77, 7590-7600.

Ehlers, A., J. Osborne, Slack, S., R. L. Roper, and C. Upton. 2002. 
Poxvirus Orthologous Clusters (POCs). Bioinformatics 18, 1544-1545

C. Upton, D. Hogg, D. Perrin, M. Boone and N. Harris, 2001.
Viral Genome Organizer: A system for analyzing complete viral genomes. Virus Research 70, 55-64.

Hoskins J, Alborn WE Jr, Arnold J, Blaszczak LC, Burgett S, DeHoff BS, Estrem ST, Fritz L, Fu DJ, Fuller W, Geringer C, Gilmour R, Glass JS, Khoja H, Kraft AR, Lagace RE, LeBlanc DJ, Lee LN, Lefkowitz EJ, Lu J, Matsushima P, McAhren SM, McHenney M, McLeaster K, Mundy CW, Nicas TI, Norris FH, O’Gara M, Peery RB, Robertson GT, Rockey P, Sun PM, Winkler ME, Yang Y, Young-Bellido M, Zhao G, Zook CA, Baltz RH, Jaskunas SR, Rosteck PR Jr, Skatrud PL, Glass JI. 2001
Genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol.183(19):5709-17.

Glass JI, Lefkowitz EJ, Glass JS, Heiner CR, Chen EY, Cassell GH. 2000
The complete sequence of the mucosal pathogen Ureaplasma urealyticum.Nature. 12;407(6805):757-62.

 


Refereed conference proceedings (considered full publications in Computer Science)

Barsky, M., U. Stege, A. Thomo, C. Upton. 2006.
A New Algorithm for Fast All-Against-All Substring Matching Proc. of String Processing and Information Retrieval SPIRE’06 Glasgow, Scotland.

Barsky, M., U. Stege, A. Thomo, C. Upton. 2007.
Shortest Path Approaches for the Longest Common Subsequence of a Set of Strings. IEEE 7th International Symposium on Bioinformatics and BioEngineering (BIBE07), pp. 327-333 IEEE. Boston, USA.

 


Book Chapters

Buller RM, Arif BM, Black DN, Dumbell KR, Esposito JJ, Lefkowitz EJ, McFadden G, Moss B, Mercer AA, Moyer RW, Skinner MA, Tripathy, DN.
Poxviridae. In Virus Taxonomy, The VIIIth Report of the International Committee on Taxonomy of Viruses. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds.) Oxford, UK, Elsevier Academic Press, 2005. ISBN: 0-12-249951-4.

Lebeda FJ, Wolinsky M, Lefkowitz EJ.
Information resources and database development for defense against biological weapons. In Biological Weapons Defense: Infectious Disease and Counterbioterrorism. Lindler LE, Lebeda FJ, Korch GW (eds.) Humana Press, 2005. ISBN: 1-58829-184-7

 

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