JCVI: About / Bios / Timothy B. Stockwell
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Timothy B. Stockwell
Assistant Professor

Research Interests and Accomplishments

Timothy B. Stockwell is an Assistant Professor and the Informatics Coordinator for the Viral Genomics Group at the J. Craig Venter Institute (JCVI). Mr. Stockwell leads informatics efforts in the area of viral genomics that have enabled JCVI to sequence and submit over 2000 H1N1pdm samples to GenBank since the pandemic outbreak in 2009, by improving the primer design, closure, and LIMS components of the system. Mr. Stockwell led the effort to integrate next-generation sequencing technologies into JCVI's viral genomics project portfolio to improve the speed of analyzing the genomes of viruses that are too variable to allow for efficient PCR primer design. He is currently leading the informatics and lab automation portions of a project to synthesize and make available to the research community 1000 HA and 1000 NA molecules from Influenza A and Influenza B. These molecules span protein diversity, coming from the four currently circulating human flu subtypes, as well as four swine flu subtypes and four avian flu subtypes that have pandemic potential. 

Mr. Stockwell has a broad background in computer hardware and software systems engineering, bioinformatics, and molecular biology, and has worked on numerous projects requiring software to adhere to stringent standards in the areas of safety, security, accuracy, and efficiency. From 1998-2002, as Senior Manager and later Director of Software Engineering at Celera Genomics, Mr. Stockwell managed the development and deployment of computational pipelines supporting mammalian transcriptome sequence analysis used for downstream annotation of whole genomes, as well as contract sequencing of bacterial and fungal genomes. After 9/11/2001, he led the development of software to automatically determine mitochondrial DNA profiles for family references, recovered human remains, and personal effects of victims of the World Trade Center attack, requiring levels of accuracy, security, and efficiency that were acceptable to the forensic and law enforcement communities. 

From 1988-1998, in his roles at The MITRE Corporation, Mr. Stockwell was responsible for systems engineering of multiple air traffic control automation systems, with significant focus on safety, security, and efficiency of software and algorithms. 

Mr. Stockwell earned a B.S. degree in Computer and Systems Engineering from Rensselaer Polytechnic Institute.

Select Publications

Poon LL, Song T, et al.
Quantifying Influenza Virus Diversity and Transmission in Humans.

Nature Genetics. 2016 Feb 01; 48: 195-200.[more]

Magagula NB, Esona MD, et al.
Whole Genome Analyses of G1P[8] Rotavirus Strains from Vaccinated and Non-vaccinated South African Children Presenting With Diarrhea.

Journal of Medical Virology. 2015 Jan 01; 87: 79-101.[more]

Shabman RS, Jabado OJ, et al.
Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells.

MBio. 2014 Nov 01; 5[more]

Nyaga MM, Stucker KM, et al.
Whole-genome Analyses of DS-1-like Human G2P[4] and G8P[4] Rotavirus Strains from Eastern, Western and Southern Africa.

Virus Genes. 2014 Oct 01; 49: 196-207.[more]

Nelson MI, Balmaseda A, et al.
The Evolutionary Dynamics of Influenza A and B Viruses in the Tropical City of Managua, Nicaragua.

Virology. 2014 Jun 21; 462: 81-90.[more]

Zhou B, Lin X, et al.
Universal Influenza B Virus Genomic Amplification Facilitates Sequencing, Diagnostics, and Reverse Genetics.

Journal of Clinical Microbiology. 2014 May 01; 52: 1330-7.[more]

Dusek RJ, Hallgrimsson GT, et al.
North Atlantic Migratory Bird Flyways Provide Routes for Intercontinental Movement of Avian Influenza Viruses.

PloS One. 2014 Apr 01; 9: e92075.[more]

Dormitzer PR, Suphaphiphat P, et al.
Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics.

Science Translational Medicine. 2013 May 15; 5: 185ra68.[more]

Ping J, Keleta L, et al.
Genomic and Protein Structural Maps of Adaptive Evolution of Human Influenza A Virus to Increased Virulence In the Mouse.

PloS one. 2011 May 01; 6: e21740.[more]

Ng, P. C., Levy, S., et al.
Genetic Variation In an Individual Human Exome

PLoS Genet. 2008 Aug 01; 4(8): e1000160.[more]

Li, K., Brownley, A., et al.
Novel Computational Methods for Increasing PCR Primer Design Effectiveness In Directed Sequencing

BMC Bioinformatics. 2008 Apr 11; 9(1): 191.[more]

Levy, S., Sutton, G., et al.
The Diploid Genome Sequence of an Individual Human

PLoS Biol. 2007 Sep 04; 5(10): e254.[more]

Lasken, R. S., Stockwell, T. B.
Mechanism of Chimera Formation During the Multiple Displacement Amplification Reaction

BMC Biotechnol. 2007 Apr 12; 7: 19.[more]

Rand, V., Huang, J., et al.
Sequence Survey of Receptor Tyrosine Kinases Reveals Mutations In Glioblastomas

Proc Natl Acad Sci U S A. 2005 Oct 04; 102(40): 14344-9.[more]