Vaughn Iverson

Vaughn Iverson Pre-doctoral Research Associate 206-685-4127 vsi at u.washington.edu

Research Interests

Microorganisms in the marine environment are always found living in association with one another. In particular, wherever there is a natural population of phytoplankton, associated heterotrophic bacteria will also be present. Traditionally in the laboratory, we go to great lengths to maintain pure cell cultures—a very unnatural act—so that we may study phytoplankton in isolation from all other types of organisms. This reductionist approach has been a valuable tool to shed light on the roles these organisms individually play in the environment; but the behaviors observed as cells adjust to a sterile lab environment are skewed, and simplified, by the absence of interaction with members of the natural communities these organisms have co-evolved with over many millions of years. I am interested in measuring and modeling the complex biochemical interactions within communities of marine microorganisms, as one would find in virtually any water sample taken from the environment. My strategy is to achieve this through the development and deployment of automated biological sensors capable of observing microbial communities in the field, and directly measuring their behaviors and interactions by quantifying specific proteins or nucleic acids of interest. Such instruments will take quite some time to develop and perfect, but my research aims to take definite steps in this direction. Biological research has been forever changed in the past 25 years by the sequencing of whole genomes for many organisms. Much of biological oceanography is being similarly transformed by the flood of genomic data now available for a wide variety of marine prokaryotic and eukaryotic organisms, with much more on the way. Using this information, I am developing ‘model systems’—relatively simple communities of organisms with sequenced genomes, living together—to study community behaviors and symbioses that are absent from pure cultures. Looking longer-term, well studied model systems such as these will facilitate the development and automation of molecular techniques and instruments targeting mixed populations; first in the lab and ultimately with natural communities in the field. My first model systems are diatom-bacteria communities designed specifically to investigate the mechanisms and potentially mutualistic behaviors leading to the exchange of B-vitamins between phytoplankton and heterotrophic bacteria. In addition, I am very interested in the study of whole genomes of sequenced marine diatoms to look for evidence of selective sweeps and skewed mutation rates through the detailed examination of patterns in the occurrence of single nucleotide polymorphisms (SNPs). This work may lead to new insights about genetic diversity, population dynamics and the role of sexual reproduction in these fascinating and globally important organisms.

Background & Bio

I grew up near Tacoma, WA and graduated from Gig Harbor High School in 1985. From there I went to Washington State University in Pullman (Go Cougs!), earning a B.S. in Computer Science and Chemistry in 1989. After a year working for Weyerhauser Corp. in 1990 designing and building some of the first computer networks and e-mail systems at the company, I attended the University of Washington in Seattle (Go Dawgs!) where I did research on artificial intelligence, computer graphics, signal processing and data compression, earning a M.S. in Computer Science and Engineering in 1993. After a short stint at IBM Corp. in Boca Raton, FL, I joined Intel Corp. in Hillsboro, OR, spending nearly 12 years there as a research scientist, inventor and engineering manager working on the development of high performance video compression algorithms and other media related graphics and signal processing technologies. During this time, I was also the lead editor of the ISO/IEC MPEG-21 (21000-2) international multimedia standard, which meant that I spent a disproportionate amount of my time in airplanes, airports and hotel conference rooms around the world. In 2002 I moved back to Seattle, working at the Intel Research lab near the University of Washington. I left Intel in early 2005 for a year of travel and time for exploration of what I might want to do next. As I followed my interests, one thing led to another and I ended up meeting Ginger Armbrust, volunteering in her lab during the summer of 2005 working with Micaela Parker on a diatom bioinformatics project, and becoming generally excited about finding a way to bring together my long-term interests in engineering, biochemistry, and the marine environment. Continuing my explorations, I spent Autumn of 2005 at the UW Friday Harbor Laboratories - Center for Cell Dynamics, studying cytoskeletal protein dynamics during cytokinesis in GFP transformed C. elegans embryos using laser confocal microscopy and computer simulations. I joined the Armbrust lab at UW Oceanography as a Ph.D. student in January 2006.

Education

M.S., University of Washington, Seattle, Computer Science and Engineering, 1993.
B.S. cum laude, Washington State University, Pullman, Computer Science and Chemistry, 1989.

Publications

Thomas Mock, Manoj Pratim Samanta, Vaughn Iverson, Chris Berthiaume, Matthew Robison, Karie Holtermann, Colleen Durkin, Sandra Splinter BonDurant, Kathryn Richmond, Matthew Rodesch, Toivo Kallas, Edward L. Huttlin, Francesco Cerrina, Michael R. Sussman, and E. Virginia Armbrust, Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses, Proceedings of the National Academy of Sciences, USA (PNAS), 105 (5): 1579-84, February 5, 2008 [Link at PNAS]
Vaughn Iverson, Jeff McVeigh and Bob Reese, Real-Time H.264/AVC Codec on Intel Architectures, Proceedings of International Conference on Image Processing (ICIP) 2004, Volume II, pp. 757-760, October 2004 [Link at IEEE]
Vaughn Iverson, Todd Schwartz, Young-Won Song, Rik Van de Walle, Mark Rowe, Doim Chang and Ernesto Santos, editors, MPEG-21 Multimedia Framework, Part 2: Digital Item Declaration, ISO/IEC International Standard, ISO/IEC 21000-2:2003, March 2004 [Link at ISO] [Free download of current version]
Bill N. Schilit, Anthony LaMarca, Gaetano Borriello, William Griswold, David McDonald, Edward Lazowska, Anand Balachandran, Jason Hong and Vaughn Iverson, Ubiquitous Location-Aware Computing and the "Place Lab" Initiative, The First ACM International Workshop on Wireless Mobile Applications and Services on WLAN (WMASH), September 2003 [Link at ACM]
Mark Walker, Todd Schwartz and Vaughn Iverson, DIDL: Packaging Digital Content, O'Reilly xml.com, May 2001 [Link at xml.com]
Vaughn Iverson and Eve A. Riskin, A Fast Method for Combining Palettes of Color Quantized Images, Proceedings of International Conference on Acoustics, Speech and Signal Processing (ICASSP) 1993, Volume V, pp. 317-320, April 1993 [Link at IEEE]

U.S. Patents (20)

Ram Rao, Jeffrey McVeigh, Sudheer Sirivara, Vaughn Iverson, Gary Martz Jr., Daniel Wagner, Kenneth Salzberg, “Transcoding media content from a personal video recorder for a portable device”, US Patent #7,365,655, April 29, 2008 [Link at USPTO]
Vaughn Iverson, “Method and apparatus for providing a location based appliance personality”, US Patent #6,957,075, October 17, 2005 [Link at USPTO]
Vaughn Iverson, Todd Schwartz, "Digital content distribution", US Patent #6,938,005, August 30, 2005 [Link at USPTO]
Ram Rao, Jeffrey McVeigh, Sudheer Sirivara, Vaughn Iverson, Gary Martz, Daniel Wagner, Kenneth Salzberg, "Transcoding media content from a personal video recorder for a portable device", US Patent #6,937,168, August 30, 2005 [Link at USPTO]
John Richardson and Vaughn Iverson, "Method and apparatus for authenticating information", US Patent #6,839,842, January 4, 2005 [Link at USPTO]
Todd Schwartz and Vaughn Iverson, "Method and apparatus for private and restricted-use electronic addresses", US Patent #6,473,758, October 29, 2002 [Link at USPTO]
Vaughn Iverson and John Richardson, "System for finding a user with a preferred communication mechanism", US Patent #6,411,696, June 25, 2002 [Link at USPTO]
Vaughn Iverson, "System for progressive transmission of compressed video including video data of first type of video frame played independently of video data of second type of video frame", US Patent #5,930,526, July 27, 1999 [Link at USPTO]
Vaughn Iverson and Thomas Walsh, "Method and apparatus for scaling image data having associated transparency data", US Patent #5,920,659, July 6, 1999 [Link at USPTO]
David Dent, Vaughn Iverson, John Richardson, Robert Adams, Jeffrey Kidder, Chihuan Lin and Thomas Gardos, "Method and apparatus for protecting user privacy by providing an inaccurate measure of network systems accessed", US Patent #5,896,498, April 20, 1999 [Link at USPTO]
Robert Adams, Vaughn Iverson and Jeffrey Kidder, "Internet browser that includes an enhanced cache for user-controlled document retention", US Patent #5,873,100, February 16, 1999 [Link at USPTO]
Vaughn Iverson and Doug Brucks, "Decode access control for encoded multimedia signals", US Patent #5,852,664, December 22, 1998 [Link at USPTO]
Vaughn Iverson and Thomas Gardos, "Encoding images using block-based macroblock-level statistics", US Patent #5,832,234, November 3, 1998 [Link at USPTO]
Vaughn Iverson and Thomas Gardos, "Adaptive block classification scheme for encoding video images", US Patent #5,815,670, September 29, 1998 [Link at USPTO]
John Richardson, Robert Adams, and Vaughn Iverson, "Method and apparatus for masquerading online", US patent #5,812,126, September 22, 1998 [Link at USPTO]
Vaughn Iverson, "Chroma-key color range determination", US patent # 5,774,191, June 30, 1998 [Link at USPTO]
Vaughn Iverson, "Method and apparatus for run-length encoding using special long-run codes", US patent #5,751,231, May 12, 1998 [Link at USPTO]
Thomas Gardos and Vaughn Iverson, "Two-measure block classification scheme for encoding video images", US patent #5,737,537, April 7, 1998 [Link at USPTO]
Robert Kantner Jr., Vaughn Iverson, Kenneth Morse, Mark Pietras and Arturo Rodriguez, "System and method for pattern-matching with error control for image and video compression", US patent #5,463,701, October 31, 1995 [Link at USPTO]
Vaughn Iverson and Eve Riskin, "Method and Apparatus for Combining Palettes of Color Quantized Images", US patent #5,459,486, October 17, 1995 [Link at USPTO]