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Vaughn Iverson


Within each liter of seawater, how do a billion individual microbial cells compete for available resources, interact with one another, shape and respond to environmental change, and ultimately reproduce or perish?

Vaughn Iverson, Ph.D. Candidate, vsi at uw.edu



Research Interests

Microorganisms in the environment are always found living in association with one another. For example, wherever there is a natural population of phytoplankton (e.g. diatoms), associated bacteria will also be present. Traditionally in the laboratory, we go to great lengths to establish and maintain pure cell cultures—a very unnatural act—so that we may study microbes in isolation from one another. This reductionist approach is a valuable tool to shed light on the roles these organisms individually play in the ecosystem; but the behaviors observed as cells adjust to a laboratory monoculture are skewed, and simplified, by the absence of interactions with members of the natural communities they have co-evolved with. Additionally, the vast majority of microbial organisms we can detect in the environment remain resistant to growth in the laboratory, limiting the utility of the traditional approach to certain groups that happen to be amenable to growth in sterile media, while excluding most of the actual participants in natural ecosystems.

I am interested in more directly observing the complex interactions likely to be occurring within communities of microorganisms; as one would find in virtually any water sample taken from the environment. The approach I am developing uses biological sensing techniques capable of inferring the behaviors and interactions within natural microbial communities by identifying and quantifying genes and proteins used by members of the community.

Biological research has been forever changed in the past 25 years by the sequencing of whole genomes for many cultured organisms; and biological oceanography is being similarly transformed by the flood of genomic data now available for a wide variety of marine isolates. Leveraging this information, together with astounding recent advances in massively parallel DNA sequencing technology, I am developing bioinformatic methods that allow us to directly sequence such communities and accurately characterize their composition (revealing who's there), while simultaneously producing very long fragments of assembled metagenomic DNA sequence (revealing what they might be doing). In many cases, this information is sufficient to reconstruct whole genome sequences representing uncultured and poorly understood groups of organisms. These reconstructed genomes allow us to shed new light on the previously unknown roles these organisms play in maintaining healthy marine ecosystems, and may ultimately provide us with the necessary clues to bring them into laboratory culture for the first time, enabling more detailed traditional physiological studies of their potential ecological functions.

 

Education

  • Ph. D. Candidate, University of Washington, Seattle, Oceanography, Presently.
  • M.S., University of Washington, Seattle, Computer Science and Engineering, 1993.
  • B.S. cum laude, Washington State University, Pullman, Computer Science and Chemistry, 1989.

 

Recent Honors

  • Mary Landsteiner Scholar, for excellence in research at the intersection of interdisciplinary ocean science with advanced computing, School of Oceanography, University of Washington, 2012.

 

Publications

  • Vaughn Iverson, Robert M. Morris, Christian D. Frazar, Chris T. Berthiaume, Rhonda L. Morales, and E. Virginia Armbrust, Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota, Science, Vol. 335 no. 6068 pp. 587-590, February 3rd, 2012 [Link at Science]
  • 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]

 

Open Source Software

 

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]