vsi at uw.edu
- Senior Research Scientist, Center for Environmental Genomics, School of Oceanography
- Senior Fellow, eScience Institute
I am interested in observing the complex interactions occurring within natural 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 specific members of the community.
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. The traditional way to study microbes is in the laboratory, by isolating and maintaining pure cell cultures which can be used to perform controlled experiments. This reductionist approach is a valuable tool to shed light on the roles these organisms may individually play in an ecosystem.
However, this approach is limited because a large majority of microscopic organisms we can detect in the environment are resistant to growth in a pure laboratory culture, which excludes most of the actual participants in natural ecosystems from study using this method. Even for those “model organisms” that do happen to grow under sterile laboratory conditions, our ability to observe their natural behaviors is limited by monoculture, which is simplified and skewed by the absence of interactions with the natural microbial communities within which these organisms have evolved.
Biological research has been revolutionized over the past several decades by the sequencing of whole genomes for many cultured organisms. Biological oceanography is being similarly transformed by the flood of genomic data now available for a wide variety of isolated marine microbes. Leveraging this information, together with astounding recent advances in massively parallel DNA sequencing technology, I am developing computational methods that allow us to effectively analyze data resulting from simultaneously sequencing the combined DNA of all members of a natural microbial community.
From these analyses, we can characterize the community composition (revealing who’s there), while also reconstructing very long stretches of DNA sequence (revealing what they might be doing). These DNA sequences are often sufficient to produce whole genomes representing uncultured, poorly understood groups of organisms. Genome sequence allows us to reveal previously unknown roles such organisms play in maintaining healthy marine ecosystems, and may ultimately provide us with the necessary clues to isolate them into culture, further extending the reach of traditional laboratory methods.
- Ph.D., University of Washington, Seattle, Oceanography. Dissertation: “Untangling Genomes from Metagenomes”.
- M.S., University of Washington, Seattle, Computer Science and Engineering.
- B.S. cum laude, Washington State University, Pullman, Computer Science and Chemistry.
- Mary Landsteiner Scholar, “For excellence in research at the intersection of interdisciplinary ocean science with advanced computing”, School of Oceanography, University of Washington, 2012.
- Julie A. Koester, Chris T. Berthiaume, Naozumi Hiranuma, Micaela S. Parker, , Rhonda Morales, Walter L. Ruzzo, E. Virginia Armbrust, Sexual ancestors generate an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana. Scientific Reports 8, Article number: 10492, 2018. [Link at Nature]
- , 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, , 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]
- , 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]
- , 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 , 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 , DIDL: Packaging Digital Content, O’Reilly xml.com, May 2001 [Link at xml.com]
- 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]
- “Untangling genomes from metagenomes: Revealing the life strategies of the uncultured majority”, Gordon Research Seminar: Marine Microbes, Lucca (Barga), Italy, 2012
- “Exploring microbial communities through next-generation metagenomic sequencing”, Life Technologies: Sequencing at the Tipping Point Meeting, San Diego, CA, USA , 2011
- “Comparative high-throughput metagenomic analysis: a deeper view into microbial diversity, metabolic potential, and community succession”, 13th International Symposium on Microbial Ecology (ISME), Seattle, WA, U.S.A., 2010
- “Novel methods for comparative high- throughput metagenomic analysis provide deeper insights into microbial diversity, metabolic potential, and community succession”, AGU Ocean Sciences Meeting, Portland, OR, U.S.A., 2010
- “Exploring Microbial Communities: Fifty billion bases at a time”, CSHL Genome Informatics Meeting, Cold Spring Harbor, NY, U.S.A., 2009
- “Exploring microbial communities six billion bases at a time: coupled metagenomic-proteomic analyses provide novel insights into diversity”, ASLO Aquatic Sciences Meeting, Nice, France, 2009
Open Source Software
U.S. Patents (20)
- Ram Rao, Jeffrey McVeigh, Sudheer Sirivara, , 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]
- , “Method and apparatus for providing a location based appliance personality”, US Patent #6,957,075, October 17, 2005 [Link at USPTO]
- , Todd Schwartz, “Digital content distribution”, US Patent #6,938,005, August 30, 2005 [Link at USPTO]
- Ram Rao, Jeffrey McVeigh, Sudheer Sirivara, , 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 , “Method and apparatus for authenticating information”, US Patent #6,839,842, January 4, 2005 [Link at USPTO]
- Todd Schwartz and , “Method and apparatus for private and restricted-use electronic addresses”, US Patent #6,473,758, October 29, 2002 [Link at USPTO]
- and John Richardson, “System for finding a user with a preferred communication mechanism”, US Patent #6,411,696, June 25, 2002 [Link at USPTO]
- , “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]
- 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, , 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, 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]
- and Doug Brucks, “Decode access control for encoded multimedia signals”, US Patent #5,852,664, December 22, 1998 [Link at USPTO]
- and Thomas Gardos, “Encoding images using block-based macroblock-level statistics”, US Patent #5,832,234, November 3, 1998 [Link at USPTO]
- 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 , “Method and apparatus for masquerading online”, US patent #5,812,126, September 22, 1998 [Link at USPTO]
- , “Chroma-key color range determination”, US patent #5,774,191, June 30, 1998 [Link at USPTO]
- , “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 , “Two-measure block classification scheme for encoding video images”, US patent #5,737,537, April 7, 1998 [Link at USPTO]
- Robert Kantner Jr., , 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]
- and Eve Riskin, “Method and Apparatus for Combining Palettes of Color Quantized Images”, US patent #5,459,486, October 17, 1995 [Link at USPTO]