Tony Chiang

Postdoctoral Research Fellow

How does the environment impact biodiversity? Specifically, how do differing oceanic regions affect the genotype - and potentially phenotype - of members of a given species.

My research focuses primarily on the mathematical and statistical modeling of polymorphic regions for seven separate oceanic strains of Thalassiosira pseudonana. Using data derived from next-generation sequencing technologies, I use simple statistical methods to model areas of significantly high or low variability such as single nucleotide polymorphisms (SNPs) or large-scale insertions or deletions. The ability to estimate regions of high variability gives clues to the adaptation mechanisms of the species for differing environments. Conversely, estimating regions of low to no variability across strains helps us determine essential genomic sequences.

I am also broadly interested in the role of theoretical computer science in biology. As data becomes larger and more abundant, it will be much more necessary to find efficient ways to store, query, and share data. My preliminary work in this area uses a graph theoretic framework to represent metagenomes. My collaborators and I are building a novel data structure for metagenomes so that we might be able to generalize the notion of comparative genomics.

Research Interests:

  • Computational Biology
  • Graphical Models
  • Learning Algorithms
  • Application of mathematics, statistics, and computer science to biologically driven problems
  • Consequences of climate change on marine ecologies

Broader Interests:

  • Politics of climate change
  • Public health policy  
  • Sustainability
  • Social Justice
  • Science Education

Positions Held:
Postdoctoral Research Fellow, School of Oceanography, University of Washington, 2011-Present
Affiliate Postdoctoral Fellow, Computer Science & Engineering, University of Washington, 2011-Present
Graduate Research Fellow - Computational Statistics, University of Cambridge, 2006-2010
Graduate Research Assistant - Pure Mathematics, University of California at Berkeley, 2001-2005

Education:
Doctor of Philosophy - King's College, University of Cambridge
Bachelor of Science - Massachusetts Institute of Technology

Honours:

  • King's College Studentship, King's College, University of Cambridge, 2008 - 2010
  • Overseas Research Studentship Fellow, University of Cambridge, 2008 - 2010
  • Ferris Fund Bursury, King's College, University of Cambridge, 2008
  • NSF EMSW21 (DMS-0354321) under Mark D. Haiman, University of California, Berkeley, 2004
  • NDSEG Graduate Student Fellowship Finalist, 2001
  • NSF Graduate Student Fellowship Honourable Mention, 2001
  • Paul Grey Fellowship Award for Undergraduate Research, MIT, 2001
  • Nankai University International Fellowship, Center for Combinatorics, Nankai University, 1999
  • Massachusetts Institute of Technology Jack C Tang Scholarship, 1997-2001

Publications:

  1. Tony Chiang, Denise Scholtens. A General Pipeline for the Quality and Statistical Assessment of Protein Interaction Data Using R and Bioconductor. Nature Protocols, 2009.
  2. Denise Scholtens, Tony Chiang, Wolfgang Huber, Robert Gentleman. Estimating Node Degree in Bait-Prey Networks. Bioinformatics, 2008.
  3. Tony Chiang, Nianhua Li, Sandra Orchard, Samuel Kerrien, Henning Hermjakob, Robert Gentleman, Wolfgang Huber. Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinformatics, 2007.
  4. Tony Chiang, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, Wolfgang Huber. Coverage and Error Models on Protein-Protein Interaction Data by a Directed Graph Analysis. Genome Biology, 2007.
  5. Tony Chiang. On the Cayley Graph of Finitely Generated Abelian Groups. Journal of Undergraduate Research, June 2001, MIT PRESS.

Contact:
phone: +1.206.685.4196
email: surname@ocean.washington.edu

My primary affiliation is within the Oceanography department; I have a secondary affiliation with the Computer Science and Engineering group. I am co-mentored by Ginger Armbrust and Larry Ruzzo of Oceans and CSE respectively.

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vitae.pdf101.45 KB
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7 Genomes Poster3.92 MB