Nicholas Chia

Photo of Nick Chia
Department of Physics
Loomis Laboratory
University of Illinois at Urbana-Champaign
1110 West Green Street
Urbana, IL 61801
USA

Tel: 217-333-4425 (IGB)
Tel: 217-244-9733 (Physics)

Email: chian [at] uiuc [dot] edu

Curriculum Vitae

Basics

I am currently working as a postdoctoral researcher working at the University of Illinois at Urbana-Champaign under the guidance of Nigel Goldenfeld and Carl Woese. I am interested in a broad range of biological phenomena with emphasis on microbiology, ecology, and evolution. Part of my focus has been examining the role of collective effects and emergent properties in biological systems, with particular interest in the role of gene transfers and mobile genetic elements such as viruses, transposons, and plasmids.

I received my Ph.D. working under Ralf Bundschuh in the Department of Physics at Ohio State University. My thesis work focused on the significance assessment of sequence alignments, but also included ties to a theoretical physical system known as the asymmetric exclusion process. At Ohio State, I also worked with a team on an alignment tool known as Hybrid PSI-BLAST that uses probabilitistic scoring in order to determine homology scores.

Abbreviated Curriculum Vitae

Research Interests

Early Life
There are many deep questions in biology that have so far gone unanswered. Some of the deepest of these questions deal with the origin of life on this planet. Central questions, such as the origin of the optimality and universality of the genetic code, codon bias, and the processes that gave rise to the three major branches of life---archaea, eukaryotes, and will ultimately help shed light on the fundemental processes of biology as well as provide answers about early life. By combining skills from quantitative biology and bioinformatics, I seek to better discern the properties and the emergence of early life.

Collective Dynamics in Microbial Populations
The goal of this work is to explore the collective dynamics of microbial ecosystems, taking into account horizontal gene transfer via viruses or other gene transfer agents. Specific examples being studied include the coevolution of microbial-virus systems, of relevance to phenomena on as small a scale as biofilms and as large a scale as ocean phytoplankton blooms, and bacterial persistence. Our ongoing work is part of an effort to form a quantitative understanding of microbial ecology from the genome upto the global scale. This includes, but is not limited to, understanding the role of horizontal gene transfers, the distributed gene pool (a.k.a. pan-genome or supra-genome), and biodiversity.

Sequence Alignment
Sequence alignment is the most widely used computational tool in molecular biology. Identification of any newly sequenced gene depends on the accuracy with which alignments can be performed. The crucial problem of sequence alignment is characterizing the background scores, i.e., scores from the alignments of random sequences. Knowledge of their background scores grants us information about the quality of any alignments between biological sequences which must be assessed in order to make a decision about their biological relevance.

Asymmetric Exclusion Process
Another system of interest is the Asymmetric Exclusion Process, a problem from statistical physics seeking to understand the properties of a system where particle movement is directionally biased. In addition to utilizing a mapping of the Asymmetric Exclusion Process onto sequence alignment for the purpose of studying sequence alignments, I have also investigated a method for efficiently and numerically assessing the universality of the Derrida-Lebowitz Scaling Function without relying on cumbersome cumulant ratios. From this method, one also may uncover the non-universal properties of various Asymmetric Exclusion Processes and more directly study its many statistical properties.

List of Publications

  • N. Chia, C. Woese, and N. Goldenfeld, A collective mechanism for phase variation in biofilms, PNAS (2008), accepted.
  • N. Chia and R. Bundschuh, Numerical Method for Assessing the Universality of the Scaling Function for a Multi-Particle Discrete Time Asymmetric Exclusion Process, Phys. Rev. E 72 (2005) 051102.
  • N. Chia and R. Bundschuh, A Practical Approach to Significance Assessment in Alignment with Gaps, in Lecture Notes in Computer Science LNBI 3500/2005, proceedings of RECOMB 2005, Cambridge, MA, USA, 2005, edited by S. Miyano et al. (Springer-Verlag Berlin, Heidelburg, 2005) p. 474; Journal of Computational Biology, 13 (2006) 429.
  • N. Chia and R. Bundschuh, Finite Width Model Sequence Comparison, Phys. Rev. E 70 (2004) 021906.

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Curriculum Vitae

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