PhD Research

Disentangling IGC tract length and initiation rate project, NC State University, 2017

Advisor: Dr. Jeff Thorne, Bioinformatics Research Center, NC State University

A shortcoming of our original approach (see the Modeling Gene Conversion project, also as in Ji et al. 2016) towards quantifying interlocus gene conversion (IGC) was its inability to infer the tract length distribution of (fixed) IGC events. I developed a method to address this and am beginning to apply it. This ongoing project can be found here on github.

IGC and gene duplication loss histories of primate ADH1 genes project, NC State University, 2016

Advisor: Dr. Jeff Thorne, Bioinformatics Research Center, NC State University

Motivated by primate ADH1 data, I extended our method (as in Ji et al. 2016) so that up to 6 paralogs per genome can be considered. I am improving my software to answer interesting biological questions (e.g., permitting asymmetry among paralogs in tendency to serve as IGC donor, investigating how distance between tandem paralogs affects IGC, summarizing how paralog divergence changes IGC). I am also considering different gene duplication loss histories and how incorporating IGC could help with orthologous mapping. This ongoing project can be found here on github.

Modeling Gene Conversion project, NC State University, 2014

Advisor: Dr. Jeff Thorne, Bioinformatics Research Center, NC State University

Interlocus gene conversion (IGC) homogenizes repeats. While genomes can be repeat-rich, the evolutionary importance of IGC is poorly understood, largely due to a lack of statistical tools. We developed a strategy for adding IGC to widely-used probabilistic models for sequence change. In 14 groups of yeast ribosomal protein genes, we estimated the percentage of codon substitutions that originate with IGC rather than point mutation. We found values ranging from 20% to 38%. Our results are consistent with an important role for IGC in the evolution of each of the 14 gene families. Our paper is published in MBE (Molecular Biology and Evolution).

Here is the github repository of the publication. This github repository keeps my under development software code.

Solvent Accessibility project, NC State University, 2013

Advisor: Dr. Jeff Thorne, Bioinformatics Research Center, NC State University

This was a ‘left-over’ project that I helped finished. I extracted solvent accessibility information from protein coding genes in several species (human, mouse and Ecoli). Another senior PhD student built probabilistic model based on these data. Details of this project can be found in this paper which I co-authored.

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Master Thesis

Laser Interference Lithography project, NC State University, 2012

Advisor: Dr. John Muth, EE Department, NC State University

The goal was to develop a fabrication process using the mask-free laser interference lithography to easily introduce periodic pattern onto devices. We wanted to use it for gas sensor fabrication to increase the surface to volumn ratio which primarily determines gas-sensor’s sensitivity. Details can be found in my ugly-written thesis.

Here are some pictures for a taste of what I did.

Periodic lines on sample Gas sensor prototype
Periodic lines on sample Gas sensor prototype

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Undergraduate Research

SPP source project, Peking University, 2011

Advisor: Dr. Zhiping Zhou, EECS Department, Peking University

I did my undergraduate thesis in this lab. Part of the work I did was to find a good doping location for SPP source design. The idea was to imbed light source inside a plasmon waveguide. You could find details in this published paper which I co-authored.

Plasmonic Lens project, Peking University, 2010

Advisor: Dr. Jiasen Zhang, Physics Department, Peking University

The Goal was to design, fabricate and test rectangular shape plasmonic lense composit of nano-scaled slots on a 200nm thin gold film on glass substrate being able to generate sharper focus. This work stays unpublished.

Due to detection limit, we could not provide direct proof that our device worked by the fact that our image detection system was only sensitive to XY plane (parallel to the device) of the optical field whereas the focus intensity mainly lied in Z direction. If possible, a near field optic probe may detect the focus point and give a direct proof. I show my simulated light intensity distribution at XY plane of the focus point together with experimental result below to give you an idea.

XY intensity plane simulated intensity experimentally detected
Simulated intensity field XY plane Big NA Experimental detected intensity field

We did have direct proof if we modified the design to have the light field mainly in XY plane, but this one didn’t have the property to generate a sharper focus. (Small Numerical Aperture)

XY intensity plane simulated intensity experimentally detected
Simulated intensity field XY plane Small NA Detected intensity field XY plane Small NA

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*All of the files in this page are copyrighted . They are provided for your convenience, yet you may download them only if you are entitled to do so by your arrangements with various publishers.

**Copyright statement copied from Dr. Jiasen Zhang’s webpage.