Student Research Spotlight

Jiajie Huang Profile Picture

Jiajie Huang

Department:

Biological Sciences

Advisor:

Dr. Michael Gribskov

Research Title:

Identification and Classification of Conserved RNA Structural Motifs Using A Theoretical Graph Approach


Research Description:

As one of the three major macromolecules (DNA, RNA, and protein) in all known forms of life, RNA (ribonucleic acid) is a ubiquitous family containing different classes that performs multiple cellular functions including coding, decoding, regulation, and expression of genes. Only a small portion of the RNA functions is studied; as modern technologies thrive (e.g. high-throughput sequencing), a plethora of novel RNAs have been found and their complex functions are yet to be revealed.

My PhD research is to identify and classify functional RNA motifs through their structures. In my study, RNA structures are represented as graphs for efficient computation; common substructures are identified by finding common (isomorphic) subgraphs among multiple structures. I have developed a subgraph sampling algorithm that efficiently identifies subgraphs in a RNA graph without exhaustive search. The set of subgraphs in an RNA structure, called its fingerprint, can be compared with the fingerprints of other RNA structures to identify conserved or common structural motifs. I have also developed a distance function for comparing RNA structural fingerprints and demonstrate that it is able to correctly identify the similarity between known classes of RNA structures. The identification of RNA with similar structural motifs is a step towards structure-based prediction of RNA function.

About Me:

Growing up in a family of healthcare providers, my dream has been to help people by research in the life science area. I spent the first 18 years of life in Canton, the south-most province in China, then went to Shanghai and got my Bachelor’s in Biology from Fudan University. After finish of college I came to Purdue and started as a PhD student in Computational Biology. Purdue is a great place and she has brought me with all kinds of excitement. I have got my first mammal pet – an American domestic short-haired cat. I have took classes in different types of dancing – belly dance, Argentina tango, and salsa. And the most importantly, I have met many great people here – they are smart, nice, and energetic. Coming to Purdue is one of the best decisions I have made in my life.


Awards:

  • Oak Ridge Institute for Science and Education (ORISE) fellowship, U.S. Department of Energy, 2014
  • College of Science Graduate Student International Travel Grant (1 out of 3 winners), Purdue University, Fall 2013
  • Interdisciplinary Life Science Travel Award, Purdue University, May 2012 and Nov 2013
  • Competent Communicator Award, Toastmasters International, 2013
  • ISMB Travel Fellowship, U.S. Department of Energy and National Science Foundation Bio-Directorate, Jul 2012
  • National People’s Scholarship, Fudan University (top 20% academic achievement), 2007 and 2008
  • Youth Excellence Annual Award (top 3% extracurricular performance), Fudan University, 2007

Publications:

  • J. Huang, K. Li, and M.R. Gribskov. “Identification of conserved RNA structural motifs using a subgraph random sampling approach.” In Preparation.
  • X. Zhu, J. Cai, J. Huang, X. Jiang, and D. Ren. “The Treatment and Prevention of Mouse Melanoma with an Oral DNA Vaccine Carried by Attenuated Salmonella Typhimurium.” Journal of Immunotherapy 33(5):453-60 (2010).

Presentations:

  • J. Huang, K. Li, and M.R. Gribskov. “Identification of conserved RNA structural motifs using a subgraph random sampling approach.” Poster Presentation, Annual International Conference on Research in Computational Molecular Biology (RECOMB), Pittsburgh, PA (2014).
  • J. Huang, K. Li, and M.R. Gribskov. “Identification and classification of conserved RNA structural motifs using a graph theoretical approach.” Poster Presentation, Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA (2012).
  • J. Huang, K. Li, and M.R. Gribskov. “A graph theoretical approach on RNA functional motif identification.” Poster Presentation, Great Lakes Bioinformatics Conference, Ann Arbor, Michigan (2012).

Personal Page:

Ernest C. Young Hall, Room 170 | 155  S. Grant Street, West Lafayette, IN 47907-2114 | 765-494-2600

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