Email: ncjones@cs.ucsd.edu
FAX: (858) 534-7029
Office: APM 3801

Mailing address:
Department of Computer Science and Engineering
University of California, San Diego
9500 Gilman Drive, Mail Code 0404
La Jolla, CA 92093-0404
USA

Biographical

Educational History

• B.S. Chemistry, California Institute of Technology (1997)
• M.S. Computer Science, UCSD (2003)
• C.Phil Computer Science, UCSD (2005)
• Ph.D. expected Jun 2007

Employment:
Graduate student, UCSD Computer Science Department (2001-present)

Fellowships:
La Jolla Interfaces in the Sciences, AY 2003-2004
Helped secure educational grant for preparation of bioinformatics class materials

Academic Activities:
Graduate Student Researcher
Teaching Associate (Graduate level algorithms class, undergraduate bioinformatics class)

Research Interests:
I am using comparative genomics techniques to locate regulatory elements in complex genomes. The particular type of regulatory elements that I am looking for involve a new class of molecule discovered in 2004 called "small modulatory" RNAs, which are RNAs that can enhance the transcription of a gene. This is in stark contrast to the other known methods of RNA regulation, namely siRNA and miRNA, both of which operate after a gene's transcription, and are only capable of silencing a gene's protein product.

Publications

Books:

1. N. Jones and P. Pevzner. Introduction To Bioinformatics Algorithms. MIT Press, Cambridge, MA

Refereed articles:

1. N. Nagarajan, N. Jones, and U. Keich, Computing the P-value of the information content from an alignment of multiple sequences, Bioinformatics. 2005 Jun 1; 21 Suppl 1:i311--8 (from ISMB 2005)
2. A. Price, N. Jones, and P. Pevzner, De novo identification of repeat families in large genomes, Bioinformatics. 2005 Jun 1; 21 Suppl 1:i351--8 (from ISMB 2005)
3. N. Jones, D. Zhi, and B. Raphael, AliWABA: Alignment on the Web through an A-Bruijn Approach, Submitted
4. N. Jones, P. Pevzner, Comparative genomics reveals unusually long motifs in mammalian genomes, Submitted
5. P. Ng, N. Nagarajan, N. Jones, and U. Keich, Apples to apples: improving the performance of motif finders and their significance analyses in the Twilight Zone, In preparation

Posters:

1. N. Jones and B. Forsgren, Improving accuracy and resolution in deuterium exchange mass spectroscopy, RECOMB 2003