I am very interested in undergraduate research and I have projects for undergraduate students from any department who are interested in the interplay of chromosome structure and cancer biology. Students are expected to be interested in applying math, stats, computer science and/or physics to biological problems.

Current Graduate students

Ari Akerstein, Biology
Daniel DeWoskin, Mathematics
Rocco Varela, Computer Science

Current Undergraduate Students

Trevor Blackstone, Computer Science.
Ben Borgo, Mathematics

Previous Students

Nasheen Mirza (Postbac, Open University Student, Fall 05, Spring 06)
Yunha Chae (Senior, CS, Fall 05, Spring 06, Fall 06),
Oswaldo Lon (Senior, CS, Spring 06, Fall 06)
Xiaou Hu (Senior, CS, Spring 06, Fall 06)
Stacey Hubbard, (Grad. student Mathematics, Fall 06)
Dane Volek, Mathematics (Junior, Mathematics,Fall 06, Spring 07)
Jupei Hsiao, Mathematics (Grad.student Mathematics, Summer 07, Fall 07)

Honors and Awards

- Nasheen Mirza was awarded 4th prize for undergraduate research in the 2006 CoSE project showcase
- Stacey Hubbard was awarded the Sergio Martens Scholarship in 2006
- Rocco Varela was awarded the Louis Stokes Alliances for Minority Participation (LSAMP) Program 2006-08
- Daniel Dewoskin was awarded the Paul Halmos Scholarship in 2007
- Daniel Dewoskin was awarded the ARCS fellowship in 2008
- Daniel Dewoskin was awarded the 1st prize for graduate research in the 2008 CoSE project showcase
- Daniel Dewoskin was awarded the SFSU alumni fellowship in 2008
-Ben Borgo was awarded an NSF-UBM from Prof. E. Connor (Biology)

Publications

1.- Arsuaga, J., Blackstone, T.*, Diao,Y., Karadayi, E. , Saito, Y.Knotting of Uniform Random Polygons in Confined Spaces. (2007) J. Phys. A: Math Gen.40; 11697-11711
2.- Arsuaga, J., Blackstone, T.*, Diao,Y., Karadayi, E. , Saito, Y. Linking of Uniform Random Polygons in Confined Spaces. (2007) J. Phys. A: Math. Gen. 40; 1925-1936
3.- Blackstone, T.*, McGuirck, P.*,Laing, C., Vazquez, M., Roca, J. and Arsuaga, J. The role of writhe in DNA knotting. Proceedings of International Workshop on Knot Theory for Scientific Objects. (2007) OCAMI Studies Volume 1 (2) Osaka Municipal Universities Press; 239-250
4.- Arsuaga, J., Vazquez, M., McGuirk, P.*, Trigueros, S., Sumners, D. W., and Roca, J. DNA knots reveal a chiral organization of DNA in phage capsids. Proceedings National Academy of Sciences U S A. 2005 Jun 28;102(26):9165-9
5.- Hua,X.*, Baghavan,B.*, Nguyen,D.*, Arsuaga,J. and Vazquez, M. Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases. Topology and its Applications (2007) 154:1381-1397.

* indicates undergraduate student

Presentations in Conferences

1.- (Talk) Hu, X.*, Chae, Y.*, Lon, O.* and Arsuaga, J. Developing a Web-based Environment for Integrating Breast Cancer "omics" data in the Clinical Setting. Northern California Undergraduate Mathematics Conference. Sonoma State University (2006).
2.- (Talk) Hubbard, S., Hu, X.*, Chae, Y.*, Lon, O.* and Arsuaga, J. Using Persitent homology to analyze Breast Cancer CGH data. Asilomar Chromatin & Chromosomes Conference (2006)
3.- (Talk) Akerstein, A., Bernstein, D., and Arsuaga, J. Analysis of FRAP data using the Gillespie algorithm . Asilomar Chromatin & Chromosomes Conference (2006)
4.- Blackstone, T.*, Diao, Y. and Arsuaga,J. Linking of Chromosomes During Interphase. RECOMB 2007. Oakland, CA.
5.- (Poster) Portillo, J.*, Blackstone, T.*, Arsuaga, J., Vazquez, M Average Writhe in the Simple Cubic Lattice. MAA NorthCal Conference, West Valley College, Saratoga, CA (2007)

underline indicates presenter

Abstracts Published

1.- Hu, X.*, Chae, Y.*, Lon, O.*, Climent, J. and Arsuaga, J. Analysis of CGH Breast Cancer Data using Algebraic homology groups. Biochemistry and Cell Biology 85(4) 532
2.- Akerstein, A., Bernstein, D. and Arsuaga, J. An in silico approach to analyzing nuclear FRAP protein recovery curves using an extension of the Gillespie algorithm. Biochemistry and Cell Biology 85(4) 521
3.- Blackstone, T.*, Diao, Y. and Arsuaga,J. Linking of Chromosomes During Interphase ( Proceedings of RECOMB 07).

Previous Mentoring

During my postdoc at UC Berkeley I was involved in undergraduate research through URAP . My students I. Renner (Senior, Chemical Eng., Fall 2000/Spring 2001), J. Lee (Sophomore, Bioeng. Spring, 2001), M. McClean (Senior, Math. Fall/Spring 2001, Fall 2002, Spring 2002-Now PhD student at harvard), B. Raghavan (Senior, CS, Spring 2002-Now PhD Student at UCSD), T. Ozdere (Senior,MCB, Fall 2002-Now PhD student at Duke) and P. McGuirk (Sophomore, Physics, Fall 2002,Spring 2002) have worked in implementing algorithms for the analysis of DNA packing in bacteriophages(I. Renner, J. Lee, B. Raghavan and P. McGuirk) and in the statistical analysis of microarray data (M. McClean, T. Ozdere). Some of these students wrote honors thesis (M. McClean) and others are coauthors in peer-reviewed papers (P.McGuirk, B. Raghavan)

Positions of some of my former students

Ms. McClean, Megan
Undergraduate UC Berkeley, Mathematics
Fall/Spring 2001, Fall/Spring 2002
Current Position: PhD student, Applied Mathematics, Harvard University

Mr. Taylan, Ozdere
Undergraduate, UC Berkeley, MCB
Current Position: PhD Student, Developmental Biology, Duke University

Mr. Barath, Raghavan
Undergraduate, UC Berkeley, CS.
Current Position: PhD Student, Computer Science, UC San Diego

Mr. Paul McGuirk
Undergraduate , UC Berkeley, Physics
Current Position: PhD Student, Physics, Madison, Wisconsin

Mr. Johnny Wu
Undergraduate, UC Berkeley, Physics
Current Position: PhD Student, Biomedical Engineering Program, UT Austin.

Mr. Oswaldo Lon
Undergraduate, SFSU, Computer Science

Ms. Yunha Chae
Undergraduate, SFSU, Computer Science
Current Position: Master's student, Software Engineering, SJSU

Mr. Xiaoyu Hu Undergraduate, SFSU, Computer Science
Current Position: Software Engineer, IBM China Global Delivery Chengdu Center