CURRICULUM VITAE

Sophia Yancopoulos

The New York Genome Center
101 Sixth Ave
New York, NY 10013
phone: (646) 977-7342
email: sopheetsa@gmail.com

EDUCATION

B.A., M.S.

Barnard College, Columbia University, Physics, 1981

Columbia University School of Engineering, Geophysics, 1981
Thesis: Reading a buried underwater tombstone with seismic waves

Ph.D.

Columbia University, Physics: May 1996

Thesis Topic: Neutron Stars in Binaries and in Isolation.
Thesis Advisor: Prof. David Helfand

RESEARCH


2004-present	*Genomics* Evolutionary Model of Genome Rearrangements Collaborations with Richard Friedberg, Oliver Attie, and others. (NYU)
2002-2003	*Bioinformatics* Search for secreted proteins in the genome (collaboration with Regeneron Pharmaceuticals)
2001-2002	*Bioinformatics* Post Doc in bioinformatics at University of Pennsylvania's Center for Bioinformatics with Artemis Hatzigeorgiou.

1999-2001	*Biophysics of Transmembrane Proteins* Postdoc at the Mount Sinai School of Medicine, NY, NY studying the role of internal waters on the structure and function of transmembrane proteins in particular the GPCR TRH-receptor, bacteriorhodopsin and rhodopsin.
1998	*Development of Novel Neural Network Model of the Brain* Worked with Prof. Richard Friedberg (Columbia University) on building a dynamically responsive brain model that can modify its functional architecture vis a vis an intrinsic means of altering the effective connections between neurons. The model is based on ternary connections between neurons.
1995-1996	*Morphology of the giant branch in globular clusters* Analysis of HST and groundbased data. Post doc with Charles Bailyn, at Yale University
1994-1995	*Search for Isolated Old Neutrons Stars* Designed and performed an automated systematic search through all soft X-ray events recorded during the Einstein mission to identify candidate isolated old neutron stars. Project provided an upper limit on density of isolated neutron stars in the solar neighborhood and posed possible candidates.
1991-1993	Detection of X-rays from a nearby Pulsar: Observed PSR1929+10 for 40 ks with the ROSAT Observatory and detected X-ray pulsations at the known radio period. The detection of apparently thermal emission from this nearby pulsar constrains models of the geometry of rotating hot spots.
1989-1991	Astrophysics of Accretion: Theoretical models and computer simulations of accretion disks around low mass X-ray binaries. Monte-Carlo simulations of Compton scattered X-rays through time dependent and independent, spherical and toroidal disk geometries performed to model the Normal Branch of Low Mass X-ray binaries.
1983	Mathematical Physics: Analytical result for the Green Function in electroastatics obtained for a Kirchoff Network on a random 2-D lattice.
1981	Experimental Particle Physics: Research Assistant on neutrino oscillations experiment at Fermi National Lab. Batavia, Illinois.
1979-1981	Acoustic Modelling: Experimental and computational modelling of acoustic waves

TEACHING


2002-2003 Spring '03	Manhattan College (Full Time) Physics with algebra, Physics with calculus, "Great Ideas in Physics", Physics for Student Teachers Manhattan College Graduate Program in Biotechnology Bioinformatics
1998-1999	Bronx High School of Science Regular and Honor's 9th grade Regents Biology Brooklyn Technical High School Regent's Chemistry and senior level Environmental Science
1997-1998	School of the Metamorphosis 6th grade General Science,7th grade Life Science, 8th grade Earth Science, 9th grade Regents Biology and 8th grade Math
1996-1997	Vassar College: Introductory Astronomy, Special Topics in Astronomy
1995	Barnard College: Introductory Astronomy for undergraduates.
1994-1995	College of Staten Island, CUNY: Introductory Astronomy for undergraduates.
1991	Steven's Institute of Technology: Introductory Graduate Level Astronomy.
1990-1991	Barnard College: Introductory Physics for undergraduates. Lab and Lecture

SKILLS

Experience in FORTRAN and C programming for Monte Carlo Simulations, Numerical Data Analysis and Image Processing. Developed scientific programs under UNIX and VAX/VMS operating systems. Familiar with Protein and Gene databases, standard online bioinformatics tools and algorithms, HTML, Java, Oracle, MacVector and CHARMM.

PUBLICATIONS

Middle School Science Textbook

Physical Science- Concepts in Action. Publisher: Prentice Hall. Edition: 2005
Michael Wysession, David Frank and Sophia Yancopoulos.

Papers

1. Yancopoulos S, Friedberg S: Sorting Genomes with Insertions, Deletions and Duplications by DCJ. RECOMB-CG 2008: 170-183

2. Yan XJ, Qi M, Telusma G, Yancopoulos S, Madaio M, Satoh M, Reeves WH, Teichberg S, Kohn N, Auborn K, Chiorazzi N. Indole-3-carbinol improves survival in lupus-prone mice by inducing tandem B- and T-cell differentiation blockades. Clin Immunol. 2009 Mar 9. [Epub ahead of print]

3. McCarthy BA, Boyle E, Wang XP, Guzowski D, Paul S, Catera R, Trott J, Yan XJ, Croce CM, Damle R, Yancopoulos S, Messmer BT, Lesser M, Allen SL, Rai KR, Chiorazzi N. Surface expression of Bcl-2 in chronic lymphocytic leukemia and other B-cell leukemias and lymphomas without a breakpoint t(14;18). Mol Med. 2008 Sep-Oct;14(9-10):618-27.

4. Damle N, Temburni S, Calissano C, Yancopoulos S, Banapur T, Sison C, Allen SL, Rai KR, Chiorazzi N. CD38 expression labels an activated subset within chronic lymphocytic leukemia clones enriched in proliferating B cells. Blood. 2007 August epub

5. Yan XJ, Albesiano E, Zanesi N, Yancopoulos S, Sawyer A, Romano E, Petlickovski A, Efremov DG, Croce CM, Chiorazzi N. B cell receptors in TCL1 transgenic mice resemble those of aggressive, treatment-resistant human chronic lymphocytic leukemia.Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11713-8.

6. Yancopoulos S, Attie O, Friedberg R. Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics. 2005 Aug 15;21(16):3340-6.

7. Yancopoulos S, Friedberg R. DCJ path formulation for genome transformations which include insertions, deletions and duplications, accepted Journal of Computational Biology. 2009

Book Chapters

Friedberg R, Darling AE, Yancopoulos S. Genome rearrangement by the double cut and join operation. Methods Mol Biol. 2008;452:385-416. Review.

Journal articles in physics and astronomy

Yancopoulos, S., Hamilton, T.T., Helfand, D.J.,1994, Pulsed X-Rays from a Nearby Radio Pulsar,ApJ, 429, 832

Alpar, A., Hasinger, G., Shaham, J. and Yancopoulos, S. 1991, 6 Hz QPO from LMXB:The Sound of anAccretionDisk?,Astronomy and Astrophysics257, 627

Friedberg, R., and Yancopoulos, S.,1983 A Rigorous Upper Bound in Electrostatics on aRandom Lattice Ensemble, Communications in Mathematical Phys89:1, 131

Conference Abstracts

Yancopoulos, S., Mezei, M., Osman, O., 2001 Internal Hydration Sites of Bacteriorhodopsin
Biophys J., 80 No1 Part 2 of 2

Yancopoulos, S., Mezei, M., Osman, O., 2000 Effect of Internal Water on Receptor
Binding and Activation, Biophys. J., 78 No1 Part 2 of 2

Yancopoulos, S.,1996, Panning for Galactic Old Local Dead Stars in the Einstein
database,Bull. Am. Astron.Soc.

Yancopoulos, S., Helfand, D.J., Hamilton, T.T., Halpern, J.P., Seward, F.D., and Becker, R.H.,

The Detection of Pulsed X-Ray Emission from a NearbyRadio Pulsar,
Bull. Am. Astron. Soc., Jan 1993

Yancopoulos, S., Becker,1991, The Normal Branch QPO in
Low Mass X-Ray Binaries, Bull. Am. Astron. Soc. 23:2 117

Shaham, J. and Yancopoulos, S. 1987, Periodic SN1987a Neutrinos:
Fact or Fancy?, News Letter of the Astronomical Society of New York
III:3 19

REFERENCES

Dr. Allan Blaer , Dept of Physics, Columbia University
(212) 854-3262; asb@phys.columbia.edu

Dr. Nicholas Chiorazzi, Center for Experimental Immunology, The Feinstein Institute for Medical Research
(516) 562-1090; nchizzi@nshs.edu
Dr. Richard Friedberg, Department of Physics, Columbia University
rfriedberg1@nyc.rr.com;

Dr. David Helfand, Department of Astronomy, Columbia University
(212) 854-2150; djh@astro.columbia.edu
Dr. Mihaly Mezei, Dept of Physiology and Biophys, Mt. Sinai School of Medicine
(212) 241-2186; mezei@physbio.mssm.edu