CURRICULUM VITAE

Sophia Yancopoulos

The Feinstein Institute for Medical Research
North Shore-LIJ Health System
350 Community Dr.
Manhasset, NY 11030
phone: (516) 562-3418
email: syancopo@nshs.edu



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
Bioinformatics
Evolutionary Model of Genome Rearrangements
Collaborations with Richard Friedberg (Columbia Physics) and Oliver Attie (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, Philadelphia, PA. Worked on the detection of signal peptides in the genome.

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
Taught 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
Taught 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

Extensive 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     

             Concepts in Action      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.


Contributed 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.
         
          In Press

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

Manuscripts in Preparation                                                                 


      Yancopoulos, S., Mezei, M., Osman, O., The Bacteriorhodopsin Bucket Brigade: 
      Internal Waters and the Mechanism of a Photon Powered Proton Pump

      Yancopoulos, S., Mezei, M., Osman, O., The Internal Waters of Rhodopsin

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 
(212) 854-3341; rmf@cuphyb.phys.columbia.edu 

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