Yuhai Tu

Manager, Theory and Computational Physics

Physical Sciences Department

Research lab: Watson Research Center (Yorktown)

Yuhai Tu

Current Position:

Research Staff Member, Physical Sciences Department
IBM research, TJ Watson Research Center

Contact Information:

(914)-945-2762
(914)-945-4506 (fax)
e-mail: yuhai@us.ibm.com

Education:

B.S., Physics, University of Science and Technology of China, 1987
M.S., Physics, University of California, San Diego, 1988
Ph. D., Physics, University of California, San Diego, 1991

Work Experience:

California Institute of Technology, Division Prize Research Fellow, 1991-1994
IBM T. J. Watson Research Center, Research Staff Member, Physical Sciences Department, 1994-present

Research Interests:

Statistical Physics

Biophysics

Dynamical Systems

Pattern Formatiom

Growth Phenomena in Material Science

Honors and Awards:

Division Prize Research Fellowship (California Institute of Technology) 1991-1994

Fellow, American Physics Society, since 2004

Other Professional Activities:

Colloquiums and seminars at many universities and research centers, including Caltech, Yale, Columbia, ITP, University of Cicago, SUNY(Stony Brook), Los Alamos National Labs, McGill University etc. in different departments, such as Physics, Applied Math, BioMedical Engineering and Genomics departments.

Workshops in related fields, including those at the Aspen Center for Physics, ITP Santa Barbara, and Los Alamos National Labs/Santa Fe.

Organized symposium and chaired sessions for major conferences, such as APS March meeting and SIAM conference. I have also organized a series of summer schools for graduate students in China.

Referee for leading Journals in Physics: Physical Review and Physical Review Letters.

Key Invited Talks:

"Noise effects in bacterial flagella motor", 2006 APS March Meeting, Baltimore, 03/2006.

"Receptor Interaction and Signal Integration in Bacterial Chemotaxis", Gordon Research Conference on Signal Transduction in Microorganism (STIM), 01/06, Ventura, CA.

"Receptor coupling and signal amplification”, BLAST ’05, Ft. Lauderdel, FL, 01/05.

"Receptor coupling and signal amplification in bacterial chemotaxis”, 2004 March Meeting of APS, Montreal, Canada.

"Noise analysis and physical modeling of gene expression microarrays", CHI conference on gene expression microarray data analysis, Baltimore, September 2003.

Tutorial on "A brief review of methods used in gene expression analysis", DIMACS workshop on gene expression analysis, Rutgers, October 17, 2001.

Analysis of gene expression microarrays for phenotype classification , 2000 ISMB meeting, San Diego.

Interface Structure of a-SiO2/c-Si , 1999 March Meeting of American Physics Society (APS), Atlanta, Georgia.

Sound Waves and the Absence of Galilean Invariance in Flocks , 1998 Dynamics Days, Chapel Hill, North Carolina.

Long Range Orientational Order in Flocks , 1997 SIAM conference on dynamical systems, Snowbird, Utah.

Flocking Dynamics: How Birds Fly Together , 1996 March Meeting of the American Physics Society (APS), St. Louis, Missouri.

Collective Behavior in Large Biological Systems , The 19th Statistical Physics Meeting, Xiamen, China, 1995.

Chaotic Domain Structure in Rotating Convection , 1993 March Meeting of American Physics Society (APS), Seattle, Washington.

Saffman-Taylor Problem in Sector Geometry , 1991 NATO Advanced Research Workshop on Asymptotic beyond All Orders, La Jolla, California

Selected Publications:

"An allosteric model for heterogeneous receptor complexes: Understanding becaterial chemotaxis responses to multiple stimuli", B. Mello and Yuhai Tu, PNAS, 102(48), 17354-17359 (2005).

"Excitation-Contraction Coupling Gain and Cooperativity of the Cardiac Ryanodine Receptors: A Modeling Approach", Kai Wang, Yuhai Tu, W. J. Rappel, H. Levine, Biophysical Journal, 89(11), 3017-3025 (2005).

"Hydrodynamics and phases of flocks", John Toner, Yuhai Tu, Sriram Ramaswamy, Annals of Physics 318(1):170-244 (2005).

“Effect of noise on bacterial flagella motors”, Y. Tu and G. Grinstein, Phys. Rev. Letts. 94, 208101 (2005). (PDF)

“Origin of apparent critical thickness for island formation in heteroepitaxy”, Y. Tu and J. Tersoff, Phys. Rev. Letts., 93, 21610(2004).

“Reconstructing biological networks using conditional correlation analysis”, J. Rice, Y. Tu, and G. Stolovitzky, Bioinformatics, October 14, (2004).

“Effects of receptor interaction in bacterial chemotaxis”, B. Mello, L. Shaw, and Yuhai, Tu, Biophysical Journal, 87(3), 1578-1595(2004).

Lepre, J., Rice, J.J., , Tu, Y., and Stolovitzky, G. Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data. Bioinformatics. May 1;20(7):1033-44 (2004). (Pubmed)

Rice, J.J., Stolovitzky, G., Tu, Y., and de Tombe, P.P. Ising model of cardiac thin filament with nearest-neighbor cooperative interactions. Biophysical Journal Feb;84(2 Pt 1):897-909. (2003). (Pubmed)

“Modeling of DNA Microarray Data Using Physical Properties of Hybridization”, G. Held, G. Grinstein, Yuhai Tu, PNAS, 100(13), 7575-7580 (2003).

“Quantitative Modeling of Sensitivity in Bacterial Chemotaxis: The Role of Coupling Between Different Chemoreceptor Species”, B. Mello and Yuhai Tu, PNAS, 100(14), 8223-8228 (2003).

“Perfect and near perfect adaptation in a model of bacterial chemotaxis”, B. Mello and Y. Tu, Biophysical Journal, 84(5), 2843-2856 (2003).

“Identification of a Global Gene Expression Signature of B-Chronic Lymphocytic Leukemia”, Diane F. Jelinek, Renee C. Tschumper, Gustavo A. Stolovitzky, Stephen J. Iturria, Yuhai Tu, Jorge Lepre, Nigam Shah, and Neil E. Kay, Molecular Cancer Research, 1(5), 346-361 (2003).

“Analysis of B-cells During Germinal Center Transition by Gene Expression Profiling”, Klein U, Tu Y, Stolovitzky GA,Jeffrey Keller, Joseph Haddad Jr., Vladan Miljkovic, Giorgio Cattoretti, Andrea Califano, and Riccardo Dalla-Favera, PNAS, 100(5), 2639-2644(2003).

“Indentification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling”, Ralf Kuppers, Ulf Klein, Ines Schwering, Verena Distler, Andreas Brauninger, Giorgio Cattoretti, Yuhai Tu, Gustavo Stolovitzky, Andrea Califano, Martin-Leo Hansmann, and Riccardo Dalla-Favera, The Journal of Clinical Investigation, 111(4), 529-537 (2003).

“Gene Expression dynamics during germinal center transition in B cells”, Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J Jr, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R., Ann. New York Acad. Sci., 987, 166-172 (2003).

“Tracking CD40 Signaling during Normal Germinal Center Development by Gene Expression Profiling”, Basso K, Klein U, Niu H, Stolovitzky GA, Tu Y, Califano A, Cattoretti G, Dalla-Favera R.. Ann N Y Acad Sci. 2003 Apr; 987:288-290 (2003).

“Can we identify cellular pathways implicated in cancer using gene expression data?”, Shah N, Lepre J, Tu Y, Stolovitzky GA, Proceedings of the 2nd IEEE Computational Systems Bioinformatics Conference, pp. 94-103, (2003)

U. Klein, Y. Tu, G. Stolovitzky, M. Mattioli, G. Cattoretti, H. Husson, A. Freedman, G. Inghirami, L. Cro, L. Baldini, A. Neri, A. Califano and R. Dalla-Favera, Gene Expression Profiling of B cell Chronic Lymphocytic Leakemia Reveals a Homogeneous Phenotype Related to Memory B Cells , submitted to JEM.

G. Gregoire, H. Chate and Y. Tu, Active boids and passive beads: modeling particles in a bacteria bath , to appear in Phys. Rev. E (2001).

S. H. Yook, H. Jeong, A. L. Barabasi and Y. Tu, Weighted Evolving Networks , to appear in Phys. Rev. Lett. (2001).

G. Gregoire, H. Chate and Y. Tu, Comment on Particle Diffusion in a Quasi-two-dimensional bacteria bath , Phys. Rev. Lett.,86, 556(2001).

Y. Tu, How Robust Is the Internet , Nature, 406, 353-354 (2000).

Y. Tu and J. Tersoff, Structure and energetics of the Si-SiO2 interface , Phys. Rev. Lett., 84(19), 4393 (2000).

A. Califano, G. Stolovitzky and Y. Tu, Analysis of Gene Expression Microarrays for Phenotype Classification , Proceeding of Intelligent System for Molecular Biology 2000.

Y. Tu, The Structure of Finite Flocks , Physica A, 281, 30-40 (2000).

Y. Tu, J. Toner and M. Ulm, Sound Waves and the Absence of Galilean Invariance in Flocks , Phys. Rev. Lett., 80(21), 4819 (1998).

J. Toner and Y. Tu, Flocks, herds, and schools: A quantitative theory of flocking , Phys. Rev. E., 58(4), 4828 (1998).

G. Grinstein, J. Tersoff and Y. Tu, Stability of Solid State Reaction Fronts , Phys. Rev. Lett., 81(12), 2490 (1998).

S. Chen, Y. Deng, X. Nie and Y. Tu, Clustering Kinetics of Granular Media in Three Dimensions , Physics Letters, 269, 218 (2000).

J. Tersoff, Y. Tu and G. Grinstein, Effect of stress on reaction rates at solid interfaces , Appl. Phys. Lett., 73(16), 2328 (1998).

Y. Tu, J. Tersoff, D. Vanderbilt and G. Grinstein, Properties of a Continuous-Random-Network Model for Amorphous Systems , Phys. Rev. Lett., 81(22), 4899(1998).

Y. Tu, G. Grinstein and M. Munoz, Systems with Multiplicative Noise: Critical Behavior From KPZ Equation and Numerics , Phys. Rev. Lett., 78 (2), 274 (1997) .

Y. Tu, Worm Structure in Modified Swift-Hohenberg Equation for Electroconvection , Phys. Rev. E , 56(4), R3765 (1997).

M. Munoz, G. Grinstein and Y. Tu, Survival probability and field theory in systems with absorbing states , Phys. Rev. E , 56(5), 5101 (1997).

G. Grinstein, M. Munoz and Y. Tu, Phase Structure of Systems with Multiplicative Noise , Phys. Rev. Lett., 76(23), 4376 (1996).

D. Ridgway, H. Levine and Y. Tu, Front Stability in Mean Field Models of Diffusion Limited Growth , Phys. Rev. E, 53(1), 861 (1996).

J. Toner and Y. Tu, Long Range Order in a 2-dimensional Dynamical XY Model: How Birds Fly Together , Phys. Rev. Lett., 75(23), 4326 (1995).

Y. Tu and H. Levine, Mean Field Theory of the Morphology Transition in Stochastic Diffusion Limited Growth , Phys. Rev. E, 52(5), 5134 (1995).

M. C. Cross and Y. Tu, Defect Dynamics for Spiral Chaos in Rayleigh-Benard Convection , Phys. Rev. Lett., 75(5), 834 (1995).

Y. Tu, Absence of Finite Upper Critical Dimension in the Spherical Kardar-Parisi-Zhang Model , Phys. Rev. Lett., 73(23), 3109 (1994).

Y. Tu and P. B. Weichman, Quantum Spherical Models for Dirty Phase Transitions , Phys. Rev. Lett., 73(1), 6 (1994).

E.S.C. Ching and Y. Tu, Passive Scalar Fluctuations with and without a Mean Gradient: A Numerical Study , Phys. Rev. E, 49(2), 1278 (1994).

M.C. Cross, Y. Tu and D. Meiron, Chaotic Domains: A Numerical Investigation , Chaos, 4(4), 607(1994).

H. Levine and Y. Tu, Theory Of Diffusion Limited Growth , Phys. Rev. E, 48(6), R4207 (1993).

Y. Tu, H. Levine and D. Ridgway, Morphological Transitions in a Mean Field Model of Diffusion Limited Growth , Phys. Rev. Lett., 71(23), 3838 (1993)

Y. Tu and M.C. Cross, Chaotic Domain Structure in Rotating Convection , Phys. Rev. Lett., 69(17), 2515 (1992).

Y. Tu, Instability in a Continuum Kinetic Growth Model with Surface Relaxation , Phys. Rev. A, 46(2), R729 (1992).

H. Levine and Y. Tu, Mean Field DLA in Radial Geometry , Phys. Rev. A, 45(2), 1053 (1992).

H. Levine and Y. Tu, Mean Field DLA and the Saffman-Taylor Problem in three Dimensions , Phys. Rev. A, 45(2), 1044 (1992).

Y. Tu, Saffman-Taylor Problem in Sector Geometry: Solution and Selection , Phys. Rev. A, 44(2), 1203 (1991).

D. Kessler, H. Levine and Y. Tu, Interface Fluctuation In Random Media , Phys. Rev. A, 43(8), R4551 (1991).

E. Brener, H. Levine and Y. Tu, Mean Field Theory for Diffusion-Limited Aggregation in Low Dimensions , Phys. Rev. Lett. 66(15), 1978 (1991).

E. Brener, H. Levine and Y. Tu, Nonsymmetric Saffman-Taylor Fingers , Physics of Fluid A, 3(4), 529 (1991).

E. Brener, H. Levine and Y. Tu, Growth of Non-reflection Symmetric Patterns , Proc. of NATO Advanced Study on Growth and Form, Cargese, France (1990).

] NoisyMotor_PRL_2005.pdf, Picture 261.jpg Last updated 10 Nov 2006