Yuhai Tu  Yuhai Tu photo         

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Foundations of AI
Thomas J. Watson Research Center, Yorktown Heights, NY USA



Precision Sensing by Two Opposing Gradient Sensors: How Does< i> Escherichia coli Find its Preferred pH Level?
Bo Hu, Yuhai Tu
Biophysical journal 105(1), 276--285, Cell Press, 2013

Synaptic gating at axonal branches, and sharp-wave ripples with replay: a simulation study
Nikita Vladimirov, Yuhai Tu, Roger D Traub
European Journal of Neuroscience, 2013

Discovery of novel chemoeffectors and rational design of Escherichia coli chemoreceptor specificity
Shuangyu Bi, Daqi Yu, Guangwei Si, Chunxiong Luo, Tongqing Li, Qi Ouyang, Vladimir Jakovljevic, Victor Sourjik, Yuhai Tu, Luhua Lai
Proceedings of the National Academy of Sciences, 201306811, National Acad Sciences

The cost of sensitive response and accurate adaptation in networks with an incoherent type-1 feed-forward loop
Ganhui Lan, Yuhai Tu
Journal of The Royal Society Interface 10(87), The Royal Society, 2013


Pathway-Based Mean-Field Model for Escherichia coli Chemotaxis
Guangwei Si, Tailin Wu, Qi Ouyang, Yuhai Tu
Physical Review Letters, 2012

The energy-speed-accuracy trade-off in sensory adaptation
Ganhui Lan, Pablo Sartori, Silke Neumann, Victor Sourjik & Yuhai Tu
Nature Physics, 2012

Frequency-Dependent Escherichia coli Chemotaxis Behavior
Xuejun Zhu, Guangwei Si, Nianpei Deng, Qi Ouyang, Tailin Wu, Zhuoran He, Lili Jiang, Chunxiong Luo, and Yuhai Tu
Physical Review Letters, 2012

Anomalous smoothing preceding island formation during growth on patterned substrates
R. Bergamaschini, J. Tersoff, Y. Tu, JJ Zhang, G. Bauer, F. Montalenti
Physical review letters 109(15), 156101, APS, 2012

Shortest loops are pacemakers in random networks of electrically coupled axons
Nikita Vladimirov, Yuhai Tu, Roger Traub
Frontiers in Computational Neuroscience, 2012


Noise Filtering Strategies in Adaptive Biochemical Signaling Networks
P Sartori, Y Tu
Journal of Statistical Physics, 1--12, Springer, 2011

Adapt locally and act globally: strategy to maintain high chemoreceptor sensitivity in complex environments
G Lan, S Schulmeister, V Sourjik, Y Tu
Molecular Systems Biology 7(1), Nature Publishing Group, 2011

Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis response
C. M. Khursigara, G. lan, S. Neumann, X. Wu, S. Ravindran, M. J. Borgnia, V. Sourjik, J. Milne, Y. Tu, and S. Subramaniam
The EMBO J., 2011


Spatiotemporal patterns of electrocorticographic very fast oscillations (> 80 Hz) consistent with a network model based on electrical coupling between principal neurons
R D Traub, R Duncan, A J C Russell, T Baldeweg, Y Tu, M O Cunningham, M A Whittington
Epilepsia 51(8), 1587--1597, Wiley Online Library, 2010

A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli
T S Shimizu, Y Tu, H C Berg
Molecular systems biology 6(1), Nature Publishing Group, 2010


Dislocation-interaction-based model of strained-layer relaxation
K W Schwarz, Y Tu
Journal of Applied Physics 106(8), 083510--083510, AIP, 2009

Dynamics of the bacterial flagellar motor with multiple stators
G Meacci, Y Tu
Proceedings of the National Academy of Sciences 106(10), 3746, National Acad Sciences, 2009

Logarithmic Sensing in Escherichia coli Bacterial Chemotaxis
Y V Kalinin, L Jiang, Y Tu, M Wu
Biophysical Journal 96(6), 2439--2448, Elsevier, 2009


Spatially-compressed cardiac myofilament models generate hysteresis that is not found in real muscle
J. J. Rice, Y. Tu, C. Poggesi, P. P. De Tombe
Pac Symp Biocomput, 366--377, 2008

The nonequilibrium mechanism for ultrasensitivity in a biological switch: Sensing by Maxwell's demons
Y Tu
Proceedings of the National Academy of Sciences 105(33), 11737, National Acad Sciences, 2008

Modeling the chemotactic response of Escherichia coli to time-varying stimuli
Y Tu, T S Shimizu, H C Berg
Proceedings of the National Academy of Sciences 105(39), 14855, National Acad Sciences, 2008



Global gene expression assays: quantitative noise analysis
G A Held, G Stolovitzky, Y Tu
Systems Biology Vol II: Networks, Models and Applications (I. Rigoutsos and G. Stephanopoulos, eds., Oxford University Press), pp. 103--136, 2006

Relationship between gene expression and observed intensities in DNA microarrays—a modeling study
GA Held, G Grinstein, Y Tu
Nucleic Acids Research 34(9), e70, Oxford Univ Press, 2006

Gene expression dynamics during germinal center transit in B cells
U Klein, Y Tu, G A Stolovitzky, J L Keller, J Haddad Jr, V Miljkovic, G Cattoretti, A Califano, R Dalla-Favera
Annals of the New York Academy of Sciences987, 166--172, 2006


Excitation-contraction coupling gain and cooperativity of the cardiac ryanodine receptor: a modeling approach
K Wang, Y Tu, W J Rappel, H Levine
Biophysical journal 89(5), 3017--3025, Elsevier, 2005

An allosteric model for heterogeneous receptor complexes: Understanding bacterial chemotaxis responses to multiple stimuli
B A Mello, Y Tu
Proceedings of the National Academy of Sciences 102(48), 17354, National Acad Sciences, 2005

Hydrodynamics and phases of flocks
J Toner, Y Tu, S Ramaswamy
Annals of Physics 318(1), 170--244, Elsevier, 2005

How white noise generates power-law switching in bacterial flagellar motors
Y Tu, G Grinstein
Physical review letters 94(20), 208101, APS, 2005

Reconstructing biological networks using conditional correlation analysis
J. J. Rice, Y. Tu, G. Stolovitzky
Bioinformatics 21(6), 765--773, 2005


Effects of receptor interaction in bacterial chemotaxis
B A Mello, L Shaw, Y Tu
Biophysical journal 87(3), 1578--1595, Elsevier, 2004

Tracking CD40 signaling during germinal center development
K Basso, U Klein, H Niu, G A Stolovitzky, Y Tu, A Califano, G Cattoretti, R Dalla-Favera
Blood 104(13), 4088, 2004


Comment on" Particle Diffusion in a Quasi-Two-Dimensional Bacterial Bath"
H Chat{'e}, G Gr{'e}goire, Y Tu
Physical Review Letters 86(03), 2003

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

Ising model of cardiac thin filament activation with nearest-neighbor cooperative interactions
J J Rice, G Stolovitzky, Y Tu, P P De Tombe
Biophysical journal 84(2), 897--909, Elsevier, 2003

Perfect and near-perfect adaptation in a model of bacterial chemotaxis
B A Mello, Y Tu
Biophysical journal 84(5), 2943--2956, Elsevier, 2003

Identification of a global gene expression signature of B-chronic lymphocytic leukemia
D F Jelinek, R C Tschumper, G A Stolovitzky, S J Iturria, Y Tu, J Lepre, N Shah, N E Kay
Molecular Cancer Research 1(5), 346, AACR, 2003

Quantitative modeling of sensitivity in bacterial chemotaxis: the role of coupling among different chemoreceptor species
B A Mello, Y Tu
Proceedings of the National Academy of Sciences 100(14), 8223, National Acad Sciences, 2003

Moving and staying together without a leader
G Gr{'e}goire, H Chat{'e}, Y Tu
Physica D: Nonlinear Phenomena 181(3-4), 157--170, Elsevier, 2003

Dynamics of coalition formation in combinatorial trading
Y Ye, Y Tu
International Joint Conference on Artificial Intelligence, pp. 625--632, 2003

Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling
R. Kuppers, U. Klein, I. Schwering, V. Distler, A. Brauninger, G. Cattoretti, Y. Tu, G. Stolovitzky, A. Califano, M.L. Hansmann, R. Dalla Favera,
Journal of Clinical Investigation 111(4), 529--537, 2003

Modeling of DNA microarray data by using physical properties of hybridization
GA Held, G Grinstein, Y Tu
Proceedings of the National Academy of Sciences 100(13), 7575, National Acad Sciences, 2003

Transcriptional analysis of the B cell germinal center reaction
U Klein, Y Tu, G A Stolovitzky, J L Keller, J Haddad, V Miljkovic, G Cattoretti, A Califano, R Dalla-Favera
Proc. Nat. Acad. Sci. U S A 100(5), 2639, 2003


Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons
A Mateos, J Dopazo, R Jansen, Y Tu, M Gerstein, G Stolovitzky
Genome Research 12(11), 1703, 2002

Quantitative noise analysis for gene expression microarray experiments
Y Tu, G Stolovitzky, U Klein
Proc. Natl. Acad. Sci. U S A 99(22), 14031, 2002

Microscopic dynamics of silicon oxidation
Y Tu, J Tersoff
Physical review letters 89(8), 86102, APS, 2002


Characterization of phenotypes by gene expression patterns and classification of samples based thereon
A Califano, G A Stolovitzky, Y Tu
US Patent App. 09/841,580, 2001 - Google Patents, Google Patents
US Patent App. 09/841,580

Structure of the silicon--oxide interface
Y Tu, J Tersoff
Thin Solid Films 400(1-2), 95--100, Elsevier, 2001

Comment on “Particle diffusion in a quasi-two-dimensional bacterial bath”
G Gr{'e}goire, H Chat{'e}, Y Tu
Physical Review Letters 86(3), 556--556, APS, 2001

Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells
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,
Journal of Experimental Medicine 194(11), 1625, 2001

Active and passive particles: Modeling beads in a bacterial bath
G Gr{'e}goire, H Chat{'e}, Y Tu
Physical Review E 64(1), 11902, APS, 2001

Weighted evolving networks
SH Yook, H Jeong, A L Barabasi, Y Tu
Physical Review Letters 86(25), 5835--5838, APS, 2001


Phases and phase transitions in flocking systems
Y Tu
Physica A: Statistical Mechanics and its Applications 281(1-4), 30--40, Elsevier, 2000

Analysis of gene expression microarrays for phenotype classification
A Califano, G Stolovitzky, Y Tu
Proceedings of the 8th Annual Intelligent Systems in Molecular Biology (ISMB) , pp. 75--85, 2000

How robust is the Internet
Y Tu
Nature 406(6794), 353--4, 2000

Structure and Energetics of the Si-SiO\_ $\{$2$\}$ Interface
Y Tu, J Tersoff
Physical Review Letters 84(19), 4393--4396, APS, 2000


Analysis of gene expression microarrays: a combinatorial multivariate approach
A Califano, G Stolovitzky, Y Tu
IBM TJ Watson Research Report, 1999

Grinstein et al. Reply
G Grinstein, Y Tu, J Tersoff
Physical Review Letters 83(3), 657--657, APS, 1999


Effect of curvature and stress on reaction rates at solid interfaces
J Tersoff, Y Tu, G Grinstein
Applied Physics Letters73, 2328, 1998

Clustering Kinetics of Granular Media in Three Dimensions
X Nie, S Chen, Y Deng, Y Tu
APS Meeting Abstracts, pp. 218--223, Elsevier, 1998

Sound waves and the absence of galilean invariance in flocks
Y Tu, J Toner, M Ulm
Physical review letters 80(21), 4819--4822, APS, 1998

Stability of solid state reaction fronts
G Grinstein, Y Tu, J Tersoff
Physical Review Letters 81(12), 2490--2493, APS, 1998

Properties of a continuous-random-network model for amorphous systems
Y Tu, J Tersoff, G Grinstein, D Vanderbilt
Physical Review Letters 81(22), 4899--4902, APS, 1998

Flocks, herds, and schools: A quantitative theory of flocking
J Toner, Y Tu
Physical Review E 58(4), 4828--4858, APS, 1998


Survival probability and field theory in systems with absorbing states
MA Munoz, G Grinstein, Y Tu
Physical Review E 56(5), 5101--5105, APS, 1997

Systems with multiplicative noise: critical behavior from KPZ equation and numerics
Y Tu, G Grinstein, MA Munoz
Physical Review Letters 78(2), 274--277, APS, 1997


Front stability in mean-field models of diffusion-limited growth
D Ridgway, H Levine, Y Tu
Physical Review E 53(1), 861--870, APS, 1996

Phase structure of systems with multiplicative noise
G Grinstein, MA Munoz, Y Tu
Physical review letters 76(23), 4376--4379, APS, 1996


Front Stability in Mean Field Models of Diffusion Limited Growth
D Ridgway, H Levine, Y Tu
Arxiv preprint patt-sol/9507004, 1995

Defect dynamics for spiral chaos in Rayleigh-B{\'e}nard convection
MC Cross, Y Tu
Physical review letters 75(5), 834--837, APS, 1995

Mean-field theory of the morphology transition in stochastic diffusion-limited growth
Y Tu, H Levine
Physical Review E 52(5), 5134--5141, APS, 1995

Long-range order in a two-dimensional dynamical XY model: How birds fly together
J Toner, Y Tu
Physical Review Letters 75(23), 4326--4329, APS, 1995


Quantum spherical models for dirty phase transitions
Y Tu, P B Weichman
Physical review letters 73(1), 6--9, APS, 1994

Passive scalar fluctuations with and without a mean gradient: A numerical study
E S C Ching, Y Tu
Physical Review E 49(2), 1278--1282, APS, 1994


Morphology transitions in a mean-field model of diffusion-limited growth
Y Tu, H Levine, D Ridgway
Physical review letters 71(23), 3838--3841, APS, 1993

Theory of diffusion-limited growth
H Levine, Y Tu
Physical Review E 48(6), 4207--4210, APS, 1993


Mean-field diffusion-limited aggregation in radial geometries
H Levine, Y Tu
Physical Review A 45(2), 1053--1057, APS, 1992

Chaotic domain structure in rotating convection
Y Tu, MC Cross
Physical review letters 69(17), 2515--2518, APS, 1992


Saffman-Taylor problem in sector geometry
Y Tu
Asymptotics beyond all orders1, 175, Plenum Pub Corp, 1991

Mean-field theory for diffusion-limited aggregation in low dimensions
E Brener, H Levine, Y Tu
Physical review letters 66(15), 1978--1981, APS, 1991

Interface fluctuations in random media
D A Kessler, H Levine, Y Tu
Physical Review A 43(8), 4551--4554, APS, 1991

Saffman-Taylor problem in sector geometry: Solution and selection
Y Tu
Physical Review A 44(2), 1203--1210, APS, 1991