Physics of Information Processing in Living Systems Publications



2013

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


2012

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

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



2011

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


2010

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


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


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

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


2007



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

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


2005

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


2004

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



2003


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

Method and apparatus for determining gene expression levels
G Grinstein, G A Held, Y Tu
US Patent App. 10/365,891

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


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


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


2001

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

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


2000

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

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


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

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


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