1. shraiman
  2. Publications

Publications

(in anti-chronological order)

  1. Streichan SJ, Noll N., Lefebvre M, Wieschaus E., Shraiman BI, Global morphogenetic flow is completely determined by myosin distribution in Drosophila embryo, arXiv:1701.07100 (2017).
  2. Noll N., Mani M., Heemskerk I., Streichan S. and Shraiman BI, “Active Tension Network model of epithelial mechanics suggests an exotic mechanical state realized in epithelial tissue”,  arXiv: 1508.00623v1 (2015) and Nature Physics, doi:10.1038/nphys4219, (2017)
  3. Hormoz S, Singer ZS, Linton JM, Antebi YE, Shraiman BI, Elowitz MB. "Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements." Cell Syst. 3(5):419-433 (2016).
  4. Alim K, Armon S, Shraiman BI, Boudaoud A, "Leaf growth is conformal." Phys Biol. 13(5):05LT01, (2016).
  5. Pan Y., Heemskerk I., Ibar C., Shraiman BI., and Irvine KD.”Differential growth triggers mechanical feedback that elevates Hippo signaling”, Proc. Nat. Acad. Sci USA113(45):E6974-83, (2016).
  6. Neher RA, Bedford T., Daniels RS, Russell CA and Shraiman BI, “Prediction, dynamics and visualization of antigenic phenotypes of seasonal influenza viruses”, Proc. Nat. Acad. Sci USA 113(12):E1701-9, (2016).
  7. Hormoz S, Desprat N, Shraiman BI. “Inferring epigenetic dynamics from kin correlations”, PNAS 112(18):E2281-9 (2015).
  8. Neher RA, Russell CA, Shraiman BI., “Predicting evolution form the shape of genealogical trees”, Elife 3: eLife.03568 (2014).
  9. Dayarian A. and Shraiman BI., "How to infer relative fitness from a sample of genomic sequences", arXiv:1208.5954 and Genetics 197(3):913-23 (2014)
  10.  Mani M., Goyal S., Irvine KD and Shraiman BI. “Collective polarization model for gradient sensing via Dachsous-Fat intercellular signaling” PNAS 110 (51): 20420-20425 (2013)
  11. Neher RA, Kessinger TA. and Shraiman BI.,” Coalescence and genetic diversity in sexual populations under selection”, PNAS 110(39): 15836-15841 (2013).
  12. Fisher DS, Laessig M and Shraiman BI, “Evolutionary dynamics and statistical physics”, JSTAT, Special Issue, N01001 (2013)
  13. Neher RA, Vucelja M, Mezard M and Shraiman BI, “Emergence of clones in sexual populations”, arXiv:1205.2059 and JSTAT Special Issue, P01008 (2013)
  14. Neher RA and Shraiman BI, “Fluctuation of Fitness Distributions and the Rate of Muller’s Ratchet”, Genetics 191(4):1283-93 (2012).
  15. Chiou K., Hufnagel L. and Shraiman B.I, “Mechanical Stress Inference for Two Dimensional Cell Arrays”, arXiv:1112.5905 and PLoS Comp Biol. 8(5):e1002512 (2012).
  16. Puliafito A, Hufnagel L, Neveu P, Streichan S, Sigal A, Fygenson DK, Shraiman BI. "Collective and single cell behavior in epithelial contact inhibition", Proc Natl Acad Sci U S A. 109(3): 739-744 (2012).
  17. Lubensky D., Shraiman B.I. and Baker N., “Dynamic patterning in Drosophila eye development”, Proc Natl Acad Sci U S A. 108(27):11145-50, (2011).
  18. Neher R. and Shraiman B.I.,"Statistical genetics and evolution of quantitative traits", Rev. Mod. Phys. 83: 1301,( 2011).
  19. Neher R. and Shraiman B.I. “Genetic Draft and Quasi-Neutrality in Large Sexual Populations”, Genetics 188(4):975-96 (2011)
  20. Callahan B., Neher R., Bachtrog D, Andolfatto P. and Shraiman B.I., “Correlated evolution of nearby residues in Drosophilid proteins”, PLoS Genet. 7(2):e1001315 (2011).
  21. Pumir A. and Shraiman B.I., "Epistasis in a model of molecular signal transduction", PLoS Comput Biol. 7(5):e1001134 (2011).
  22. Neveu P, Kye MJ, Qi S, Buchholz DE, Clegg DO, Sahin M, Park IH, Kim KS, Daley GQ, Kornblum HI, Shraiman BI, Kosik KS, "MicroRNA profiling reveals two distinct p53-related human pluripotent stem cell states." Cell Stem Cell. 2010 Dec 3;7(6):671-81.
  23. Neher R., Shraiman B.I. and Fisher D.S. "Rate of adaptation in large sexual populations." Genetics 184(2):467-81 (2010).
  24. Burak Y. and Shraiman B.I. “Order and stochastic dynamics in Planar Cell Polarity”, PLoS Comp Biol. 5(12):e1000628 (2009).
  25. Callahan B., Thattai M. and  Shraiman B.I. “Emergent gene order in the model of  the modular polyketide syntase system”, Proc. Natl. Acad. Sci. USA,  106(46):19410-5 (2009).
  26. Neher R. and Shraiman B.I., “Competition between recombination and epistasis can cause a transition from allele to genotype selection”, Proc. Natl. Acad. Sci. USA,  106(16)6866-71, (2009).
  27. Pumir A., Graves J., Ranganathan R. and Shraiman BI, “Systems Analysis of the Single Photon Response in Invertebrate Photoreceptors”, Proc. Natl. Acad. Sci. USA,  105(30):10354-9 (2008).
  28. Thattai M, Burak Y, Shraiman BI., “The origins of specificity in polyketide synthase protein interactions”, PLoS Comp Biol. 3(9):1827-35, (2007).
  29. Liu T, Papagiannakopoulos T, Puskar K, Qi S, Santiago F, Clay W, Lao K, Lee Y, Nelson SF, Kornblum HI, Doyle F, Petzold L, Shraiman BI, Kosik KS., “Detection of a microRNA signal in an in vivo expression set of mRNAs”, PLoS ONE, 2(8): e804, (2007).
  30. Hufnagel, L., Teleman, A., Rouault, H., Cohen S.M. and Shraiman B.I., On the mechanism of wing size determination in fly development”, Proc. Natl. Acad. Sci. USA, 104(10):3835-40, (2007).
  31. Vergassola M, Villermaux E, Shraiman B.I., “'Infotaxis' as a strategy for searching without gradients”, Nature, 445(7126):406-9, (2007).
  32. Hufnagel, L., Kreuger J.,  Cohen S.M. and Shraiman B.I., “On the role of glypicans in the process of morphogen gradient formation”, Dev Biol. 300(2):512-22, (2006).
  33. Djordjevic M, Semenova E, Shraiman B.I. and Severinov K., “Quantitative analysis of a virulent bacteriophage transcription strategy”, Virology 354(2):240-51, (2006).
  34. Shraiman B.I., “Mechanical feedback as a possible regulator of tissue growth”, Proc. Natl. Acad. Sci. USA: 102, 3318-23, (2005).
  35. Ramanathan S., Detwiler P., Sengupta A. and Shraiman, B.I. “G-protein-coupled enzyme cascades have intrinsic properties that improve signal localization and fidelity”, Biophys J. 88: 3063-71,(2005).
  36. Semenova E., Djordjevic M, Shraiman, B.I., and Severinov K., “The tale of two RNA polymerases: transcription profiling and gene expression strategy of bacteriophage Xp10”, Mol Microbiol. 55: 764-77, (2005).
  37. Mucha P.J., Shang-You T., Weitz D.A, Shraiman B.I. and Brenner M.P., “A model for velocity fluctuations in sedimentation”, J. of Fluid Mechanics 501: 71-104 (2004).
  38. Ozbudak E., Thattai M, Lim H, Shraiman, B.I., and van Oudenaarden A., “Global analysis of multistability in the lactose utilization network of E. Coli”, Nature 427:737-40, (2004).
  39. Thattai M. and Shraiman B.I, “Metabolic switching in the sugar phosphotransferase system of Escherichia coli”,Biophys J. 85: 744-54, (2003).
  40. Djordjevic, M., Sengupta A.M., and Shraiman, B.I., “A biophysical approach to transcription factor binding site discovery”, Genome Res. 13: 2381-90, (2003).
  41. Pumir, A and Shraiman, B.I., “Lagrangian Particle Approach to Large Eddy Simulations of Hydrodynamic Turbulence”, J. of Statistical Physics 113:693-700,  (2003)
  42. Ronen M, Rosenberg, R., Shraiman, B.I., and Alon, U. “Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics”, Proc. Natl. Acad. Sci. USA, 99: 10555-60 (2002).
  43. “Specificity and Robustness in Transcription Control Networks”, A.Sengupta, M. Djordjevic,  and B.I. Shraiman, Proc. Natl. Acad. Sci. USA, 99, 2072-2077,  (2002).
  44. Balkovsky E. and Shraiman, B.I. “Olfactory search at high Reynolds number”, Proc Natl Acad Sci USA.99,12589-93 (2002).
  45.  “Lagrangian View of Turbulent Energy Transfer”, A. Pumir, B.I. Shraiman and M. Chertkov, Europhys. Lett., 56, 379-85, (2001).
  46. “Engineering Aspects of Enzymatic Signal Transduction: Photoreceptors in the Retina”, P.Detwiler, S. Ramanathan, A.Sengupta and B.I. Shraiman, Biophys.J., 79, 2801-2817, (2000).
  47.  “Scalar Turbulence”, B.I. Shraiman and E.D. Siggia, Nature, 405, 639-646, (2000).
  48. “Geometry of Lagrangian Dispersion”, A.Pumir and B.I. Shraiman and M.Chertkov, Phys.Rev.Lett., 85, 5324-5327,(2000).
  49. “Towards the Clarity Limit in Optical Fibers”, G.Thomas, B.I.Shraiman and M.Stevens, Nature, 404, (2000)
  50. “Lagrangian Tetrad Dynamics and the Phenomenology of Turbulence”, M. Chertkov, A. Pumir, and B. I. Shraiman, Phys. of Fluids, 11, 2394-2410, (1999).
  51. “Longitudinal Spread of Second Messenger Signals in Rod Outer Segments”, M.Gray-Keller, W. Denk, B. I. Shraiman, and P. Detwiler, J. Physiology, 519, 679-692 (1999).
  52. “Intergrain Magnetoresistance via Second Order Tunneling in Perovskite Manganites”, S. Lee, S-W.Cheong, H. Hwang, J.Ratcliff, B.I. Shraiman, Phys.Rev. Lett. 82, 4508-4511, (1999).
  53. “Anomalous Hall Effect in Double Exchange Magnets”, J-W. Ye, Y-B. Kim, P. Majumdar, A. Millis , B.I. Shraiman and Z. Tesanovich, Phys. Rev. Lett. 83, 3737-3740, (1999).
  54. “The Role of Nonlinear Dynamics of the Syrinx in Birdsong Production”, M. S. Fee, B. I. Shraiman, B. Pesaran, and P. P. Mitra, Nature, 395, 67-71 (1998).
  55. “Structures and Multipoint Correlations for Turbulent Advection: Predictions and Experiments”, L. Mydlarski, A. Pumir, B. I. Shraiman, E. D. Siggia and Z. Warhaft, Phys. Rev. Lett., 81, 4373 (1998).
  56. “Anomalous Scaling for a Passive Scalar near the Batchelor limit”, B. I. Shraiman and E. D. Siggia, Phys. Rev. E, 57, 2965, (1998).
  57.  “Assembly of Ordered Colloidal Aggregates by Electric Field Induced Fluid Flow”,    S.R.Yeh, M.Seul and B.I. Shraiman, Nature, 386, 57-59, (1997)
  58. “Perturbation Theory for the Delta-Correlated Model of Passive Scalar Advection Near Batchelor Limit”, A. Pumir, B. I. Shraiman and E. D. Siggia, Phys. Rev. E, Rapid Comm., 55, R1263, (1997).
  59. “Microtubules and Vesicles Under Controlled Tension”, D. Fygenson, M. Elbaum, B. I. Shraiman, and A. Libchaber, Phys. Rev. E, 55, 850, (1997).
  60. “On the Role of Assembly Kinetics in Determining the Structure of Clathrin Cages”, Biophysical Journal, 72, 935, (1997).
  61. “’Zipper’ Model of Enveloped Virus Budding”, preprint, (1996).
  62. “Symmetry and Scaling in Turbulent Mixing”, B. I. Shraiman and E. D. Siggia, Phys. Rev. Lett., 77, 2463, (1996).
  63. “High Rayleigh Number Convection and Turbulent Mixing”, B. I. Shraiman and E. D. Siggia, Physica D, 97, 286, (1996).
  64. “Fluctuations and Mixing of a Passive Scalar in Turbulent Flow”, B. I. Shraiman and E. D. Siggia, Proceedings of the Cargese Summer School on "Chaos, Mixing and Turbulence", ed. H.Chate and E.Villermaux, Plenum (1996).
  65. “Dynamic Jahn-Teller Effect and Colossal Magnetoresistance in La1-xSrxMnO3”, A. J. Millis, B. I. Shraiman, and R. Mueller, Phys. Rev. Lett., 77, 175, (1996).
  66. “On the Fermi Liquid to Polaron Crossover I: General Results”, A. J. Millis, R. Mueller and B. I. Shraiman, Phys. Rev. B 54,5389, (1996).
  67. “On the Fermi Liquid to Polaron Crossover II: Double Exchange and the Physics of ‘Colossal’ Magnetoresistance”, A. J. Millis, R. Mueller and B. I. Shraiman, Phys. Rev. B 54, 5405, (1996).
  68. “Persistent Small Scale Anisotropy in Homogeneous Shear Flow”, A. Pumir and B. I. Shraiman, Phys. Rev. Lett., 75, 3114 (1995).
  69. “Anomalous Scaling of a Passive Scalar in Turbulent Flow”, B. I. Shraiman and E. D. Siggia, CRAS (Paris) 321, s. II, p. 279 (1995).
  70. “Double Exchange Alone Does not Explain the Resistivity of La1-x Srx MnO3”, A. J. Millis, P. B. Littlewood and B. I. Shraiman, Phys. Rev. Lett.. 74, 5144 (1995)
  71. “Lagrangian Path Integrals and Fluctuations in Random Flows”, B. I. Shraiman and E. D. Siggia, Phys. Rev. E 49,2912, (1994).
  72. “Temporal Coding and the Spatiotemporal Response of Neurons in the Lateral Geniculate Nucleus”, D. Golomb, D. Kleinfeld, R. C. Reid, R. M. Shapley and B. I. Shraiman, J. of Neurophys., 72, 2990 (1994).
  73. “Decorrelation and Feature Discovery”, AT&T Bell Laboratories Technical Memorandum #11111-930805-33, (1993).
  74. “Faraday Rotation and the Hall Constant in Strongly Correlated Fermi Systems”, B. S. Shastry, B. I. Shraiman and R. R. P. Singh, Phys. Rev. Lett., 70, 2004 (1993).
  75. “Curie and Non-Curie Behavior of Impurity Spins in Quantum Antiferromagnets”, D. Clarke, T. Giamarchi and B. I. Shraiman, Phys. Rev. B 48, 7070 (1993).
  76. “Vortex Morphology and Kelvin's Theorem”, A. Pumir, B. I. Shraiman and E. D. Siggia, Phys. Rev. A 45, R5351 (1992).
  77. “Spatiotemporal Chaos in the One-Dimensional Complex Ginzburg-Landau Equation”, B. I. Shraiman, A. Pumir, W. van Saarloos, P. C. Hohenberg, H. Chate and M. Holen, Physica D 57, 241 (1992).
  78. “Theory of Optical Absorption by a Localized Carrier in a Antiferromagnetic Insulator”, A. J. Millis and B. I. Shraiman, Phys. Rev. B 46, 14834 (1992).
  79. “Clustering in Globally Coupled Oscillators”, with D. Golomb, D. Hansel, B. I. Shraiman and H. Sompolinsky, Phys. Rev. A 45, 3516 (1992).
  80. “On the Excitation Spectrum of a Spiral State of a Doped Antiferromagnet”, B. I. Shraiman and E. D. Siggia, Phys. Rev. B 46, 8305 (1992).
  81. “Exponential Tails and Random Advection”, A. Pumir, B. I. Shraiman and E. D. Siggia, Phys. Rev. Lett., 66, 2984 (1991)
  82. “Raman Scattering in Mott-Hubbard Systems”, B. S. Shastry and B. I. Shraiman, Int. Journal of Modern Phys. B 5, 365 (1991).
  83. “Heat Transport in High Rayleigh Number Convection”, B. I. Shraiman and E. D. Siggia, Phys. Rev. A 42, 3650 (1990).
  84. “Spiral Phases of Doped Antiferromagnets”, B. I. Shraiman and E. D. Siggia, Proceedings of the Trieste Conference on Strongly Correlated Electron Systems, ed. Yu Lu, World Scientific, Singapore (1990).
  85. “Mobile Vacancy in a Quantum Antiferromagnet:  Effective Hamiltonian”, B. I. Shraiman and E. D. Siggia, Phys. Rev. B 42, 2485 (1990).
  86. “Theory of Raman Scattering in Mott-Hubbard Systems”, B. S. Shastry and B. I. Shraiman, Phys. Rev. Lett., 65, 1068 (1990).
  87. “Ground State Properties of a Single Oxygen Hole in a CuO2 Plane”, D. Frenkel, R. Gooding, B. I. Shraiman and E. D. Siggia, Phys. Rev. B, 41, 350, (1990).
  88. “The Ground State of a Mobile Vacancy in a Quantum Antiferromagnet: Small Cluster Study”, V. Elser, D. Huse, B. I. Shraiman and E. D. Siggia, Phys. Rev. B 41, 6715 (1990).
  89. “Chaotic Behavior of a Spatially Extended System”, P. C. Hohenberg and B. I. Shraiman, Physica D, 37, 109 (1989).
  90. “Nonlinear Theory of Traveling Wave Convection in Binary Mixtures”, D. Bensimon, A. Pumir and B. I. Shraiman, J. Physique, 50, 3089 (1989).
  91. “The Spiral Phase of a Doped Quantum Antiferromagnet”, B. I. Shraiman and E. D. Siggia, Phys. Rev. Lett., 62, 1564 (1989).
  92. “Mean Field Theory of a Doped Antiferromagnet”, B. I. Shraiman and E. D. Siggia, Phys. Rev. B 40, 9162 (1989).
  93. “Mobile Vacancies in Quantum Heisenberg Antiferromagnets”, B. I. Shraiman and E. D. Siggia, Phys. Rev. Lett., 61, 467 (1988).
  94. “Two-Particle Excitations in Antiferromagnetic Insulators”, B. I. Shraiman and E. D. Siggia, Phys. Rev. Lett., 60, 740 (1988).
  95. “Zero-point Motion and the Isotope Effect in Oxide Superconductors”, D. S. Fisher, A. J. Millis, B. I. Shraiman and R. N. Bhatt, Phys. Rev. Lett., 61, 482 (1988).
  96. “Non-Adiabatic Effects in Convection”, D. Bensimon, B. I. Shraiman and V. Croquette, Phys. Rev. A, 38, 5461 (1988).
  97. “Hydrodynamic Dispersion in Laminar Flows”, A. Pumir and B. I. Shraiman, "Disorder and Mixing" ed., E. Guyon, J.-P. Nadal, Y. Pomeau, Kluwer Academic Pub. (1988).
  98. “Diffusive Transport in a Rayleigh-Benard Convection Cell”, Phys. Rev. A. 36, 261 (1987).
  99. “Dynamics of Curved Fronts and Pattern Selection”, D. Bensimon, P. Pelce and B. I. Shraiman, J. Physique 48, 2081 (1987).
  100. “Velocity Selection and the Saffman-Taylor Problem”, Phys. Rev. Lett., 56, 2028 (1986).
  101. “Order, Disorder and Phase Turbulence”, Phys. Rev. Lett., 57, 325 (1986).
  102. “Fractal Measures and their Singularities: the Characterization of Strange Sets”, T. Halsey, M. Jensen, L. Kadanoff, I.  Procaccia and B. I. Shraiman, Phys. Rev. A 33, 1141 (1986).
  103. “Viscous Fingering”, D. Bensimon, L. Kadanoff, S. Liang, B. I. Shraiman and C. Tang, Rev. Mod. Phys. 58, 977 (1986).
  104. “On the Dynamical Mechanism for Velocity Selection”, D. Bensimon and B. I. Shraiman, Proceedings Nobel Symposium, June 1984, Physica Scripta, T9, 123 (1985).
  105. “Scaling Laws for Mode Locking in Circle Maps”, P.  Cvitanovic, B. Soderberg and B. I. Shraiman, Physica Scripta 32, 263 (1985).
  106. “Singularities in Nonlocal Interface Dynamics”, B. I. Shraiman and D. Bensimon, Phys. Rev. A 30, 2840 (1984).
  107. “Mean Field Theory for a Ballistic Model of Aggregation”, D. Bensimon, L. P. Kadanoff and B.I. Shraiman, Proceedings of Conference on Kinetics of Aggregration and Gelation, ed., D. Landau and F. Family, Atlanta, GA. (1984).
  108. “On the Ballistic Model of Aggregation”, D. Bensimon, B. I. Shraiman and S. Liang, Phys. Lett., 102A, 238 (1984).
  109. “Transition from Quasiperiodicity to Chaos: A Perturbative Renormalization Group Approach”, Phys. Rev. A 29, 3464 (1984).
  110. “2-D XY Magnets with Random Dzyaloshinski-Moriya Interactions”, M. Rubinstein, B. I. Shraiman and D. Nelson, Phys. Rev. B 27, 1800 (1982).
  111. “Scaling Theory for Noisy Period Doubling Transitions to Chaos”, B. I. Shraiman, C. E. Wayne and P. C. Martin, Phys. Rev. Lett., 46, 935 (1981).