Gasper Tkacik

Summary

Affiliation: Princeton University
Country: USA

Publications

  1. pmc The role of input noise in transcriptional regulation
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 3:e2774. 2008
  2. pmc Information capacity of genetic regulatory elements
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 78:011910. 2008
  3. ncbi request reprint Diffusion, dimensionality, and noise in transcriptional regulation
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 79:051901. 2009
  4. pmc Information flow and optimization in transcriptional regulation
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 105:12265-70. 2008
  5. pmc The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA
    Shawn C Little
    Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
    PLoS Biol 9:e1000596. 2011
  6. doi request reprint Learning quadratic receptive fields from neural responses to natural stimuli
    Kanaka Rajan
    Joseph Henry Laboratories of Physics and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Neural Comput 25:1661-92. 2013
  7. pmc Positional information, in bits
    Julien O Dubuis
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, and Department of Molecular Biology, Princeton University, Princeton, NJ 08544
    Proc Natl Acad Sci U S A 110:16301-8. 2013
  8. pmc Precise physical models of protein-DNA interaction from high-throughput data
    Justin B Kinney
    Physics Department and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 104:501-6. 2007
  9. ncbi request reprint Statistical thermodynamics of natural images
    Greg J Stephens
    Joseph Henry Laboratories of Physics and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev Lett 110:018701. 2013
  10. ncbi request reprint Optimizing information flow in small genetic networks. II. Feed-forward interactions
    Aleksandra M Walczak
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, and Princeton Center for Theoretical Science, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 81:041905. 2010

Detail Information

Publications12

  1. pmc The role of input noise in transcriptional regulation
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 3:e2774. 2008
    ....
  2. pmc Information capacity of genetic regulatory elements
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 78:011910. 2008
    ..The question whether real systems actually exploit this richer possibility is beyond the scope of this investigation...
  3. ncbi request reprint Diffusion, dimensionality, and noise in transcriptional regulation
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 79:051901. 2009
    ..With realistic parameters, sliding along DNA has surprisingly little effect on the physical limits to the precision of transcriptional regulation...
  4. pmc Information flow and optimization in transcriptional regulation
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 105:12265-70. 2008
    ....
  5. pmc The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA
    Shawn C Little
    Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
    PLoS Biol 9:e1000596. 2011
    ..We conclude that the spatial distribution of bicoid mRNA contributes to, but cannot account for, protein gradient formation, and therefore that protein movement, either active or passive, is required for gradient formation...
  6. doi request reprint Learning quadratic receptive fields from neural responses to natural stimuli
    Kanaka Rajan
    Joseph Henry Laboratories of Physics and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Neural Comput 25:1661-92. 2013
    ..We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus...
  7. pmc Positional information, in bits
    Julien O Dubuis
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, and Department of Molecular Biology, Princeton University, Princeton, NJ 08544
    Proc Natl Acad Sci U S A 110:16301-8. 2013
    ..We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network...
  8. pmc Precise physical models of protein-DNA interaction from high-throughput data
    Justin B Kinney
    Physics Department and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 104:501-6. 2007
    ..Results from in vivo and in vitro experiments also provide highly consistent characterizations of Abf1p, a result that contrasts with a previous analysis of the same data...
  9. ncbi request reprint Statistical thermodynamics of natural images
    Greg J Stephens
    Joseph Henry Laboratories of Physics and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev Lett 110:018701. 2013
    ..We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations...
  10. ncbi request reprint Optimizing information flow in small genetic networks. II. Feed-forward interactions
    Aleksandra M Walczak
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, and Princeton Center for Theoretical Science, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 81:041905. 2010
    ..Even with this limitation, the networks that optimize information transmission have a structure reminiscent of the networks found in real biological systems...
  11. pmc Information-based clustering
    Noam Slonim
    Joseph Henry Laboratories of Physics, and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 102:18297-302. 2005
    ..Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures...
  12. pmc Decoding spike timing: the differential reverse-correlation method
    Gasper Tkacik
    Joseph Henry Laboratories of Physics, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Biosystems 93:90-100. 2008
    ..We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel...