1. Computing continuous core/periphery structures for social relations data with MINRES/SVD

    Social Networks 32(2):125 (2010)

    When diagonal values are missing or excluded, MINRES is a natural continuous model for the core/periphery structure of a symmetric social network matrix. Symmetric models, however, are not so useful when dealing with asymmetric data. Singular value decomposition (SVD) is a natural choice to...
  2. Automated quantification of cellular traffic in living cells.

    Journal of Neuroscience Methods 178(2):378 (2009) PMID 19146878

    Cellular traffic is a central aspect of cell function in health and disease. It is highly dynamic, and can be investigated at increasingly finer temporal and spatial resolution due to new imaging techniques and probes. Manual tracking of these data is labor-intensive and observer-biased and exis...
  3. Automated quantification of cellular traffic in living cells.

    Journal of Neuroscience Methods 178(2):378 (2009) PMID 19146878

    Cellular traffic is a central aspect of cell function in health and disease. It is highly dynamic, and can be investigated at increasingly finer temporal and spatial resolution due to new imaging techniques and probes. Manual tracking of these data is labor-intensive and observer-biased and exis...
  4. Automated quantification of cellular traffic in living cells

    Journal of Neuroscience Methods 178(2):378 (2009)

    Cellular traffic is a central aspect of cell function in health and disease. It is highly dynamic, and can be investigated at increasingly finer temporal and spatial resolution due to new imaging techniques and probes. Manual tracking of these data is labor-intensive and observer-biased and...
  5. Bayesian inference for improved single molecule fluorescence tracking.

    Biophysical Journal 94(12):4932 (2008) PMID 18339757 PMCID PMC2397372

    Single molecule tracking is widely used to monitor the change in position of lipids and proteins in living cells. In many experiments in which molecules are tagged with a single or small number of fluorophores, the signal/noise ratio may be limiting, the number of molecules is not known, and flu...
  6. Bayesian inference for improved single molecule fluorescence tracking.

    Biophysical Journal 94(12):4932 (2008) PMID 18339757 PMCID PMC2397372

    Single molecule tracking is widely used to monitor the change in position of lipids and proteins in living cells. In many experiments in which molecules are tagged with a single or small number of fluorophores, the signal/noise ratio may be limiting, the number of molecules is not known, and flu...
  7. Automated analysis of the architecture of receptors, imaged by atomic force microscopy.

    Micron 39(2):101 (2008) PMID 17296302

    Fast neurotransmission involves the operation of ionotropic receptors, which are multi-subunit proteins that respond to activation by opening an integral ion channel. Examples of such channels include the GABA(A) receptor, the 5-HT(3) receptor and the P2X receptor for ATP. These receptors contai...
  8. Automated analysis of the architecture of receptors, imaged by atomic force microscopy

    Micron 39(2):101 (2008)

    Fast neurotransmission involves the operation of ionotropic receptors, which are multi-subunit proteins that respond to activation by opening an integral ion channel. Examples of such channels include the GABA A receptor, the 5-HT 3 receptor and the P2X receptor for ATP. These r...
  9. Bayesian Inference for Improved Single Molecule Fluorescence Tracking

    Biophysical Journal 94(12):4932 (2008)

    Single molecule tracking is widely used to monitor the change in position of lipids and proteins in living cells. In many experiments in which molecules are tagged with a single or small number of fluorophores, the signal/noise ratio may be limiting, the number of molecules is not known, an...
  10. Automated analysis of the architecture of receptors, imaged by atomic force microscopy.

    Micron 39(2):101 (2008) PMID 17296302

    Fast neurotransmission involves the operation of ionotropic receptors, which are multi-subunit proteins that respond to activation by opening an integral ion channel. Examples of such channels include the GABA(A) receptor, the 5-HT(3) receptor and the P2X receptor for ATP. These receptors contai...
  11. Single-molecule level analysis of the subunit composition of the T cell receptor on live T cells.

    PNAS 104(45):17662 (2007) PMID 17971442 PMCID PMC2077052

    The T cell receptor (TCR) expressed on most T cells is a protein complex consisting of TCRalphabeta heterodimers that bind antigen and cluster of differentiation (CD) 3epsilondelta, epsilongamma, and zetazeta dimers that initiate signaling. A long-standing controversy concerns whether there is o...
  12. Single-molecule level analysis of the subunit composition of the T cell receptor on live T cells.

    PNAS 104(45):17662 (2007) PMID 17971442 PMCID PMC2077052

    The T cell receptor (TCR) expressed on most T cells is a protein complex consisting of TCRalphabeta heterodimers that bind antigen and cluster of differentiation (CD) 3epsilondelta, epsilongamma, and zetazeta dimers that initiate signaling. A long-standing controversy concerns whether there is o...
  13. A sequential Monte Carlo EM approach to the transcription factor binding site identification problem.

    PMID 17387112

    A significant and stubbornly intractable problem in genome sequence analysis has been the de novo identification of transcription factor binding sites in promoter regions. Although theoretically pleasing, probabilistic methods have faced difficulties due to model mismatch and the nature of the b...
  14. A sequential Monte Carlo EM approach to the transcription factor binding site identification problem.

    PMID 17387112

    A significant and stubbornly intractable problem in genome sequence analysis has been the de novo identification of transcription factor binding sites in promoter regions. Although theoretically pleasing, probabilistic methods have faced difficulties due to model mismatch and the nature of the b...
  15. Computing core/periphery structures and permutation tests for social relations data

    Social Networks 28(2):165 (2006)

    The core/periphery structure is ubiquitous in network studies. The discrete version of the concept is that individuals in a group belong to either the core, which has a high density of ties, or to the periphery, which has a low density of ties. The density of ties between the core and the p...
  16. Atomic force microscopy study of the structural effects induced by echinomycin binding to DNA.

    Journal of Molecular Biology 345(4):745 (2005) PMID 15588823

    Atomic force microscopy (AFM) has been used to examine the conformational effects of echinomycin, a DNA bis-intercalating antibiotic, on linear and circular DNA. Four different 398 bp DNA fragments were synthesized, comprising a combination of normal and/or modified bases including 2,6-diaminopu...
  17. Atomic force microscopy study of the structural effects induced by echinomycin binding to DNA.

    Journal of Molecular Biology 345(4):745 (2005) PMID 15588823

    Atomic force microscopy (AFM) has been used to examine the conformational effects of echinomycin, a DNA bis-intercalating antibiotic, on linear and circular DNA. Four different 398 bp DNA fragments were synthesized, comprising a combination of normal and/or modified bases including 2,6-diaminopu...
  18. Atomic Force Microscopy Study of the Structural Effects Induced by Echinomycin Binding to DNA

    Journal of Molecular Biology 345(4):745 (2005)

    Atomic force microscopy (AFM) has been used to examine the conformational effects of echinomycin, a DNA bis-intercalating antibiotic, on linear and circular DNA. Four different 398 bp DNA fragments were synthesized, comprising a combination of normal and/or modified bases including 2,...
  19. Bayesian estimation of quantum optical phase by photon counting

    Signal Processing 84(8):1461 (2004)

    Photon count distributions at the outputs of a Mach–Zehnder interferometer are highly dependent on the phase difference between the two arms of the apparatus. Experimental results have shown that phase information can be inferred from the data even at low mean intensities of ≲10 photons. He...
  20. Bayesian estimation of quantum optical phase by photon counting

    Signal Processing 84(8):1461 (2004)

    Photon count distributions at the outputs of a Mach–Zehnder interferometer are highly dependent on the phase difference between the two arms of the apparatus. Experimental results have shown that phase information can be inferred from the data even at low mean intensities of ≲10 photons. He...