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56 Janelia Publications

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    01/01/09 | Imaging informatics for personalised medicine: applications and challenges.
    Liu T, Peng H, Zhou X
    International Journal of Functional Informatics and Personalised Medicine. 2009;2(2):125-35. doi: 10.1007/s12021-010-9090-x

    Imaging informatics has emerged as a major research theme in biomedicine in the last few decades. Currently, personalised, predictive and preventive patient care is believed to be one of the top priorities in biomedical research and practice. Imaging informatics plays a major role in biomedicine studies. This paper reviews main applications and challenges of imaging informatics in biomedicine.

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    Simpson Lab
    01/01/09 | Mapping and manipulating neural circuits in the fly brain.
    Simpson JH
    Advances in Genetics. 2009;65:79-143. doi: 10.1016/S0065-2660(09)65003-3

    Drosophila is a marvelous system to study the underlying principles that govern how neural circuits govern behaviors. The scale of the fly brain (approximately 100,000 neurons) and the complexity of the behaviors the fly can perform make it a tractable experimental model organism. In addition, 100 years and hundreds of labs have contributed to an extensive array of tools and techniques that can be used to dissect the function and organization of the fly nervous system. This review discusses both the conceptual challenges and the specific tools for a neurogenetic approach to circuit mapping in Drosophila.

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    01/01/09 | Modulating protein interactions by rational and computational design.
    Marvin JS, Looger LL
    Protein Engineering and Design. 2009:343-66
    Chklovskii Lab
    01/01/09 | Reconstruction of sparse circuits using multi-neuronal excitation (RESCUME).
    Hu T, Chklovskii DB
    Neural Information Processing Systems. 2009;22:790-8

    One of the central problems in neuroscience is reconstructing synaptic connectivity in neural circuits. Synapses onto a neuron can be probed by sequentially stimulating potentially pre-synaptic neurons while monitoring the membrane voltage of the post-synaptic neuron. Reconstructing a large neural circuit using such a "brute force" approach is rather time-consuming and inefficient because the connectivity in neural circuits is sparse. Instead, we propose to measure a post-synaptic neuron's voltage while stimulating sequentially random subsets of multiple potentially pre-synaptic neurons. To reconstruct these synaptic connections from the recorded voltage we apply a decoding algorithm recently developed for compressive sensing. Compared to the brute force approach, our method promises significant time savings that grow with the size of the circuit. We use computer simulations to find optimal stimulation parameters and explore the feasibility of our reconstruction method under realistic experimental conditions including noise and non-linear synaptic integration. Multineuronal stimulation allows reconstructing synaptic connectivity just from the spiking activity of post-synaptic neurons, even when sub-threshold voltage is unavailable. By using calcium indicators, voltage-sensitive dyes, or multi-electrode arrays one could monitor activity of multiple postsynaptic neurons simultaneously, thus mapping their synaptic inputs in parallel, potentially reconstructing a complete neural circuit.

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    Eddy/Rivas Lab
    01/01/09 | Rfam: updates to the RNA families database.
    Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A
    Nucleic Acids Research. 2009 Jan;37(Database issue):D136-40. doi: 10.1093/nar/gkn766

    Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at

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    01/01/09 | Stochastic resonance-enhanced laser-based particle detector.
    Dutta A, Werner C
    Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society.. 2009;2009:785-7. doi: 10.1109/IEMBS.2009.5332748

    This paper presents a Laser-based particle detector whose response was enhanced by modulating the Laser diode with a white-noise generator. A Laser sheet was generated to cast a shadow of the object on a 200 dots per inch, 512 x 1 pixels linear sensor array. The Laser diode was modulated with a white-noise generator to achieve stochastic resonance. The white-noise generator essentially amplified the wide-bandwidth (several hundred MHz) noise produced by a reverse-biased zener diode operating in junction-breakdown mode. The gain in the amplifier in the white-noise generator was set such that the Receiver Operating Characteristics plot provided the best discriminability. A monofiber 40 AWG (approximately 80 microm) wire was detected with approximately 88% True Positive rate and approximately 19% False Positive rate in presence of white-noise modulation and with approximately 71% True Positive rate and approximately 15% False Positive rate in absence of white-noise modulation.

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