@article {3930,
	title = {Imaging light responses of targeted neuron populations in the rodent retina.},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	volume = {31},
	year = {2011},
	month = {2011 Feb 23},
	pages = {2855-67},
	abstract = {<p>Decoding the wiring diagram of the retina requires simultaneous observation of activity in identified neuron populations. Available recording methods are limited in their scope: electrodes can access only a small fraction of neurons at once, whereas synthetic fluorescent indicator dyes label tissue indiscriminately. Here, we describe a method for studying retinal circuitry at cellular and subcellular levels combining two-photon microscopy and a genetically encoded calcium indicator. Using specific viral and promoter constructs to drive expression of GCaMP3, we labeled all five major neuron classes in the adult mouse retina. Stimulus-evoked GCaMP3 responses as imaged by two-photon microscopy permitted functional cell type annotation. Fluorescence responses were similar to those measured with the small molecule dye OGB-1. Fluorescence intensity correlated linearly with spike rates \&gt;10 spikes/s, and a significant change in fluorescence always reflected a significant change in spike firing rate. GCaMP3 expression had no apparent effect on neuronal function. Imaging at subcellular resolution showed compartment-specific calcium dynamics in multiple identified cell types.</p>
},
	keywords = {Action Potentials, Animals, Female, Inbred C57BL, Male, Mice, Neurons, Ocular, Organ Culture Techniques, Retina, Vision, Voltage-Sensitive Dye Imaging},
	issn = {1529-2401},
	doi = {10.1523/JNEUROSCI.6064-10.2011},
	author = {Borghuis, Bart G and Tian, Lin and Xu, Ying and Nikonov, Sergei S and Vardi, Noga and Zemelman, Boris V and Looger, Loren L}
}
@article {2157,
	title = {Mapping of microbial pathways through constrained mapping of orthologous genes.},
	journal = {Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference},
	year = {2004},
	month = {2004},
	pages = {363-70},
	abstract = {<p>We present a novel computer algorithm for mapping biological pathways from one prokaryotic genome to another. The algorithm maps genes in a known pathway to their homologous genes (if any) in a target genome that is most consistent with (a) predicted orthologous gene relationship, (b) predicted operon structures, and (c) predicted co-regulation relationship of operons. Mathematically, we have formulated this problem as a constrained minimum spanning tree problem (called a Steiner network problem), and demonstrated that this formulation has the desired property through applications. We have solved this mapping problem using a combinatorial optimization algorithm, with guaranteed global optimality. We have implemented this algorithm as a computer program, called PMAP. Our test results on pathway mapping are highly encouraging {\textendash} we have mapped a number of pathways of H. influenzae, B. subtilis, H. pylori, and M. tuberculosis to E. coli using P-MAP, whose homologous pathways in E coli. are known and hence the mapping accuracy could be checked. We have then mapped known E. coli pathways in the EcoCyc database to the newly sequenced organism Synechococcus sp WH8102, and predicted 158 Synechococcus pathways. Detailed analyses on the predicted pathways indicate that P-MAP{\textquoteright}s mapping results are consistent with our general knowledge about (local) pathways. We believe that P-MAP will be a useful tool for microbial genome annotation projects and inference of individual microbial pathways.</p>
},
	keywords = {Algorithms, Amino Acid, Bacterial, Bacterial Physiological Phenomena, Bacterial Proteins, Biological, Chromosome Mapping, Computer Simulation, Conserved Sequence, Genome, Models, Sequence Homology, Signal Transduction},
	issn = {1551-7497},
	doi = {10.1007/s12021-010-9090-x},
	author = {Olman, Victor and Peng, Hanchuan and Su, Zhengchang and Xu, Ying}
}
