@article {1627497,
	title = {Modulating mesendoderm competence during human germ layer differentiation},
	journal = {Cell Reports},
	volume = {37},
	number = {6},
	year = {2021},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601596/},
	author = {Valcourt, JR, Huang, RE, Kundu, Sharmistha, Venkatasubramanian, D, Kingston, RE, Ramanathan, S.}
}
@article {1627496,
	title = {Discovering a sparse set of pairwise discriminating features in high-dimensional data.},
	journal = {Bioinformatics },
	volume = {37},
	number = {2},
	year = {2021},
	pages = {202-212},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8599814/},
	author = {Melton, S., Ramanathan, S.}
}
@article {1627495,
	title = {Discovering a sparse set of pairwise discriminating features in high-dimensional data},
	journal = {Bioinformatics},
	year = {2020},
	url = {https://doi.org/10.1093/bioinformatics/btaa690},
	author = {Melton, S., Ramanathan, S.}
}
@article {1627494,
	title = {Changing the Waddington landscape to control mesendoderm competence},
	journal = {biorxiv},
	year = {2020},
	url = {https://doi.org/10.1101/867010},
	author = {Valcourt JR, Huang R, Kundu S, Venkatasubramanian D, Kingston RE, Ramanathan S.}
}
@article {1627493,
	title = {A compressed sensing framework for efficient dissection of neural circuits.},
	journal = {Nature Methods},
	volume = {16},
	year = {2019},
	pages = {126-133},
	url = {https://doi.org/10.1038/s41592-018-0233-6},
	author = {Lee, J.B., Yonar, A., Hallacy, T. et al.}
}
@article {1627488,
	title = {Mouse embryo geometry drives formation of robust signaling gradients through receptor localization.},
	journal = {Nature Communication},
	volume = {10},
	number = {4516},
	year = {2019},
	url = {https://doi.org/10.1038/s41467-019-12533-7 (https://doi.org/10.1038/s41467-019-12533-7)},
	author = {Zhang, Z., Zwick, S., Loew, E. et al.}
}
@article {1479367,
	title = {A compressed sensing framework for efficient dissection of neural circuits},
	journal = {Nature Methods},
	volume = {16},
	number = {1},
	year = {2018},
	url = {https://doi.org/10.1038/s41592-018-0233-6},
	author = {Lee JB, Yonar A, Hallacy T, Shen CH, Milloz J, Srinivasan J, Kocabas A, Ramanathan S}
}
@article {1016431,
	title = {Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation},
	journal = {Neuron},
	volume = {93},
	number = {5},
	year = {2017},
	pages = {1035{\textendash}1048.e5},
	author = {J Close and Z Yao and B Levi and J Miller and T Bakken and V Menon and J Ting and A Wall and A Krostag and E Thomsen and Nelson, A and S Bort and N Shapovalova and K Ngo and J Grimley and J Phillips and C Thompson and Ramanathan, S. and E Lein}
}
@article {1016421,
	title = {Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states},
	journal = {eLife},
	volume = {6:e20487},
	year = {2017},
	url = {https://elifesciences.org/articles/20487},
	author = {S Jang and L Furchtgott and Choubey, S and L-N Zou and A Doyle and V Menon and E Loew and A-R Krostag and R.A. Martinez and L Madisen and B.P. Levi and Ramanathan, S.}
}
@article {1016396,
	title = {Discovering sparse transcription factor codes for cell states and state transitions during development},
	journal = {eLife},
	volume = {2017;6:e20488},
	year = {2017},
	url = {https://elifesciences.org/articles/20488},
	author = {L Furchtgott and S Melton and V Menon and Ramanathan, S.}
}
@article {1016391,
	title = {A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development.},
	journal = {Cell Stem Cell},
	volume = {20},
	number = {1},
	year = {2016},
	pages = {120-134},
	author = {Z Yao and V Menon and J.K. Mich and S Ku and A Krostag and R.A. Martinez and L Furchtgott and H Mulholland and S Bort and M.A. Fuqua and B.W. Gregor and R.D. Hodge and A Jayabalu and R.C. May and S Melton and A.M. Nelson and N.K. Ngo and N.V. Shapovalova and S.I. Shehata and M.W. Smith and L.J. Tait and E.R. Thomsen and C Ye and I.A. Glass and C.L. Thompson and J.W. Phillips and J.S. Grimley and B.P. Levi and Wang, Y. and Ramanathan, S.}
}
@article {677016,
	title = {Fixed single-cell transcriptomic characterization of human radial glial diversity.},
	journal = {Nat Methods},
	volume = {13},
	number = {1},
	year = {2016},
	month = {2016 Jan},
	pages = {87-93},
	abstract = {The diverse progenitors that give rise to the human neocortex have been difficult to characterize because progenitors, particularly radial glia (RG), are rare and are defined by a combination of intracellular markers, position and morphology. To circumvent these problems, we developed Fixed and Recovered Intact Single-cell RNA (FRISCR), a method for profiling the transcriptomes of individual fixed, stained and sorted cells. Using FRISCR, we profiled primary human RG that constitute only 1\% of the midgestation cortex and classified them as ventricular zone-enriched RG (vRG) that express ANXA1 and CRYAB, and outer subventricular zone-localized RG (oRG) that express HOPX. Our study identified vRG and oRG markers and molecular profiles, an essential step for understanding human neocortical progenitor development. FRISCR allows targeted single-cell profiling of any tissues that lack live-cell markers.},
	issn = {1548-7105},
	doi = {10.1038/nmeth.3629},
	author = {Thomsen, Elliot R and Mich, John K and Yao, Zizhen and Hodge, Rebecca D and Doyle, Adele M and Jang, Sumin and Shehata, Soraya I and Nelson, Angelique M and Shapovalova, Nadiya V and Levi, Boaz P and Ramanathan, Sharad}
}
@article {677021,
	title = {Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behaviour.},
	journal = {Nature},
	volume = {490},
	number = {7419},
	year = {2012},
	month = {2012 Oct 11},
	pages = {273-7},
	abstract = {Animals locate and track chemoattractive gradients in the environment to find food. With its small nervous system, Caenorhabditis elegans is a good model system in which to understand how the dynamics of neural activity control this search behaviour. Extensive work on the nematode has identified the neurons that are necessary for the different locomotory behaviours underlying chemotaxis through the use of laser ablation, activity recording in immobilized animals and the study of mutants. However, we do not know the neural activity patterns in C. elegans that are sufficient to control its complex chemotactic behaviour. To understand how the activity in its interneurons coordinate different motor programs to lead the animal to food, here we used optogenetics and new optical tools to manipulate neural activity directly in freely moving animals to evoke chemotactic behaviour. By deducing the classes of activity patterns triggered during chemotaxis and exciting individual neurons with these patterns, we identified interneurons that control the essential locomotory programs for this behaviour. Notably, we discovered that controlling the dynamics of activity in just one interneuron pair (AIY) was sufficient to force the animal to locate, turn towards and track virtual light gradients. Two distinct activity patterns triggered in AIY as the animal moved through the gradient controlled reversals and gradual turns to drive chemotactic behaviour. Because AIY neurons are post-synaptic to most chemosensory and thermosensory neurons, it is probable that these activity patterns in AIY have an important role in controlling and coordinating different taxis behaviours of the animal.},
	keywords = {Animals, Behavior, Animal, Caenorhabditis elegans, Chemotaxis, Electric Stimulation, Interneurons, Neurons},
	issn = {1476-4687},
	doi = {10.1038/nature11431},
	author = {Kocabas, Askin and Shen, Ching-Han and Guo, Zengcai V and Ramanathan, Sharad}
}
@article {677026,
	title = {Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system.},
	journal = {Science},
	volume = {336},
	number = {6082},
	year = {2012},
	month = {2012 May 11},
	pages = {721-4},
	abstract = {Biological systems involving short-range activators and long-range inhibitors can generate complex patterns. Reaction-diffusion models postulate that differences in signaling range are caused by differential diffusivity of inhibitor and activator. Other models suggest that differential clearance underlies different signaling ranges. To test these models, we measured the biophysical properties of the Nodal/Lefty activator/inhibitor system during zebrafish embryogenesis. Analysis of Nodal and Lefty gradients revealed that Nodals have a shorter range than Lefty proteins. Pulse-labeling analysis indicated that Nodals and Leftys have similar clearance kinetics, whereas fluorescence recovery assays revealed that Leftys have a higher effective diffusion coefficient than Nodals. These results indicate that differential diffusivity is the major determinant of the differences in Nodal/Lefty range and provide biophysical support for reaction-diffusion models of activator/inhibitor-mediated patterning.},
	keywords = {Animals, Blastula, Body Patterning, Diffusion, Embryonic Development, Fluorescence Recovery After Photobleaching, Half-Life, Intracellular Signaling Peptides and Proteins, Kinetics, Left-Right Determination Factors, Models, Biological, Nodal Signaling Ligands, Recombinant Fusion Proteins, Zebrafish, Zebrafish Proteins},
	issn = {1095-9203},
	doi = {10.1126/science.1221920},
	author = {M{\"u}ller, Patrick and Rogers, Katherine W and Jordan, Ben M and Lee, Joon S and Robson, Drew and Ramanathan, Sharad and Schier, Alexander F}
}
@article {677036,
	title = {Measuring in vivo signaling kinetics in a mitogen-activated kinase pathway using dynamic input stimulation.},
	journal = {Methods Mol Biol},
	volume = {734},
	year = {2011},
	month = {2011},
	pages = {101-19},
	abstract = {Determining the in vivo kinetics of a signaling pathway is a challenging task. We can measure a property we termed pathway bandwidth to put in vivo bounds on the kinetics of the mitogen-activated protein kinase (MAPk) signaling cascade in Saccharomyces cerevisiae that responds to hyperosmotic stress [the High Osmolarity Glycerol (HOG) pathway]. Our method requires stimulating cells with square waves of oscillatory hyperosmotic input (1 M sorbitol) over a range of frequencies and measuring the activity of the HOG pathway in response to this oscillatory input. The input frequency at which the pathway{\textquoteright}s steady-state activity drops precipitously because the stimulus is changing too rapidly for the pathway to respond faithfully is defined as the pathway bandwidth. In this chapter, we provide details of the techniques required to measure pathway bandwidth in the HOG pathway. These methods are generally useful and can be applied to signaling pathways in S. cerevisiae and other organisms whenever a rapid reporter of pathway activity is available.},
	keywords = {Biochemistry, Culture Media, Image Processing, Computer-Assisted, Kinetics, MAP Kinase Signaling System, Microfluidics, Mitogen-Activated Protein Kinases, Saccharomyces cerevisiae, Software, Solutions, Time Factors},
	issn = {1940-6029},
	doi = {10.1007/978-1-61779-086-7_6},
	author = {McClean, Megan N and Hersen, Pascal and Ramanathan, Sharad}
}
@article {677031,
	title = {Pluripotency factors in embryonic stem cells regulate differentiation into germ layers.},
	journal = {Cell},
	volume = {145},
	number = {6},
	year = {2011},
	month = {2011 Jun 10},
	pages = {875-89},
	abstract = {Cell fate decisions are fundamental for development, but we do not know how transcriptional networks reorganize during the transition from a pluripotent to a differentiated cell state. Here, we asked how mouse embryonic stem cells (ESCs) leave the pluripotent state and choose between germ layer fates. By analyzing the dynamics of the transcriptional circuit that maintains pluripotency, we found that Oct4 and Sox2, proteins that maintain ESC identity, also orchestrate germ layer fate selection. Oct4 suppresses neural ectodermal differentiation and promotes mesendodermal differentiation; Sox2 inhibits mesendodermal differentiation and promotes neural ectodermal differentiation. Differentiation signals continuously and asymmetrically modulate Oct4 and Sox2 protein levels, altering their binding pattern in the genome, and leading to cell fate choice. The same factors that maintain pluripotency thus also integrate external signals and control lineage selection. Our study provides a framework for understanding how complex transcription factor networks control cell fate decisions in progenitor cells.},
	keywords = {Animals, Cell Differentiation, Embryonic Stem Cells, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Germ Layers, Homeodomain Proteins, Mice, Octamer Transcription Factor-3, Pluripotent Stem Cells, SOXB1 Transcription Factors},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2011.05.017},
	author = {Thomson, Matt and Liu, Siyuan John and Zou, Ling-Nan and Smith, Zack and Meissner, Alexander and Ramanathan, Sharad}
}
@article {677051,
	title = {In vivo measurement of signaling cascade dynamics.},
	journal = {Cell Cycle},
	volume = {8},
	number = {3},
	year = {2009},
	month = {2009 Feb 1},
	pages = {373-6},
	abstract = {Genetic and biochemical studies yield information about the component proteins and interactions involved in a cellular signaling pathway. However this parts inventory often does not immediately reveal the in vivo signal processing capabilities and function of the pathway. Signaling pathways are complex systems with dynamic behavior and a systems level approach is needed to understand the physiological roles they play within the cell. We recently used such an approach to measure the signal processing behavior of the budding yeast HOG MAP kinase pathway in response to precisely varied temporal stimuli controlled with a microfluidic device. Despite being a well-studied pathway with well-known components the signaling dynamics and biochemical parameters of this pathway were not known. Our approach allowed us to characterize the pathway{\textquoteright}s in vivo signal processing and put bounds on all of the in vivo reaction rates. The experimental and theoretical techniques used in our study are general and can be applied to understanding other signaling pathways in a range of biological systems.},
	keywords = {Microfluidics, Mitogen-Activated Protein Kinases, Recombinant Fusion Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Signal Transduction},
	issn = {1551-4005},
	author = {McClean, Megan N and Hersen, Pascal and Ramanathan, Sharad}
}
@article {677046,
	title = {Modularity of MAP kinases allows deformation of their signalling pathways.},
	journal = {Nat Cell Biol},
	volume = {11},
	number = {4},
	year = {2009},
	month = {2009 Apr},
	pages = {484-91},
	abstract = {Eukaryotic protein kinase pathways have both grown in number and changed their network architecture during evolution. We wondered if there are pivotal proteins in these pathways that have been repeatedly responsible for forming new connections through evolution, thus changing the topology of the network; and if so, whether the underlying properties of these proteins could be exploited to re-engineer and rewire these pathways. We addressed these questions in the context of the mitogen-activated protein kinase (MAPK) pathways. MAPK proteins were found to have repeatedly acquired new specificities and interaction partners during evolution, suggesting that these proteins are pivotal in the kinase network. Using the MAPKs Fus3 and Hog1 of the Saccharomyces cerevisiae mating and hyper-osmolar pathways, respectively, we show that these pivotal proteins can be re-designed to achieve a wide variety of changes in the input-output properties of the MAPK network. Through an analysis of our experimental results and of the sequence and structure of these proteins, we show that rewiring of the network is possible due to the underlying modular design of the MAPKs. We discuss the implications of our findings on the radiation of MAPKs through evolution and on how these proteins achieve their specificity.},
	keywords = {Conserved Sequence, Enzyme Activation, Evolution, Molecular, Glycerol, MAP Kinase Signaling System, Mitogen-Activated Protein Kinases, Models, Molecular, Osmolar Concentration, Pheromones, Protein Binding, Protein Structure, Secondary, Recombinant Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Sequence Analysis, Protein},
	issn = {1476-4679},
	doi = {10.1038/ncb1856},
	author = {Mody, Areez and Weiner, Joan and Ramanathan, Sharad}
}
@article {677041,
	title = {Optical interrogation of neural circuits in Caenorhabditis elegans.},
	journal = {Nat Methods},
	volume = {6},
	number = {12},
	year = {2009},
	month = {2009 Dec},
	pages = {891-6},
	abstract = {The nematode Caenorhabditis elegans has a compact nervous system with only 302 neurons. Whereas most of the synaptic connections between these neurons have been identified by electron microscopy serial reconstructions, functional connections have been inferred between only a few neurons through combinations of electrophysiology, cell ablation, in vivo calcium imaging and genetic analysis. To map functional connections between neurons, we combined in vivo optical stimulation with simultaneous calcium imaging. We analyzed the connections from the ASH sensory neurons and RIM interneurons to the command interneurons AVA and AVD. Stimulation of ASH or RIM neurons using channelrhodopsin-2 (ChR2) resulted in activation of AVA neurons, evoking an avoidance behavior. Our results demonstrate that we can excite specific neurons expressing ChR2 while simultaneously monitoring G-CaMP fluorescence in several other neurons, making it possible to rapidly decipher functional connections in C. elegans neural circuits.},
	keywords = {Animals, Caenorhabditis elegans, Calcium, Interneurons, Optics and Photonics},
	issn = {1548-7105},
	doi = {10.1038/nmeth.1397},
	author = {Guo, Zengcai V and Hart, Anne C and Ramanathan, Sharad}
}
@article {677066,
	title = {HIV-1 positive feedback and lytic fate.},
	journal = {Nat Genet},
	volume = {40},
	number = {4},
	year = {2008},
	month = {2008 Apr},
	pages = {382-3},
	keywords = {Feedback, Physiological, Gene Expression Regulation, Viral, HIV-1, Humans, tat Gene Products, Human Immunodeficiency Virus, Transcription, Genetic, Transcriptional Activation, Virus Replication},
	issn = {1546-1718},
	doi = {10.1038/ng0408-382},
	author = {Nachman, Iftach and Ramanathan, Sharad}
}
@article {677056,
	title = {[Dynamic analysis of cell signalling: the example of the Saccharomyces cerevisiae osmotic response].},
	journal = {Med Sci (Paris)},
	volume = {24},
	number = {12},
	year = {2008},
	month = {2008 Dec},
	pages = {1020-2},
	keywords = {Cytoplasm, MAP Kinase Signaling System, Membrane Proteins, Mitogen-Activated Protein Kinase Kinases, Mitogen-Activated Protein Kinases, Osmotic Pressure, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins},
	issn = {0767-0974},
	doi = {10.1051/medsci/200824121020},
	author = {Hersen, Pascal and McClean, Megan and Ramanathan, Sharad}
}
@article {677061,
	title = {Signal processing by the HOG MAP kinase pathway.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {105},
	number = {20},
	year = {2008},
	month = {2008 May 20},
	pages = {7165-70},
	abstract = {Signaling pathways relay information about changes in the external environment so that cells can respond appropriately. How much information a pathway can carry depends on its bandwidth. We designed a microfluidic device to reliably change the environment of single cells over a range of frequencies. Using this device, we measured the bandwidth of the Saccharomyces cerevisiae signaling pathway that responds to high osmolarity. This prototypical pathway, the HOG pathway, is shown to act as a low-pass filter, integrating the signal when it changes rapidly and following it faithfully when it changes more slowly. We study the dependence of the pathway{\textquoteright}s bandwidth on its architecture. We measure previously unknown bounds on all of the in vivo reaction rates acting in this pathway. We find that the two-component Ssk1 branch of this pathway is capable of fast signal integration, whereas the kinase Ste11 branch is not. Our experimental techniques can be applied to other signaling pathways, allowing the measurement of their in vivo kinetics and the quantification of their information capacity.},
	keywords = {Gene Deletion, Gene Expression Regulation, Gene Expression Regulation, Fungal, Image Processing, Computer-Assisted, Inflammation, MAP Kinase Kinase Kinases, MAP Kinase Signaling System, Microfluidic Analytical Techniques, Microfluidics, Mitogen-Activated Protein Kinases, Models, Biological, Plasmids, Saccharomyces cerevisiae, Signal Transduction},
	issn = {1091-6490},
	doi = {10.1073/pnas.0710770105},
	author = {Hersen, Pascal and McClean, Megan N and Mahadevan, L and Ramanathan, Sharad}
}
@article {677081,
	title = {Cross-talk and decision making in MAP kinase pathways.},
	journal = {Nat Genet},
	volume = {39},
	number = {3},
	year = {2007},
	month = {2007 Mar},
	pages = {409-14},
	abstract = {Cells must respond specifically to different environmental stimuli in order to survive. The signal transduction pathways involved in sensing these stimuli often share the same or homologous proteins. Despite potential cross-wiring, cells show specificity of response. We show, through modeling, that the physiological response of such pathways exposed to simultaneous and temporally ordered inputs can demonstrate system-level mechanisms by which pathways achieve specificity. We apply these results to the hyperosmolar and pheromone mitogen-activated protein (MAP) kinase pathways in the yeast Saccharomyces cerevisiae. These two pathways specifically sense osmolar and pheromone signals, despite sharing a MAPKKK, Ste11, and having homologous MAPKs (Fus3 and Hog1). We show that in a single cell, the pathways are bistable over a range of inputs, and the cell responds to only one stimulus even when exposed to both. Our results imply that these pathways achieve specificity by filtering out spurious cross-talk through mutual inhibition. The variability between cells allows for heterogeneity of the decisions.},
	keywords = {MAP Kinase Signaling System, Models, Biological, Pheromones, Receptor Cross-Talk, Saccharomyces cerevisiae},
	issn = {1061-4036},
	doi = {10.1038/ng1957},
	author = {McClean, Megan N and Mody, Areez and Broach, James R and Ramanathan, Sharad}
}
@article {677076,
	title = {Dissecting timing variability in yeast meiosis.},
	journal = {Cell},
	volume = {131},
	number = {3},
	year = {2007},
	month = {2007 Nov 2},
	pages = {544-56},
	abstract = {Cell-to-cell variability in the timing of cell-fate changes can be advantageous for a population of single-celled organisms growing in a fluctuating environment. We study timing variability during meiosis in Saccharomyces cerevisiae, initiated upon nutritional starvation. We use time-lapse fluorescence microscopy to measure the timing of meiotic events in single cells and find that the duration of meiosis is highly variable between cells. This variability is concentrated between the beginning of starvation and the onset of early meiosis genes. Cell-cycle variability and nutritional history have little effect on this timing variability. Rather, variation in the production rate of the meiotic master regulator Ime1 and its gradual increase over time govern this variability, and cell size effects are channeled through Ime1. These results tie phenotypic variability with expression dynamics of a transcriptional regulator and provide a general framework for the study of temporal developmental processes.},
	keywords = {Cell Cycle Proteins, Cell Nucleus, DNA-Binding Proteins, Food, Genes, Fungal, Genes, Reporter, Meiosis, Nuclear Proteins, Phenotype, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Signal Transduction, Time Factors, Transcription Factors},
	issn = {0092-8674},
	doi = {10.1016/j.cell.2007.09.044},
	author = {Nachman, Iftach and Regev, Aviv and Ramanathan, Sharad}
}
@article {677071,
	title = {Genetic drift at expanding frontiers promotes gene segregation.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {104},
	number = {50},
	year = {2007},
	month = {2007 Dec 11},
	pages = {19926-30},
	abstract = {Competition between random genetic drift and natural selection play a central role in evolution: Whereas nonbeneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer a selective advantage. Here, however, we observe chance effects during range expansions that dramatically alter the gene pool even in large microbial populations. Initially well mixed populations of two fluorescently labeled strains of Escherichia coli develop well defined, sector-like regions with fractal boundaries in expanding colonies. The formation of these regions is driven by random fluctuations that originate in a thin band of pioneers at the expanding frontier. A comparison of bacterial and yeast colonies (Saccharomyces cerevisiae) suggests that this large-scale genetic sectoring is a generic phenomenon that may provide a detectable footprint of past range expansions.},
	keywords = {Escherichia coli, Genetic Drift, Genetic Markers, Models, Genetic, Saccharomyces cerevisiae, Selection, Genetic},
	issn = {1091-6490},
	doi = {10.1073/pnas.0710150104},
	author = {Hallatschek, Oskar and Hersen, Pascal and Ramanathan, Sharad and Nelson, David R.}
}
@article {677091,
	title = {G-protein-coupled enzyme cascades have intrinsic properties that improve signal localization and fidelity.},
	journal = {Biophys J},
	volume = {88},
	number = {5},
	year = {2005},
	month = {2005 May},
	pages = {3063-71},
	abstract = {G-protein-coupled enzyme cascades are used by eukaryotic cells to detect external signals and transduce them into intracellular messages that contain biological information relevant to the cell{\textquoteright}s function. Since G-protein-coupled receptors that are designed to detect different kinds of external signals can generate the same kind of intracellular response, effective signaling requires that there are mechanisms to increase signal specificity and fidelity. Here we examine the kinetic equations for the initial three stages in a generic G-protein-coupled cascade and show that the physical properties of the transduction pathway result in two intrinsic features that benefit signaling. 1), The response to a single activated receptor is naturally confined to a localized spatial domain, which could improve signal specificity by reducing cross talk. 2), The peak of the response generated by such a signaling domain is limited. This saturation effect reduces trial-to-trial variability and increases signaling fidelity by limiting the response to receptors that remain active for longer than average. We suggest that this mechanism for reducing response fluctuations may be a contributing factor in making the single photon responses of vertebrate retinal rods so remarkably reproducible.},
	keywords = {Animals, Biophysics, Catalysis, Gene Expression Regulation, GTP-Binding Proteins, Kinetics, Models, Biological, Models, Statistical, Photons, Protein Structure, Tertiary, Receptors, Cell Surface, Retinal Rod Photoreceptor Cells, Signal Transduction, Time Factors},
	issn = {0006-3495},
	doi = {10.1529/biophysj.103.039321},
	author = {Ramanathan, Sharad and Detwiler, Peter B and Sengupta, Anirvan M and Shraiman, Boris I}
}
@article {677086,
	title = {Tracing the sources of cellular variation.},
	journal = {Dev Cell},
	volume = {9},
	number = {5},
	year = {2005},
	month = {2005 Nov},
	pages = {576-8},
	abstract = {As the adage says, variety is the spice of life, and despite our best attempts, cells, even those with the same genome, never seem to behave the same. By combining mathematical and experimental analyses, Colman-Lerner and colleagues propose, in a recent issue of Nature, a method to delicately unravel the sources of this variation. Applying their technique to the pheromone response in budding yeast, they show that much of the observed variation originates from cell cycle effects and is dependent on levels of pathway input.},
	keywords = {Cell Cycle, Genetic Variation, Pheromones, Ribosomes, Saccharomyces cerevisiae},
	issn = {1534-5807},
	doi = {10.1016/j.devcel.2005.10.004},
	author = {Ramanathan, Sharad and Swain, Peter S}
}
@article {677096,
	title = {Influence of scattering on transmission through long-period fiber gratings and tunable microstructure fibers.},
	journal = {Appl Opt},
	volume = {41},
	number = {33},
	year = {2002},
	month = {2002 Nov 20},
	pages = {7018-24},
	abstract = {Controlled optical scattering within or around an optical fiber provides a potentially useful mean for adjusting its transmission characteristic. This approach can complement conventional methods based on the establishment of well-defined variations in the index of refraction of the core or the cladding of the fiber. We describe the use of a highly scattering submonolayer of nanoparticles deposited onto the fiber surface for adjusting the resonance wavelength, depth, and width of an in-fiber long-period grating filter. We also introduce a polymer-dispersed liquid-crystal material that has a thermally tunable scattering cross section and can be incorporated into the channels of a microstructure optical fiber; this system may provide the means for a fiber-based scattering switch.},
	issn = {0003-6935},
	author = {Mach, Peter and Kerbage, Charles and Ramanathan, Sharad and Windeler, Robert S and Eggleton, Benjamin J and Rogers, John A}
}
