Genome Dashboards: Framework and Examples.


:Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics- and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.


Biophys J


Biophysical journal


Li Z,Sun R,Bishop TC




Has Abstract


2020-05-05 00:00:00














  • Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study.

    abstract::Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates rev...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Nguyen PH,Gorbunov RD,Stock G

    更新日期:2006-08-15 00:00:00

  • Codon-dependent tRNA fluctuations monitored with fluorescence polarization.

    abstract::During protein synthesis dictated by the codon sequence of messenger RNA, the ribosome selects aminoacyl-tRNA (aa-tRNA) with high accuracy, the exact mechanism of which remains elusive. By using a single-molecule fluorescence resonance energy transfer method coupled with fluorescence emission anisotropy, we provide ev...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Mishra PP,Qureshi MT,Ren W,Lee TH

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  • Self-segregation of myelin membrane lipids in model membranes.

    abstract::Rapid conduction of nerve impulses requires coating of axons by myelin sheaths, which are multilamellar, lipid-rich membranes produced by oligodendrocytes in the central nervous system. To act as an insulator, myelin has to form a stable and firm membrane structure. In this study, we have analyzed the biophysical prop...

    journal_title:Biophysical journal

    pub_type: 杂志文章


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  • Some self-consistent two-state sliding filament models of muscle contraction.

    abstract::The general formalism required to treat two-state sliding filament models of muscle contraction, including free energy considerations, is first reviewed and amplified. This formalism is then used to examine, and modify as needed, three models studied previously by Podolsky and Nolan, in which cross-bridge attachment-d...

    journal_title:Biophysical journal

    pub_type: 杂志文章


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  • Secondary flow as a mechanism for the formation of biofilm streamers.

    abstract::In most environments, such as natural aquatic systems, bacteria are found predominantly in self-organized sessile communities known as biofilms. In the presence of a significant flow, mature multispecies biofilms often develop into long filamentous structures called streamers, which can greatly influence ecosystem pro...

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  • Dynamic studies of proton diffusion in mesoscopic heterogeneous matrix: I. Concentrated solutions of sucrose.

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  • Gap junction gating sensitivity to physiological internal calcium regardless of pH in Novikoff hepatoma cells.

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  • 2H NMR determination of the global correlation time of the gramicidin channel in a lipid bilayer.

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    journal_title:Biophysical journal

    pub_type: 杂志文章


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  • Electrochemical healing similarities between animals and plants.

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    pub_type: 杂志文章


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  • Effects of hydrostatic pressure on bilayer phase behavior and dynamics of dilauroylphosphatidylcholine.

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    pub_type: 杂志文章


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  • Modeling the step of endosomal escape during cell infection by a nonenveloped virus.

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    journal_title:Biophysical journal

    pub_type: 杂志文章


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    pub_type: 杂志文章


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  • Benjamin Franklin, Philadelphia's favorite son, was a membrane biophysicist.

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    journal_title:Biophysical journal

    pub_type: 传,历史文章,杂志文章


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  • Intermediate and stable redox states of cytochrome c studied by low temperature resonance Raman spectroscopy.

    abstract::Stabilized intermediate redox states of cytochrome c are generated by radiolytic reduction of initially oxidized enzyme in glass matrices at liquid nitrogen temperature. In the intermediate states the heme group is reduced by hydrated electrons, whereas the protein conformation is restrained close to its oxidized form...

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    pub_type: 杂志文章


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  • Bioelectrorheological model of the cell. VI. Experimental verification of the rheological model of cytoplasmic membrane.

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  • Quantitative analysis of G-actin transport in motile cells.

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    pub_type: 杂志文章


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    journal_title:Biophysical journal

    pub_type: 杂志文章


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  • Hofmeister effect in ion transport: reversible binding of halide anions to the roflamycoin channel.

    abstract::We have studied the anion-dependent gating of roflamycoin ion channels using spectral analysis of noise in currents through multichannel planar lipid bilayers. We have found that in addition to low frequency current fluctuations that may be attributed to channel switching between open and closed conformations, roflamy...

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    pub_type: 杂志文章


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  • The effects of thermal disorder on the solution-scattering profiles of macromolecules.

    abstract::The solution-scattering profiles of macromolecules are significantly affected by the thermal motions of their atoms, especially at wide scattering angles, even when only a single conformational state is significantly populated in solution. Here it is shown that the impact thermal motions have on the molecular componen...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Moore PB

    更新日期:2014-04-01 00:00:00

  • Light harvesting by lamellar chromatophores in Rhodospirillum photometricum.

    abstract::Purple photosynthetic bacteria harvest light using pigment-protein complexes which are often arranged in pseudo-organelles called chromatophores. A model of a chromatophore from Rhodospirillum photometricum was constructed based on atomic force microscopy data. Molecular-dynamics simulations and quantum-dynamics calcu...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Chandler DE,Strümpfer J,Sener M,Scheuring S,Schulten K

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  • Specific ion effects: why the properties of lysozyme in salt solutions follow a Hofmeister series.

    abstract::Protein solubility in aqueous solutions depends in a complicated and not well understood way on pH, salt type, and salt concentration. Why for instance does the use of two different monovalent salts, potassium thiocyanate and potassium chloride, produce such different results? One important and previously neglected so...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Boström M,Williams DR,Ninham BW

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  • Epithelial water transport in a balanced gradient system.

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    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Mathias RT

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  • Gating of the mechanosensitive channel protein MscL: the interplay of membrane and protein.

    abstract::The mechanosensitive channel of large conductance (MscL) belongs to a family of transmembrane channel proteins in bacteria and functions as a safety valve that relieves the turgor pressure produced by osmotic downshock. MscL gating can be triggered solely by stretching of the membrane. This work reports an effort to u...

    journal_title:Biophysical journal

    pub_type: 杂志文章


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  • Acyl chain length and saturation modulate interleaflet coupling in asymmetric bilayers: effects on dynamics and structural order.

    abstract::A long-standing question about membrane structure and function is the degree to which the physical properties of the inner and outer leaflets of a bilayer are coupled to one another. Using our recently developed methods to prepare asymmetric vesicles, coupling was investigated for vesicles containing phosphatidylcholi...

    journal_title:Biophysical journal

    pub_type: 杂志文章


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  • An x-ray diffraction study on early structural changes in skeletal muscle contraction.

    abstract::Structural changes in frog skeletal muscle were studied using x-ray diffraction with a time resolution of 0.53-1.02 ms after a single electrical stimulus at 8 degrees C. Tension began to drop at 6 ms (latency relaxation), reached a minimum at 8 ms, and then twitch tension developed. The intensity of the meridional ref...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Yagi N

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  • Regular gaits and optimal velocities for motor proteins.

    abstract::It has been observed in numerical experiments that adding a cargo to a motor protein can regularize its gait. Here we explain these results via asymptotic analysis on a general stochastic motor protein model. This analysis permits a computation of various observables (e.g., the mean velocity) of the motor protein and ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: DeVille RE,Vanden-Eijnden E

    更新日期:2008-09-15 00:00:00

  • On mutations that uncouple sodium channel activation from inactivation.

    abstract::Computations on sodium channel gating were conducted using a closed-open-inactivated coupled kinetic scheme. The time constant of inactivation (tauh) derives a voltage dependency from coupling to voltage-dependent activation even when rate constants between inactivated and other states are strictly voltage independent...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Goldman L

    更新日期:1999-05-01 00:00:00

  • Quantitative intensity-based FRET approaches--a comparative snapshot.

    abstract::Förster resonance energy transfer (FRET) has become an important tool for analyzing different aspects of interactions among biological macromolecules in their native environments. FRET analysis has also been successfully applied to study the spatiotemporal regulation of various cellular processes using genetically enc...

    journal_title:Biophysical journal

    pub_type: 杂志文章,评审


    authors: Zeug A,Woehler A,Neher E,Ponimaskin EG

    更新日期:2012-11-07 00:00:00

  • Polarization-modulated infrared spectroscopy and x-ray reflectivity of photosystem II core complex at the gas-water interface.

    abstract::The state of photosystem II core complex (PS II CC) in monolayer at the gas-water interface was investigated using in situ polarization-modulated infrared reflection absorption spectroscopy and x-ray reflectivity techniques. Two approaches for preparing and manipulating the monolayers were examined and compared. In th...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Gallant J,Desbat B,Vaknin D,Salesse C

    更新日期:1998-12-01 00:00:00

  • The effect of thin filament activation on the attachment of weak binding cross-bridges: A two-dimensional x-ray diffraction study on single muscle fibers.

    abstract::To study possible structural changes in weak cross-bridge attachment to actin upon activation of the thin filament, two-dimensional (2D) x-ray diffraction patterns of skinned fibers from rabbit psoas muscle were recorded at low and high calcium concentration in the presence of saturating concentrations of MgATPgammaS,...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kraft T,Xu S,Brenner B,Yu LC

    更新日期:1999-03-01 00:00:00