Conrad J. Burden

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

BackgroundRNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods.ResultsDifferential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices.ConclusionsThis work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates.

Ground state spectrum of light quark mesons

A confining, Goldstone theorem preserving, separable ansatz for the ladder kernel of the two-body Bethe-Salpeter equation is constructed from phenomenologically efficacious u, d, and s dressed-quark propagators. The simplicity of the approach is its merit. It provides a good description of the ground-state flavor-octet pseudoscalar, vector, and axial-vector meson spectrum facilitates an exploration of the relative importance of various components of the two-body Bethe-Salpeter amplitudes, showing that subleading Dirac components are quantitatively important in the flavor-octet pseudoscalar meson channels, and allows a scrutiny of the domain of applicability of ladder truncation studies. A color-antitriplet diquark spectrum is obtained. The shortcomings of separable {ital Ans{umlt a}tze} and the ladder kernel are highlighted. {copyright} {ital 1997} {ital The American Physical Society}

Singularity structure of a model quark propagator

Abstract A model Schwinger-Dyson equation for the fermion self-energy is solved for both spacelike and timelike momenta. The singularity structure of the quark propagator obtained as a solution of this equation is studied. It is found to be an entire function (except for an essential singularity at p2 = −∞; timelike in our metric): a property that may be indicative of confinement. The absence of singularities is a non-trivial feature that arises only as a result of the cancellation of zeros in the numerator and denominator of the propagator.

Gravitational Radiation From a Particular Class of Cosmic Strings

Abstract The gravitational radiation from closed loops of superheavy cosmic string is studied. For a broad class of string trajectories including non self intersecting loops an analytic expression is given for the power radiated in gravitational waves per unit solid angle. The total power radiated per loop is evaluated for several loop trajectories in the class, the results being similar to the values obtained in a previous numerical calculation of specific trajectories by Vachaspati and Vilenkin.

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.

Lattice Fermions in Odd Dimensions

Euclidean lattice fermions are examined in odd dimensions. The continuum flavours are identified and it is found that the flavours fall into two equal groups requiring inequivalent representations of the Dirac matrices. The relationship of this result to the parity transformation and the role of chiral symmetry are elucidated.

Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays

Recent analyses have shown that the relationship between intensity measurements from high density oligonucleotide microarrays and known concentration is non linear. Thus many measurements of so-called gene expression are neither measures of transcript nor mRNA concentration as might be expected. Intensity as measured in such microarrays is a measurement of fluorescent dye attached to probe-target duplexes formed during hybridization of a sample to the probes on the microarray. We develop several dynamic adsorption models relating fluorescent dye intensity to target RNA concentration, the simplest of which is the equilibrium Langmuir isotherm, or hyperbolic response function. Using data from the Affymerix HG-U95A Latin Square experiment, we evaluate various physical models, including equilibrium and non-equilibrium models, by applying maximum likelihood methods. We show that for these data, equilibrium Langmuir isotherms with probe dependent parameters are appropriate. We describe how probe sequence information may then be used to estimate the parameters of the Langmuir isotherm in order to provide an improved measure of absolute target concentration.

Electromagnetic from factors of charged and neutral kaons

Abstract The charged and neutral kaon form factors are calculated as a phenomenological application of model QCD Dyson-Schwinger equations. The results are compared with the pion form factor calculated in the same framework and yield FK±(Q2) > Fπ±(Q2) on Q2 ϵ [0, 3] GeV2; and a negative charge radius for the neutral kaon. These results are sensitive to the difference between the kaon and pion Bethe-Salpeter amplitude and the u- and s-quark propagation characteristics.

Adsorption models of hybridization and post-hybridization behaviour on oligonucleotide microarrays

Analysis of data from an Affymetrix Latin Square spike-in experiment indicates that measured fluorescence intensities of features on an oligonucleotide microarray are related to spike-in RNA target concentrations via a hyperbolic response function, generally identified as a Langmuir adsorption isotherm. Furthermore, the asymptotic signal at high spike-in concentrations is almost invariably lower for a mismatch feature than for its partner perfect match feature. We survey a number of theoretical adsorption models of hybridization at the microarray surface and find that in general they are unable to explain the differing saturation responses of perfect and mismatch features. On the other hand, we find that a simple and consistent explanation can be found in a model in which equilibrium hybridization is followed by partial dissociation of duplexes during the post-hybridization washing phase.

Diquarks and the Bosonisation of QCD

Previously the functional integral formulation of quantum chromodynamics <QCD) has been transformed into one involving colour singlet and colour octet bilocal fields describing qq states. While useful in determining the effective action for the observable colour singlet mesons, this formulation is of no use in determining the effective action for the baryon states. Here we show that there exists an alternative bosonisation of QCD in which the colour singlet meson fields and the colour triplet diquark fields form a complete set of functional integration variables. These diquark fields play an essential role in the colour singlet baryon states.