FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads

Do the quark masses run? Extracting mb(mZ)m_b(m_Z) from LEP data

We present the first results of next-to-leading order QCD corrections to three jet heavy quark production at LEP including mass effects. Among other applications, this calculation can be used to extract the bottom quark mass from LEP data, and therefore to test the running of masses as predicted by QCD.Comment: 6 pages + 2 figures, LaTeX, uses ReVTe

m(b)(m(z)) from jet production at the Z peak in the Cambridge algorithm

We consider the production of heavy quark jets at the Z-pole at the next-to-leading order (NLO) using the {\it Cambridge jet-algorithm}. We study the effects of the quark mass in two- and three-jet observables and the uncertainty due to unknown higher order corrections as well as due to fragmentation. We found that the three-jet observable has remarkably small NLO corrections, which are stable with respect to the change of the renormalization scale, when expressed in terms of the {\it running quark mass} at the mZ-scale. The size of the hadronization uncertainty for this observable remains reasonably small and is very stable with respect to changes in the jet resolution parameter yc

An analytical program for fermion pair production in e+e- annihilation

We describe how to use {\tt ZFITTER}, a program based on a semi-analytical approach to fermion pair production in e^+ e^- annihilation and Bhabha scattering. A flexible treatment of complete {\cal O}(\alpha) QED corrections, also including higher orders, allows for three calculational {\bf chains} with different realistic sets of restrictions in the photon phase space. {\tt ZFITTER} consists of several {\bf branches} with varying assumptions on the underlying hard scattering process. One includes complete {\cal O}(\alpha) weak loop corrections with a resummation of leading higher-order terms. Alternatively, an ansatz inspired from S-matrix theory, or several model-independent effective Born cross sections may be convoluted. The program calculates cross sections, forward-backward asymmetries, and for \tau~pair production also the final-state polarization. Various {\bf interfaces} allow fits to be performed with different sets of free parameters

Search for composite and exotic fermions at LEP 2

A search for unstable heavy fermions with the DELPHI detector at LEP is reported. Sequential and non-canonical leptons, as well as excited leptons and quarks, are considered. The data analysed correspond to an integrated luminosity of about 48 pb^{-1} at an e^+e^- centre-of-mass energy of 183 GeV and about 20 pb^{-1} equally shared between the centre-of-mass energies of 172 GeV and 161 GeV. The search for pair-produced new leptons establishes 95% confidence level mass limits in the region between 70 GeV/c^2 and 90 GeV/c^2, depending on the channel. The search for singly produced excited leptons and quarks establishes upper limits on the ratio of the coupling of the excited fermio

Search for lightest neutralino and stau pair production in light gravitino scenarios with stau NLSP

Promptly decaying lightest neutralinos and long-lived staus are searched for in the context of light gravitino scenarios. It is assumed that the stau is the next to lightest supersymmetric particle (NLSP) and that the lightest neutralino is the next to NLSP (NNLSP). Data collected with the Delphi detector at centre-of-mass energies from 161 to 183 \GeV are analysed. No evidence of the production of these particles is found. Hence, lower mass limits for both kinds of particles are set at 95% C.L.. The mass of gaugino-like neutralinos is found to be greater than 71.5 GeV/c^2. In the search for long-lived stau, masses less than 70.0 to 77.5 \GeVcc are excluded for gravitino masses from 10 to 150 \eVcc . Combining this search with the searches for stable heavy leptons and Minimal Supersymmetric Standard Model staus a lower limit of 68.5 \GeVcc may be set for the stau mas