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Search Results: 1 - 10 of 503757 matches for " David A Nix "
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GATA: a graphic alignment tool for comparative sequence analysis
David A Nix, Michael B Eisen
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-9
Abstract: To address some of these issues, we created a stand alone, platform independent, graphic alignment tool for comparative sequence analysis (GATA http://gata.sourceforge.net/ webcite). GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF) file.GATA uses the NCBI-BLASTN program in conjunction with post-processing to exhaustively align two DNA sequences. It provides researchers with a fine-grained alignment and visualization tool aptly suited for non-coding, 0–200 kb, pairwise, sequence analysis. It functions independent of sequence feature ordering or orientation, and readily visualizes both large and small sequence inversions, duplications, and segment shuffling. Since the alignment is visual and does not contain gaps, gene annotation can be added to both sequences to create a thoroughly descriptive picture of DNA conservation that is well suited for comparative sequence analysis.The most widely used methods for aligning DNA sequences rely on dynamic programming algorithms initially developed by Smith-Waterman and Needleman-Wunsch [1,2]. These algorithms create the mathematically best possible alignment of two sequences by inserting gaps in either sequence to maximize the score of base pair matches and minimize penalties for base pair mismatches and sequence gaps. Although these methods have proven invaluable in understanding sequence conservation and gene relatedness, they make several assumptions. One of their assumptions in generating the "best" alignment is that sequence features are collinear. For
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
David A Nix, Samir J Courdy, Kenneth M Boucher
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-523
Abstract: Here we present a package of algorithms and software that makes use of control input data to reduce false positives and estimate confidence in ChIP-Seq peaks. Several different methods were compared using two simulated spike-in datasets. Use of control input data and a normalized difference score were found to more than double the recovery of ChIP-Seq peaks at a 5% false discovery rate (FDR). Moreover, both a binomial p-value/q-value and an empirical FDR were found to predict the true FDR within 2–3 fold and are more reliable estimators of confidence than a global Poisson p-value. These methods were then used to reanalyze Johnson et al.'s neuron-restrictive silencer factor (NRSF) ChIP-Seq data without relying on extensive qPCR validated NRSF sites and the presence of NRSF binding motifs for setting thresholds.The methods developed and tested here show considerable promise for reducing false positives and estimating confidence in ChIP-Seq data without any prior knowledge of the chIP target. They are part of a larger open source package freely available from http://useq.sourceforge.net/ webcite.Chromatin immunoprecipitation (chIP) is a well-characterized technique for enriching regions of DNA that are marked with a modification (e.g. methylation), display a particular structure (e.g. DNase hypersensitivity), or are bound by a protein (e.g. transcription factor, polymerase, modified histone), in vivo, across an entire genome [1]. Chromatin is typically prepared by fixing live cells with a DNA-protein cross-linker, lysing the cells, and randomly fragmenting the DNA. An antibody that selectively binds the target of interest is then used to immunoprecipitate the target and any associated nucleic acid. The cross-linker is then reversed and DNA fragments of approximately 200–500 bp in size are isolated. The final chIP DNA sample contains primarily background input DNA plus a small amount (<1%) of additional immunoprecipitated target DNA.Several methods have been used to ide
Flexible promoter architecture requirements for coactivator recruitment
Derek Y Chiang, David A Nix, Ryan K Shultzaberger, Audrey P Gasch, Michael B Eisen
BMC Molecular Biology , 2006, DOI: 10.1186/1471-2199-7-16
Abstract: A Cbf1 binding site was required upstream of a Met31/32 binding site for full reporter gene expression. Distance constraints on coactivator recruitment were more flexible than those for cooperatively binding transcription factors. Distances from 18 to 50 bp between binding sites support efficient recruitment of Met4, with only slight modulation by helical phasing. Intriguingly, we found that certain sequences located between the binding sites abolished gene expression.These results yield insight to the influence of both binding site architecture and local DNA flexibility on gene expression, and can be used to refine computational predictions of gene expression from promoter sequences. In addition, our approach can be applied to survey promoter architecture requirements for arbitrary combinations of transcription factor binding sites.In most eukaryotes, the sequences that regulate transcription integrate multiple signals, through the binding of different transcription factors, to modulate levels of gene expression. When bound to DNA, transcription factors anchor the assembly of multiprotein complexes that influence the recruitment of RNA polymerase. Efficient assembly depends on optimally spaced protein-protein interactions among transcription factors and auxiliary proteins [1-4]. Since transcription factors recognize specific sites on DNA, the distance between these binding sites can influence how transcription factors interact with each other and other proteins. For example, overlapping sites may prevent two transcription factors from binding simultaneously, while sites too distant from each other may hinder bound transcription factors from recruiting necessary cofactors. Furthermore, some distantly spaced sites can only properly interact when the DNA between them is looped, a process influenced by the composition of the looped DNA.Computational approaches take into account the multifactorial nature of transcriptional regulation when discovering transcription facto
ENCODE Tiling Array Analysis Identifies Differentially Expressed Annotated and Novel 5′ Capped RNAs in Hepatitis C Infected Liver
Milan E. Folkers,Don A. Delker,Christopher I. Maxwell,Cassie A. Nelson,Jason J. Schwartz,David A. Nix,Curt H. Hagedorn
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014697
Abstract: Microarray studies of chronic hepatitis C infection have provided valuable information regarding the host response to viral infection. However, recent studies of the human transcriptome indicate pervasive transcription in previously unannotated regions of the genome and that many RNA transcripts have short or lack 3′ poly(A) ends. We hypothesized that using ENCODE tiling arrays (1% of the genome) in combination with affinity purifying Pol II RNAs by their unique 5′ m7GpppN cap would identify previously undescribed annotated and unannotated genes that are differentially expressed in liver during hepatitis C virus (HCV) infection. Both 5′-capped and poly(A)+ populations of RNA were analyzed using ENCODE tiling arrays. Sixty-four annotated genes were significantly increased in HCV cirrhotic as compared to control liver; twenty-seven (42%) of these genes were identified only by analyzing 5′ capped RNA. Thirty-one annotated genes were significantly decreased; sixteen (50%) of these were identified only by analyzing 5′ capped RNA. Bioinformatic analysis showed that capped RNA produced more consistent results, provided a more extensive expression profile of intronic regions and identified upregulated Pol II transcriptionally active regions in unannotated areas of the genome in HCV cirrhotic liver. Two of these regions were verified by PCR and RACE analysis. qPCR analysis of liver biopsy specimens demonstrated that these unannotated transcripts, as well as IRF1, TRIM22 and MET, were also upregulated in hepatitis C with mild inflammation and no fibrosis. The analysis of 5′ capped RNA in combination with ENCODE tiling arrays provides additional gene expression information and identifies novel upregulated Pol II transcripts not previously described in HCV infected liver. This approach, particularly when combined with new RNA sequencing technologies, should also be useful in further defining Pol II transcripts differentially regulated in specific disease states and in studying RNAs regulated by changes in pre-mRNA splicing or 3′ polyadenylation status.
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
Alan M Moses,Daniel A Pollard,David A Nix,Venky N Iyer,Xiao-Yong Li,Mark D Biggin,Michael B Eisen
PLOS Computational Biology , 2006, DOI: 10.1371/journal.pcbi.0020130
Abstract: The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an evolutionary model to study binding-site turnover that uses multiple sequence alignments to assess the evolutionary constraint on individual binding sites, and to map gain and loss events along a phylogenetic tree. We apply this model to study the evolutionary dynamics of binding sites of the Drosophila melanogaster transcription factor Zeste, using genome-wide in vivo (ChIP–chip) binding data to identify functional Zeste binding sites, and the genome sequences of D. melanogaster, D. simulans, D. erecta, and D. yakuba to study their evolution. We estimate that more than 5% of functional Zeste binding sites in D. melanogaster were gained along the D. melanogaster lineage or lost along one of the other lineages. We find that Zeste-bound regions have a reduced rate of binding-site loss and an increased rate of binding-site gain relative to flanking sequences. Finally, we show that binding-site gains and losses are asymmetrically distributed with respect to D. melanogaster, consistent with lineage-specific acquisition and loss of Zeste-responsive regulatory elements.
Next generation tools for genomic data generation, distribution, and visualization
David A Nix, Tonya L Di Sera, Brian K Dalley, Brett A Milash, Robert M Cundick, Kevin S Quinn, Samir J Courdy
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-455
Abstract: Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser.These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/ webcite, http://sourceforge.net/projects/genoviz/ webcite, and http://sourceforge.net/projects/useq webcite.The post-genomic era holds many promises for addressing fundamental questions regarding biology and improving patient outcome through personalized medicine. It also presents several unique challenges that need to be addressed to maximize the effectiveness of using genomic data in the laboratory and clinic. One key issue is the exponential growth in the number, size, and complexity of datasets generated from genomic experiments. The bottleneck is less the cost and difficulty of generating the data but, more so, efficiently managing, analyzing, and distributing it. Here, we present three, open source, platform independent, software tools that we have developed to address each of th
Effects of Syngas Particulate Fly Ash Deposition on the Mechanical Properties of Thermal Barrier Coatings on Simulated Film-Cooled Turbine Vane Components  [PDF]
Kevin Luo, Andrew C. Nix, Bruce S. Kang, Dumbi A. Otunyo
International Journal of Clean Coal and Energy (IJCCE) , 2014, DOI: 10.4236/ijcce.2014.34006
Abstract: Research is being conducted to study the effects of particulate deposition from contaminants in coal synthesis gas (syngas) on the mechanical properties of thermal barrier coatings (TBC) employed on integrated gasification combined cycle (IGCC) turbine hot section airfoils. West Virginia University (WVU) had been working with US Department of Energy, National Energy Technology Laboratory (NETL) to simulate deposition on the pressure side of an IGCC turbine first stage vane. To model the deposition, coal fly ash was injected into the flow of a combustor facility and deposited onto TBC coated, angled film-cooled test articles in a high pressure (approximately 4 atm) and a high temperature (1560 K) environment. To investigate the interaction between the deposition and the TBC, a load-based multiple-partial unloading micro-indentation technique was used to quantitatively evaluate the mechanical properties of materials. The indentation results showed the Young’s Modulus of the ceramic top coat was higher in areas with deposition formation due to the penetration of the fly ash. This corresponds with the reduction of strain tolerance of the 7% yttria-stabilized zirconia (7YSZ) coatings.
First search for $K_{L}\toπ^{0}π^{0}ν\barν$
J. Nix,for the E391a Collaboration
Physics , 2007, DOI: 10.1103/PhysRevD.76.011101
Abstract: The first search for the rare kaon decay $\kppnn$ has been performed by the E391a collaboration at the KEK 12-GeV proton synchrotron. An upper limit of $4.7\times10^{-5}$ at the 90 % confidence level was set for the branching ratio of the decay $\kppnn$ using about 10 % of the data collected during the first period of data taking. First limits for the decay mode $\kppP$, where $P$ is a pseudoscalar particle, were also set.
ARQ-Aware Scheduling and Link Adaptation for Video Transmission over Mobile Broadband Networks
Victoria Sgardoni,David R. Bull,Andrew R. Nix
Journal of Computer Networks and Communications , 2012, DOI: 10.1155/2012/369803
Abstract: This paper studies the effect of ARQ retransmissions on packet error rate, delay, and jitter at the application layer for a real-time video transmission at 1.03?Mbps over a mobile broadband network. The effect of time-correlated channel errors for various Mobile Station (MS) velocities is evaluated. In the context of mobile WiMAX, the role of the ARQ Retry Timeout parameter and the maximum number of ARQ retransmissions is taken into account. ARQ-aware and channel-aware scheduling is assumed in order to allocate adequate resources according to the level of packet error rate and the number of ARQ retransmissions required. A novel metric, namely, goodput per frame, is proposed as a measure of transmission efficiency. Results show that to attain quasi error free transmission and low jitter (for real-time video QoS), only QPSK 1/2 can be used at mean channel SNR values between 12?dB and 16?dB, while 16QAM 1/2 can be used below 20?dB at walking speeds. However, these modes are shown to result in low transmission efficiency, attaining, for example, a total goodput of 3?Mbps at an SNR of 14?dB, for a block lifetime of 90?ms. It is shown that ARQ retransmissions are more effective at higher MS speeds. 1. Introduction Mobile WiMAX (IEEE 802.16e) [1] and 3GPP LTE (Long-Term Evolution) [2] represent mobile broadband standards that offer high user data rates and support for bandwidth hungry video applications. Both standards use very similar PHY and MAC layer techniques, especially for downlink (DL) transmission. In order to provide strong QoS, cross-layer adaptive strategies must be implemented in the wireless network [3, 4]. Video applications demand a low Packet Error Rate (PER), which may be achieved via the use of MAC layer Automatic Repeat ReQuest (ARQ) and the choice of suitable Modulation and Coding Schemes (MCS). However, ARQ consumes additional bandwidth and causes increased end-to-end latency and jitter. ARQ is controlled in the MAC layer by the block lifetime and ARQ Retry Timer parameters, which define how many and how frequently retransmissions may occur. Link adaptation is used in mobile broadband networks to improve the PER by matching the QAM constellation and forward error correction coding rate to the time varying channel quality. The impact of specific ARQ parameters and mechanisms has been extensively studied in the literature, for example, [5–9]. In [8], the authors analyze delay and throughput using probabilistic PHY layer error modelling. In [9], packet errors were modelled as an uncorrelated process in time. Often packet errors are modelled
Distortion-Based Link Adaptation for Wireless Video Transmission
Pierre Ferré,James Chung-How,David Bull,Andrew Nix
EURASIP Journal on Advances in Signal Processing , 2008, DOI: 10.1155/2008/253706
Abstract: Wireless local area networks (WLANs) such as IEEE 802.11a/g utilise numerous transmission modes, each providing different throughputs and reliability levels. Most link adaptation algorithms proposed in the literature (i) maximise the error-free data throughput, (ii) do not take into account the content of the data stream, and (iii) rely strongly on the use of ARQ. Low-latency applications, such as real-time video transmission, do not permit large numbers of retransmission. In this paper, a novel link adaptation scheme is presented that improves the quality of service (QoS) for video transmission. Rather than maximising the error-free throughput, our scheme minimises the video distortion of the received sequence. With the use of simple and local rate distortion measures and end-to-end distortion models at the video encoder, the proposed scheme estimates the received video distortion at the current transmission rate, as well as on the adjacent lower and higher rates. This allows the system to select the link-speed which offers the lowest distortion and to adapt to the channel conditions. Simulation results are presented using the MPEG-4/AVC H.264 video compression standard over IEEE 802.11g. The results show that the proposed system closely follows the optimum theoretic solution.
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