analysis of high throughput ancient dna sequencing data

... Principles of the Sanger sequencing technology 21 1.6 Principles of pyrosequencing 24 1.7 Principles of the 454 pyrosequencer 25 1.8 Principles of sequencing- by-synthesis ... Tassell et al., 2008) The development of DNA sequencing technologies is briefly reviewed in this section 1.3.1 The Sanger Sequencing Technology One of the first DNA sequencing methods was developed ... Variation xiii LIST OF TABLES xiv ddNTP 2’,3’-dideoxynucleotide DECIPHER Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources DGV Database of Genomic Variants DNA Deoxyribonucleic...

Ngày tải lên: 11/09/2015, 10:01

... use this as an indication of systematic error affecting at least part of the data for that protein An application of this criterion to the subgraph GBP of the data of Krogan et al [11] is shown ... grouping of objects They have two distinct types of nodes, and edges only connect a node of one type to a node of the other For example, the proteins of a biological system could be the nodes of one ... terminology of graphs Undirected graphs An undirected graph consists of a set of nodes V and a set of edges E and is denoted as G = (V,E) Each element of the edge set E is an unordered pair (u,v) of nodes,...

Ngày tải lên: 14/08/2014, 08:20

... networks Bulyk introduced a DNA microarray-based in vitro assay that enables high- throughput characterization of the binding sites for specific transcription factors in DNA and identifies the combinatorial ... the combinatorial co-regulation of certain genes Walhout reported the development of an in vivo yeast one-hybrid system for the high- throughput identification of interactions Volume 8, Issue ... protein-interaction networks and to reveal kinetic aspects of the control of signaling by protein phosphorylation The abundance of high- quality data confirms that quantitative MS is here to stay and...

Ngày tải lên: 14/08/2014, 08:20

... THE GROWTH OF THE HIGH THROUGHPUT SEQUENTIAL AND STRUCTURAL DATA HUGO WILLY B Comp (Hons.), NUS A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN COMPUTER SCIENCE DEPARTMENT OF COMPUTER ... structural data in the PDB database We characterized 452 distinct SLiMs from the Protein Data Bank (PDB), of which 155 are validated by either literature validations or over-representation in high throughput ... interaction data of a single organism (called the interactome) Thus it would be beneficial to have a high confidence set of SLiMs to reduce the number of validations To this end, a number of computational...

Ngày tải lên: 10/09/2015, 15:52

Ngày tải lên: 31/03/2014, 05:21

... and analysis of RT and protease sequences and data from persons infected with non-B HIV-1 subtypes Currently, the workgroup consists of investigators from 15 sites in 13 countries The goal of ... there are insufficient data, even in subtype B HIV-1 Worldwide collaboration, using common data collection instruments and uniform protocols, is essential to the analysis of non-B resistance This ... Journal of the International AIDS Society 2005, 7:71 increasing data on the genotype of B and non-B viruses among drug-naive and -experienced...

Ngày tải lên: 20/06/2014, 08:20

... paired-t test of hypotheses (1) with fcmin = at a FDR level of 20% The second stage of the “Two-stage FDR-CI” algorithm selects Ᏻ2 as a subset of Ᏻ1 at the prescribed FDR-CI level of 20% Stage of the ... populations The data from this experiment fall into the category of a two-way layout [21], where each cell in the layout corresponds to a set of replicates of samples from one of the two populations ... and biological level of significance The statistical level of significance of the test is specified by the false positive rate In contrast, the biological level of significance of the test is specified...

Ngày tải lên: 23/06/2014, 01:20

... sensitive alignment of reads with longer indels to the approximate correct genomic position Results and discussion Local re-alignment of simulated data Local re-alignment of empirical data To assess ... observed indels within the sequencing data and indels reported in dbSNP The discordance rate of indels is inflated due to the lack of completeness within the variant databases, as well as artifacts ... assumed DNA microarray error rate, thus limiting further utility of this type of comparison The variant calls of SRMA are improved genome-wide by SRMA, and several dramatic examples of sequence...

Ngày tải lên: 09/08/2014, 22:23

... efficiency of translation and hence overall expression of the gene product It functions by slowing down the rate of scanning by the ribosome and improving the chance of it recognising the start of translation ... HSA-gene Figure format of the vectors used in the study Linearized Linearized format of the vectors used in the study G1: pcDNA3.1/GS-HSA, H1: pcDNA3.1/V5-His+HSA, H2: pcDNA3.1/V5-His+HSA with ... using Lipofectamine 2000, cultured for 48 h, harvested and applied to Western blot Control (C) cells treated the same way without DNA HSA vectors: pcDNA3.1/GS (G1), pcDNA3.1/V5-His (H1), pcDNA3.1/V5-His...

Ngày tải lên: 12/08/2014, 18:22

... of onset of asthma or amount of maintenance therapy), management, ventilation strategies, complications and detailed evolution of the condition within the ICU stay are not collected as part of ... in the ICU were excluded from calculation of Acute Physiology Score and APACHE II score Data A history of steroid treatment was defined as the receipt of at least 0.3 mg/kg per day prednisolone ... length of stay was 1.5 days in the ICU and days in hospital Referrals from other hospitals accounted for 11.8% of admissions, and 2.3% of admissions were identified as being readmissions of the...

Ngày tải lên: 12/08/2014, 20:20

... Relationship of case mix factors with ultimate hospital mortality Table presents the results of the multiple logistic regression analysis of case mix factors on ultimate hospital mortality in the group of ... Survival data were extracted at discharge from the CMP unit and at ultimate discharge from hospital Activity Length of stay in ICU was calculated in fractions of days from the dates and times of admission ... with number of organ system failures (Table 3) It was higher in patients requiring chronic renal dialysis, particularly at low numbers of organ system failures Case mix adjusted effect of chronic...

Ngày tải lên: 13/08/2014, 03:21

... is enhanced by the number of units contributing data The CMPD is recognised to be of high quality, meaning that the data used in this study are reliable Limitations of the study The CMPD was ... factors, 70.2% of intubated patients died compared with 45.3% of nonintubated patients Two thousand eight hundred admissions were included in the subgroup analysis of the effect of diagnosis on ... Calibration plot of SAPS II, APACHE II and ICNARC physiology scores scores A comparison of the goodness -of- fit of the SAPS II, APACHE II and ICNARC physiology scores Strengths of the study The...

Ngày tải lên: 13/08/2014, 18:22

... the time of the publication of the review in [1.1] Historically, the performance of the voltage-source inverter was essentially ignored because of poor load regulation, slow turn-off time of the ... representing the underlying physical structure of the system, is often sufficient for off-line simulation of highly complex non-linear systems ANFIS uses a combination of neural networks and fuzzy logic ... current injection High efficiency, high power factor, low THD at input supply, and ripple-free dc output of high quality are obtainable with these converters 41 Nam Nguyen-Quang High- frequency matrix...

Ngày tải lên: 13/11/2014, 06:49

... methods for comparison and analysis of these high- dimensional datasets, especially among a large group of subjects There remain several challenges in using HARDI-based brain analysis across populations ... failure of the mapping Thus, one of the fundamental limitations of choosing the anatomy of a single subject as an atlas is the introduction of a statistical bias based on the arbitrary choice of the ... 21 3.1 The role of Chapter in the ODF-based analysis framework 24 3.2 Illustration of affine transformation on square-root ODFs (Similar to the shape of ODF, the colors of ODF also indices...

Ngày tải lên: 08/09/2015, 19:24

... as atlas, Iatlas , the space of the initial momentum m0 , provides a linear representation of the nonlinear diffeomorphic shape space in which linear statistical analysis can be applied 21 BACKGROUND ... maps, are available in closed form, as illustrated in Figure 2.1 Figure 2.1: Illustration of the manifold of square-root ODFs (picture token and modified from [1])) √ The square-root ODF ( ODF) is ... non-negative to ensure uniqueness The space of such functions is defined as Ψ = {ψ : S2 → R+ |∀s ∈ S2 , ψ(s) ≥ 0; 16 s∈S2 ψ (s)ds = 1} (2.1) 2.1 Riemannian Manifold of ODFs We see that from Eq (2.1), the...

Ngày tải lên: 08/09/2015, 19:26

... CST-right), using 50 3.5 HARDI Data of Children Brains Figure 3.8: Panels (a-d) show the maps of mean squared error of spherical harmonics coefficients (MSE of SH) of the ODFs between the template ... generation and group analysis of HARDI for a variety of clinical studies 55 DIFFEOMORPHIC METRIC MAPPING OF HIGH ANGULAR RESOLUTION DIFFUSION IMAGING BASED ON RIEMANNIAN STRUCTURE OF ORIENTATION DISTRIBUTION ... (Similar to the shape of ODF, the colors of ODF also indices the relative values of ODF in each direction, where blue stands for low ODF value and red for high value.) First of all, we denote s...

Ngày tải lên: 08/09/2015, 19:27

... ESTIMATION OF WHITE MATTER ATLAS FROM HIGH ANGULAR RESOLUTION DIFFUSION IMAGING a shape prior of the white matter anatomy and the likelihood of individual observed HARDI datasets First of all, we ... Conditional Likelihood of the ODF Data In this section, we will derive the construction of the conditional likelihood of the ODF data fσ (J (i) |φ(i) , φ, I0 ) From the field of information geometry ... a Riemannian structure of the ODFs 62 4.2 The Shape Prior of the Atlas and the Distribution of Random Diffeomorphisms Figure 4.2: Illustration of the general framework of the Bayesian HARDI atlas...

Ngày tải lên: 08/09/2015, 19:27

... for each row Under one type of ODF ¯ metrics of that row, the mean variance of synthetic data, M SE(ψi , ψ); the mean squared of the geodesic regression are ˆ residuals of the geodesic regression, ... this experiment, the higher level of noise, the larger the mean variance of the synthetic data (see the first column) From the results, 98 5.2 Experiments Figure 5.6: Consistency of results under ... geodesic explains a small portion of the variance of the synthetic data This finding is expected due to the noise being large (for M ≥ 0.5) and high- dimensionality of the underlying space However,...

Ngày tải lên: 08/09/2015, 19:27

... the shape prior of the HARDI atlas can be modeled using a centered Gaussian random field (GRF) model of the initial momentum In order to construct the likelihood of observed HARDI datasets, it is ... is a lack of fundamental image analysis tools, such as registration, that can fully utilize their information Our future work will also include the extension of our framework to HDYI dataset 114 ... Registration of 3D Tensor Medical Data Medical Image Analysis, 6(2):143–161, 2002 [17] H UI Z HANG , PAUL A Y USHKEVICH , DANIEL C A LEXANDER , AND JAMES C G EE Deformable registration of diffusion...

Ngày tải lên: 08/09/2015, 19:27

... from S pombe 2.2.4 Preparation of A tumefaciens genomic DNA 2.2.5 Preparation of S pombe genomic DNA 2.2.6 Preperation of S cerevisiae genomic DNA 2.3 Analysis of potential integrant into the ... T -DNA extraction and analysis Fig 3.7 Border analysis of S pombe transformants Fig 3.8 Comparison of S pombe binary vectors Fig 3.9 Comparison of S pombe and binary vectors Fig 3.10 Affect of ... Construction of pUPT301 Fig 3.2 Construction of pAPT301 Fig 3.3 Construction of pLPT19 Fig 3.4 Development of a method for Agrobacterium-mediated transformation of S pombe Fig 3.5 Transformation of S...

Ngày tải lên: 12/09/2015, 08:20