analysis of high throughput ancient dna sequencing data

... Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data Tianyu Wang1, Boyang Li2, Craig E Nelson3 and Sheida Nabavi4* Abstract Background: The analysis of ... RNAseq data Data multimodality and abundance of zero read counts are the main characteristics of scRNAseq data, which play important roles in the performance of differential gene expression analysis ... data, three of which are for bulk RNAseq data analysis Miao et al [41] evaluated 14 differential expression analysis tools, three of which are newly developed for scRNAseq data and 11 of which are

Ngày tải lên: 25/11/2020, 13:14

... Varsani et al.: Analysis of high- time-resolution observations of an FTE Sonnerup, B U Ö and Scheible, M.: Minimum and maximum variance analysis, in: Analysis Methods for Multi-Spacecraft Data, edited ... 1096 A Varsani et al.: Analysis of high- time-resolution observations of an FTE Figure Position of Cluster and Geotail in GSE and LMN coordinates Top three panels: the location of the Cluster spacecraft ... observations of two distinguishable populations of electrons: (i) those in a relatively wide band of energy (30 eV to ∼ keV) but Ann Geophys., 32, 1093–1117, 2014 1102 A Varsani et al.: Analysis of high- time-resolution

Ngày tải lên: 01/11/2022, 09:12

... ANALYSIS OF ADAPTIVE RESPONSE TO DNA DAMAGE CHECKPOINT INDUCED ARREST YIO WEE KHENG NATIONAL UNIVERSITY OF SINGAPORE 2009 ANALYSIS OF ADAPTIVE RESPONSE TO DNA DAMAGE CHECKPOINT ... with the initiating ssDNA, resulting in the extension of the initial DNA joint This process is termed "DNA strand exchange" or "DNA branch migration" The extent of DNA branch migration ... ectopic expression of Cdc5 84 4.2.4 High level of Cdc5 inhibits Ddc2 foci formation 87 4.2.5 Cdc5 inhibits formation of Ddc2 foci assembled at the site of DNA damage 93 4.2.6

Ngày tải lên: 14/09/2015, 08:23

... GENETIC ANALYSIS OF THE TRANSCRIPTIONAL REGULATORY DNA OF THE OXYTOCIN AND VASOPRESSIN GENES Patrick Gilligan (M.Sc. University of Waikato) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY ... expression of a cDNA encoding the human V1b vasopressin receptor. J Biol Chem 269, 27088-27092. Suzuki, M., Kubokawa, K., Nagasawa, H., and Urano, A. (1995) Sequence analysis of vasotocin cDNAs of the ... alignment of sequences 3’ of the mouse and human oxytocin polyA signals 92 5.2 The alignment of sequence 3’ of the mouse and human vasopressin polyA signals 93 5.3 Apparent “blocks” of contiguous

Ngày tải lên: 15/09/2015, 22:13

... -III- Table of Contents Table of Contents SUMMARY I ACKNOWLEDGEMENTS III TABLE OF CONTENTS IV LIST OF SYMBOLS VIII LIST OF TABLES XIII LIST OF FIGURES XIV LIST OF ACRONYMS XXI ... high- speed transmission needs of chips despite further scaling of feature sizes [1] 1.1.1.2 High- Speed Interconnect Effects The term, high- speed, is usually defined in terms of ... be common for high speed or high frequencies Therefore, the research in this thesis will focus on developing numerical methods for the electrical analysis of high- speed interconnects

Ngày tải lên: 16/09/2015, 15:55

... (i)) Thus, the result of Part B is immediate. (4.27) Chapter 4 Analysis of the Data Allocation Algorithm With Finite-size Buffers 53 The usefulness of proof of Part B of Lemma 1 is identical ... proof of Theorem 3, we follow the same analysis as we did in the proof of Theorem 2 and prove the following lemma before we realize the result of the theorem. Similarly, we split the proof of ... part of control-message cost with m · np (1) · Cc in the proof of Part A of Lemma 2, where np (1) is the number of different reading processors of ψo (1) which are not in IAo (1). Proof of Part

Ngày tải lên: 04/10/2015, 10:24

... personal use only Analysis of High- Speed Rail irregularity of wavelength of m is considered for all cases Note that “Irregularity 1” pertains to that of a near smooth track The degree of track irregularity ... alternative to other modes of transportation for long distance travel Due to the high speed of train moving over the track, the chance of occurrence of the “jumping wheel” phenomenon is high in particular ... 05/07/15 For personal use only Analysis of High- Speed Rail Fig Effect of foundation stiffness ratio on contact force transition of stiffness ratio For a larger stiffness ratio of 16, the phenomenon is

Ngày tải lên: 16/12/2017, 04:55

... Access Comparing very low birth weight versus very low gestation cohort methods for outcome analysis of high risk preterm infants Louise IM Koller-Smith1, Prakesh S Shah2,3, Xiang Y Ye3, Gunnar ... Wang1, Sharon S W Chow1, Brian A Darlow5, Shoo K Lee2,3, Stellan Håkanson6, Kei Lui1,7*, on behalf of the Australian and New Zealand Neonatal Network, Canadian Neonatal Network and Swedish Neonatal

Ngày tải lên: 20/02/2020, 22:20

... suitable for the analysis of high- throughput sequencing data and compared their performance to identify the best software Using a simulated test set of Illumina reads and a set of artificial isomiRs, ... suitable for smaller datasets or the selected analysis of a few miRNAs In contrast, isomiR-SEA gained a low score overall, but it allows the analysis of diverse mutations in large datasets because ... next generation sequencing data Results: We compared the performance of isomiRID, isomiR-SEA and miraligner using simulated Illumina HiSeq2000 and MiSeq data to test the impact of technical errors

Ngày tải lên: 25/11/2020, 17:15

... methylation profile is now available in the form of count-based data, with which it is often of interests to study the dynamics at epitranscriptomic layer However, the sample size of RNA methylation ... to be of crucial biological significance [16] Previously, there have been a number of computational approaches developed for differential methylation analysis of DNA [17–22] Similar to DNA methylation, ... amount of methylation and the relative amount, which calls for a precise estimation of the basal background and makes it different from the differential analysis of DNA methylation or DNAprotein

Ngày tải lên: 25/11/2020, 17:24

... odds of IPV [9, 31, 32] Study in Canada and Zimbabwe show that a high socio-economic status evidenced by a level of education and wealth is protective against IPV [5–7, 33] A high level of education ... Disability status, partner behavior, and the risk of sexual intimate partner violence in Uganda: An analysis of the demographic and health survey data Betty Kwagala1* and Johnstone Galande2 Abstract ... levels of education [6, 34] Relational or interpersonal factors are central to the analysis of risk factors for sexual IPV Partner-related characteristics were found to be strong predictors of IPV

Ngày tải lên: 31/10/2022, 03:36

... Elements, and Contact Analysis Methods in the Analysis of High Concrete-Faced Rockfill Dams Xiao-xiang Qian, Hui-na Yuan, Quan-ming Li, and Bing-yin Zhang State Key Laboratory of Hydroscience and ... comparison of different interface analysis methods through the analysis of stress and displacement distributions near the interface in the Tianshengqiao-I CFRD project The accuracy and limitations of ... Separation of the stage-I slab (b) Separation of the stage-II slab Figure 12: Separation of the slab from the cushion layer at different stages (contact analysis method) Table 4: Parameters of the

Ngày tải lên: 01/11/2022, 09:06

... Energy and Exergy Analysis of High Temperature Agent Gasification of Biomass Yueshi Wu *, Weihong Yang and Wlodzimierz Blasiak Division of Energy and Furnace Technology, Department of Material Science ... diameter of 0.008 m and an average ratio of length/diameter, l/d, of The properties of the feedstock are shown in Table The feedstock was supplied and analyzed by an external supplier, Booforssjö ... exergy Introduction As one of the most promising technologies for the thermochemical conversion of biomass fuels, high temperature agent gasification (HTAG) using highly preheated oxidizing agents

Ngày tải lên: 02/11/2022, 09:22

... 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

... 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

... 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

... 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