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Jan Voges - Compression of DNA Sequencing Data

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Jan Voges

Compression of DNA Sequencing Data

Series: Informatik/ Kommunikation

Volume 878 2022

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Introduction S. 1-11

„… development of compres-sion technology that facilitates scalable DNA sequencing data storage,transmission, and …” „… the use of high-performance compression techniquesspecifically designed for HTS data.Viewed from …” „… enable the widespreadadoption of compression technologies to democratize the use of DNAsequencing data …”

Conclusions S. 129-132

„… compression technologies that facilitate scalableDNA sequencing data storage, transmission, and processing.In …” „… and bioinformatics to data compression. Withregard to data compression, we put a special emphasis on …” „… investigated entropy coding methods in the contextof compression of DNA sequencing data. We reviewed the state …”

Publications S. 153-166

„… reference-based compression of FASTQ data.” In:BMC Bioinformatics 16.1 (2015), p. 188. doi: 10.1186/s …” „… 12859-015-0628-7.[ZL77] J. Ziv and A. Lempel. “A universal algorithm for sequen-tial data compression.” In: IEEE …” „… . Sahinalp. “Comparisonof high-throughput sequencing data compression tools.” In:Nature Methods 13.12 (2016 …”

Entropy Coding of DNA Sequencing Data S. 91-111

„… data compression,we conceived a well-grounded experiment setup, which we lay out inSection 5.3. We …” „… GABAC in typical DNAsequencing data compression scenarios. Therefore, to simulate such ascenario, and to …” „… the compres-sion of DNA sequencing data. The development of GABAC overlappedtemporally with the …”

Compression of Aligned Reads S. 45-60

„… corresponding Section 3.1.3.3.1.1 Genome CompressionThe first DNA-related compression tools aimed at the …” „… only 1 MB.463.1 state of the art and contribution3.1.2 Read CompressionThe compression of reads differs …” „… the actual compression.While read compression tools are focused on the efficient compression ofthe …”

Bibliography S. 133-152

„… Compression.”In: 2007 Data Compression Conference (DCC). 2007, pp. 43–52.doi: 10.1109/DCC.2007.7.[Dud14] J. Duda …” „… /bioinformatics/btu390.[BM13] J. K. Bonfield and M. V. Mahoney. “Compression of FASTQand SAM Format Sequencing Data …” „… .” In: 2016 DataCompression Conference (DCC). 2016, pp. 261–270. doi: 10.1109/DCC.2016.49.[Her+19] M …”

Titelei/Inhaltsverzeichnis S. I-XVIII

„… INFORMATIK/KOMMUNIKATIONVogesCompression of DNA Sequencing DataREIHE 10 | NR. 878ISBN 987-3-18-387810-9 E-ISBN 978-3-18-687810-6Institut …” „… _Reihe_10_878_Cover.pdf · Seite 222Compression of DNA Sequencing DataVon der Fakultät für Elektrotechnik …” „… . Dr.-Ing. Bodo RosenhahnTag der Promotion: 13. Mai 2022Compression of DNA Sequencing DataDipl.-Ing. Jan …”

Preliminaries S. 12-44

„… 24, which is essentially a collectionof offsets into the BGZF file.2.4 data compressionData …” „… ”) information.242.4 data compressionThe performance of different compression methods can be analyzedacross three …” „… ). Its positivesquare root is the standard deviation σx.282.4 data compressionThe covariance provides …”

Standards and Implementations S. 112-128

„… sequencing data compression:the SequenceSqueeze contest [BM13].Furthermore, the WHO Expert Committee on …” „… data needs to be transmitted to a remotedevice “on-the-fly”.• High compression: High compression is …” „… avail-ability of the entire data, as well as some preprocessing steps thatmay affect compression latency. It is …”

Compression of Quality Scores S. 61-90

„… amount of loss that can be accepted after reconstruction of the data,and the compression that can be …” „… shows the details of the selected data. Following the approach81compression of quality scoresof [Och+17 …” „… compressionis already included, in contrast to Crumble and Quartz. With QVZ2 weperformed the compression for the …”

doi.org/10.51202/9783186878106

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VDI Wissensforum GmbH (ed.)

Automation 2021

Series: VDI-Berichte

Volume 2392 2021

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I. Amihai, R. Gitzel, A. Boyaci Compression and Fault Diagnosis of High Frequency Sensor Data S. 545-556

„… Compression and Fault Diagnosis of High Frequency Sensor Data Dr. I. Amihai, Dr. R. Gitzel …” „… relevant for high-dimensional data. In this paper, we tested several dimensionality reduction methods to …” „… . enabled better compression of the acceleration signals. Secondly, we used the best performing model to …”

Titelei/Inhaltsverzeichnis S. I-XVI

„… publication in the Deutsche Nationalbibliographie (German National Bibliography); detailed bibliographic data …” „… Künstliche Intelligenz & Autonome Systeme – Datenanalyse Compression and Fault Diagnosis of High Frequency …” „… Sensor Data . . . . . . . . . . . . . . . . . . . 545 I. Amihai, R. Gitzel, A. Boyaci …”

doi.org/10.51202/9783181023921

VDI Wissensforum GmbH - 28. Deutscher Flammentag

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VDI Wissensforum GmbH (ed.)

28. Deutscher Flammentag

Series: VDI-Berichte

Volume 2302 2017

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C.-P. Ding, A. Renaud, R. Honza, A. Dreizler, B. Böhm Characterization of near-wall flows in a SI engine using high-speed PIV and high-resolution PI S. 345-356

„… the density changes during the compression stroke. The quality of the data provides new opportunities …” „… compression-ignition engines--understanding the incylinder processes,’’ Proceedings of the Combustion Institute, vol …” „… boundary layer impacts heat loss [1, 2] and, in case of compression ignition engines, ignition timing [3 …”

doi.org/10.51202/9783181023020

Christian Woitzik - Experimental testing and numerical simulation of granules as crash absorber for double hull structures

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Christian Woitzik

Experimental testing and numerical simulation of granules as crash absorber for double hull structures

Series: Mechanik/Bruchmechanik

Volume 356 2021

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Determination of bulk particle properties S. 40-63

„… model with experimental data up to 10% compression. Material hs n ϕ α β ed0 ei0 ec0 [ MPa …” „… is performed to adjust the material parameters with respect to compression ratios for the uniaxial …” „… compression used in the previous chapter for the selection of granules. In this inverse problem, the …”

Selection of granules and description of single grains S. 24-39

„… detail. In doing so, particle parameters are determined using a single particle compression test …” „… compression test is used to break down the selection to one granular material of primary interest. The setup …” „… is shown in Figure 3.1. The particles of interest are subjected to a uniaxial compression load in a …”

Introduction S. 1-5

„… tests are required to gather data for numerical modelling and verification. The modelling on particle …” „… breakage behaviour of granules, compression tests are performed for single grains. Based on this, a …” „… setting with higher compression ratios. On the other hand, the parameters for the collision scenario are …”

Numerical investigation S. 88-112

„… , the optimization process governing the material parameters using only the uniaxial compression data is …” „… resolution is favourable for comparisons with experimental data. The initial model used for the calculations …” „… is shown in Figure 6.1. This model has been used to design the experimental setup with material data …”

Titelei/Inhaltsverzeichnis S. I-VIII

„… Nationalbibliographie (German National Bibliography); detailed bibliographic data is available via Internet at …” „… test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 4.4 Uniaxial compression …” „… , triaxial test, and friction test are performed. This test data is used to calibrate and validate the …”

Bibliography S. 119-136

„… , A. Levy, H. Kalman, S. Aman, J. Tomas, Strength distribution of particles under compression, Powder …” „… of elastic properties of particles using single particle compression test, Powder Technology 268 (1 …” „… .2018.02.022. [70] Z. Wang, G. Wang, Q. Ye, A constitutive model for crushable sands involving compression and …”

Experimental investigation S. 64-87

„… results from the uniaxial compression test – see Section 70 5.2 Experiments without stiffener Figure 5.10 …” „… additional layer. Compared to the uniaxial compression test in Section 4.4.2, an almost vertical slope can be …” „… seen in the high compression region – as shown in Figure 3.2. The chosen setup – allowing movement in …”

Constitutive equations and numerical implementation S. 6-23

„… parameter e describing the out-of-roundness between the extension meridian and the compression meridian, see …” „… by compression tests. The friction angle ϕ, dilatancy angle ψ, and cohesion parameter c can be …” „… identified using triaxial compression tests with different confining pressures [61] using the resulting …”

doi.org/10.51202/9783186356185

Manuel Dahmen - Model-Based Design of Pure and Multicomponent Cellulosic Biofuels for Advanced Engine Concepts

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Manuel Dahmen

Model-Based Design of Pure and Multicomponent Cellulosic Biofuels for Advanced Engine Concepts

Series: Verfahrenstechnik

Volume 954 2017

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Introduction S. 1-9

„… refunctionalization producing oxygenated fuel components. 1 1 Introduction premixed air/fuel compression-ignition …” „… reduction of engine-out emissions of NOx and soot (primarily compression-ignition engine). As illustrated in …” „… spark-ignition (SI) end compression-ignition (CI) engines. Burning pure ethanol instead of RON95 gasoline, for …”

Titelei/Inhaltsverzeichnis S. I-XVIII

„… of identifying oxygenated fuel candidates for both spark-ignition and compression-ignition engines …” „… . . . . . . . . . . . . . . . . . . 107 6.2 Candidates for compression-ignition (CI) engines . . . . . . . . . . . . . . . 120 6.3 …” „… compression-ignition CN cetane number CPD conceptual process design CPM conversion pathway map CRPM chemical reaction …”

Conclusions and outlook S. 175-178

„… biofuel candidates for spark-ignition (SI) and compression-ignition (CI) engines. Compared to earlier …” „… a candidate for spark-ignition (DCN<20) or compression-ignition (DCN>40) engines (cf. Chapter 6 …” „… numbers with high volatilities (cf. Chapter 6). • High-quality ignition delay data from a single …”

Bibliography S. 227-276

„… . (2008). The potential of di-methyl ether (DME) as an alternative fuel for compression-ignition engines …” „… compression-ignition engines - Understanding the in-cylinder processes. Proceedings of the Combustion Institute …” „… components in a compression ignition engine. Energy & Fuels, 29(11):7317–7326. Baumlin, S., Broust, F …”

Basic concepts of fuel design S. 10-39

„… et al., 2009; Rothamer and Jennings, 2012). Compared to SI engines, compression-ignition (CI) engines …” „… considered unlikely. However, (partially) premixed compression-ignition (PCI) combustion is a promising …” „… ) derived cetane number DCN [-] compression ratio → efficiency ignition control, (soot) enthalpy of …”

Model-based identification of biofuel candidates S. 107-129

„… compression-ignition engines like those studied within TMFB (Janssen et al., 2011; Thewes et al., 2011a,b; Heuser et al …” „… compression-ignition (CI) engines The second case study targets pure-component biofuels for the compression-ignition …” „… mentioned in Table 2.3, high productivity 120 6.2 Candidates for compression-ignition (CI) engines and high …”

Blend formulation by simultaneous product and pathway design S. 130-174

„… compression-ignition (CI) engines, too heavy components can cause engine oil dilution (Fisher et al., 2010; Thewes et …” „… molecule should be included in the set of palette compounds include pure-component properties, yield data …” „… as well as additional process-related data if available. automatic generation of palette compounds …”

doi.org/10.51202/9783186954039

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