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Vandenplas, Jeremie (author), Nguyen, B. (author), Vuik, Cornelis (author)In this paper, we consider a block Jacobi preconditioner and various deflation techniques applied in the Deflated Preconditioned Conjugate Gradient (DPCG) method for solving a sparse system of linear equations derived from a statistical linear mixed model that analyses simultaneously phenotypic and pedigree information of genotyped and...journal article 2023
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Izquierdo-Lara, Ray W. (author), Heijnen, Leo (author), Oude Munnink, Bas B. (author), Schapendonk, Claudia M.E. (author), Elsinga, Goffe (author), Langeveld, J.G. (author), Post, Johan (author), Prasad, Divyae K. (author), Medema, G.J. (author)Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the...journal article 2023
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Bennis, N.X. (author), Kostanjsek, M. (author), van den Broek, M.A. (author), Daran, J.G. (author)Saccharomyces pastorianus is not a classical taxon, it is an interspecific hybrid resulting from the cross of Saccharomyces cerevisiae and Saccharomyces eubayanus. Exhibiting heterosis for phenotypic traits such as wort α-oligosaccharide consumption and fermentation at low temperature, it has been domesticated to become the main workhorse of...journal article 2023
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Mahler, M.S. (author), Malone Portu, L.M. (author), van den Berg, D.F. (author), Smith, Leah M. (author), Brouns, S.J.J. (author), Fineran, Peter C. (author)Serratia sp. ATCC 39006 is a Gram-negative bacterium that has been used to study the function of phage defences, such as CRISPR-Cas, and phage counter-defence mechanisms. To expand our phage collection to study the phage-host interaction with Serratia sp. ATCC 39006, we isolated the T4-like myovirus LC53 in Ōtepoti Dunedin, Aotearoa New...journal article 2023
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Sarkar, A. (author)Efforts to realize a sufficiently large controllable quantum processor are actively being pursued globally. These quantum devices are programmed by specifying the manipulation of quantum information via quantum algorithms. This doctoral research provides an application perspective to the design requirements of a quantum accelerator architecture....doctoral thesis 2022
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Ahmad, T. (author)The ever increasing pace of advancements in sequencing technologies has enabled rapid DNA/genome sequencing to become much more accessible. In particular, next (second) and third generation sequencing technologies offer high throughput, massively parallel and cost effective sequencing solutions. Individual sample sequencing data volumes as well...doctoral thesis 2022
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- Mikuš, Matus (author) master thesis 2022
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Dekker, W.J.C. (author), Jürgens, H. (author), Ortiz Merino, R.A. (author), Mooiman, C. (author), van den Berg, Remon (author), Kaljouw, Astrid (author), Mans, R. (author), Pronk, J.T. (author)While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha...journal article 2022
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Kouba, V. (author), Bachmannová, Ch (author), Podzimek, T. (author), Lipovová, P. (author), van Loosdrecht, Mark C.M. (author)The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies...review 2022
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Barth, R. (author), Shaban, Haitham A. (author)Gene transcription by RNA polymerase II (RNAPol II) is a tightly regulated process in the genomic, temporal, and spatial context. Recently, we have shown that chromatin exhibits spatially coherently moving regions over the entire nucleus, which is enhanced by transcription. Yet, it remains unclear how the mobility of RNA Pol II molecules is...journal article 2022
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Ahmad, T. (author), Ma, Chengxin (author), Al-Ars, Z. (author), Hofstee, H.P. (author)Current cluster scaled genomics data processing solutions rely on big data frameworks like Apache Spark, Hadoop and HDFS for data scheduling, processing and storage. These frameworks come with additional computation and memory overheads by default. It has been observed that scaling genomics dataset processing beyond 32 nodes is not efficient on...conference paper 2022
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Chardon, Florian (author), Japaridze, A. (author), Witt, Hannes (author), Velikovsky, Leonid (author), Chakraborty, Camellia (author), Wilhelm, Therese (author), Dumont, Marie (author), Yang, W.W.W. (author), Dekker, C. (author)Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA...journal article 2022
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Postma, E.D. (author), Couwenberg, Lucas G.F. (author), van Roosmalen, Roderick N. (author), Geelhoed, J. (author), de Groot, P.A. (author), Daran-Lapujade, P.A.S. (author)Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterized by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of “minor” paralogs and complicates modular and...journal article 2022
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Postma, E.D. (author), Else-Hassing, J. (author), Mangkusaputra, Venda (author), Geelhoed, J. (author), de la Torre, P. (author), van den Broek, M.A. (author), Mooiman, C. (author), Pabst, Martin (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)The construction of powerful cell factories requires intensive genetic engineering for the addition of new functionalities and the remodeling of native pathways and processes. The present study demonstrates the feasibility of extensive genome reprogramming using modular, specialized de novo-assembled neochromosomes in yeast. The in vivo...journal article 2022
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Holub, M. (author), Birnie, A.T.F. (author), Japaridze, A. (author), van der Torre, J. (author), Ridder, Maxime den (author), de Ram, C. (author), Pabst, Martin (author), Dekker, C. (author)Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the...journal article 2022
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Koster, C.C. (author), Postma, E.D. (author), Knibbe, E. (author), Cleij, C.V. (author), Daran-Lapujade, P.A.S. (author)Synthetic Genomics focuses on the construction of rationally designed chromosomes and genomes and offers novel approaches to study biology and to construct synthetic cell factories. Currently, progress in Synthetic Genomics is hindered by the inability to synthesize DNA molecules longer than a few hundred base pairs, while the size of the...review 2022
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Park, Seongyeon (author), Kim, Hajin (author), Ahmad, T. (author), Ahmed, N. (author), Al-Ars, Z. (author), Hofstee, H.P. (author), Kim, Youngsok (author), Lee, Jinho (author)Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit...conference paper 2022
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Anyansi, C.A. (author)This thesis represents one small step in the battle with TB, where we apply WGS approaches to explore different topics of TB research. Here we offer the global community a method to diagnose complex TB infections consisting of multiple distinct strains. We show that this functionality is necessary and has been overlooked by the TB community in...doctoral thesis 2021
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Cao, Qingyuan (author)This project is dedicated to implementing an unsupervised learning clustering method system for processing big data applied in Intel SGX. Intel SGX is a technology developed to meet the needs of the trusted computing industry similarly to ARM TrustZone, but this time for desktop and server platforms. It is a set of safety-related instruction...master thesis 2021
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Nguyen, Buu-Van (author)The single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) model can potentially be used in animal breeding for genetic evaluations. It has been reported that this model has convergence issues when the Preconditioned Conjugate Gradient (PCG) method is applied. This is due to the linear system being ill-conditioned...master thesis 2021