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Mans, R. (author), Else-Hassing, J. (author), Wijsman, M. (author), Giezekamp, Annabel (author), Pronk, J.T. (author), Daran, J.G. (author), van Maris, A.J.A. (author)CRISPR/Cas9-based genome editing allows rapid, simultaneous modification of multiple genetic loci in Saccharomyces cerevisiae. Here, this technique was used in a functional analysis study aimed at identifying the hitherto unknown mechanism of lactate export in this yeast. First, an S. cerevisiae strain was constructed with deletions in 25...journal article 2017
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van Dijk, Lucas (author)Capturing all genetic variation within a polyploid organism is a challenge. Most current de novo assemblers have no notion of the concept “ploidy”. Consequently, when assembling the genome of diploid or higher ploidy organisms, the assembler mixes reads coming from either chromosome copy and builds a single DNA sequence representing an arbitrary...master thesis 2017
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Bracher, J.M. (author), de Hulster, A.F. (author), Koster, C.C. (author), van den Broek, M.A. (author), Daran, J.G. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)Biotin prototrophy is a rare, incompletely understood, and industrially relevant characteristic of Saccharomyces cerevisiae strains. The genome of the haploid laboratory strain CEN.PK113-7D contains a full complement of biotin biosynthesis genes, but its growth in biotin-free synthetic medium is extremely slow (specific growth rate [μ] ≈ 0.01...journal article 2017
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Gorter de Vries, A.R. (author), Pronk, J.T. (author), Daran, J.G. (author)Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact, and evolutionary significance of CCNV. Fundamental studies of this yeast have contributed to an extensive set of methods for...journal article 2017
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Mouzos, L. (author)In recent years, cheap sequencing has resulted in hundreds or thousands of individual genomes available for many species. Therefore, it is logical to rethink the concept of the reference genome; as consisting of a population of genomes rather than being a single one. The term pan-genome describes a population of genomes of the same species or a...master thesis 2017
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Mouzos, L. (author)In recent years, cheap sequencing has resulted in hundreds or thousands of individual genomes available for many species. Therefore, it is logical to rethink the concept of the reference genome; as consisting of a population of genomes rather than being a single one. The term pan-genome describes a population of genomes of the same species or a...master thesis 2017
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Gorter de Vries, A.R. (author), de Groot, P.A. (author), van den Broek, M.A. (author), Daran, J.G. (author)Background: The ease of use of CRISPR-Cas9 reprogramming, its high efficacy, and its multiplexing capabilities have brought this technology at the forefront of genome editing techniques. Saccharomyces pastorianus is an aneuploid interspecific hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus that has been domesticated for...journal article 2017
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Speth, Daan R. (author), Lagkouvardos, Ilias (author), Wang, Yong (author), Qian, Pei Yuan (author), Dutilh, Bas E. (author), Jetten, M.S.M. (author)Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using...journal article 2017
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Salazar, A.N. (author), Gorter de Vries, A.R. (author), van den Broek, M.A. (author), Wijsman, M. (author), de la Torre, P. (author), Brickwedde, A. (author), Brouwers, N. (author), Daran, J.G. (author), Abeel, T.E.P.M.F. (author)The haploid Saccharomyces cerevisiae strain CEN.PK113–7D is a popular model system for metabolic engineering and systems biology research. Current genome assemblies are based on short-read sequencing data scaffolded based on homology to strain S288C. However, these assemblies contain large sequence gaps, particularly in subtelomeric regions, and...journal article 2017
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Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)DNA read alignment is a major step in genome analysis. However, as DNA reads continue to become longer, new approaches need to be developed to effectively use these longer reads in the alignment process. Modern aligners commonly use a two-step approach for read alignment: 1. seeding, 2. extension. In this paper, we have investigated various...conference paper 2016
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Roshchupkin, G. V. (author), Adams, H. H H (author), Vernooij, M. W. (author), Hofman, A. (author), Van Duijn, C. M. (author), Ikram, M. A. (author), Niessen, W.J. (author)High-throughput technology can now provide rich information on a person's biological makeup and environmental surroundings. Important discoveries have been made by relating these data to various health outcomes in fields such as genomics, proteomics, and medical imaging. However, cross-investigations between several high-throughput...journal article 2016
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Sorokin, Dimitry Y. (author), Rakitin, Andrey L. (author), Gumerov, Vadim M. (author), Beletsky, Alexey V. (author), Sinninghe Damsté, Jaap S. (author), Mardanov, Andrey V. (author), Ravin, Nikolai V. (author)Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5-10.5 and total Na<sup>+</sup> concentrations...journal article 2016
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Bolat, I. (author)One of the best guarded secrets of brewers is represented by the brewing yeast employed in beer fermentation, due to its profound impact upon the specific flavour profile of the final product. The current research tackles the genome diversity of lager brewing strains as well as their impact on important phenotypic traits. Furthermore, the...doctoral thesis 2016
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Moolman, M.C. (author), Tiruvadi Krishnan, S. (author), Kerssemakers, J.W.J. (author), de Leeuw, R. (author), Lorent, V.J.F. (author), Sherratt, David J. (author), Dekker, N.H. (author)Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood....journal article 2016
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Knijnenburg, Theo A. (author), Klau, Gunnar W (author), Lorio, Francesco (author), Garnett, Mathew J. (author), McDermott, Ultan (author), Shmulevich, I (author), Wessels, L.F.A. (author)Mining large datasets using machine learning approaches often leads to models that are hard to interpret and not amenable to the generation of hypotheses that can be experimentally tested. We present ‘Logic Optimization for Binary Input to Continuous Output’ (LOBICO), a computational approach that infers small and easily interpretable logic...journal article 2016
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Schlicker, A (author), Michaut, Magali (author), Rahman, Rubayte (author), Wessels, L.F.A. (author)Although large-scale efforts for molecular profiling of cancer samples provide multiple data types for many samples, most approaches for finding candidate cancer genes rely on somatic mutations and DNA copy number only. We present a new method, OncoScape, which exploits five complementary data types across 11 cancer types to identify new...journal article 2016
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Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array...conference paper 2015
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Babaei, S. (author)Cancer is a complex disease that results from alterations in genes that control the growth and division mechanisms of the cell. Identifying cancer-associated genes and pathways through which these genes influence cellular function is the key challenge in cancer re- search. This thesis proposes novel computational approaches that integrate data...doctoral thesis 2015
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Paclt, J. (author)Informed Transformations looks into revamp of Marconi Towers in Rotterdam in light of Information Age, as Tofflers describe it. Information processing though IT resonates with todays rhizomatic distribution of power, insfluence, data and space as well. Everchanging socio-economic context can be treated by a meta-design that binds input of...master thesis 2015
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Babaei, S. (author), Mahfouz, A.M.E.T.A. (author), Hulsman, M. (author), Lelieveldt, B.P.F. (author), De Ridder, J. (author), Reinders, M.J.T. (author)The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains...journal article 2015