Searched for: subject%3A%22Genomics%22
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Shirali Hossein Zade, R. (author)
The genome encompasses an organism’s full DNA, organized into chromosomes within the cell nucleus. Humans have 46 paired chromosomes, and within these pairs, genetic information is grouped as haplotypes—genetic packages passed from one generation to the next, ensuring genetic diversity. While DNA sequencing produces short fragments or reads,...
doctoral thesis 2024
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de Jong, S.I. (author)
Alkaliphiles thrive in environments with a pH of 8.5 or above, while maintaining an internal pH closer to neutral. Thus, alkaliphilic microorganisms have a proton gradient inverted with respect to the normal orientation. Intuitively, this would nullify the potential to generate energy via respiration with regularly oriented respiratory chains...
doctoral thesis 2024
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Hoencamp, C. (author)
Every human being originates from a single fertilized egg cell, continuously duplicating to form a body consisting of trillions of cells in a process known as the cell cycle. This cycle involves two major stages: interphase, where the cell prepares for division, and mitosis, where it divides into two daughter cells. The accurate duplication and...
doctoral thesis 2024
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Rojas-Padilla, Eduardo (author), Metze, T.A.P. (author), Dewulf, Art (author)
The influence of visualizations on decision-making about controversial policy issues is increasingly recognized in the political and policy sciences. In this paper, we explore how combinations of visuals and text on Twitter (now X) lead to the formation of networks of actors sharing similar textual and visual framings about a policy issue in...
journal article 2024
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Páez Watson, T.W. (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)
With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic...
journal article 2024
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Hiralal, Anwar (author), Geelhoed, Jeanine S. (author), Hidalgo-Martinez, Silvia (author), Smets, Bent (author), van Dijk, Jesper R. (author), Meysman, F.J.R. (author)
Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in...
journal article 2024
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Firtina, Can (author), Pillai, Kamlesh (author), Kalsi, Gurpreet S. (author), Suresh, Bharathwaj (author), Cali, Damla Senol (author), Kim, Jeremie S. (author), Shahroodi, Taha (author), Cavlak, Meryem Banu (author), Lindegger, Joël (author)
Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequences. In pHMMs, sequences are represented as graph structures, where states and edges capture modifications (i.e., insertions, deletions, and substitutions) by...
journal article 2024
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Schwartzman, Julia A. (author), Lebreton, Francois (author), Salamzade, Rauf (author), Shea, Terrance (author), Martin, Melissa J. (author), Schaufler, Katharina (author), Urhan, A. (author), Abeel, T.E.P.M.F. (author), Camargo, Ilana L.B.C. (author)
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common...
journal article 2024
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Haenen, Jasper (author)
Genomics has revolutionized our understanding of evolution, hereditary diseases, and more. The advent of long-read DNA sequencers i.e. Oxford Nanopore Technologies' innovations, has opened many new research potentials in genomics. These sequencers produce significantly longer DNA reads, facilitating novel applications. However, this...
master thesis 2023
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Koster, C.C. (author)
Building synthetic cells is extremely interesting from a fundamental perspective, as the ability to rationally build viable, dividing, and self-maintaining cells provides knowledge on the minimal requirements to sustain life. This should enhance our understanding about which biological parts are minimally required for a cell to live, and how...
doctoral thesis 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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Cosma, Bianca-Maria (author), Shirali Hossein Zade, R. (author), Jordan, E.N. (author), van Lent, P.H. (author), Peng, C. (author), Pillay, S. (author), Abeel, T.E.P.M.F. (author)
Background: Assembly algorithm choice should be a deliberate, well-justified decision when researchers create genome assemblies for eukaryotic organisms from third-generation sequencing technologies. While third-generation sequencing by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) has overcome the disadvantages of short...
journal article 2023
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Depuydt, Lore (author), Renders, Luca (author), Abeel, T.E.P.M.F. (author), Fostier, Jan (author)
Background: Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, as their graph topology naturally reveals similarity and divergence within the pan-genome. Most state-of-the-art pan-genome...
journal article 2023
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Frkatović-Hodžić, Azra (author), Mijakovac, Anika (author), Miškec, Karlo (author), Nostaeva, Arina (author), Sharapov, Sodbo Z. (author), Landini, Arianna (author), Haller, Toomas (author), van den Akker, E.B. (author), Sharma, Sapna (author)
Glycans are an essential structural component of immunoglobulin G (IgG) that modulate its structure and function. However, regulatory mechanisms behind this complex posttranslational modification are not well known. Previous genome-wide association studies (GWAS) identified 29 genomic regions involved in regulation of IgG glycosylation, but...
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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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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Bennis, N.X. (author), Anderson, Jonah P. (author), Kok, Siebe M.C. (author), Daran, J.G. (author)
ErCas12a is a class 2 type V CRISPR-Cas nuclease isolated from Eubacterium rectale with attractive fundamental characteristics, such as RNA self-processing capability, and lacks reach-through royalties typical for Cas nucleases. This study aims to develop a ErCas12a-mediated genome editing tool applicable in the model yeast Saccharomyces...
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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Kim, Eugene (author), Barth, R. (author), Dekker, C. (author)
SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have...
review 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
Searched for: subject%3A%22Genomics%22
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