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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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Carvalho Teixeira, M.T. (author), Pillay, S. (author), Urhan, A. (author), Abeel, T.E.P.M.F. (author)Motivation: Plasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of...journal article 2023
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Peng, C. (author), May, Ali (author), Abeel, T.E.P.M.F. (author)BackgroundEnteric methane from cow burps, which results from microbial fermentation of high-fiber feed in the rumen, is a significant contributor to greenhouse gas emissions. A promising strategy to address this problem is microbiome-based precision feed, which involves identifying key microorganisms for methane production. While machine...journal article 2023
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Henao, Laura (author), Shirali Hossein Zade, R. (author), Restrepo, Silvia (author), Husserl, Johana (author), Abeel, T.E.P.M.F. (author)Genomes of four Streptomyces isolates, two putative new species (Streptomyces sp. JH14 and Streptomyces sp. JH34) and two non thaxtomin-producing pathogens (Streptomyces sp. JH002 and Streptomyces sp. JH010) isolated from potato fields in Colombia were selected to investigate their taxonomic classification, their pathogenicity, and the...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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Calderon Franco, D. (author), van Loosdrecht, Mark C.M. (author), Abeel, T.E.P.M.F. (author), Weissbrodt, D.G. (author)The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to...journal article 2023
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van Lent, P.H. (author), Schmitz, Joep (author), Abeel, T.E.P.M.F. (author)Combinatorial pathway optimization is an important tool in metabolic flux optimization. Simultaneous optimization of a large number of pathway genes often leads to combinatorial explosions. Strain optimization is therefore often performed using iterative design-build-test-learn (DBTL) cycles. The aim of these cycles is to develop a product...journal article 2023
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Buisma-Yi, S.C. (author), Heijbroek, A.C. (author), Cutz, L. (author), Pillay, S. (author), de Jong, W. (author), Abeel, T.E.P.M.F. (author), Gebert, J. (author)Application of biochar to landfill cover soils can purportedly improve methane (CH4) oxidation rates, but understanding the combined effects of soil texture, compaction, and biochar on the activity and composition of the methanotrophs is limited. The amendment of wood biochar on two differently textured landfill cover soils at three compaction...journal article 2023
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Wen, J. (author), Abeel, T.E.P.M.F. (author), de Weerdt, M.M. (author)Global soft fruit supply chains rely on trustworthy descriptions of product quality. However, crucial criteria such as sweetness and firmness cannot be accurately established without destroying the fruit. Since traditional alternatives are subjective assessments by human experts, it is desirable to obtain quality estimations in a consistent and...journal article 2023
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Calderon Franco, D. (author), Sarelse, R.G. (author), Christou, S. (author), Pronk, M. (author), van Loosdrecht, Mark C.M. (author), Abeel, T.E.P.M.F. (author), Weissbrodt, D.G. (author)In the One Health context, wastewater treatment plants (WWTPs) are central to safeguarding water resources. Nonetheless, many questions remain about their effectiveness in preventing antimicrobial resistance (AMR) dissemination. Most surveillance studies monitor the levels and removal of selected antibiotic resistance genes (ARGs) and mobile...journal article 2022
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Veldhuis, M.S. (author), Ariëns, Simone (author), Ypma, Rolf J.F. (author), Abeel, T.E.P.M.F. (author), Benschop, Corina C.G. (author)Machine learning obtains good accuracy in determining the number of contributors (NOC) in short tandem repeat (STR) mixture DNA profiles. However, the models used so far are not understandable to users as they only output a prediction without any reasoning for that conclusion. Therefore, we leverage techniques from the field of explainable...journal article 2022
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Shirali Hossein Zade, R. (author), Urhan, A. (author), Assis de Souza, A. (author), Singh, A. (author), Abeel, T.E.P.M.F. (author)Motivation: Haplotypes are the set of alleles co-occurring on a single chromosome and inherited together to the next generation. Because a monoploid reference genome loses this co-occurrence information, it has limited use in associating phenotypes with allelic combinations of genotypes. Therefore, methods to reconstruct the complete...journal article 2022
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Pillay, S. (author), Calderon Franco, D. (author), Urhan, A. (author), Abeel, T.E.P.M.F. (author)The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic...journal article 2022
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StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communitiesvan Dijk, L.R. (author), Walker, Bruce J. (author), Straub, Timothy J. (author), Worby, Colin J. (author), Grote, Alexandra (author), Schreiber, Henry L. (author), Anyansi, C.A. (author), Pickering, Amy J. (author), Hultgren, Scott J. (author), Manson, Abigail L. (author), Abeel, T.E.P.M.F. (author), Earl, Ashlee M. (author)Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which...journal article 2022
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Ruibal, Paula (author), Franken, Kees L.M.C. (author), van Meijgaarden, Krista E. (author), van Wolfswinkel, Marjolein (author), Derksen, Ian (author), Scheeren, Ferenc A. (author), van Veelen, Peter A. (author), Abeel, T.E.P.M.F. (author), Joosten, Simone A. (author)Tuberculosis (TB) remains one of the deadliest infectious diseases worldwide, posing great social and economic burden to affected countries. Novel vaccine approaches are needed to increase protective immunity against the causative agent Mycobacterium tuberculosis (Mtb) and to reduce the development of active TB disease in latently infected...journal article 2022
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Urhan, A. (author), Abeel, T.E.P.M.F. (author)Coronavirus disease 2019 (COVID-19) has emerged in December 2019 when the first case was reported in Wuhan, China and turned into a pandemic with 27 million (September 9th) cases. Currently, there are over 95,000 complete genome sequences of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, in...journal article 2021
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Urhan, A. (author), Abeel, T.E.P.M.F. (author)Microbial organisms have diverse populations, where using a single linear reference sequence in comparative studies introduces reference-bias in downstream analyses, and leads to a failure to account for variability in the population. Recently, pan-genome graphs have emerged as an alternative to the traditional linear reference with many...journal article 2021
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Calderon Franco, D. (author), van Loosdrecht, Mark C.M. (author), Abeel, T.E.P.M.F. (author), Weissbrodt, D.G. (author)The free-floating extracellular DNA (exDNA) fraction of microbial ecosystems harbors antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Natural transformation of these xenogenetic elements can generate microbial cells resistant to one or more antibiotics. Isolating and obtaining high yield exDNA is challenging due to its low...journal article 2020
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Boonekamp, F.J. (author), Dashko, S. (author), Duiker, Donna (author), Gehrmann, T. (author), van den Broek, M.A. (author), den Ridder, M.J. (author), Pabst, Martin (author), Robert, Vincent (author), Abeel, T.E.P.M.F. (author), Postma, E.D. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)The construction of powerful cell factories requires intensive and extensive remodelling of microbial genomes. Considering the rapidly increasing number of these synthetic biology endeavors, there is an increasing need for DNA watermarking strategies that enable the discrimination between synthetic and native gene copies. While it is well...journal article 2020