Thomas Abeel
@ThomasAbeel
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Associate professor at @TUDelft and visiting scientist at @broadinstitute. Interested in computational (microbial) genomics and precision medicine.
Joined July 2012
An interesting large-scale co-assembly of soil metagenome: 8 TB of FASTQs altogether fed to an assembler, resulting in a 75 Gbp assembly. https://t.co/vsbrTTE4Gs "Terabase-Scale Coassembly of a Tropical Soil Microbiome"
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With this article, I close my PhD thesis🥳. Give it a try! It's about transformation as gene transfer, complex microbial communities, and a bit about plasmids and mobility...also a nice "catchy" title. Thanks @MarkvLoosdrecht @ThomasAbeel @WeissbrodtLab ! https://t.co/vTdVZT3z3K
link.springer.com
Antonie van Leeuwenhoek - The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition...
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APA on How to cite ChatGPT. Seems reasonable to me; anyone disagree?
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Interested in genome-scale modeling? Struggling with commercial solver licenses? This pre-print shows the result of benchmarking 6 optimization solvers: 2 commercial and 4 open-source. Please drop me a message if you'd like to be a potential reviewer. https://t.co/hTLAzdY0g5
biorxiv.org
Genome-scale metabolic modeling is a powerful framework for predicting metabolic phenotypes of any organism with an annotated genome. For two decades, this framework has been used for rational design...
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My 8yo came across my bound thesis in the basement, "read" it, and spontaneously wrote me this note. I will now be listing her as a suggested reviewer for all my manuscript submissions. ❤️
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Last Friday I successfully defended my Ph.D at TUDelft. Special thanks to my promoters @MarkvLoosdrecht @WeissbrodtLab and @ThomasAbeel, for all the guidance during these years. Thanks to the committee members, paranymphs, and everyone who joined me on this amazing day.
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Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings https://t.co/tyVjS7PKEv Nice review by Stephanie Pillay et al. @ThomasAbeel
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New preprint ⚠️ Catch me if you can: capturing #exDNA transformation in mixed cultures via Hi-C sequencing 🧬 🦠 💧 Get to know more at #EDAR6 🤓 @MarkvLoosdrecht @ThomasAbeel @WeissbrodtLab
https://t.co/8RpRfdyGu0
biorxiv.org
Environmental microorganisms evolve constantly under various stressors using different adaptive mechanisms, including horizontal gene transfer. Microorganisms benefit from transferring genetic...
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💧 🦠 🧬 🏭 Check our last preprint on transfer dynamics of resistance determinants through granular sludge systems. Who, what and where? New actors such as #exDNA may play an important role 😎 #WWTP fighting #antibioticresistance 💪🏻
Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant https://t.co/lwyQNdAXqK
#bioRxiv
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Recruiting a four year fully-paid PhD position in precision medicine and artificial intelligence at @TUDelft in collaboration with Grace Systems. https://t.co/tmpk6oeTSY
#phd #artificialintelligence #precisionmedicine #tudelft
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Recruiting a four year fully-paid PhD position in Computer Science and Artificial Intelligence at @TUDelft in collaboration with @DSM. https://t.co/SJSprcHuma
#phd #artificialintelligence #metabolomics #tudelft
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New machine learning PhD positions in my group in collaboration with @DSM in the context of #AI4B.io. First one:
academictransfer.com
DNA is the blueprint of all organisms and large amounts of DNA and RNA sequences of microbes and microbial communities are determined with widespread biotechnological applications. Predicting the...
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Looks interesting
Benchmarking metagenomic classification tools for long-read sequencing data
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Whenever I discover that I am writing a *long* review (meaning I am opinionated and have expertise), I try to force myself to propose acceptance of the paper, despite the many problems I see. This research explains why this might make sense. 👇
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"Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020" - now peer-reviewed and out in @Eurosurveillanc
eurosurveillance.org
We whole-genome sequenced 55 SARS-CoV-2 isolates from Germany to investigate SARS-CoV-2 outbreaks in 2020 in the Heinsberg district and Düsseldorf. While the genetic structure of the Heinsberg...
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Thanks to #opendata sharing by @ErasmusMC @MarionKoopmans @ReinaSikkema @1986Bom @Rimo42 & @GISAID we've updated https://t.co/SDPCOcsnMX with *48* new #COVID19 #SARSCoV2
#HCoV19 sequences from the Netherlands - a total of 73 dutch seqs! They are positioned across the tree.
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@PLOSCompBiol @StanBrouns @TNWTUDelft @EEMCS_TUD Special thanks to @NobregaFL, @an_salazan and the rest of the team to make this happen.
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