Rob Edwards (@linsalrob) profile picture

Rob Edwards

@linsalrob

Matthew Flinders Fellow in Bioinformatics. 'The David Attenborough of Phages' mastadon: @linsalrob@genomic.social

 Adelaide, South Australia
edwards.sdsu.edu/research
Joined June 2008
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Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)Photo by Rob Edwards (@linsalrob)
🔬 Meet Prof. @linsalrob: A creator of RAST and MG-RAST 🌟 🌐 From coral reefs to remote islands, he's pushed the limits of sequencing and bioinformatics. 🔬 Catch his talk at #ICBRAR2023: "PhageCraft: From Sewage to Synthesis." Get ready for a journey that goes beyond the lab!
Image from Phages for Life 2023 (Hybrid Conference) (@phagesymp2023)
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Rob Edwards retweeted
Zamin Iqbal (@ZaminIqbal) profile picture
Zamin Iqbal@ZaminIqbal12 Apr 2023
Replying to @linsalrob
(I have no expertise but) maybe one that relies on plasmid encoded genes to get in? Eg biorxiv.org/content/10.1101/… From @baym and Natalia QO , whose twitter is I can't find oddly
Diverse and abundant viruses exploit conjugative plasmids

Diverse and abundant viruses exploit conjugative plasmids

Viruses exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of bacterial viruses, phages, use chromosomally-...

biorxiv.org
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Rob Edwards retweeted
Xin😼 (@EnViruSoil) profile picture
Xin😼@EnViruSoil12 Apr 2023
Replying to @linsalrob
One idea: you may have a look at the tremendous EOP assays (S1 data) performed for the BASEL E.coli phage collection by @AHarms485 & colleagues @PLOSBiology journals.plos.org/plosbiolog…
Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection

Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection

This study presents the BASEL collection of phages that infect the model bacterium Escherichia coli; this resource for the community is representative of natural E. coli phage diversity and has been...

journals.plos.org
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Replying to @linsalrob
That depends a bit on your definition of host range. Just recognition / lysis or also plaque formation? Phages targeting the highly conserved NGR glycan of enterobacteria are quite broad or those targeting conjugative pili of broad host-range plasmids (even cross-genus for PRD1).
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We are happy to announce the final speaker in our list of keynote speakers! Rob Edwards @linsalrob will join us in Valencia at #ViBioM2023 to speak about the promise and pitfalls of #prophages. Registration is still open: evbc.uni-jena.de/events/vibi…
Image from European Virus Bioinformatics Center (@EVirusBioinfC)
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The preprint of Phables is up on biorxiv! Phables can resolve high-quality bacteriophage genomes in metagenomic data using assembly graphs. @BeardyMcFace @BhavyaPapudeshi @susiegriggo_ @PDecewicz @GB13Faithless @linsalrob @LauraInglis13 @Marine_Rycrobe #phages #Bioinformatics
bioRxiv Bioinfo (@biorxiv_bioinfo) profile picturebioRxiv Bioinfo@biorxiv_bioinfo5 Apr 2023
Phables: from fragmented assemblies to high-quality bacteriophage genomes biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Do you have problems assembling high-quality phage genomes from viral metagenomes? Come find me at my poster (# A3) at #abacbs22 where I talk about Phables which can resolve phage genomes. #phage #phages #genomics #metagenomics #Bioinformatics #software #abacbs #ABACBS2022
Image from Vijini Mallawaarachchi (@viji112)
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Plenary speaker Rob Edwards @linsalrob presenting the impressive diversity of crAssphages now at #AusME22. They are everywhere, but took several years to cultivate. Awesome example of the power of metagenomics.
Image from AusME2022 (@AusME_microbes)
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DinsdaleLab (@DinsdaleLab) profile picture
DinsdaleLab@DinsdaleLab9 Nov 2022
The Dinsdale Lab had a great time at #AusMe22! We learned so much and loved sharing our cool sharkrobiomes! @Marine_Rycrobe @AmberSkyeCook4
Image from DinsdaleLab (@DinsdaleLab)
Image from DinsdaleLab (@DinsdaleLab)
Image from DinsdaleLab (@DinsdaleLab)
Image from DinsdaleLab (@DinsdaleLab)
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Wait.. what? UniProt hosting embeddings? That's cool! uniprot.org/help/embeddings Imagine if they did that for all of UniRef90 and also predicted a bunch of stuff... What? We did? Database update coming soon. Loooooots of predicted data, all those sweet embeddings, much goodness.

UniProt

UniProt is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.

uniprot.org
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Replying to @GB13Faithless @RhysTWhite @Shijie_Zhao
Checkout @linsalrob github.com/linsalrob/Prophag… for a collection of a bunch of command-line tools as well, from my experience with s aureus at least phispy is trivial to install and run does a good job of getting most of the likely prophage regions (if not the perfect boundaries)

GitHub - linsalrob/ProphagePredictionComparisons: Comparisons of multiple different prophage...

Comparisons of multiple different prophage predictions - linsalrob/ProphagePredictionComparisons

github.com
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Rob Edwards retweeted
lone brøndsted (@LNdsted) profile picture
lone brøndsted@LNdsted9 Oct 2022
I’m looking for a #postdoc for an exciting project developing #phage #enzymes to target #salmonella! A collaborative project with @BriersYves and open lab foundation. You must have a strong #molecular background. Is this you? #phagebio #unicph apply online jobportal.ku.dk/alle-opslag/…
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Rob Edwards retweeted
Titus Brown (@ctitusbrown) profile picture
Titus Brown@ctitusbrown8 Oct 2022
Hey I don't know if anyone saw this but it's a nice paper (COI: I'm an author ;) - Ten simple rules and a template for creating workflows-as-applications scholar.google.com/citations… w/@BeardyMcFace @linsalrob @watsonhaigh @saltyscientist and others!

Ten simple rules and a template for creating workflows-as-applications

MJ Roach, NT Pierce-Ward, R Suchecki, V Mallawaarachchi, B Papudeshi, SA Handley, CT Brown, NS Watson-Haigh, RA Edwards, PLoS computational biology, 2022 - Cited by 29

scholar.google.com
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The first paper of my PhD has been published in BMC Bioinformatics! I show that amino acid sequence embeddings may be used as a systematic framework for generating more robust protein annotations. You can read it here: bmcbioinformatics.biomedcent…

Organizing the bacterial annotation space with amino acid sequence embeddings

BMC Bioinformatics - Due to the ever-expanding gap between the number of proteins being discovered and their functional characterization, protein function inference remains a fundamental challenge...

link.springer.com
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Rob Edwards retweeted
Sen (@DrSenWang) profile picture
Sen@DrSenWang22 Sep 2022
We are adding 1x NGS Specialist and 1x Partnerships Manager to the team. Please feel free to share and forward if you know anyone who might be interested. #Genomics #sequencing – at Adelaide, South Australia
South Australian Genomics Centre (SAGC) (@SA_genomics) profile pictureSouth Australian Genomics Centre (SAGC)@SA_genomics22 Sep 2022
Welcome to SA! Two more positions are available at the SAGC. Partnerships Manager seek.com.au/job/58577683 NGS Specialist seek.com.au/job/58578010
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Extremely honoured to receive the ‘Outstanding Science Prize to a scientific poster’ at #GenomesMicrobiomes22 🤩 A huge thank you to the conference organisers and my lab FAME @FlindersCSE @Flinders #metagenomics #mags #phage #research
Microbiology Society (@MicrobioSoc) profile pictureMicrobiology Society@MicrobioSoc16 Sep 2022
Huge congratulations to Vijini Mallawaarachchi (@viji112) from @FlindersCSE for winning the ‘Outstanding Science Prize to a scientific poster’ at #GenomesMicrobiome22! 🎉 Sponsored by Microbial Genomics (#MGen): microb.io/MGen 👈 #PublishingForTheCommunity
Image from Microbiology Society (@MicrobioSoc)
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Want to replace your most dominant E coli? Go do some international travel. #GenomesMicrobiome22
Image from Rasmus Kirkegaard (@kirk3gaard)
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We resolve bacteriophage genomes using assembly graphs from metagenomic data. #phage #bacteriophage #metagenomics #assemblygraphs
Vijini Mallawaarachchi (@viji112) profile pictureVijini Mallawaarachchi@viji11216 Sep 2022
Come find my poster on phage bubbles at Genomes of Microbiomes 2022. 🦠🧬 Such a wonderful event with lots of exciting research to see. @MicrobioSoc #GenomesMicrobiome22
Image from Vijini Mallawaarachchi (@viji112)
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Come find my poster on phage bubbles at Genomes of Microbiomes 2022. 🦠🧬 Such a wonderful event with lots of exciting research to see. @MicrobioSoc #GenomesMicrobiome22
Image from Vijini Mallawaarachchi (@viji112)
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Anuradha (@Anuradhawick) profile picture
Anuradha@Anuradhawick16 Sep 2022
Attending genomes of microbiomes. Such a great event with amazing researchers presenting their wonderful work. It’s great to be a poster presenter too. #GenomesMicrobiome22 #metagenomics #Bioinformatics @MicrobioSoc
Image from Anuradha (@Anuradhawick)
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