@brjoris

Senior bioinformatician at @CeragenGrow

 Kitchener, Ontario
bjoris33.github.io/
Joined October 2016
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2Media
My first research paper of my PhD is out as a preprint (and under review)! Here we show that: 1. bacterial conjugation systems are differentially abundant between populations and 2. they are systematically excluded from metagenomic bins. 1/ biorxiv.org/content/10.1101/…

Separation of cohorts on the basis of bacterial type IV conjugation systems identified from...

Conjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways...

biorxiv.org
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First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset) biorxiv.org/content/10.1101/…
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Ben Joris retweeted
Kait Al@kait_al28 Nov 2023
Very excited to share our latest work in @MicrobiomeJ, where we take a deep dive into the #microbiome at multiple body sites in #kidneystone formers. TLDR? The microbiome plays a massive part in this disease but Oxalobacter doesn't! doi.org/10.1186/s40168-023-0…
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Ben Joris retweeted
David Edgell@megatev8 Sep 2023
Latest pub from Edgell/Gloor labs. Better sgRNA predictions in bacteria with crisprHAL. nature.com/articles/s41467-0… Huge effort (Dalton Ham @nortnlentivirus @gbgloor @tesseraqtinc). @gbgloor tweetorial (xitter.cf/gbgloor/status/1700200…). Thanks @CIHR_IRSC @westernuBiochem @SchulichMedDent

A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality...

Nature Communications - Current bacterial sgRNA activity models struggle with accurate predictions and generalizations. Here the authors report crisprHAL, a machine learning architecture that can...

nature.com
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BioCreate Showcase 3: @CeragenGrow
Ontario Genomics@ontariogenomics14 Jun 2023
Meet the 1st cohort of our #BioCreate program and hear about their pathbreaking innovations! Featuring: ▶️@aimalabs_inc ▶️@Biofectinc ▶️@CeragenGrow ▶️@GBioindustries ▶️@index_bio ▶️@KrakenSense ▶️ Liven Proteins ▶️@PerfPlants
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Check out our latest pre-print on animating conjugative systems from metagenomic data for delivery of Cas9 antimicrobials. Ever wonder if metagenomic sequences are 'real'? Or how to build from scratch a 54-kb genetic element with 47 genes? biorxiv.org/content/10.1101/…

De novo synthesis of a conjugative system from human gut metagenomic data for targeted delivery of...

Metagenomic sequence represents an untapped source of genetic novelty, particularly for conjugative systems that could be used for plasmid-based delivery of Cas9-derived antimicrobial agents....

biorxiv.org
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Happy #InternationalWomensDay ! A special shout out to all of the awesome #WomenInSTEM on the Ceragen R&D team and all of their hard work and dedication to increasing crop yields through plant growth promoting bacteria!
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Latest pub from Edgell lab now online at NAR! academic.oup.com/nar/advance… Awesome work from @GregP_47 & collab with @gbgloor @EmmaAllenVercoe. Thanks to @CIHR @SchulichMedDent @westernuBiochem. Want to link dCas9 activity to a metabolic pathway? Read on!
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📢#ForbesUnder30: @CeragenGrow founders are making headlines and we couldn't be more excited! @ontariogenomics is a proud supporter & investor in their work as they continue to assist growers to increase crop yields by 10-20% 🤝
CeragenGrow@CeragenGrow29 Nov 2022
Congratulations to our founders for making the #forbes30under30 list for 2023! We at Ceragen look forward to continuing to help growers increase crop yields into 2023 and beyond! #hydroponicfarming #greenhouse #tomatoes #lettuce
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Congratulations to our founders for making the #forbes30under30 list for 2023! We at Ceragen look forward to continuing to help growers increase crop yields into 2023 and beyond! #hydroponicfarming #greenhouse #tomatoes #lettuce
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SEE EVERYONE GOES ON ABOUT LONG READS MAKING BETTER MAGS BUT REALLY IT'S ALL ABOUT DNA EXTRACTION AND YOU CAN'T GET LONG DNA FROM BEAD BEATING AND IF YOU DON'T BEAD BEAT HARD ENOUGH YOU BIAS THE SAMPLE AND IF YOU SIZE SELECT YOU BIAS THE SAMPLE AND U WON'T HAVE ENOUGH DNA
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🇨🇦 Canadian full plasmid sequencing is here! 🇨🇦
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How do we compare MAGs and microbial genomes with different degrees of completeness? Wonder no more! 🤔➡️🥳 Preprint out today with Pauline Trinh & David Clausen @paulinetrinh @davidandacat #microbiome #MAGs #methods biorxiv.org/content/10.1101/…

happi: a Hierarchical Approach to Pangenomics Inference

Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both...

biorxiv.org
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Less input DNA is a positive, but only a maximum of 10kb read lengths is less than desirable.
Illumina
@illumina10 Jan 2022
Replying to @illumina
Infinity also enables 10x greater throughput with 90% less #DNA input than legacy long reads. We anticipate an early access launch for Infinity technology in the second half of the year.
Co-first authorship order was determined through a mushrooming contest. 😂 academic.oup.com/nar/advance…
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"It’s pretty amazing how much you can learn about a novel organism just from sitting at your computer." - anonymous peer's feedback for symposium talk
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"Just from sitting" 🥲
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.@uOttawa announces that vaccination will be mandatory for all students, faculty, staff, and anyone returning to or visiting campus as of September 7th, 2021. fal.cn/3hlMo #COVID19On #Covidvaccine
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I repeat- I haven’t been this excited about a discovery since CRISPR. We found something enigmatic that, like CRISPR, is associated with microbial genomes. We have named these unique entities #BORGs
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Hey! Looking for something to do on this rainy afternoon?? #GetVaxxed at #MLHU’s Pop-up COVID-19 Vaccination Clinic inside Citi Plaza (Southeast Corner of Clarence and King St). Just walk-in and get your first or second dose. No appointment necessary! #LdnOnt #Middlesex

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