Bioinformatician interested in pathogen genomics. Loves all things Apple, Unix, Python and Ruby. Views & opinions my own, retweets not necessarily endorsements.
London
Joined July 2008
- Tweets3.3K
- Following454
- Followers1.6K
- Likes2.7K
Anthony Underwood retweeted
Machine learning (ML) is revolutionizing genomics, but common pitfalls can lead to misleading results. Here's a thread on how to avoid them 🧵
Anthony Underwood retweeted
I built a tool that can help open the black box of AIs.
It is called ‘Programmed Conceptual Deconstruction’. It systematically breaks down any initial concept (Ci) into its constituent, related concepts through an iterative process until further decomposition is no longer possible.
It is convenient since it reveals the complete network of concepts that an LLM might associate with the initial concept, which helps seeing the understanding that any LLM might have of any topic.
The relationships between concepts are then visualized in a graph.
A demonstration follows below.
At @BrokenStringBio we've been investigating many PaaS to make the software aspect of our INDUCE-seq® technology available to all irrespective of bioinformatics experience. One observation: the only workflow manager common to all is @nextflowio. Glad I plumped for it 7 years back
Anthony Underwood retweeted
Very productive day working with @ncdcgov scientists to move our @ghruamr genomic surveillance of #AntimicrbialResistance work forward, and towards planning initiation of wastewater pathogen surveillance
Anthony Underwood retweeted
INDUCE-seq™ is a game changing #technology for development of advanced #therapies, but what is it?
Watch this video to learn how the platform precisely characterises breaks in the #genome, to inform the development of cutting edge therapeutics that are safer by design!🧪
Anthony Underwood retweeted
Register for free to attend our webinar on the 29th Feb, 5PM GMT, and learn more about how our technology is helping to unlock the next wave of cell & gene therapies!
Join our webinar! Our CEO, Felix, will be sharing an educational session on off-target #geneediting events, and how our INDUCE-seq™ platform can provide the actionable insights to advance cell & gene therapy programs.
📆29 Feb🕑5pm GMT
Free registration: zoom.us/webinar/register/WN_…
It's so good to see the basic training for Nextflow in multiple languages
youtube.com/@nf-core/playlis…
For fireside style chats about all things nextfkow see the podcast
nextflow.io/podcasts.html
#NextflowSummit
Awesome new pipeline automation functionality made possible by seqera-kit (github.com/seqeralabs/seqera…) and @nextflowio as tooled by @aka_hpatel and team at @SeqeraLabs #NextflowSummit
Anthony Underwood retweeted
Thanks to @MonicaAbrudan for guiding us all along and making this publication happen. @TheCGPS for all the support and @NIHRglobal for funding. @bioinformAnt @silargi @cake_ray @sndigregorio @Geetha66538200 for their technical expertise.@nanopore
WGS #surveillance study describes two novel hospital-acquired sublineages of Staphylococcus aureus in India, both #AMR, which limits treatment options for patients. @CrlKims @varunshamanna @KLRavikumar @MonicaAbrudan @TheCGPS @GHRUamr @NIHRresearch journals.asm.org/doi/10.1128…
I'm excited to be part of Broken String's journey as we use NGS and integrated wet and dry lab processes to make cell and gene therapies safer, and affordable for patients. Heading up the bioinformatics and data science aspects has been challenging yet immensely rewarding.
We're excited to announce that we have closed our $15M Series A #funding!
The investment will support further development of our INDUCE-seq™ #technology, designed to drive development of #cellandgene therapies that are safer by design.
Read more: rb.gy/t9r7t
#DNA
It's a privilege to work in a dynamic joined-up team working together to help bring about the therapeutic promise of gene editing.
We are hiring brokenstringbio.com/#careers. Come and join a great team in the Cambridge region
Anthony Underwood retweeted
🔥 Exciting discussions at #SeqeraSessions in Cambridge with our CEO @EvanFloden, Adrianto Wirawan from @GenomicsEngland, @bioinformAnt
from @BrokenStringBio, Miika Ahdesmaki and Jennifer Harrow from @AstraZeneca.
🙏Thanks for sharing your expertise with us today!
Anthony Underwood retweeted
🔥 Bactopia v3 is here! 🔥
The @nextflowio pipeline for bacterial genomes is now faster, packed with more tools, updated docs, and much much more!
Get started at: bactopia.github.io/v3.0.0/
#bioinformatics #genomics
Anthony Underwood retweeted
"🎉 Birthday wish granted! 📚 My latest paper, born from the @SandraReuter9 lab, just hit the shelves. Explore how three tenacious Klebsiella pneumoniae lineages ruled the roost in a Greek hospital for a whopping 15 years! 🏥🧫 - go.shr.lc/44AEB4E
Anthony Underwood retweeted
Blogged: precise removal of host DNA sequences
log.bede.im/2023/08/29/preci…
Anthony Underwood retweeted
We've released v5.1.0 of our desktop bioinformatics platform! We've overhauled the installer for better support in Windows, made it easier to report problems to us and added new UI to show workflow progress. More info and download link on release note: labs.epi2me.io/epi2me-23.07-…
Excited to be a part of the @wellcomegenome Bioinformatics Workflows Community. Enjoyed meeting other @nextflowio users and sharing how @BrokenStringBio leverages it for reproducible, scalable, and auditable workflows in the cloud.
youtube.com/watch?v=GKMR-k7m…
Anthony Underwood retweeted
New funded PhD studentship!
Work with me and some amazing colleagues @unibirmingham using NLP, ML and electronic health records to improve antibiotic prescribing for emergency admissions in partnership with Shionogi (shionogi.com/global/en/)
findaphd.com/phds/project/na…
Anthony Underwood retweeted
The twinning between CPHL @OmaniMOH and WPHL has been such a great experience.
Lots accomplished in a few days: capacity building, facilitating conversations with IT, introductions to @nextflowio, @nf_core and @SingularityApp 🎉
Already missing our family in Oman!🇴🇲 🦬
@APHL 🌍 had an amazing lab/NGS/bioinformatics twinning (Wyoming PHL) visit with CPHL @OmaniMOH. They are all now family - such a talented group of dedicated public health professionals. Can’t wait to continue to see what we accomplish together! 🇴🇲 @nextflowio @CDCGlobal
ALT Oman CPHL, APHL, and, consultants from Wyoming Public Health Laboratory at Mutrah Fort in Muscat, Oman. If Oman isn’t on your bucket list, it should be.
ALT Marie Gosselin, MSc addressing QMS for public health laboratories and leading a discussion on QMS for NGS and bioinformatics.
ALT Dr. Petit III doing a training on NextFlow Core.
ALT Discussion with CPHL Director, Dr. Hanan and APHL and consultants from the Wyoming Public Health Laboratory.
Anthony Underwood retweeted
I've just added Day 1 AND Day 2 into 100 Days Of Containers And Orchestration.
You'll be learning about:
- Docker
- What containers are
- Why containers are important
- Container runtimes
and A LOT more.
github.com/AdminTurnedDevOps…
#kubernetes #devops #docker
