Moved to Bluesky : bsky.app/profile/bedec.bsky.…
Joined February 2010
- Tweets 4,997
- Following 3,778
- Followers 1,256
- Likes 11,818
367 Photos and videos
Pinned Tweet
6 Jul 2023
Preprint: How best to remove human reads from microbial FASTQs? Our tool Hostile removed >99.6% of human reads while retaining >99.997% and 100% of simulated reads in bacterial and mycobacterial metagenomes
biorxiv.org/content/10.1101/…
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Bede Constantinides retweeted
16 Sep 2024
Check out our latest blog from Dr. Inês Mendes and Dr. Bryan A. Wee, members of the Public Health Alliance for Genomic Epidemiology @pha4ge . They show how ‘bad data’ can be made more valuable by tagging them with information about their potential issues. microb.io/3Xrg9kH
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Bede Constantinides retweeted
10 Sep 2024
Air purifiers in Finnish daycare reduced children's illnesses by 18% in a carefully controlled study. This implies huge potential for better public health and cost savings from sick leaves, with a simple intervention against airborne infections.
yle.fi/a/74-20089670
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Bede Constantinides retweeted
1 Sep 2024
Great pleasure to work with @shenwei356 on a new indexing and alignment scheme, called LexicMap:
biorxiv.org/content/10.1101/…
We have been working on uniformly reassembling, QC-ing and annotating all bacterial ( now archaeal) data, & wanted to be able to do full alignment to it....
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Bede Constantinides retweeted
29 Aug 2024
I find it really interesting that biotechs & institutes often build their own bioinformatics workflow managers:
- Insitro: Redun
- GRAIL: Reflow
- 10X Genomics: Martian
- Invitae: in-house engine
- CZI: Swipe
- Broad: Cromwell
- UCSC: Toil
What does the future look like?
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More workflow engines
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More convergence
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Just show me the results
466 votes • Final results
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Bede Constantinides retweeted
27 Aug 2024
Incredibly excited for the launch of Pathoplexus, which I've spent quite a bit of time helping with over the past year. New, open-source, infrastructure for sharing viral sequence data!
27 Aug 2024
📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬
Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing.
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Bede Constantinides retweeted
27 Aug 2024
📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬
Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing.
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Bede Constantinides retweeted
20 Aug 2024
Kicking off a new series of #TheLifeScientific today, @jimalkhalili talks to Microsoft founder @BillGates about science-driven philanthropy, the power of vaccines and having a sense of humour about conspiracy theories… from 9am @BBCRadio4 or @BBCSounds: bbc.co.uk/programmes/m00224g…
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Bede Constantinides retweeted
4 Aug 2024
🦠 Working around the clock over the past 10 days to investigate the rapid viral expansion of OROV beyond the Amazon Basin! @fiocruz @LACENs @lalcan40 @vagnerf0nseca @Tuliodna @LourencoJML - climade.health/2024/08/04/ra…
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Bede Constantinides retweeted
2 Aug 2024
Allright, I think my blogpost on computing random minimizers is ready to share.
Runs in just under 0.5s for a full human genome :)
That's 60x-160x faster than some other implementations.
As part of this, there's also a 30x faster ntHash implementation.
curiouscoding.nl/posts/fast-…
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Bede Constantinides retweeted
19 Jul 2024
Overhauling pandemic plans and increasing pandemic response capacity is urgent. It is a mistake to think of it as a long-term aspiration against a theoretical risk. The risk posed by H5N1 influenza, uncertain as it is, is certainly higher than it has been for a long time.
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Bede Constantinides retweeted
14 Jul 2024
Oxford brewery helps cut reoffending rates by training jail-leavers to make ale theguardian.com/society/arti…
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Bede Constantinides retweeted
10 Jul 2024
Our new preprint showing how protein language models (PLMs) can help us understand viral proteins is now available! We used ESM-2 to investigate what PLMs know about the SARS-CoV-2 spike protein from a single sequence to evolutionary trajectories.
biorxiv.org/content/10.1101/…
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Take it in. The first female chancellor. The first housing secretary who's actually lived in social housing. The first education secretary who was on free school meals. An energy secretary who actually believes in aggressively fighting climate change. Not a bad afternoon.
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Bede Constantinides retweeted
4 Jul 2024
GE2024 Results Spreadsheet!
Those who helped with the nominations sheet should all have access to add vote totals for each seat :)
docs.google.com/spreadsheets…
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5 Jul 2024
The greens beat the tories in 80/650 (12%) of UK constituencies #UKGE2024 @TheGreenParty
gist.github.com/bede/821a8bd…
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Bede Constantinides retweeted
3 Jul 2024
When writing bioinformatics tools, I often need small datasets to test edge cases or invalid file formats, e.g. files that are truncated, unsorted, have extraneous whitespace, etc.
I started compiling examples here: github.com/omgenomics/bio-da…, contributions are welcome!
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Bede Constantinides retweeted
21 Jun 2024
Got milk virus genomes? (or any H5N1?) Throw them at usher.bio and see where they land in per-segment trees of tens of thousands of public Influenza A H5N1 sequences!
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19 Jun 2024
UK folk: just 1.5hrs left to apply for a postal vote to ensure that you can vote however busy / wherever you are on election day:
gov.uk/apply-postal-vote
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Analysis of 170 @PacBio HiFi genomes identified 7000 segmentation duplications (SD) that comprise 6.1% of the (T2T CHM13) genome. African genomes show higher copy number of multi-copy SDs. Comparing to Iso-Seq data finds 201 novel protein-coding gene in multicopy SDs.
biorxiv.org/content/10.1101/…
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