First paper from my student Daria Frolova's PhD now on biorxiv:
www.biorxiv.org/content/10.1...
The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes?
1/n
In 1995 computer pioneer Niklaus Wirth wrote "A Plea for Lean Software". Today it is normal to ship simple software as a 350MB package, or with 1600 dependencies. In appreciation of Wirth's legacy, I wrote a Plea for Lean Software, updated for today's computing horrors: berthub.eu/articles/pos...
18.01.2024 14:28 — 👍 10 🔁 3 💬 0 📌 1Awesome!
08.11.2023 00:17 — 👍 1 🔁 0 💬 0 📌 0Gute Besserung
25.10.2023 13:59 — 👍 0 🔁 0 💬 0 📌 0Carp is everywhere, as the platypus.
12.10.2023 21:53 — 👍 0 🔁 0 💬 0 📌 0I'm recruiting PhD students for Oct 24 start at University of Bath. Fully funded for UK students only. If interested in developing data structures/algorithms for bacterial genomics, or exploring plasmid epidemiology, or ML/AI on bacterial/phage geno/pheno data, give me a call!
04.10.2023 18:28 — 👍 48 🔁 56 💬 2 📌 5
👩🔬New **PostDoc** Opportunity!👨🔬
My new Epidemiology & Virus Evolution (EVE) group at SwissTPH is looking for a PostDoc in evolution & phylogenetics of respiratory viruses 🦠🌳
Interested? See here for more details & to apply!
jobs.swisstph.ch/Vacancies/92...
Please share!😁
Excited to share our preprint introducing MGX 2.0, which
adds metagenome (co-)assembly (including binning and bin assessment) as well as de novo metatranscriptome assembly.
Wow. Ok. Normally I feel like it's a bit overplayed to individually comment on #MDPI in the whole #AcademicChatter conversation, but this is really a must-see:
A Special Issue where the guest editors are lead or senior author on 27 of the 28 papers it published 🤯
www.mdpi.com/journal/proc...
Bar chart showing increase in throughput for nanopore flow cells if shielded from light during run. Most dramatic increase is on 10.4.1 minion flow cells with 488% increase in yield. Prom flow cells and flongles show much more modest increase at 11-34%.
Image showing new light shields that will be shipped with new flow cells.
Breaking news! Time to get the tinfoil out for existing flow cells...
20.09.2023 08:23 — 👍 35 🔁 17 💬 6 📌 7So, 'responsible release' seems to be equal to 'no release' now...
19.09.2023 15:13 — 👍 1 🔁 0 💬 0 📌 0
As an unpaid anonymous peer reviewer who handles probably 30 manuscripts a year, I am absolutely not in the position of running and evaluating code any more than I am in the position of running gels to evaluate lab results. If this is important to you, I suspect you can find a consultant who will do it at a reasonable rate.
AITA, academic publishing edition.
Flashy for-profit journal sends a review back to me for further consideration because as reviewer I did not run the code and replicate the results.
My reply is below.
Am I the asshole?
