Yes, but for optimization, I was just cloning and transforming the products into E. coli and doing 10 cheap Sanger reactions per condition.
06.03.2026 17:02
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Yes, but for optimization, I was just cloning and transforming the products into E. coli and doing 10 cheap Sanger reactions per condition.
I just add a small amount of MnCl2 to the mastermix (play with concentrations to optimize for the number of point mutations). Itβs cheap and works great (feel free to DM me).
Genome modelling and design across all domains of life - Evo2
A biological foundation model trained on 9 trillion DNA base pairs to predict the functional impacts of genetic variation
www.nature.com/articles/s41...
Really nice to see @marstonlab.bsky.social's News & Views piece cover the evolution of budding yeast centromeres in @nature.com. Check it out for a clear and concise breakdown of @maxhaase.bsky.socialβs new paper and ours! π§¬
In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! π¨
Let me hit you with some highlights on why spatial structure matters. (and why you should care!)
Sharing is appreciated π π§΅π
doi.org/10.1093/fems...
Amazing, thank you! π
Posting into the void again :P Any ideas?
Looks like it could be a dyerβs polypore?
I'm looking for a textbook / workbook for using Bash and other things bioinformatics-related in the command line (e.g. making phylogenic trees, genome alignments, SNP calling, etc.). Thanks in advance!
Our paper is now out in Nature:
βAncient co-option of LTR retrotransposons as yeast centromeresβ
www.nature.com/articles/s41...
A short thread on how retrotransposons helped give rise to yeast point centromeres.
1/14
Amazing work, Edoardo!
The replicase???
Figure 1. The genome is enriched with active promoters relative to random DNA. (A) We cloned the random library of 150 bp N-mer sequences (n=17,129, purple), and the genomic library of 100-300 bp sequences (n=91,866, magenta) into the dual-reporter plasmid MR1 (pMR1), which drives the expression of green fluorescent protein (GFP, teal) from inserts on the top DNA strand, and that of red fluorescent protein (RFP, orange) on the bottom strand. We transformed E. coli cells with the plasmid libraries. (B) We sorted the bacterial libraries into fluorescence bins at four fluorescence strengths: none, weak, moderate, and strong for both GFP and RFP (eight bins total) with a cell-sorter. We bulk-sequenced the library inserts from each bin and calculated fluorescence scores in arbitrary units (a.u.) ranging between one (none) and four (strongest) (Methods). (C) The probability that a DNA sequence in the random (purple) and genomic (magenta) libraries is a promoter relative to its AT-content. (D) For 102 position-weight matrices (PWMs) for transcription factors and sigma (Ο) factors, we plot the percentage of sequences in each library (purple: random, magenta: genome) that encode at least one putative factor binding site (vertical axis) against the respective PWMβs information content in bits. We test for equality of the frequency distributions between the random and genome libraries with a paired t-test (p=7.48Γ10β12).
De-novo promoters emerge more readily from random DNA than from genomic DNA
www.biorxiv.org/content/10.1...
I'm looking for a Swiss department to host me for an SNSF Starting Grant.
I research how gene expression evolves and emerges by combining wet lab + computational work in a variety of model systems (E. coli, Drosophila, yeast). More: timothyfuqua.com
If your department might be a match, letβs chat!
Can you infer cause and effect between genes without disturbing the cell? π§¬
This study shows how natural βnoiseβ in gene expression can reveal directed geneβgene interactions.
buff.ly/mruUeLZ
Now published in @science.org
www.science.org/doi/10.1126/...
Wanna read about yeasts and heat waves? π₯΅ Check out our new preprint with @jennifermolinet.bsky.social and @stelkens.bsky.social!
doi.org/10.64898/202...
New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes βmulti-way regulatory hubsβ in early Drosophila embryos.
www.biorxiv.org/content/10.6...
I just did my first tetrad dissection! π𧫠Am I a yeast person now?
New online! Emergence and evolution of protein-coding de novo genes
2026 has just begun and we are looking forward to welcoming you to EMBL for another year of groundbreaking science.
Our programme now features even more events, check it out β‘οΈ s.embl.org/2026-poster
Claudia Bank's (@cbank.bsky.social) research group, Theoretical Ecology and Evolution (THEE) is now on Bluesky! I posted a thread showing some of the group's publications from 2025 to get the account going. Please consider following the group for updates related to ecology and evolution π
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
We lost a legendβ¦
TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread
Schematic representation of fitness landscapes. (A) Orange lines show maximum (dashed) and average (dotted) fitness of a population on a narrower peak (yellow circles), blue lines show the same for a wider peak (blue circles). (B) Trajectory of a population in a periodically changing environment with respect to a given fitness landscape (solid arrow) and with respect to an unseen other fitness landscape (dashed arrow). (C) Hypothetical βtrappingβ of the population in variable environments.
One of the most-viewed PNAS articles in the last week is βThe variability of evolvability: Properties of dynamic fitness landscapes determine how phenotypic variability evolves.β Explore now: https://ow.ly/XouU50XWiiV
For more trending articles, visit https://ow.ly/AiXL50XWi81.
π£ #EMBOEvoEco returns in 2026 to uncover the mechanistic foundations of ecological and evolutionary change!
Keynote lectures will spotlight the ecology and evolution of symbiosis.
Submit your abstract for the EMBO Workshop: https://s.embl.org/eae26-01-bl!
Come to my talk today :)
If you're at the Karolinska @ki.se next Monday and are interested in #transcription or #generegulation then consider coming to my guest talk, "The biases and mechanisms of regulatory DNA evolution and emergence." Cheers!
More info here: news.ki.se/calendar/the...
New year, new conferences! Consider submitting to the symposium on Fitness landscapes and Genotype-phenotype maps, linking computational and experimental approaches (organising with @n-martin.bsky.social; @dbajic.bsky.social invited spreaker) at SMBE (28/6-2/7)! Abstract deadline February 3rd!
