Why are evolved networks (such as gene and metabolic webs) different from engineering designs? One lesson is provided by generating electronic circuits using Darwinian evolution, as shown in this Scientific American paper by John Koza Víctor de Lorenzo Michael Levin jstor.org/stable/pdf/260…

Two papers in nature present a new genome editing technique that enables the insertion, inversion and deletion of long DNA sequences at user-specified genome positions. The approach may provide an easier method of genome editing. go.nature.com/3RGkI8M go.nature.com/3RHBvIs

Great, we are now also in Science! GeneticsUB Universitat de Barcelona Facultat de Biologia UB science.org/content/articl…

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era academic.oup.com/mbe/advance-ar… Molecular Biology and Evolution

Nice - cohesin may only be required for enhancer-promoter comm for distal enhancers (>50kb). This nicely extends (and generalises) findings from Wendy Bickmore at shh locus, tethering a TF at different distances. There 100kb was the tested cut off - interesting to see even 50kb

We are excited to share our latest work: biorxiv.org/content/10.110… in which we show that local DNA compaction creates TF-DNA clusters that enable transcription.

FoldMason progressively aligns thousands of protein structures in seconds, enabling remote MSA for distant phylogeny. Highlights: structural flexible MSA, LDDT conservation score, friendly webserver🧵 💾github.com/steineggerlab/… 🌐search.foldseek.com/foldmason 📄biorxiv.org/content/10.110…

BertSNR: an interpretable deep learning framework for single nucleotide resolution identification of transcription factor binding sites based on DNA language model academic.oup.com/bioinformatics…

Tokenized and Continuous Embedding Compressions of Protein Sequence and Structure biorxiv.org/content/10.110…

Our latest: "Reverse development in the ctenophore Mnemiopsis leidyi" out in bioRxiv, Pawel Burkhardt Michael Sars Centre Universitetet i Bergen. Check it out: biorxiv.org/content/10.110… Illustrations by talented Nicholas Bezio (Bezio Studios) . [🧵1/6]

We present The Transcription Factor Binding Landscape of Mouse Development🐭🧬 #DevBio We use CUT&RUN-LoV-U to map Many SignalingPathways X 4tissue X 2stages It is a huge dataset - yet only the beginning of the TranscriptionFactorBinding(TFB)-OMICS biorxiv.org/content/10.110…

Very happy to see the “optoscillator” - a synthetic optogenetic oscillator - published! By applying light pulses on growing E. coli colonies and analysing the ring patterns, we observed synchronisation, (subharmonic) resonance, period doubling and chaos! nature.com/articles/s4146…

There's a new paper by Simone Tiberi et al. from the Mark Robinson @[email protected] lab on a method for finding differentially regulated genes: "spliced and unspliced (or precursor) mRNA..can be used to study gene regulation and changes in gene expression production" 1/ nature.com/articles/s4159…

Major effort from the lab (💪Robert Frömel), finally on biorxiv: We built 60,000 fully synthetic enhancers and measured their cell state specific activity during blood stem cell differentiation. Why did we do that and what did we learn🧵? biorxiv.org/content/10.110…

A gene coding for a small non-coding RNA seems to be associated with a surprising number of developmental disorders - another indicator of the significance of ncRNA. A short 🧵 nature.com/articles/d4158…

(1/12) Our brain network study of religious fundamentalism is out in PNAS. We identified brain networks associated with religious fundamentalism and found shared neuroanatomy with lesions linked to confabulation and criminal behavior: pnas.org/doi/10.1073/pn…

Wouldn’t it be great to test how individual transcription factors engage with their motif in the nucleus? We tried exactly that in a study lead by Ralph (Ralph Grand) and Marco (Marco Pregnolato) now out in Molecular Cell authors.elsevier.com/sd/article/S10…. 1/7

Happy to share our new paper on the characterization of MSTV1, an archaeal virus infecting Methanobrevibacter smithii, the dominant archaeon in the human gut. This was a beautiful collaboration between Mart Krupovic and Simonetta Gribaldo labs. 👇🧵nature.com/articles/s4146…

I am thrilled to announce I have secured an European Research Council (ERC) Starting Grant (1.5 MILLION euros!) to study the #genomics of miniaturisation in vertebrates! Press release: news.ku.dk/all_news/2024/…

My favorate piece of my postdoc work is published! We fused our favorite TFs with a deaminase domain that induces point mutations in DNA, mutagenizing TF binding sites across the genome. Will be a great reagent for exp. evo., as its name suggests :) academic.oup.com/mbe/article/41…