ComparativeSystemsBiologyGroup_unimi

@MartinJLercher @67250Old @ItaiYanai @ScienceMagazine I think it holds. If interested in the theoretical basis, I will give a seminar tomorrow online, the zoom link is available by Jindrich Brejcha, matbio.natur.cuni.cz/contacts or write to me matteo.brilli@unimi.it and I will forward it.

@67250Old @ItaiYanai @ScienceMagazine Why? The selection coefficients are small, which is also clear from the remaining variation in gene positions (our figure 3C). Such weak selection would be very difficult to detect experimentally.

Is the genome just a bag of genes? A new paper in @ScienceMagazine now reports that for two thirds of an organisms' genes the position along the chromosome is actually very tightly constrained! Amazing work from my favorite night scientist @MartinJLercher and his team!

@rravi @ItaiYanai @ScienceMagazine @MartinJLercher well, there are many papers saying this. Only, this got published on Science. Rocha did a lot about this. But some of those patterns are somehow known since Sharp and Li in 88. What is really new, is the theoretical framework that can explain it. A draft: biorxiv.org/content/10.110…

@ItaiYanai @ScienceMagazine @MartinJLercher Amazing that such basic knowledge is decoded after decades of genomics data. This is wow.

@ItaiYanai @ScienceMagazine @MartinJLercher Very interesting! I take the occasion for advertising my seminar online tomorrow (April, 15, 1:00 pm), about models of interaction of DNA replication and gene expression with theoretical expl. for what they find in the paper. zoom link contacting matbio.natur.cuni.cz/contacts

doi.org/10.1103/PhysRe… doi.org/10.1103/PhysRe… doi.org/10.1103/PhysRe… doi.org/10.1140/epje/i… doi.org/10.1073/pnas.1… doi.org/10.1103/PhysRe…

Reading lots of papers about scaling laws in bacterial growth. But, why no one has considered that variance is also introduced through the changes in copy number introduced by DNA replication? doi.org/10.2142/biophy… doi.org/10.1016/j.cub.… doi.org/10.1103/PhysRe…

8th grade graduation exam from 1912. This wasn’t for affluent kids in New England. This was rural Kentucky.

Be less curious about people and more curious about ideas. -- Marie Skłodowska Curie

Congratulations to @dendenesara and @EmanueleBiondi5 for this important work. It was a long and tiring process, but it ended in the best possible way! Sinorhizobium meliloti FcrX coordinates cell cycle and division[...] pnas.org/doi/10.1073/pn…

@schwabpa maybe you are right, in general you should not trust names, and use sequences, but this is normal to me. But, I am writing because the picture is really appalling and wrong. the generating AI does not even know that there are 10 bases per full turn, in DNA.

A central mistake in biology was to name genes. This over-simplification made reconciling what is happening on the molecular level a mess - it's not rare to find reports of opposite mechanisms in different contexts, claimed involvement in dozens if not hundreds of different processes, sometimes inhibiting and sometimes amplifying and most of the time being oblivious to the potential for sequence-level variation. Nobody would be surprised about this diversity of findings if we instead recognized genes as (sometimes quite lengthy and complex) pieces of sequence that carry state and interact with and are interpreted by their environment - often producing dozens of gene products that are in turn themselves context-dependent and modulated. Naturally, such a highly amorphous composition of objects has many diverse effects, and masking this complexity behind a single name more often than not ends up being a harmful abstraction. The primary role of gene names then is to give us the false appearance of comfort in the face of enormous biological complexity. One under-appreciated potential of the emergence of AI tools in biology is to undo this mistake, and - instead of assuming it away - extend our ability to lean further into this complexity.

@Maths__Physics1 but wait..if you need first, middle bla.bla, it means you have no idea of why is that way!

It was time! After two revisions at @MolBioEvol , and the incomprehensible decision to reject it based on mysterious simulations performed by the reviewer, we are proud to announce that @mSystemsJ liked it! A novel hypothesis on the origin of operons: journals.asm.org/doi/10.1128/ms…

Paul Dirac explains the deep connection between mathematics and theoretical physics, highlighting how mathematical beauty often guides the discovery of new physical laws. ✍️

very easy to get fascinated by seeing things. I used to spend hours decorating my homology networks back in 2006-2008 but it is much more rewarding to exploit network theory to extract non trivial information about the biological system. So, go on!

“Man is the most insane species. He worships an invisible God and destroys a visible Nature. Unaware that this Nature he’s destroying is this God he’s worshiping.” -- Hubert Reeves (1932 - 2023) He would have turned 92 today. He passed away last year in Paris.

Update -- Brownian motion evolution on a phylogeny (a GIF) using #phytools, plus the #Rstats code here: blog.phytools.org/2024/07/an-ani….

@razoralign I think you miss references to similar works. It is becoming increasingly common to realize that people nowadays do not pay attention to previous works. this is not entirely new. we worked on the same kind of graph in 2012. we called them gene neighborhood graphs

Pangene: Exploring gene content with pangene graphs academic.oup.com/bioinformatics…

76 years ago #Today, Claude Shannon published the article 'A Mathematical Theory of Communication', cited over 100,000 times, which is rare for a scientific article and gave rise to the field of information theory.

@ashleyruba_phd it's not the number that matters.

In a blog post, she tells the story of the reaction she received when she pointed this out to her (tenured) professor at the time, and to others. She was basically told not to waste her time: "a lot of the scientific literature has problems". liorpachter.wordpress.com/2024/07/02/the… 7/

My book Interpretable Machine Learning has been career-defining. Even though the book is available on the web for free, many have supported me by buying the ebook or paperback, which ultimately helped me become a full-time writer. I'm grateful for all your support 🙏