Barak Raveh @ravehlab.bsky.social · 10/12/2025We introduce multiscale Markov state models (mMSMs), compact summaries of molecular dynamics (MD) simulation trajectories simultaneously capturing multiple temporal resolutions. In this example, we used mMSM to describe the folding process of the HP35 miniprotein: 1/3 #mMSM #MD 100
Barak Raveh @ravehlab.bsky.social · 04/12/2025Cool work by Rod Lim’s lab on transport through nuclear pore complexes, the gateways to the nucleus, with contributions from our own Roi Eliasian, who developed a simulator to directly compare imaging data to our modeling. #npc #transport www.nature.com/articles/s41... m.youtube.com/watch?v=9FPX...m.youtube.comKaryopherins remodel the dynamic organization of the nuclear pore complex transport barrierYouTube video by Swiss Nanoscience Institute 121
Reposted by Barak RavehBarak Raveh @ravehlab.bsky.social · 22/10/2025The integrative model enables us to visualize how the flexible FG chains lining the NPC’s central channel filter molecular traffic between the nucleus and the cytoplasm at picosecond resolution, well beyond the capabilities of any existing imaging technology. #NPC #transport 011
Barak Raveh @ravehlab.bsky.social · 19/10/2025Years of work, finally out! Nuclear Pore Complexes (NPCs) are the gateways to the nucleus, but how can they be both rapid and picky, even for very large cargoes? To answer this question, we built the most detailed data-driven model to date of transport through NPCs. / www.pnas.org/doi/10.1073/...pnas.orgIntegrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport | PNASNuclear pore complexes (NPCs) enable rapid, selective, and robust nucleocytoplasmic transport. To explain how transport emerges from the system com... 172
Barak Raveh @ravehlab.bsky.social · 09/07/2025Check out the TEMPO algorithm from our lab by the incredible Reshef Mintz. By recursively forecasting future timesteps from recent ones across scales, TEMPO accelerates the costly integration step of molecular dynamics, even for complex biomolecular processes such as nucleocytoplasmic transport. 020
Barak Raveh @ravehlab.bsky.social · 11/03/2025Kudos to #kaplanlab@huji for this exciting work, identifying 1000s of genomic regions showing allele-specific DNA methylation, including novel cell-type-specific imprinted regions.nature.comAtlas of imprinted and allele-specific DNA methylation in the human body - Nature CommunicationsDNA methylation drives parental expression differences at imprinted genes. Here, the authors uncover hundreds of ubiquitous and tissue-specific differentially methylated regions, offering insights int... 040
Reposted by Barak RavehMor Nitzan @mornitzan.bsky.social · 08/12/2024Characterizing single-cell and spatial data structure and identifying gaps in our knowledge of their annotations by analyzing deep learning training dynamics! Led by @jonathankarin.bsky.social and Reshef Mintz, with @ravehlab.bsky.social 092
Reposted by Barak RavehJonathan Karin @jonathankarin.bsky.social · 08/12/20241/3 Annotatability is out in Nature Computational Science! With Reshef Mintz, @ravehlab.bsky.social and @mornitzan.bsky.social www.nature.com/articles/s43...nature.comInterpreting single-cell and spatial omics data using deep neural network training dynamics - Nature Computational ScienceThe Annotatability framework analyzes neural network training dynamics to interpret single-cell and spatial omics data. It identifies erroneous annotations and ambiguous cell states, infers trajectori... 121
