
#Biology, from the molecular to #cellular - beyond the biomedical. Maintained by David Kirschtel. #microbiology #microbialecology #molecularbiology #evolution
College Park, MD
Joined April 2017
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Cell Bio News retweeted
New online! Ciliate hydrogen organelles fuel rumen methanogenesis dlvr.it/TScgKf
Cell Bio News retweeted
==Monthly Reminder ===
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Postings will remain indefinitely - or until closed down for lack of activity.
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Cell Bio News retweeted
ESMfold2, includes support for protein-protein interactions, DNA/RNA, small molecules. Including colab notebook!
colab.research.google.com/gi…
Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology.
The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics.
We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity.
We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures.
ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences.
A world model of protein biology emerges through language modeling.
We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins.
The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science.
This understanding emerges without prior knowledge, just from language modeling of protein sequences.
Language models are becoming a powerful substrate to understand and program biology.
The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders.
I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.
Cell Bio News retweeted
Nifty work on plasmid chromatinization from @stergachislab !
"plasmids are indeed capable of recapitulating nuclear genome-encoded chromatin architectures, ... However, plasmids consistently adopt a heterogeneous and incomplete chromatin architecture relative to nuclear-encoded chromatin fibers, and surrounding sequence context plays an integral role in modulating whether a plasmid-encoded regulatory element will recapitulate nuclear genome-encoded chromatin architectures."
Online Now: Chromatin architectures underlying plasmid-based assays for regulatory variant effects dlvr.it/TSkLhj
Cell Bio News retweeted
Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes nature.com/articles/s41597-0…
Cell Bio News retweeted
My entire team wrote an opinion paper about Common misconceptions of speciation research. Each section is written by 1-2 team members. The bulk of the writing happened during two writing retreats. It was a lot of fun and I am very happy with the result. academic.oup.com/evolinnean/…
Cell Bio News retweeted
📌 6 years Postdoc Position in Microbial Biotechnology 🦠🧬; Metabolic Modelling and Bioprocess Engineering of Microorganisms at BOKU University in Vienna 🇦🇹... Please share and spread the word! For details visit: wp.me/pbv48T-9MK
Cell Bio News retweeted
The microbial phosphorus cycle in aquatic ecosystems nature.com/articles/s41579-0…
Cell Bio News retweeted
(1/🧵) How much of Earth's phytoplankton do space satellites not "see"? Can chlorophyll from satellites reliably describe phytoplankton biomass? 🛰️🦠
In our new paper in @PNAS, we answer these questions with a fleet of undersea Argo robots 🤖🌊:
doi.org/10.1073/pnas.2405354…
Cell Bio News retweeted
A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities
@mSystemsJ from @PSchneeb
journals.asm.org/doi/10.1128…
Cell Bio News retweeted
New PhD position in plant-microbe interactions!
Our newly established DFG Research Unit "MadFungi" will study mechanisms of competition in plant-colonizing fungi: portal.uni-koeln.de/en/unive…
Within MadFungi, our lab is offering a PhD position:
jobportal.uni-koeln.de/aussc…
Cell Bio News retweeted
Learn more about our open PhD position!🌊🦠Chat with me if you are excited about marine microbes + numerical modeling + experimental evolution. ALL students encouraged to apply! Please DM me if you can help spread the word at local universities in Texas.
Cell Bio News retweeted
📌 PhD Fully Funded Position in (Food🦠🧬) Microbiology / Bioinformatics / Biotechnology at Wageningen University in The Netherlands and Kapodistrian University of Athens in Greece 🇳🇱🇬🇷... Please share and spread the word! For details visit: wp.me/pbv48T-9ok
Cell Bio News retweeted
Setting the stage for plant–soil feedback: Mycorrhizal influences over conspecific recruitment, plant and fungal communities, and coevolution - Eagar et al - Journal of Ecology - besjournals.onlinelibrary.wi…
Cell Bio News retweeted
The role of cyclic nucleotides in bacterial antimicrobial resistance and tolerance
@gLarrouyM_Lab
dlvr.it/TCwkTr
Cell Bio News retweeted
Phylogenomic analysis uncovers an unexpected capacity for the biosynthesis of secondary metabolites in Pseudoalteromonas
-in European Journal of Medicinal Chemistry
sciencedirect.com/science/ar…
Cell Bio News retweeted
Pseudomonas fragariae sp. nov., a novel bacterial species causing leaf spots on strawberry (Fragaria×ananassa). Published #OpenAccess and fee-free in #IJSEM using a #PublishAndRead agreement: doi.org/10.1099/ijsem.0.0064…
Cell Bio News retweeted
Looking for the best conference choice next year? Check this: lyyti.fi/p/Ecology_of_Soil_M…!
Cell Bio News retweeted
📌 4 Year PhD Funded Position in Plant Breeding 🌱🧬 at Swedish University of Agricultural Sciences in Sweden 🇸🇪... Please share and spread the word! For details visit: wp.me/pbv48T-9rO































